Davis Project

Davis Project
• All clinicians should keep

themselves updated about recent developments including global spread of
the disease.
• Non-essential international travel should be avoided at this time.
• People should stop spreading myths and false information about the disease
and try to allay panic and anxiety of the public.
Conclusions
This new virus outbreak has challenged the economic, medical and public
health infrastructure of China and to some extent, of other countries
especially, its neighbours. Time alone will tell how the virus will impact our
lives here in India. More so, future outbreaks of viruses and pathogens of
zoonotic origin are likely to continue. Therefore, apart from curbing this
outbreak. efforts should be made to
category A agents (cholera, plague). Patients should be placed in separate

rooms or cohorted together. Negative pressure rooms are not generally
needed. The rooms and surfaces and equipment should undergo regular
decontamination preferably with sodium hypochlorite. Healthcare workers
should be provided with fit tested N95 respirators and protective suits and
goggles. Airborne transmission precautions should be taken during aerosol
generating procedures such as intubation, suction and tracheostomies. All
contacts including healthcare workers should be monitored for development
of symptoms of COVID-19. Patients can be discharged from isolation once
they are afebrile for atleast 3 d and have two consecutive negative molecular
tests at 1 d sampling interval. This recommendation is different from
pandemic flu where patients were
considerable protection in mice against a MERS- CoV lethal challenge. Such

antibodies may play a crucial role in enhancing protective humoral responses
against the emerging CoVs by aiming appropriate epitopes and functions of
the S protein. The cross-neutralization ability of SARS-CoV RBD- specific
neutralizing MAbs considerably relies on the resemblance between their
RBDs; therefore, SARS-COV RBD-specific antibodies could cross- neutralized
SL CoVs, i.e., bat-SL-CoV strain WIV1 (RBD with eight amino acid differences
from SARS- COV) but not bat-SL-CoV strain SHC014 (24 amino acid
differences) (200).
Appropriate RBD-specific MAbs can be recognized by a relative analysis of
RBD of SARS- CoV-2 to that of SARS-CoV, and cross-neutralizing SARS-COV
RBD-specific MAbs could be explored for their effectiveness against COVID-19
and further need to be assessed clinically. The U.S. biotechnology company
Regeneron is attempting to recognize potent and specific MAbs to combat
COVID-19. An ideal therapeutic option suggested for SARS-CoV-2 (COVID-19)
is the combination therapy comprised of MAbs and the drug remdesivir
(COVID-19) (201). The SARS-CoV-specific human MAb CR3022 is found to
bind with SARS-CoV-2 RBD, indicating its potential as a therapeutic agent
other clinical trials in different phases are still ongoing elsewhere.

Immunomodulatory agents. SARS-CoV-2 triggers a strong immune response
which may cause cytokine storm syndrome 60,61. Thus, immunomodulatory
agents that inhibit the excessive inflammatory response may be a potential
adjunctive therapy for COVID-19. Dexamethasone is a corticosteroid often
used in a wide range of conditions to relieve inflammation through its anti-
inflammatory and immunosuppressant effects. Recently, the RECOVERY trial
found dexamethasone reduced mortality by about one third in hospitalized
patients with COVID-19 who received invasive mechanical ventilation and by
one fifth in patients receiving oxygen. By contrast, no benefit was found in
patients without respiratory support146.
Tocilizumab and sarilumab, two types of interleukin-6 (IL-6) receptor-specific
antibodies previously used to treat various types of arthritis, including
rheumatoid arthritis, and cytokine release syndrome, showed effectiveness
in the treatment of severe COVID-19 by attenuating the cytokine storm in a
small uncontrolled trial147. Bevacizumab is an anti-vascular endothelial
growth factor (VEGF) medication that could potentially reduce pulmonary
oedema in patients with severe COVID-19. Eculizumab is a specific
monoclonal antibody that inhibits the proinflammatory complement protein
C5. Preliminary results showed that it induced a drop of inflammatory markers
and C-reactive protein levels, suggesting its potential to be an option for the
treatment of severe COVID-19 (REF.148).
another study, the average reproductive number of COVID-19 was found to be

3.28, which is significantly higher than the initial WHO estimate of 1.4 to 2.5
(77). It is too early to obtain the exact Ro value, since there is a possibility of
bias due to insufficient data. The higher Ro value is indicative of the more
significant potential of SARS-CoV-2 transmission in a susceptible population.
This is not the first time where the culinary practices of China have been
blamed for the origin of novel coronavirus infection in humans. Previously, the
animals present in the live-animal market were identified to be the
intermediate hosts of the SARS outbreak in China (78). Several wildlife
species were found to harbor potentially evolving coronavirus strains that can
overcome the species barrier (79). One of the main principles of Chinese food
culture is that live- slaughtered animals are considered more nutritious (5).
After 4 months of struggle that lasted from December 2019 to March 2020,
the COVID-19 situation now seems under control in China. The wet animal
markets have reopened, and people have started buying bats, dogs, cats,
birds, scorpions, badgers, rabbits, pangolins (scaly anteaters), minks, soup
from palm civet, ostriches, hamsters, snapping turtles, ducks, fish, Siamese
crocodiles, and other
proteins without the presence of S protein would not confer any noticeable
protection, with the absence of detectable serum SARS-CoV-neutralizing
antibodies (170). Antigenic determinant sites present over S and N structural
proteins of SARS-CoV-2 can be explored as suitable vaccine candidates (294).
In the Asian population, S, E, M, and N proteins of SARS- CoV-2 are being
targeted for developing subunit vaccines against COVID-19 (295).
The identification of the immunodominant region among the subunits and
domains of S protein is critical for developing an effective vaccine against the
coronavirus. The C-terminal domain of the S1 subunit is considered the
immunodominant region of the porcine deltacoronavirus S protein (171).
Similarly, further investigations are needed to determine the immunodominant
regions of SARS- CoV-2 for facilitating vaccine development.
However, our previous attempts to develop a universal vaccine that is
effective for both SARS- CoV and MERS-CoV based on T-cell epitope similarity
pointed out the possibility of cross- reactivity among coronaviruses (172).
That can be made possible by selected potential vaccine targets that are
common to both viruses. SARS-CoV-2 has been reported to be closely related
to SARS-COV (173, 174). Hence, knowledge and understanding of
extended to other cities of Hupel

province. Cases of COVID-19 in countries outside China were reported in
those with no history of travel to China suggesting that local human-to- human
transmission was occurring in these countries [9]. Airports in different
countries including India put in screening mechanisms to detect symptomatic
people returning from China and placed them in isolation and testing them for
COVID-19. Soon it was apparent that the infection could be transmitted from
asymptomatic people and also before onset of symptoms. Therefore,
countries including India who evacuated their citizens from Wuhan through
special flights or had travellers returning from China, placed all people
symptomatic or otherwise in isolation for 14 d and tested them for the virus.
Cases continued to increase
exponentially and modelling studies
had >95% homology with the bat coronavirus and > 70% similarity with the
SARS-COV. Environmental samples from the Huanan sea food market also
tested positive, signifying that the virus originated from there [7]. The number
of cases started increasing exponentially, some of which did not have
exposure to the live animal market, suggestive of the fact that human-to-
human transmission was occurring [8]. The first fatal case was reported on
11th Jan 2020. The massive migration of Chinese during the Chinese New
Year fuelled the epidemic. Cases in other provinces of China, other countries
(Thailand, Japan and South Korea in quick succession) were reported in
people who were returning from Wuhan. Transmission to
healthcare workers caring for patients was described on 20th Jan, 2020. By
23rd January, the 11 million population of Wuhan was placed under lock down
been used based on the experience

with SARS and MERS. In a historical control study in patients with SARS,
patients treated with lopinavir-
ritonavir with ribavirin had better
outcomes as compared to those given ribavirin alone [15].
In the case series of 99 hospitalized patients with COVID-19 infection from
Wuhan, oxygen was given to 76%, non-
invasive ventilation in 13%,
mechanical ventilation in 4%,
extracorporeal membrane oxygenation
(ECMO) in 3%, continuous renal replacement therapy (CRRT) in 9%, antibiotics
in 71%, antifungals in 15%, glucocorticoids in 19% and intravenous
immunoglobulin therapy in 27% [15]. Antiviral therapy consisting of
oseltamivir, ganciclovir and lopinavir-
ritonavir was given to 75% of the
patients. The duration of non-invasive ventilation was 4-22 d [median 9 d]
Epidemiology and Pathogenesis

[10, 11]
All ages are susceptible. Infection is transmitted through large droplets
generated during coughing and sneezing by symptomatic patients but can
also occur from asymptomatic
people and before onset of symptoms [9]. Studies have shown higher viral
loads in the nasal cavity as compared to the throat with no difference in viral
burden between symptomatic and asymptomatic people [12]. Patients can be
infectious for as long as the symptoms last and even on clinical recovery.
Some people may act as
super spreaders; a UK citizen who attended a conference in Singapore
infected 11 other people while staying in a resort in the French Alps and upon
return to the UK [6]. These infected
droplets can spread 1-2 m and deposit
fever, cough, and sputum (83). Hence, the clinicians must be on the look-out
for the possible occurrence of atypical clinical manifestations to avoid the
possibility of missed diagnosis. The early
transmission ability of SARS-CoV-2 was found to be similar to or slightly
higher than that of SARS-CoV, reflecting that it could be controlled despite
moderate to high transmissibility (84).
Increasing reports of SARS-CoV-2 in sewage and wastewater warrants the
need for further investigation due to the possibility of fecal-oral transmission.
SARS-CoV-2 present in environmental compartments such as soil and water
will finally end up in the wastewater and sewage sludge of treatment plants
(328). Therefore, we have to reevaluate the current wastewater and sewage
sludge treatment procedures and introduce advanced techniques that are
specific and effective against SARS-CoV-2. Since there is active shedding of
SARS-CoV-2 in the stool, the prevalence of infections in a large population can
be studied using wastewater-based epidemiology. Recently,
reverse transcription-
quantitative PCR (RT-qPCR) was used to enumerate the copies of SARS-CoV-2
RNA concentrated from wastewater collected from a wastewater treatment
plant (327). The calculated viral RNA copy numbers determine the number of
infected individuals. The
13 CONVALESCENT PLASMA THERAPY

Guo Yanhong, an official with the National Health Commission (NHC), stated
that convalescent plasma therapy is a significant method for treating severe
COVID-19 patients. Among the COVID-19 patients currently receiving
convalescent plasma therapy in the virus-hit Wuhan, one has been discharged
from hospital, as reported by Chinese science authorities on Monday, 17th
February 2020 in Beijing. The first dose of convalescent plasma from a COVID-
19 patient was collected on 1st and 9th February 2020 from a severely ill
patient who was given treatment at a hospital in Jiangxia District in Wuhan.
The presence of the virus in patients is minimised by the antibodies. in the
convalescent plasma. Guiqiang stated that donating plasma may cause
minimal harm to the donor and that there is nothing to be worried about.
Plasma donors must be cured patients and discharged from hospital. Only
plasma is used, whereas red blood cells (RBC), white blood cells (WBC) and
blood platelets are transfused back into the donor's body. Wang alleged that
donor's plasma will totally improve to its initial state after one or 2 weeks from
the day of plasma donation of around 200 to 300 millilitres.61
Prevention [21, 30]

Since at this time there are no
approved treatments for this infection,
prevention is crucial. Several
properties of this virus make
prevention difficult namely, non- specific features of the disease, the infectivity
even before onset of
symptoms in the incubation period, transmission from asymptomatic
people, long incubation period, tropism for mucosal surfaces such as the
conjunctiva, prolonged duration of the illness and transmission even after
clinical recovery.
Isolation of confirmed or suspected cases with mild illness at home is
recommended. The ventilation at home
should be good with sunlight to allow for destruction of virus. Patients should
be asked to wear a simple surgical
mask and practice cough hygiene.
prongs, face mask, high flow nasal cannula (HFNC) or non-invasive ventilation
is indicated. Mechanical ventilation and even extra corporeal membrane
oxygen support may be needed. Renal replacement therapy may be needed in
some. Antibiotics and antifungals are required if co- infections are suspected
or proven. The role of corticosteroids is unproven; while current international
consensus and WHO advocate against their use, Chinese guidelines do
recommend short term therapy with low-to-
moderate dose corticosteroids in
COVID-19 ARDS [24, 25]. Detailed
guidelines for critical care
management for COVID-19 have been published by the WHO [26]. There is, as
of now, no approved treatment for COVID-19. Antiviral drugs such as ribavirin,
lopinavir-ritonavir have been used based on the experience with SARS and
MERS. In a historical
absence of this protein is related to the altered virulence of coronaviruses due

to changes in morphology and tropism (54). The E protein consists of three
domains, namely, a short hydrophilic amino terminal, a large hydrophobic
transmembrane domain, and an efficient C-terminal domain (51). The SARS-
CoV-2 E protein reveals a similar amino acid constitution without any
substitution (16).
N Protein
The N protein of coronavirus is multipurpose. Among several functions, it
plays a role in complex formation with the viral genome, facilitates M protein
interaction needed during virion assembly, and enhances the transcription
efficiency of the virus (55, 56). It contains three highly conserved and distinct
domains, namely, an NTD, an RNA-binding domain or a linker region (LKR), and
a CTD (57). The NTD binds with the 3' end of the viral genome, perhaps via
electrostatic interactions, and is highly diverged both in length and sequence
(58). The charged LKR is serine and arginine rich and is also known as the SR
(serine and arginine) domain (59). The LKR is capable of direct interaction
with in vitro RNA interaction and is responsible for cell signaling (60, 61). It
also modulates the antiviral response of the host by working as an antagonist
for interferon
this emerging virus will establish a niche in humans and coexist with us for a
long time166. Before clinically approved vaccines are widely available, there is
no better way to protect us from SARS-CoV-2 than personal preventive
behaviours such as social distancing and wearing masks, and public health
measures, including active testing, case tracing and restrictions on social
gatherings. Despite a flood of SARS-CoV-2 research published every week,
current knowledge of this novel coronavirus is just the tip of the iceberg. The
animal origin and cross-species infection route of SARS-CoV-2 are yet to be
uncovered. The molecular mechanisms of SARS-COV-2 infection
pathogenesis and virus-host
including IL2, IL7, IL10, GCSF, IP10,

MCP1, MIP1A, and TNFa [15]. The median time from onset of symptoms
to dyspnea was 5 d, hospitalization 7 d and acute respiratory distress
syndrome (ARDS) 8 d. The need for intensive care admission was in 25- 30%
of affected patients in published series. Complications witnessed included
acute lung injury, ARDS, shock and acute kidney injury.
Recovery started in the 2nd or 3rd wk. The median duration of hospital stay in
those who recovered was 10 d. Adverse outcomes and death are more
common in the elderly and those with
underlying co-morbidities (50-75% of fatal cases). Fatality rate in hospitalized
adult patients ranged from 4 to 11%. The overall case fatality rate is
estimated to range between 2 and 3% [2].
Interestingly, disease in patients outside Hubei province has been
system (30).
Bovine coronaviruses (BoCoVs) are known to infect several domestic and wild
ruminants (126). BoCoV inflicts neonatal calf diarrhea in adult cattle, leading
to bloody diarrhea (winter dysentery) and respiratory disease complex
(shipping fever) in cattle of all age groups (126). BoCoV-like viruses have been
noted in humans, suggesting its zoonotic potential as well (127). Feline
enteric and feline infectious peritonitis (FIP) viruses are the two major feline
CoVs (128), where feline CoVs can affect the gastrointestinal tract, abdominal
cavity (peritonitis), respiratory tract, and central nervous system (128).
Canines are also affected by CoVs that fall under different genera, namely,
canine enteric coronavirus in Alphacoronavirus and canine respiratory
coronavirus in Betacoronavirus, affecting the enteric and respiratory tract,
respectively (129, 130). IBV, under Gammacoronavirus, causes diseases of
respiratory, urinary, and reproductive systems, with substantial economic
losses in chickens (131, 132). In small laboratory animals, mouse hepatitis
virus, rat sialodacryoadenitis coronavirus, and guinea pig and rabbit
coronaviruses are the major CoVs associated with disease manifestations like
enteritis, hepatitis, and respiratory infections (10, 133).
Swine acute diarrhea syndrome coronavirus
Interestingly, disease in patients outside Hubei province has been reported to

be milder than those from
Wuhan [17]. Similarly, the severity and case fatality rate in patients outside
China has been reported to be milder [6]. This may either be due to selection
bias wherein the cases reporting from Wuhan included only the severe cases
or due to predisposition of the Asian population to the virus due to higher
expression of ACE2 receptors on the respiratory mucosa [11].
Disease in neonates, infants and children has been also reported to be
significantly milder than their adult counterparts. In a series of 34 children
admitted to a hospital in Shenzhen, China between January 19th and February
7th, there were 14 males and 20 females. The median age was 8 y 11 mo and
in 28 children the infection was linked to a family member and 26
uroplets can spread 1-2 il ditu deposit

on surfaces. The virus can remain
viable on surfaces for days in
favourable atmospheric conditions but are destroyed in less than a minute by
common disinfectants like sodium hypochlorite, hydrogen peroxide etc. [13].
Infection is acquired either by inhalation of these droplets or touching
surfaces contaminated by them and then touching the nose, mouth and eyes.
The virus is also present in the stool and contamination of the water supply
and subsequent transmission via aerosolization/feco oral route is also
hypothesized [6]. As per current information, transplacental transmission from
pregnant women to their fetus has not been described [14]. However, neonatal
disease due to post natal transmission is described [14]. The incubation
period varies from 2 to 14 d [median 5 d]. Studies have
identified angiotensin receptor 2
(ACE) as the recentor through which
Cases continued to increase

exponentially and modelling studies reported an epidemic doubling time of
1.8 d [10]. In fact on the 12th of February, China changed its definition of
confirmed cases to include patients with negative/ pending molecular tests
but with clinical, radiologic and epidemiologic features of COVID-19 leading to
an increase in cases by 15,000 in a single day [6]. As of 05/03/2020 96,000
cases worldwide (80,000 in China) and 87 other
countries and 1 international
conveyance (696, in the cruise ship Diamond Princess parked off the coast of
Japan) have been reported [2]. It is important to note that while the
number of new cases has reduced in China lately, they have increased
exponentially in other countries
including South Korea, Italy and Iran.
Of those infected, 20% are in critical
condition 250% haTO POCovered
and
SARS- or MERS-CoV outbreak (120). However, there has been concern

regarding the impact of SARS-CoV-2/COVID-19 on pregnancy. Researchers
have mentioned the probability of in utero transmission of novel SARS-CoV-2
from COVID- 19-infected mothers to their neonates in China based upon the
rise in IgM and IgG antibody levels and cytokine values in the blood obtained
from newborn infants immediately postbirth; however, RT-PCR failed to
confirm the presence of SARS-CoV-2 genetic material in the infants (283).
Recent studies show that at least in some cases, preterm delivery and its
consequences are associated with the virus. Nonetheless, some cases have
raised doubts for the likelihood of vertical transmission (240-243).
associated with
COVID-19 infection was pneumonia, and some developed acute respiratory
distress syndrome (ARDS). The blood biochemistry indexes, such as albumin,
lactate dehydrogenase, C- reactive protein, lymphocytes (percent), and
neutrophils (percent) give an idea about the disease severity in COVID-19
infection (121). During COVID-19, patients may present leukocytosis,
leukopenia with lymphopenia (244), hypoalbuminemia, and an increase of
lactate dehydrogenase, aspartate transaminase, alanine aminotransferase,
bilirubin, and, especially, D-dimer
comprised a small population and, hence, the possibility of misinterpretation

could arise. However, in another case study, the authors raised concerns over
the efficacy of hydroxychloroquine- azithromycin in the treatment of COVID-19
patients, since no observable effect was seen when they were used. In some
cases, the treatment was discontinued due to the prolongation of the QT
interval (307). Hence, further randomized clinical trials are required before
concluding this matter.
Recently, another
FDA-approved
drug,
ivermectin, was reported to inhibit the in vitro replication of SARS-CoV-2. The
findings from this study indicate that a single treatment of this drug was able
to induce an ~5,000-fold reduction in the viral RNA at 48 h in cell culture.
(308). One of the main disadvantages that limit the clinical utility of ivermectin
is its potential to cause cytotoxicity. However, altering the vehicles used in the
formulations, the pharmacokinetic properties can be modified, thereby having
significant control over the systemic concentration of ivermectin (338). Based
on the pharmacokinetic simulation, it was also found that ivermectin may
have limited therapeutic utility in managing COVID-19, since the inhibitory
concentration that has to be achieved for effective anti-SARS-CoV-2 activity is
far higher than the
only a matter of time before another zoonotic coronavirus results in an
epidemic by jumping the so-called species barrier (287).
The host spectrum of coronavirus increased when a novel coronavirus,
namely, SW1, was recognized in the liver tissue of a captive beluga whale
(Delphinapterus leucas) (138). In recent decades, several novel coronaviruses
were identified from different animal species. Bats can harbor these viruses
without manifesting any clinical disease but are persistently infected (30).
They are the only mammals with the capacity for self-powered flight, which
enables them to migrate long distances, unlike land mammals. Bats are
distributed worldwide and also account for about a fifth of all mammalian
species (6). This makes them the ideal reservoir host for many viral agents
and also the source of novel coronaviruses that have yet to be identified. It
has become a necessity to study the diversity of coronavirus in the bat
population to prevent future outbreaks that could jeopardize livestock and
public health. The repeated outbreaks caused by bat-origin coronaviruses
calls for the development of efficient molecular surveillance strategies for
studying Betacoronavirus among animals (12), especially in the Rhinolophus
bat family (86). Chinese bats have high commercial value, since they are used
in
of persistent local transmission or contact with patients with similar travel

history or those with confirmed COVID-19 infection. However cases
may be asymptomatic or even without fever. A confirmed case is a suspect
case with a positive molecular test.
Specific diagnosis is by specific molecular tests on respiratory samples
(throat swab/ nasopharyngeal swab/ sputum/ endotracheal aspirates and
bronchoalveolar lavage). Virus may also be detected in the stool and in severe
cases, the blood. It must be
remembered that the multiplex PCR panels currently available do not
include the COVID-19. Commercial tests are also not available at present. In a
suspect case in India, the appropriate sample has to be sent to designated
reference labs in India or the National
Institute of Virology in Pune. As the
epidemic progresses, commercial tests
or even die, whereas most young people and children have only mild diseases
(non-pneumonia or mild pneumonia) or are asymptomatic9,81,82. Notably, the
risk of disease was not higher for pregnant women. However, evidence of
transplacental transmission of SARS-CoV-2 from an infected mother to a
neonate was reported, although it was an isolated case83,84. On infection, the
most common symptoms are fever, fatigue and dry cough13,60,80,81. Less
common symptoms include sputum production, headache, haemoptysis,
diarrhoea, anorexia, sore throat, chest pain, chills and nausea and vomiting in
studies of patients in China13,60,80,81. Self-reported olfac- tory and taste
disorders were also reported by patients in Italy. Most people showed signs of
diseases after an incubation period of 1-14 days (most commonly around 5
days), and dyspnoea and pneumonia developed within a median time of 8
days from illness onset.
In a report of 72,314 cases in China, 81% of the cases were classified as mild,
14% were severe cases that required ventilation in an intensive care unit (ICU)
and a 5% were critical (that is, the patients had respiratory failure, septic shock
and/or multiple organ dysfunction or failure)9,86. On admission, ground-glass
opacity was the most common radiologic finding on chest computed
tomography (CT) 13,60,80,81. Most patients also developed marked
lymphopenia, similar to what was observed in patients with SARS and MERS,
and non-survivors developed severer lymphopenia over time 13,60,80,81.
Compared with non-ICU patients, ICU patients had higher levels
was linked to a family member and 26

children had history of
travel/residence to Hubei province in China. All the patients were either
asymptomatic (9%) or had mild disease. No severe or critical cases were
seen. The most common
symptoms were fever (50%) and cough (38%). All patients recovered with
symptomatic therapy and there were no deaths. One case of severe
pneumonia and multiorgan
dysfunction in a child has also been reported [19]. Similarly the neonatal
cases that have been reported have been mild [20].
Diagnosis [21]
A suspect case is defined as one with fever, sore throat and cough who has
history of travel to China or other areas of persistent local transmission or
contact with patients with similar
travel history or those with confirmed
in Yunnan. This novel bat virus, denoted 'RmYN02, is 93.3% identical to SARS-
CoV-2 across the genome. In the long lab gene, it exhibits 97.2% identity to
SARS-COV-2, which is even higher than for RaTG13 (REF.28). In addition to
RaTG13 and RmYN02, phylogenetic analysis shows that bat coronaviruses
ZC45 and ZXC21 previously detected in Rhinolophus pusillus bats from
eastern China also fall into the SARS-CoV-2 lineage of the subgenus
Sarbecovirus36 (FIG. 2). The dis- covery of diverse bat coronaviruses closely
related to SARS-CoV-2 suggests that bats are possible reservoirs of SARS-
CoV-2 (REF.37). Nevertheless, on the basis of current findings, the divergence
between SARS-CoV-2 and related bat coronaviruses likely represents more
than 20 years of sequence evolution, suggesting that these bat coronaviruses
can be regarded only as the likely evolu- tionary precursor of SARS-CoV-2 but
not as the direct progenitor of SARS-CoV-2 (REF.38).
Beyond bats, pangolins are another wildlife host probably linked with SARS-
CoV-2. Multiple SARS-CoV-2- related viruses have been identified in tissues of
Malayan pangolins smuggled from Southeast Asia into southern China from
2017 to 2019. These viruses from pangolins independently seized by Guangxi
and Guangdong pro- vincial customs belong to two distinct sublineages39-41.
The Guangdong strains, which were isolated or sequenced by different
research groups from smuggled pangolins, have 99.8% sequence identity
with each other11. They are very closely related to SARS-CoV-2, exhibiting
92.4% sequence similarity. Notably, the RBD of Guangdong pangolin
coronaviruses is highly similar to that of SARS-CoV-2. The receptor-binding
motif (RBM; which is part of the RBD) of these viruses has only one amino
acid variation from SARS-CoV-2, and it is identical to that of SARS-CoV-2 in all
five critical
recovered patients and used for plasma transfusion twice in a volume of 200
to 250 ml on the day of collection (310). At present, treatment for sepsis and
ARDS mainly involves antimicrobial therapy, source control, and supportive
care. Hence, the use of therapeutic plasma exchange can be considered an
option in managing such severe conditions. Further randomized trials can be
designed to investigate its efficacy (311).
Potential Therapeutic Agents
Potent therapeutics to combat SARS-CoV-2 infection include virus binding
molecules, molecules or inhibitors targeting particular enzymes implicated in
replication and transcription process of the virus, helicase inhibitors, vital viral
proteases and proteins, protease inhibitors of host cells, endocytosis
inhibitors, short interfering RNA (siRNA), neutralizing antibodies, MAbs
against the host receptor, MAbs interfering with the S1 RBD, antiviral peptide
aimed at S2, and natural drugs/medicines (7, 166, 186). The S protein acts as
the critical target for developing CoV antivirals, like inhibitors of S protein and
S cleavage, neutralizing antibodies, RBD-ACE2 blockers, siRNAs, blockers of
the fusion core, and proteases (168).
All of these therapeutic approaches have revealed
identified angiotensin receptor 2 (ACE2) as the receptor through which

the virus enters the respiratory mucosa [11].
The basic case reproduction rate (BCR) is estimated to range from 2 to 6.47 in
various modelling studies [11]. In comparison, the BCR of SARS was 2 and 1.3
for pandemic flu H1N1 2009 [2].
Clinical Features [8, 15-18]
The clinical features of COVID-19 are varied, ranging from asymptomatic state
to acute respiratory distress
syndrome and multi organ dysfunction. The common clinical features include
fever (not in all), cough, sore throat, headache, fatigue, headache, myalgia and
breathlessness. Conjunctivitis has also been described. Thus, they are
indistinguishable from
other respiratoru infections. In a subset
Origin and Spread of COVID-19 [1, 2, 6]

In December 2019, adults in Wuhan, capital city of Hubei province and a major
transportation hub of China started presenting to local hospitals with severe
pneumonia of unknown cause. Many of the initial cases had a common
exposure to the Huanan wholesale seafood market that also
traded live animals. The surveillance system (put into place after the SARS
outbreak) was activated and
respiratory samples of patients were sent to reference labs for etiologic
investigations. On December 31st 2019, China notified the outbreak to the
World Health Organization and on 1st January the Huanan sea food market
was closed. On 7th January the virus was identified as a coronavirus that had
>95% homology with the bat
with COVID-19 showed typical features on initial CT, including bilateral

multilobar ground-glass opacities with a peripheral or posterior distribution
118,119. Thus, it has been suggested that CT scanning combined with
repeated swab tests should be used for individuals with high clinical
suspicion of COVID-19 but who test negative in initial nucleic acid
screening118. Finally, SARS-COV-2 serological tests detecting antibodies to N
or S protein could complement molecular diagnosis, particularly in late phases
after disease onset or for retrospective studies 116,120,121. However, the
extent and duration of immune responses are still unclear, and available
serological tests differ in their sensitivity and specificity, all of which need to
be taken into account when one is deciding on serological tests and
interpreting their results or potentially in the future test for T cell
responses.
Therapeutics
.
To date, there are no generally proven effective therapies for COVID-19 or
antivirals against SARS-CoV-2, although some treatments have shown some
benefits in certain subpopulations of patients or for certain end points (see
later). Researchers and manufacturers are conducting large-scale clinical
trials to evaluate various therapies for COVID-19. As of 2 October 2020, there
were about 405 therapeutic drugs in development for COVID-19, and nearly
318 in human clinical trials (COVID-19 vaccine and therapeutics tracker). In
the following sections, we summarize potential therapeutics against SARS-
CoV-2 on the basis of published clinical data and experience.
infections clinically or through routine lab tests. Therefore travel history

becomes important. However, as the epidemic spreads, the travel history
will become irrelevant.
Treatment [21, 23]
Treatment is essentially supportive and symptomatic.
The first step is to ensure adequate isolation (discussed later) to prevent
transmission to other contacts, patients
and healthcare workers. Mild illness should be managed at home with
counseling about danger signs. The usual principles are maintaining hydration
and nutrition and
controlling fever and cough. Routine
use of antibiotics and antivirals such as
oseltamivir should be avoided in
confirmed cases. In hypoxic patients, provision of oxygen through nasal
prongs, face mask, high flow nasal
epidemic progresses, commercial tests

will become available.
Other laboratory investigations are usually non specific. The white cell count is
usually normal or low. There may be lymphopenia; a lymphocyte count <1000
has been associated with severe disease. The platelet count is usually normal
or mildly low. The CRP and ESR are generally elevated but procalcitonin levels
are usually
normal. A high procalcitonin level may indicate a bacterial co-infection. The
ALT/AST, prothrombin time, creatinine, D-dimer, CPK and LDH may be elevated
and high levels are associated with severe disease.
The chest X-ray (CXR) usually shows bilateral infiltrates but may be normal in
early disease. The CT is more sensitive and specific. CT imaging generally
shows infiltrates, ground glass opacities and sub segmental
comorbidities), it may progress to

pneumonia, acute respiratory distress syndrome (ARDS) and multi organ
dysfunction. Many people are
asymptomatic. The case fatality rate is estimated to range from 2 to 3%.
Diagnosis is by demonstration of the virus in respiratory secretions by special
molecular tests. Common laboratory findings include normal/ low white cell
counts with elevated C- reactive protein (CRP). The
computerized tomographic chest scan. is usually abnormal even in those with
no symptoms or mild disease.
Treatment is essentially supportive; role of antiviral agents is yet to be
established. Prevention entails home isolation of suspected cases and those
with mild illnesses and strict infection control measures at hospitals that
include contact and droplet
precautions. The virus spreads faster
than its two ancestors the SARS-COV
and chest discomfort, and in severe cases dyspnea and bilateral lung
infiltration67. Among the first 27 documented hospitalized patients, most
cases were epidemi- ologically linked to Huanan Seafood Wholesale Market a
wet market located in downtown Wuhan, which sells not only seafood but also
live animals, including poultry and wildlife48. According to a retrospective
study, the onset of the first known case dates back to 8 December 2019 (REF).
On 31 December, Wuhan Municipal Health Commission notified the public of a
pneumonia outbreak of unidentified cause and informed the World Health
Organization (WHO) (FIG. 1).
By metagenomic RNA sequencing and virus isola tion from bronchoalveolar
lavage fluid samples from patients with severe pneumonia, independent
teams of Chinese scientists identified that the causative agent of this
emerging disease is a betacoronavirus that had never been seen
before6,10,11. On 9 January 2020, the result of this etiological identification
was publicly announced (FIG. 1). The first genome sequence of the novel
coronavirus was published on the Virological website on 10 January, and
more nearly complete genome sequences determined by different research
institutes were then released via the GISAID database on 12 January Later,
more patients with no history of exposure to Huanan Seafood Wholesale
Market were identified. Several familial clusters of infection were reported and
nosocomial infection also occurred in health-care facilities. All these cases
provided clear evidence for human-to-human transmission of the new
virus4,12-14 As the outbreak coincided with the approach of the lunar New
Year, travel between cities before the festival facilitated virus transmission in
China. This novel coronavirus pneumonia soon spread to other cities in Hube
province and to other parts of China. Within 1 month.
such instance was in 2002-2003 when a

new coronavirus of the ß genera and
with origin in bats crossed over to
humans via the intermediary host of palm civet cats in the Guangdong
province of China. This virus,
designated as severe acute respiratory syndrome coronavirus affected 8422
people mostly in China and Hong Kong and caused 916 deaths (mortality rate
11%) before being contained [4].
Almost a decade later in 2012, the Middle East respiratory syndrome
coronavirus (MERS-CoV), also of bat origin, emerged in Saudi Arabia with
dromedary camels as the intermediate host and affected 2494 people and
caused 858 deaths (fatality rate 34%) [5].
Origin and Spread of COVID-19 [1, 2, 6]
In December 2019, adults in Wuhan, capital city of Hubei province and a
[median 17 d]. In the case series of

children discussed earlier, all children recovered with basic treatment and did
not need intensive care [17].
There is anecdotal experience with use of remdeswir, a broad spectrum anti
RNA drug developed for Ebola in management of COVID-19 [27]. More
evidence is needed before these drugs are recommended. Other drugs
proposed for therapy are arbidol (an antiviral drug available in Russia and
China), intravenous immunoglobulin, interferons, chloroquine and plasma of
patients recovered from COVID-19 [21, 28, 29]. Additionally, recommendations
about using traditional Chinese herbs find place in the Chinese guidelines [21].
Prevention [21, 30]
exponentially in other countries including South Korea, Italy and Iran.

condition, 25% have recovered, and 3310 (3013 in China and 297 in other
countries) have died [2]. India, which had reported only 3 cases till 2/3/2020,
has also seen a sudden spurt in cases. By 5/3/2020, 29 cases had been
reported; mostly in Delhi, Jaipur and Agra in Italian tourists and their contacts.
One case was reported in an Indian who traveled back from Vienna and
exposed a large number of school children in a birthday party at a city hotel.
Many of the contacts of these cases have been quarantined.
These numbers are possibly an
underestimate of the infected and dead
due to limitations of surveillance and testing. Though the SARS-CoV-2
originated from bats, the intermediary
(entertainment parks etc). China is also

considering introducing legislation to prohibit selling and trading of wild
animals [32].
The international response has been dramatic. Initially, there were massive
travel restrictions to China and people returning from China/ evacuated from
China are being evaluated for clinical symptoms, isolated and tested for
COVID-19 for 2 wks even if
asymptomatic. However, now with rapid world wide spread of the virus these
travel restrictions have extended
to other countries. Whether these
efforts will lead to slowing of viral spread is not known.
A candidate vaccine is under
development.
Practice Points from an Indian
Perspective
article gives a bird's eye view about

this new virus. Since knowledge about this virus is rapidly evolving, readers
are urged to update themselves
regularly.
History
Coronaviruses are enveloped positive sense RNA viruses ranging from 60 nm
to 140 nm in diameter with spike like projections on its surface giving it a
crown like appearance under the electron microscope; hence the name
coronavirus [3]. Four corona viruses namely HKU1, NL63, 229E and OC43 have
been in circulation in humans,
and generally cause mild respiratory disease.
There have been two events in the past two decades wherein crossover of
animal betacorona viruses to humans
has resulted in severe disease. The first such instance was in 2002-2003
when a
in of the monone and
lower respiratory tracts. Acute viral interstitial pneumonia and humoral and
cellular immune responses were observed 48,75. Moreover, prolonged virus
shedding peaked early in the course of infection in asymptomatic macaques,
and old monkeys showed severer interstitial pneumonia than young
monkeys", which is similar to what is seen in patients with COVID-19. In
human ACE2-transgenic mice infected with SARS-CoV-2, typical interstitial
pneumonia was present, and viral anti- gens were observed mainly in the
bronchial epithelial cells, macrophages and alveolar epithelia. Some human
ACE2-transgenic mice even died after infection70,71, In wide-type mice, a
SARS-CoV-2 mouse-adapted strain with the N501Y alteration in the RBD of the
S protein was generated at passage 6. Interstitial pneumonia and
inflammatory responses were found in both young and aged mice after
infection with the mouse-adapted strain. Golden hamsters also showed
typical symptoms after being infected with SARS-CoV-2 (REF.77). In other
animal models, including cats and ferrets, SARS-CoV-2 could efficiently
replicate in the upper respiratory tract but did not induce severe clinical
symptoms43,78. As transmission by direct contact and air was observed in
infected ferrets and hamsters, these animals could be used to model different
transmission modes of COVID-19 (REFS77-79). Animal models offer
important information for understanding the pathogenesis of SARS-CoV-2
infection and the transmission dynamics of SARS- CoV-2, and are important to
evaluate the efficacy of antiviral therapeutics and vaccines.
Clinical and epidemiological features
It appears that all ages of the population are susceptible to SARS-CoV-2
infection, and the median age of infection is around 50 years"," $9,13,60,80,81.
However, clinical manifestations differ with age. In general, older men (>60
years old) with co-morbidities are more likely to develop severe respiratory
disease that requires hospitalization
mask and practice cough hygiene. Caregivers should be asked to wear a

surgical mask when in the same room as patient and use hand hygiene every
15-20 min.
The greatest risk in COVID-19 is transmission to healthcare workers. In the
SARS outbreak of 2002, 21% of those affected were healthcare workers [31].
Till date, almost 1500 healthcare workers in China have been infected
with 6 deaths. The doctor who first warned about the virus has died too. It is
important to protect healthcare workers to ensure continuity of care and to
prevent transmission of
infection to other patients. While COVID-19 transmits as a droplet pathogen
and is placed in Category B of infectious agents (highly pathogenic H5N1 and
SARS), by the China National Health Commission, infection control measures
recommended are those for
pandemic flu where patients were asked to resume work/school once afebrile
for 24 h or by day 7 of illness. Negative molecular tests were not a
prerequisite for discharge.
At the community level, people should be asked to avoid crowded areas and
postpone non-essential travel to places with ongoing transmission. They
should be asked to practice cough hygiene by coughing in sleeve/ tissue
rather than hands and practice hand hygiene frequently every 15-20 min.
Patients with respiratory symptoms should be asked to use surgical masks.
The use of mask by healthy people in public places has not shown to protect
against respiratory viral infections and is currently not recommended by WHO.
However, in China, the public has been asked to wear masks in public and
especially in crowded places and large scale gatherings are prohibited
(entertainment parks etc). China is also
risk regions. It is derived from a live attenuated strain of Mycobacterium

bovis. At present, three new clinical trials have been registered to evaluate the
protective role of BCG vaccination against SARS- CoV-2 (363). Recently, a
cohort study was conducted to evaluate the impact of childhood BCG
vaccination in COVID-19 PCR positivity rates. However, childhood BCG
vaccination was found to be associated with a rate of COVID-19-positive test
results similar to that of the nonvaccinated group (364). Further studies are
required to analyze whether BCG vaccination in childhood can induce
protective effects against COVID-19 in adulthood. Population genetic studies
conducted on 103 genomes identified that the SARS-CoV-2 virus has evolved
into two major types, L and S. Among the two types, L type is expected to be
the most prevalent (~70%), followed by the S type (~30%) (366). This finding
has a significant impact on our race to develop an ideal vaccine, since the
vaccine candidate has to target both strains to be considered effective. At
present, the genetic differences between the L and S types are very small and
may not affect the immune response. However, we can expect further genetic
variations in the coming days that could lead to the emergence of new strains
(367).
exponentially in other countries including South Korea, Italy and Iran.

condition, 25% have recovered, and 3310 (3013 in China and 297 in other
countries) have died [2]. India, which had reported only 3 cases till 2/3/2020,
has also seen a sudden spurt in cases. By 5/3/2020, 29 cases had been
reported; mostly in Delhi, Jaipur and Agra in Italian tourists and their contacts.
One case was reported in an Indian who traveled back from Vienna and
exposed a large number of school children in a birthday party at a city hotel.
Many of the contacts of these cases have been quarantined.
These numbers are possibly an
underestimate of the infected and dead
due to limitations of surveillance and testing. Though the SARS-CoV-2
originated from bats, the intermediary
other emerging viral diseases. Several therapeutic and preventive strategies,

including vaccines, immunotherapeutics, and antiviral drugs, have been
exploited against the previous CoV outbreaks (SARS-CoV and MERS-CoV) (8,
104, 164-167). These valuable options have already been evaluated for their
potency, efficacy, and safety, along with several other types of current
research that will fuel our search for ideal therapeutic agents against COVID-
19 (7, 9, 19, 21, 36). The primary cause of the unavailability of approved and
commercial vaccines, drugs, and therapeutics to counter the earlier SARS-CoV
and MERS-CoV seems to owe to the lesser attention of the biomedicine and
pharmaceutical companies, as these two CoVs did not cause much havoc,
global threat, and panic like those posed by the SARS-CoV-2 pandemic (19).
Moreover, for such outbreak situations, the requirement for vaccines and
therapeutics/drugs exists only for a limited period, until the outbreak is
controlled. The proportion of the human population infected with SARS-CoV
and MERS-CoV was also much lower across the globe, failing to attract drug
and vaccine manufacturers and producers. Therefore, by the time an effective
drug or vaccine is designed against such disease outbreaks, the virus would
have been controlled by adopting appropriate and strict
Splits Tree phylogeny analysis.

In the unrooted phylogenetic tree of different betacoronaviruses based on the
S protein, virus sequences from different subgenera grouped into separate
clusters. SARS-CoV-2 sequences from Wuhan and other countries exhibited a
close relationship and appeared in a single cluster (Fig. 1). The CoVs from the
subgenus Sarbecovirus appeared jointly in Splits Tree and divided into three
subclusters, namely, SARS-CoV-2, bat-SARS-like- CoV (bat-SL-CoV), and SARS-
CoV (Fig. 1). In the case of other subgenera, like Merbecovirus, all of the
sequences grouped in a single cluster, whereas in Embecovirus, different
species, comprised of canine respiratory CoVs, bovine CoVs, equine CoVs,
and human CoV strain (OC43), grouped in a common cluster. Isolates in the
subgenera Nobecovorus and Hibecovirus were found to be placed separately
away from other reported SARS-CoVS but shared a bat origin.
CURRENT WORLDWIDE SCENARIO OF SARS-COV-2
This novel virus, SARS-CoV-2, comes under the subgenus Sarbecovirus of the
Orthocoronavirinae subfamily and is entirely different from the viruses
Practice Points from an Indian

Perspective
At the time of writing this article, the risk of coronavirus in India is
extremely low. But that may change in the next few weeks. Hence the
following is recommended:
• Healthcare providers should take travel history of all patients with respiratory
symptoms, and any international travel in the past 2
•
wks as well as contact with sick
people who have travelled
internationally.
They should set up a system of
triage of patients with respiratory
illness in the outpatient
department and give them a
simple surgical mask to wear.
They should use surgical masks themselves while examining such
themselves while examining such

patients and practice hand
hygiene frequently.
Suspected cases should be referred to government designated centres for
isolation and testing (in
Mumbai, at this time, it is Kasturba
hospital). Commercial kits for
testing are not yet available in India.
Patients admitted with severe
pneumonia and acute respiratory
distress syndrome should be
evaluated for travel history and
placed under contact and droplet isolation. Regular
decontamination of surfaces
should be done. They should be tested for etiology using multiplex PCR panels
if logistics permit and if no pathogen is identified, refer the samples for testing
for SARS- CoV-2.
specimens, like bronchoalveolar lavage fluid, sputum, nasal swabs,

fibrobronchoscope brush biopsy specimens, pharyngeal swabs, feces, and
blood (246).
The presence of SARS-CoV-2 in fecal samples has posed grave public health
concerns. In addition to the direct transmission mainly occurring via droplets
of sneezing and coughing, other routes, such as fecal excretion and
environmental and fomite contamination, are contributing to SARS-CoV-2
transmission and spread (249–252). Fecal excretion has also been
documented for SARS-CoV and MERS-CoV, along with the potential to stay
viable in situations aiding fecal-oral transmission. Thus, SARS-CoV-2 has every
possibility to be transmitted through this mode. Fecal-oral transmission of
SARS- CoV-2, particularly in regions having low standards of hygiene and poor
sanitation, may have grave consequences with regard to the high spread of
this virus. Ethanol and disinfectants containing chlorine or bleach are effective
against coronaviruses (249-252). Appropriate precautions need to be followed
strictly while handling the stools of patients infected with SARS-CoV-2.
Biowaste materials and
sewage from hospitals must be adequately disinfected, treated, and disposed
of properly. The significance of frequent and good hand hygiene and
To assess the genetic variation of different SARS- CoV-2 strains, the 2019
Novel Coronavirus Resource of China National Center for Bioinformation
aligned 77,801 genome sequences of SARS-CoV-2 detected globally and
identified a total of 15,018 mutations, including 14,824 single-nucleotide
polymorphisms (BIGD)31. In the S protein, four amino acid alterations, V483A,
L4551, F456V and G476S, are located near the binding interface in the RBD,
but their effects on binding to the host receptor are unknown. The alteration
D614G in the S1 subunit was found far more frequently than other S variant
sites, and it is the marker of a major subclade of SARS-CoV-2 (clade G). Since
March 2020, SARS-CoV-2 variants with G614 in the S protein have replaced the
original D614 variants and become the dominant form circulating globally.
Compared with the D614 variant, higher viral loads were found in patients
infected with the G614 variant, but clinical data suggested no significant link
between the D614G alteration and disease severity32. Pseudotyped viruses
carrying the S protein with G614 generated higher infectious titres than
viruses carrying the S protein with D614, suggesting the alteration may have
increased the infectivity of SARS-COV-2 (REF. 32). However, the results of in
vitro experiments based on pseudovirus models may not exactly reflect
natural infection. This preliminary finding should be validated by more studies
using wild-type SARS-CoV-2 variants to infect different target cells and animal
models. Whether this amino acid change enhanced virus transmissibility is
also to be determined. Another marker mutation for SARS-CoV-2 evolution is
the single-nucleotide
the SARS-COV. Environmental samples

from the Huanan sea food market also tested positive, signifying that the virus
originated from there [7]. The number of cases started increasing
exponentially, some of which did not have exposure to the live animal market,
suggestive of the fact that human-to-human transmission was occurring [8].
The first fatal case was reported on 11th Jan 2020. The massive migration of
Chinese during the Chinese New Year fuelled the epidemic. Cases in other
provinces of China, other countries (Thailand, Japan and South Korea in quick
succession) were reported in people who were returning from Wuhan.
Transmission to
healthcare workers caring for patients was described on 20th Jan, 2020. By
23rd January, the 11 million population of Wuhan was placed under lock down
with restrictions of entry and exit from the region. Soon this lock down was
respiratory infection (SARI) and respiratory distress, shock or hypoxaemia.

Patients with SARI can be given conservative fluid therapy only when there is
no evidence of shock. Empiric antimicrobial therapy must be started to
manage SARI. For patients with sepsis, antimicrobials must be administered
within 1 hour of initial assessments. The WHO and CDC recommend that
glucocorticoids not be used in patients with COVID-19 pneumonia except
where there are other indications (exacerbation of chronic obstructive
pulmonary disease).59
Patients' clinical deterioration is closely observed with SARI; however, rapidly
progressive respiratory failure and sepsis. require immediate supportive care
interventions comprising quick use of neuromuscular blockade and sedatives,
hemodynamic management, nutritional support, maintenance of blood
glucose levels, prompt assessment and treatment of nosocomial pneumonia,
and prophylaxis
against deep venous thrombosis (DVT) and
60
gastrointestinal (GI) bleeding. Generally, such
patients give way to their primary illness to secondary complications like
sepsis or multiorgan system failure.48
consolidation. It is also abnormal in

asymptomatic patients/ patients with no clinical evidence of lower
respiratory tract involvement. In fact, abnormal CT scans have been used to
diagnose COVID-19 in suspect cases with negative molecular diagnosis; many
of these patients had positive molecular tests on repeat testing [22].
Differential Diagnosis [21]
The differential diagnosis includes all types of respiratory viral infections
[influenza, parainfluenza, respiratory syncytial virus (RSV), adenovirus, human
metapneumovirus, non COVID- 19 coronavirus], atypical organisms
(mycoplasma, chlamydia) and bacterial infections. It is not possible to
differentiate COVID-19 from these infections clinically or through routine lab
tests. Therefore travel history
becomes important. However, as the epidemic spreads, the travel history
variant group. The receptor-binding gene region appears to be very similar to

that of the SARS-
CoV and it is believed that the same receptor would be used for cell entry."
17
4.1 Virion structure and its
genome
Coronaviruses are structurally enveloped,
belonging to the positive-strand RNA viruses category that has the largest
known genomes of RNA. The structures of the coronavirus are
more spherical in shape, but their structure has the potential to modify their
morphology in response to environmental conditions, being pleomorphic. The
capsular membrane which represents the outer envelope usually has
glycoprotein projection and covers the nucleus, comprising a matrix protein
containing a positive-strand RNA. Since the structure possesses 5'-capped
and 3'-polyadenylated ends, it remains identical to the cellular mRNAs.18 The
structure is comprised of hemagglutinin esterase (HE) (present only in some
beta-coronaviruses), spike (S), small membrane (E), membrane (M) and
nucleocapsid (N), as shown (Figure 1). The envelope containing glycoprotein
is responsible for attachment to the host cell, which possesses the primary
anti-genic epitopes mainly those
glass opacities and sub segmental consolidation. It is also abnormal in

asymptomatic patients/ patients with no clinical evidence of lower
respiratory tract involvement. In fact, abnormal CT scans have been used to
diagnose COVID-19 in suspect cases with negative molecular diagnosis; many
of these patients had positive molecular tests on repeat testing [22].
Differential Diagnosis [21]
The differential diagnosis includes all types of respiratory viral infections
[influenza, parainfluenza, respiratory syncytial virus (RSV), adenovirus, human
metapneumovirus, non COVID- 19 coronavirus], atypical organisms
(mycoplasma, chlamydia) and bacterial infections. It is not possible to
differentiate COVID-19 from these
infections clinically or through routine
(using suitable animal models) should be conducted to evaluate the risk of

future epidemics. Presently, licensed antiviral drugs or vaccines against SARS-
CoV, MERS-CoV, and SARS-CoV-2 are lacking. However, advances in designing
antiviral drugs and vaccines against several other emerging diseases will help
develop suitable therapeutic agents against COVID-19 in a short time. Until
then, we must rely exclusively on various control and prevention measures to
prevent this new disease from becoming a pandemic.
mice, and hDPP4-Tg mice (transgenic for expressing hDPP4) for MERS-CoV
infection (221). The CRISPR-Cas9 gene-editing tool has been used for
inserting genomic alterations in mice, making them susceptible to MERS-CoV
infection (222). Efforts are under way to recognize suitable animal models for
SARS-CoV2/COVID-19, identify the receptor affinity of this virus, study
pathology in experimental animal models, and explore virus-specific immune
responses and protection studies, which together would increase the pace of
efforts being made for developing potent vaccines and drugs to counter this
emerging virus. Cell lines, such as monkey epithelial cell lines (LLC-MK2 and
Vero-B4), goat lung cells, alpaca kidney cells, dromedary umbilical cord cells,
and advanced ex vivo three-dimensional tracheobronchial tissue, have been
explored to study human CoVs (MERS-CoV) (223, 224). Vero and Huh-7 cells
(human liver cancer cells) have been used for isolating SARS-CoV-2 (194).
Recently, an experimental study with rhesus monkeys as animal models
revealed the absence of any viral loads in nasopharyngeal and anal swabs,
and no viral replication was recorded in the primary tissues at a time interval
of 5 days post-reinfection in reexposed monkeys (274). The subsequent and
pathological
virological, radiological,
developed for rapid and colorimetric detection of this virus (354). RT-LAMP
serves as a simple, rapid, and sensitive diagnostic method that does not
require sophisticated equipment or skilled personnel (349). An interactive
web-based dashboard for tracking SARS-CoV-2 in a real-time mode has been
designed (238). A smartphone-integrated home-based point- of-care testing
(POCT) tool, a paper-based POCT combined with LAMP, is a useful point-of-
care diagnostic (353). An Abbott ID Now COVID-19 molecular POCT-based
test, using isothermal nucleic acid amplification technology, has been
designed as a point-of-care test for very rapid detection of SARS-CoV-2 in just
5 min (344). A CRISPR-based SHERLOCK (specific high-sensitivity enzymatic
reporter unlocking) diagnostic for rapid detection of SARS-CoV-2 without the
requirement of specialized instrumentation has been reported to be very
useful in the clinical diagnosis of COVID-19 (360). A CRISPR-Cas 12-based
lateral flow assay also has been developed for rapid detection of SARS-CoV-2
(346). Artificial intelligence, by means of a three- dimensional deep-learning
model, has been developed for sensitive and specific diagnosis of COVID-19
via CT images (332).
Tracking and mapping of the rising incidence rates, disease outbreaks.
community spread,
Inhibition of virus replication. Replication inhibitors include remdesivir (GS-

5734), favilavir (T-705), ribavirin, lopinavir and ritonavir. Except for lopinavir
and ritonavir, which inhibit 3CLpro, the other three all target RdRp128,135 (FIG.
5). Remdesivir has shown activity against SARS-CoV-2 in vitro and in vivo
128,136. A clinical study revealed a lower need for oxygen support in patients
with COVID-19 (REF.137). Preliminary results of the Adaptive COVID-19
Treatment Trial (ACTT) clinical trial by the National Institute of Allergy and
Infectious Diseases (NIAID) reported that remdesivir can shorten the recovery
time in hospitalized adults with COVID-19 by a couple days compared with
placebo, but the difference in mortality was not statistically significant138.
The FDA has issued an emergency use authorization for remdesivir for the
treatment of hospitalized patients with severe COVID-19. It is also the first
approved option by the European Union for treatment of adults and adoles-
cents with pneumonia requiring supplemental oxygen. Several international
phase III clinical trials are contin- uing to evaluate the safety and efficacy of
remdesivir for the treatment of COVID-19.
Favilavir (T-705), which is an antiviral drug developed in Japan to treat
influenza, has been approved in China, Russia and India for the treatment of
COVID-19. A clinical study in China showed that favilavir significantly
reduced the signs of improved disease signs on chest imaging and shortened
the time to viral clearance139. A preliminary report in Japan showed rates of
clinical improvement of 73.8% and 87.8% from the start of favilavir therapy in
patients with mild COVID-19 at 7 and 14 days, respectively, and 40.1% and
60.3% in patients with severe COVID-19 at 7 and 14 days,
might be lower. Further genetic analysis is required between SARS-CoV-2 and

different strains of SARS-CoV and SARS-like (SL) CoVs to evaluate the
possibility of repurposed vaccines against COVID-19. This strategy will be
helpful in the scenario of an outbreak, since much time can be saved, because
preliminary evaluation, including in vitro studies, already would be completed
for such vaccine candidates.
Multiepitope subunit vaccines can be considered a promising preventive
strategy against the ongoing COVID-19 pandemic. In silico and advanced
immunoinformatic tools can be used to develop multiepitope subunit
vaccines. The vaccines that are engineered by this technique can be further
evaluated using docking studies and, if found effective, then can be further
evaluated in animal models (365). Identifying epitopes that have the potential
to become a vaccine candidate is critical to developing an effective vaccine
against COVID-19. The immunoinformatics approach has been used for
recognizing essential epitopes of cytotoxic T lymphocytes and B cells from
the surface glycoprotein of SARS-CoV-2. Recently, a few epitopes have been
recognized from the SARS-CoV- 2 surface glycoprotein. The selected epitopes
explored targeting molecular dynamic simulations,
6.1 Laboratory testing for coronavirus disease 2019 (COVID- 19) in suspected
human cases
The assessment of the patients with COVID-19 should be based on the clinical
features and also epidemiological factors. The screening protocols must be
prepared and followed per the native context.31 Collecting and testing of
specimen samples from the suspected individual is considered to be one of
the main principles for controlling and managing the outbreak of the disease
in a country. The suspected cases must be screened thoroughly in order to
detect the virus with the help of nucleic acid amplification tests such as
reverse transcription polymerase chain reaction (RT- PCR). If a country or a
particular region does not have the facility to test the specimens, the
specimens of the suspected individual should be sent to the nearest reference
laboratories per the list provided by WHO.32
It is also recommended that the suspected patients be tested for the other
respiratory pathogens by performing the routine laboratory investigation per
the local guidelines, mainly to differentiate from other viruses that include
influenza virus, parainfluenza virus, adenovirus, respiratory syncytial virus,
rhinovirus, human
respectively140. However, this study did not include
a control arm, and most of the trials of favilavir were based on a small sample
size. For more reliable assessment of the effectiveness of favilavir for
treating COVID-19, large-scale randomized controlled trials should be
conducted.
Lopinavir and ritonavir were reported to have in vitro inhibitory activity against
SARS-CoV and MERS-CoV141,142. Alone, the combination of lopinavir
virological,
radiological, and pathological
observations indicated that the monkeys with reexposure had no recurrence
of COVID-19, like the SARS-CoV-2-infected monkeys without rechallenge.
These findings suggest that primary infection with SARS-CoV-2 could protect
from later exposures to the virus, which could help in defining disease
prognosis and crucial inferences for designing and developing potent
vaccines against COVID-19 (274).
PREVENTION, CONTROL, AND MANAGEMENT
In contrast to their response to the 2002 SARS outbreak, China has shown
immense political openness in reporting the COVID-19 outbreak promptly.
They have also performed rapid sequencing of COVID-19 at multiple levels
and shared the findings globally within days of identifying the novel virus
(225). The move made by China opened a new chapter in global health
security and diplomacy. Even though complete lockdown was declared
following the COVID-19 outbreak in Wuhan, the large-scale movement of
people has resulted in a radiating spread of infections in the surrounding
provinces as well as to several other countries. Large-scale screening
programs might
there, there is an increase in the outbreak of this virus through human-to-

human
transmission, with the fact that it has become widespread around the globe.
This confirms the fact similar to the previous epidemics, including SARS and
MERS, that this coronavirus exhibited potential human-to-human
transmission, as it was recently declared a pandemic by WHO.26
Respiratory droplets are the major carrier for coronavirus transmission. Such
droplets can either stay in the nose or mouth or enter the lungs via the inhaled
air. Currently, it is known that COVID-19's transmission from one person to
another also occurs through touching either an infected surface or even an
object. With the current scant awareness of the transmission systems
however, airborne safety measures with a high-risk procedure have been
proposed in many countries. Transmission levels, or the rates from one
person to another, reported differ by both location and interaction with
involvement in infection control. It is stated that even asymptomatic
individuals or those individuals in their incubation period can act as carrier of
SARS-CoV2.27, 28 With the data and
evidence provided by the CDC, the usual incubation period is probably 3 to 7
days, sometimes being prolonged up to even 2 weeks, and the typical
symptom occurrence
dogs have low susceptibility, while the chickens, ducks, and pigs are not at all
susceptible to SARS- CoV-2 (329).
Similarly, the National Veterinary Services Laboratories of the USDA have
reported COVID-19 in tigers and lions that exhibited respiratory signs like dry
cough and wheezing. The zoo animals are suspected to have been infected by
an asymptomatic zookeeper (335). The total number of COVID-19- positive
cases in human beings is increasing at a high rate, thereby creating ideal
conditions for viral spillover to other species, such as pigs. The evidence
obtained from SARS-CoV suggests that pigs can get infected with SARS-CoV-
2 (336). However, experimental inoculation with SARS-CoV-2 failed to infect
pigs (329).
Further studies are required to identify the possible animal reservoirs of SARS-
CoV-2 and the seasonal variation in the circulation of these viruses in the
animal population. Research collaboration between human and animal health
sectors is becoming a necessity to evaluate and identify the possible risk
factors of transmission between animals and humans. Such cooperation will
help to devise efficient strategies for the management of emerging zoonotic
diseases (12).
snakes, and various other wild animals (20, 30, 79, 93, 124, 125, 287).
Coronavirus infection is linked to different kinds of clinical manifestations,
varying from enteritis in cows and pigs, upper respiratory disease in chickens,
and fatal respiratory infections in humans (30).
Among the CoV genera, Alphacoronavirus and Betacoronavirus infect
mammals, while Gammacoronavirus and Deltacoronavirus mainly infect birds,
fishes, and, sometimes, mammals (27, 29, 106). Several novel coronaviruses
that come under the genus Deltacoronavirus have been discovered in the past
from birds, like Wigeon coronavirus HKU20, Bulbul coronavirus HKU11, Munia
coronavirus HKU13, white-eye coronavirus HKU16, night-heron coronavirus
HKU19, and common moorhen coronavirus HKU21, as well as from pigs
(porcine coronavirus HKU15) (6, 29). Transmissible gastroenteritis virus
(TGEV), porcine epidemic diarrhea virus (PEDV), and porcine hemagglutinating
encephalomyelitis virus (PHEV) are some of the coronaviruses of swine.
Among them, TGEV and PEDV are responsible for causing severe
gastroenteritis in young piglets with noteworthy morbidity and mortality.
Infection with PHEV also causes enteric infection but can cause encephalitis
due to its ability to infect the nervous
prevailing chronic medical conditions such as lung disease, heart failure,

cancer, cerebrovascular disease, renal disease, diabetes, liver disease and
immunocompromising conditions and
pregnancy are risk factors for developing severe illness. Management
includes implementation of prevention and control measures and supportive
therapy to manage the complications, together with advanced organ
support.57
Corticosteroids must be avoided unless specified for chronic obstructive
pulmonary disease exacerbation or septic shock, as it is likely to prolong viral
replication as detected in MERS-CoV patients.58
12 EARLY SUPPORTIVE THERAPY AND MONITORING
Management of patients with suspected or documented COVID-19 consists of
ensuring appropriate infection control and supportive care. WHO and the CDC
posted clinical guidance for COVID-19.59
Immediate therapy of add-on oxygen must be started for patients with severe
acute
respiratory infection (SARI) and respiratory
Abstract
There is a new public health crises
threatening the world with the
emergence and spread of 2019 novel coronavirus (2019-nCoV) or the severe
acute respiratory syndrome
coronavirus 2 (SARS-CoV-2). The virus originated in bats and was transmitted
to humans through yet unknown intermediary animals in Wuhan, Hubei
province, China in December 2019. There have been around 96,000
reported cases of coronavirus disease 2019 (COVID-2019) and 3300 reported
deaths to date (05/03/2020). The disease is transmitted by inhalation or
contact with infected droplets and the incubation period ranges from 2 to 14
d. The symptoms are usually fever, cough, sore throat, breathlessness, fatigue,
malaise among others. The disease is mild in most people; in some (usually
the elderly and those with comorbidities) it may progress to
prevent further spread of disease at mass gatherings, functions remain

canceled in the affected cities, and persons are asked to work from home
(232). Hence, it is a relief that the current outbreak of COVID-19 infection can
be brought under control with the adoption of strategic preventive and control
measures along with the early isolation of subsequent cases in the coming
days. Studies also report that since air traffic between China and African
countries increased many times over in the decade after the SARS outbreak,
African countries need to be vigilant to prevent the spread of novel
coronavirus in Africa (225). Due to fear of virus spread, Wuhan City was
completely shut down (233). The immediate control of the ongoing COVID-19
outbreaks appears a mammoth task, especially for developing countries, due
to their inability to allocate quarantine stations that could screen infected
individuals' movements (234). Such underdeveloped countries should divert
their resources and energy to enforcing the primary level of preventive
measures, like controlling the entry of individuals from China or countries
where the disease has flared up, isolating the infected individuals, and
quarantining individuals with suspected infection. Most of the sub-Saharan
African countries have a fragile health system that can be
vaccine that can produce cross-reactive antibodies. However, the success of

such a vaccine relies greatly on its ability to provide protection not only
against present versions of the virus but also the ones that are likely to
emerge in the future. This can be achieved by identifying antibodies that can
recognize relatively conserved epitopes that are maintained as such even
after the occurrence of considerable variations (362). Even though several
vaccine clinical trials are being conducted around the world, pregnant women
have been completely excluded from these studies. Pregnant women are
highly vulnerable to emerging diseases such as COVID-19 due to alterations in
the immune system and other physiological systems that are associated with
pregnancy. Therefore, in the event of successful vaccine development,
pregnant women will not get access to the vaccines (361). Hence, it is
recommended that pregnant women be included in the ongoing vaccine trials,
since successful vaccination in pregnancy will protect the mother, fetus, and
newborn.
The heterologous immune effects induced by Bacillus Calmette Guérin (BCG)
vaccination is a promising strategy for controlling the COVID-19 pandemic and
requires further investigations. BCG is a widely used vaccine against
tuberculosis in high-
populations. The in vitro and in vivo studies carried out on the isolated virus
confirmed that there is a potential risk for the reemergence of SARS-CoV
infection from the viruses that are currently circulating in the bat population
(105).
CLINICAL PATHOLOGY OF SARS-CoV-2 (COVID-19)
The disease caused by SARS-CoV-2 is also named severe specific contagious
pneumonia (SSCP), Wuhan pneumonia, and, recently, COVID- 19 (110).
Compared to SARS-CoV, SARS-CoV-2 has less severe pathogenesis but has
superior transmission capability, as evidenced by the rapidly increasing
number of COVID-19 cases (111). The incubation period of SARS-CoV-2 in
familial clusters was found to be 3 to 6 days (112). The mean incubation
period of COVID-19 was found to be 6.4 days, ranging from 2.1 to 11.1 days
(113). Among an early affected group of 425 patients, 59 years was the
median age, of which more males were affected (114). Similar to SARS and
MERS, the severity of this nCoV is high in age groups above 50 years (2, 115).
Symptoms of COVID-19 include fever, cough, myalgia or fatigue, and, less
commonly, headache, hemoptysis, and diarrhea (116, 282). Compared to the
SARS-CoV-2-infected patients in Wuhan during
specifically in the respiratory tract will help to reduce virus-triggered immune

pathologies in COVID-19 (209). The later stages of coronavirus- induced
inflammatory cascades are characterized by the release of proinflammatory
interleukin-1 (IL-1) family members, such as IL-1 and IL-33. Hence, there exists
a possibility that the inflammation associated with coronavirus can be
inhibited by utilizing anti-inflammatory cytokines that belong to the IL-1 family
(92). It has also been suggested that the actin protein is the host factor that is
involved in cell entry and pathogenesis of SARS-CoV-2. Hence, those drugs
that modulate the biological activity of this protein, like ibuprofen, might have
some therapeutic application in managing the disease (174). The plasma
angiotensin 2 level was found to be markedly elevated in COVID-19 infection
and was correlated with viral load and lung injury. Hence, drugs that block
angiotensin receptors may have potential for treating COVID-19 infection
(121). A scientist from Germany, named Rolf Hilgenfeld, has been working on
the identification of drugs for the treatment of coronaviral infection since the
time of the first SARS outbreak (19).
The SARS-CoV S2 subunit has a significant function in mediating virus fusion
that provides entry into the host cell. Heptad repeat 1 (HR1) and heptad
high commercial value, since they are used in traditional Chinese medicine
(TCM). Therefore, the handling of bats for trading purposes poses a
considerable risk of transmitting zoonotic COV epidemics (139).
Due to the possible role played by farm and wild animals in SARS-CoV-2
infection, the WHO, in their novel coronavirus (COVID-19) situation report,
recommended the avoidance of unprotected contact with both farm and wild
animals (25). The live- animal markets, like the one in Guangdong, China,
provides a setting for animal coronaviruses to amplify and to be transmitted
to new hosts, like humans (78). Such markets can be considered a critical
place for the origin of novel zoonotic diseases and have enormous public
health significance in the event of an outbreak. Bats are the reservoirs for
several viruses; hence, the role of bats in the present outbreak cannot be ruled
out (140). In a qualitative study conducted for evaluating the zoonotic risk
factors among rural communities of southern China, the frequent human-
animal interactions along with the low levels of environmental biosecurity
were identified as significant risks for the emergence of zoonotic disease in
local communities (141, 142).
The comprehensive sequence analysis of the
Initially, the epicenter of the SARS-CoV-2 pandemic was China, which reported
a significant number of deaths associated with COVID-19, with 84,458
laboratory-confirmed cases and 4,644 deaths as of 13 May 2020 (Fig. 4). As
of 13 May 2020, SARS-COV-2 confirmed cases have been reported in more
than 210 countries apart from China (Fig. 3 and 4) (WHO Situation Report
114) (25, 64). COVID-19 has been reported on all continents except Antarctica.
For many weeks, Italy was the focus of concerns regarding the large number
of cases, with 221,216 cases and 30,911 deaths, but now, the United States is
the country with the largest number of cases, 1,322,054, and 79,634 deaths.
Now, the United Kingdom has even more cases (226,4671) and deaths
(32,692) than Italy. A John Hopkins University web platform has provided daily
updates on the basic epidemiology of the COVID-19 outbreak
transmission risk (228). Considering the zoonotic links associated with SARS-
CoV-2, the One Health approach may play a vital role in the prevention and
control measures being followed to restrain this pandemic virus (317-319).
The substantial importation of COVID-19 presymptomatic cases from Wuhan
has resulted in independent, self- sustaining outbreaks across major cities
both within the country and across the globe. The majority of Chinese cities
are now facing localized outbreaks of COVID-19 (231). Hence, deploying
efficient public health interventions might help to cut the spread of this virus
globally.
The occurrence of COVID-19 infection on several cruise ships gave us a
preliminary idea regarding the transmission pattern of the disease. Cruise
ships act as a closed environment and provide an ideal setting for the
occurrence of respiratory disease outbreaks. Such a situation poses a
significant threat to travelers, since people from different countries are on
board, which favors the introduction of the pathogen (320). Although nearly 30
cruise ships from different countries have been found harboring COVID-19
infection, the major cruise ships that were involved in the COVID-19 outbreaks
are the Diamond Princess, Grand Princess, Celebrity Apex, and Ruby Princess.
The
viruses in nasal washes, saliva, urine and faeces for up to 8 days after
infection, and a few naive ferrets with only indirect contact were positive for
viral RNA, suggesting airborne transmission78. In addition, transmission of
the virus through the ocular surface and prolonged presence of SARS-CoV-2
viral RNA in faecal samples were also documented 101,102. Coronaviruses
can persist on inanimate surfaces for days, which could also be the case for
SARS-CoV-2 and could pose a prolonged risk of infection 103. These findings
explain the rapid geographic spread of COVID-19, and public health
interventions to reduce transmission will provide benefit to mitigate the
epidemic, as has proved successful in China and several other countries, such
as South Korea89,104,105.
Diagnosis
time
Early diagnosis is crucial for controlling the spread of COVID-19. Molecular
detection of SARS-CoV-2 nucleic acid is the gold standard. Many viral nucleic
acid detection kits targeting ORF1b (including RdRp), N, E or S genes are
commercially available 11,106-109. The detection ranges from several
minutes to hours depending on the technology10 106,107,109-111. The
molecular detection can be affected by many factors. Although SARS-CoV-2
has been detected from a variety of respiratory sources, including throat
swabs, posterior oropharyngeal saliva, nasopharyngeal swabs, sputum and
bronchial fluid, the viral load is higher in lower respiratory tract sam- ples1
11,96,112-115. In addition, viral nucleic acid was also found in samples from
the intestinal tract or blood even when respiratory samples were negative116.
Lastly, viral load may already drop from its peak level on disease onset 96,97.
Accordingly, false negatives can be common when oral swabs and used, and
so multiple detection methods should be adopted to confirm a COVID-19
diagnosis 117,118. Other detection methods were therefore used to
overcome this problem. Chest CT was used to quickly identify a patient when
the capacity of molecular detection was overloaded in Wuhan. Patients
polymorphism at nucleotide position 28,144, which results in amino acid

substitution of Ser for Lys at residue 84 of the ORF8 protein. Those variants
with this mutation make up a single subclade labelled as 'clade S'33,34
Currently, however, the available sequence data are not sufficient to interpret
the early global transmission history of the virus, and travel patterns, founder
effects and public health measures also strongly influence the spread of
particular lineages, irrespective of potential biological differences between
different virus variants.
Animal host and spillover
Bats are important natural hosts of alphacoronavi- ruses and
betacoronaviruses. The closest relative to SARS-CoV-2 known to date is a bat
coronavirus detected in Rhinolophus affinis from Yunnan province, China,
named 'RaTG13', whose full-length genome sequence is 96.2% identical to
that of SARS-CoV-2 (REF.). This bat virus shares more than 90% sequence
identity with SARS-CoV-2 in all ORFs throughout the genome, including the
highly variable S and ORF8 (REF.). Phylogenetic analysis confirms that SARS-
CoV-2 closely clusters with RaTG13 (FIG. 2). The high genetic similarity
between SARS-CoV-2 and RaTG13 supports the hypothesis that SARS-CoV-2
likely originated from bats 35. Another related coronavirus has been reported
more recently in a Rhinolophus malayanus bat sampled
in Yunnan This novel hat virus denoted 'RmYN02'
in asymptomatic patients. These abnormalities progress from the initial focal

unilateral to diffuse bilateral ground-glass opacities and will further progress
to or coexist with lung consolidation changes within 1 to 3 weeks (159). The
role played by radiologists in the current scenario is very important.
Radiologists can help in the early diagnosis of lung abnormalities associated
with COVID-19 pneumonia. They can also help in the evaluation of disease
severity, identifying its progression to acute respiratory distress syndrome and
the presence of secondary bacterial infections (160). Even though chest CT is
considered an essential diagnostic tool for COVID-19, the extensive use of CT
for screening purposes in the suspected individuals might be associated with
a disproportionate risk-benefit ratio due to increased radiation exposure as
well as increased risk of cross- infection. Hence, the use of CT for early
diagnosis of SARS-CoV-2 infection in high-risk groups should be done with
great caution (292).
More recently, other advanced diagnostics have been designed and developed
for the detection of SARS-CoV-2 (345, 347, 350-352). A reverse transcriptional
isothermal
loop-mediated
amplification (RT-LAMP), namely, iLACO, has been
developed for rapid and colorimetric detection of this
adaptive evolution, close monitoring of the viral mutations that occur during
subsequent human-to- human transmission is warranted.
M Protein
The M protein is the most abundant viral protein present in the virion particle,
giving a definite shape to the viral envelope (48). It binds to the nucleocapsid
and acts as a central organizer of coronavirus assembly (49). Coronavirus M
proteins are highly diverse in amino acid contents but maintain overall
structural similarity within different genera (50). The M protein has three
transmembrane domains, flanked by a short amino terminus outside the virion
and a long carboxy terminus inside the virion (50). Overall, the viral scaffold is
maintained by M-M interaction. Of note, the M protein of SARS-CoV-2 does not
have an amino acid substitution compared to that of SARS-CoV (16).
E Protein
The coronavirus E protein is the most enigmatic and smallest of the major
structural proteins (51). It plays a multifunctional role in the pathogenesis,
assembly, and release of the virus (52). It is a small integral membrane
polypeptide that acts as а viroporin (ion channel) (53). The inactivation or
vitro antiviral potential of FAD-approved drugs, viz., ribavirin, penciclovir,

nitazoxanide, nafamostat, and chloroquine, tested in comparison to
remdesivir and favipiravir (broad-spectrum antiviral drugs) revealed remdesivir
and chloroquine to be highly effective against SARS-CoV-2 infection in vitro
(194). Ribavirin, penciclovir, and favipiravir might not possess noteworthy in
vivo antiviral actions for SARS-CoV-2, since higher concentrations of these
nucleoside analogs are needed in vitro to lessen the viral infection. Both
remdesivir and chloroquine are being used in humans to treat other diseases,
and such safer drugs can be explored for assessing their effectiveness in
COVID-19 patients.
Several therapeutic agents, such as lopinavir/ritonavir, chloroquine,
and
hydroxychloroquine, have been proposed for the clinical management of
COVID-19 (299). A molecular docking study, conducted in the RNA- dependent
RNA polymerase (RdRp) of SARS-CoV-2 using different commercially available
antipolymerase drugs, identified that drugs such as ribavirin, remdesivir,
galidesivir, tenofovir, and sofosbuvir bind RdRp tightly, indicating their vast
potential to be used against COVID-19 (305). A broad-spectrum antiviral drug
that was developed in the United States, tilorone dihydrochloride (tilorone),
N Protein
The N protein of coronavirus is multipurpose. Among several functions, it
plays a role in complex formation with the viral genome, facilitates M protein
interaction needed during virion assembly, and enhances the transcription
efficiency of the virus (55, 56). It contains three highly conserved and distinct
domains, namely, an NTD, an RNA-binding domain or a linker region (LKR), and
a CTD (57). The NTD binds with the 3' end of the viral genome, perhaps via
electrostatic interactions, and is highly diverged both in length and sequence
(58). The charged LKR is serine and arginine rich and is also known as the SR
(serine and arginine) domain (59). The LKR is capable of direct interaction
with in vitro RNA interaction and is responsible for cell signaling (60, 61). It
also modulates the antiviral response of the host by working as an antagonist
for interferon (IFN) and RNA interference (62). Compared to that of SARS-CoV,
the N protein of SARS-CoV-2 possess five amino acid mutations, where two
are in the intrinsically dispersed region (IDR; positions 25 and 26), one each in
the NTD (position 103), LKR (position 217), and CTD (position 334) (16).
nsps and Accessory Proteins
nsps and Accessory Proteins

Besides the important structural proteins, the SARS-CoV-2 genome contains
15 nsps, nspl to nsp10 and nsp12 to nsp16, and 8 accessory proteins (3a, 3b,
p6, 7a, 7b, 8b, 9b, and ORF14) (16). All these proteins play a specific role in
viral replication (27). Unlike the accessory proteins of SARS-CoV, SARS-COV-2
does not contain 8a protein and has a longer 8b and shorter 3b protein (16).
The nsp7, nsp13, envelope, matrix, and p6 and 8b accessory proteins have not
been detected with any amino acid substitutions compared to the sequences
of other coronaviruses (16).
HOST Immate
systems could enigten our
understanding of the lung inflammation associated with this infection (24).
SARS is a viral respiratory disease caused by a formerly unrecognized animal
CoV that originated from the wet markets in southern China after adapting to
the human host, thereby enabling transmission between humans (90). The
SARS outbreak reported in 2002 to 2003 had 8,098 confirmed cases with 774
total deaths (9.6%) (93). The outbreak severely affected the Asia Pacific
region, especially mainland China (94). Even though the case fatality rate
(CFR) of SARS-CoV-2 (COVID-19) is lower than that of SARS-CoV, there exists
a severe concern linked to this outbreak due to its epidemiological similarity
to influenza viruses (95, 279). This can fail the public health system, resulting
in a pandemic (96).
MERS is another respiratory disease that was first reported in Saudi Arabia
during the year 2012. The disease was found to have a CFR of around 35%
(97). The analysis of available data sets suggests that the incubation period of
SARS-CoV-2, SARS-CoV, and MERS-CoV is in almost the same range. The
longest predicted incubation time of SARS-CoV-2 is 14 days. Hence,
suspected individuals are isolated for 14 days to avoid the risk of further
spread (98). Even though a high similarity has been reported
All of these therapeutic approaches have revealed

both in vitro and in vivo anti-CoV potential. Although in vitro research carried
out with these therapeutics showed efficacy, most need appropriate support
from randomized animal or human trials. Therefore, they might be of limited
applicability and require trials against SARS-CoV-2 to gain practical
usefulness. The binding of SARS-CoV-2 with ACE2 leads to the exacerbation
of pneumonia as a consequence of the imbalance in the renin- angiotensin
system (RAS). The virus-induced pulmonary inflammatory responses may be
reduced by the administration of ACE inhibitors (ACEI) and angiotensin type-1
receptor (ATIR) (207).
Several investigations have suggested the use of small-molecule inhibitors for
the potential control of SARS-CoV infections. Drugs of the FDA-approved
compound library were screened to identify four small-molecule inhibitors of
MERS-COV (chlorpromazine, chloroquine, loperamide, and lopinavir) that
inhibited viral replication. These compounds also hinder SARS-CoV and
human CoVs (208). Therapeutic strategies involving the use of specific
antibodies or compounds that neutralize cytokines and their receptors will
help to restrain the host inflammatory responses. Such drugs acting
specifically in the respiratory tract will help to
respiratory syncytial virus, rhinovirus, human metapneumovirus and SARS

coronavirus. It is advisable to distinguish COVID-19 from other pneumonias
such as mycoplasma pneumonia, chlamydia pneumonia and bacterial
pneumonia.33 Several published pieces of literature based on the novel
coronavirus reported in China declared that stool and blood samples can also
collected from the suspected persons in order to detect the virus. However,
respiratory samples show better viability in identifying the virus, in comparison
with the other specimens.34-36
6.2 Nucleic acid amplification tests (NAAT) for COVID-19 virus
The gold standard method of confirming the suspected cases of COVID-19 is
carried out by detecting the unique sequences of virus RNA through reverse
transcription polymerase chain reaction (RT-PCR) along with nucleic acid
sequencing if needed. The various genes of virus identified so far include N, E,
S (N: nucleocapsid protein, E: envelope protein gene, S: spike protein gene)
and RdRP genes (RNA- dependent RNA polymerase gene).32
severe illness, to minimise the risk of exposure to COVID-19 during

outbreaks.53
9 VACCINES
The strange coronavirus outbreak in the Chinese city of Wuhan, now termed
COVID-19, and its rapid transmission, threatens people around the world.
Because of its pandemic nature, the National Institutes of Health (NIH) and
pharmaceutical companies are involved in the development of COVID-19
vaccines. Xu Nanping, China's vice-minister of science and technology,
announced that the first vaccine is expected to be ready for clinical trials in
China at the end of April 2020.54 There is no approved
vaccine and treatment for COVID-19 infections.
Vaccine development is sponsored and supported by the Biomedical
Advanced Research and Development Authority (BARDA), a component of the
Office of the Assistant Secretary for Preparedness and Response (ASPR).
Sanofi will use its egg-free, recombinant DNA technology to produce an exact
genetic match to proteins of the virus.55
of plasma cytokines, which suggests an immunopatho- logical process

caused by a cytokine storm 60,86,87. In this cohort of patient, around 2.3%
people died within a median time of 16 days from disease onset9,8%. Men
older than 68 years had a higher risk of respiratory failure, acute cardiac
injury and heart failure that led to death, regardless of a history of
cardiovascular disease86 (FIG. 4). Most patients recovered enough to be
released from hospital in 2 weeks 9,80 (FIG. 4).
Early transmission of SARS-CoV-2 in Wuhan in December 2019 was initially
linked to the Huanan Seafood Wholesale Market, and it was suggested as the
source of the outbreak9,22,60. However, community transmission might have
happened before that. Later, ongoing human-to-human transmission
propagated the outbreak. It is generally accepted that SARS-CoV-2 is more
transmissible than SARS-CoV and MERS-CoV; however, determination of an
accurate reproduction number (RO) for COVID-19 is not possible yet, as many
asymptomatic infections cannot be accurately accounted for at this stage9.
An estimated RO of 2.5 (ranging from 1.8 to 3.6) has been proposed for SARS-
CoV-2 recently, compared with 2.0-3.0 for SARS-CoV90. Notably, most of the
SARS-CoV-2 human-to-human transmission early in China occurred in family
clusters, and in other countries large outbreaks also happened in other set-
tings, such as migrant worker communities, slaughter- houses and meat
packing plants, indicating the necessity of isolating infected people,12,91-93.
Nosocomial transmission was not the main source of transmission in China
because of the implementation of infection control measures in clinical
settings'. By contrast, a high risk of nosocomial transmission was reported in
some other
major problem associated with this diagnostic kit is that it works only when
the test subject has an active infection, limiting its use to the earlier stages of
infection. Several laboratories around the world are currently developing
antibody-based diagnostic tests against SARS-CoV-2 (157).
Chest CT is an ideal diagnostic tool for identifying viral pneumonia. The
sensitivity of chest CT is far superior to that of X-ray screening. The chest CT
findings associated with COVID-19- infected patients include characteristic
patchy infiltration that later progresses to ground-glass opacities (158). Early
manifestations of COVID-19 pneumonia might not be evident in X-ray chest
radiography. In such situations, a chest CT examination can be performed, as
it is considered highly specific for COVID-19 pneumonia (118). Those patients
having COVID-19 pneumonia will exhibit the typical ground-glass opacity in
their chest CT images (154). The patients infected with COVID-19 had
elevated plasma angiotensin 2 levels. The level of angiotensin 2 was found to
be linearly associated with viral load and lung injury, indicating its potential as
a diagnostic biomarker (121). The chest CT imaging abnormalities associated
with COVID-19 pneumonia have also been observed even in asymptomatic
patients. These abnormalities
and other SARSr-CoVs (FIG. 2). Using sequences of five conserved replicative
domains in pplab (3C-like protease (3CLpro), nidovirus RNA-dependent RNA
polymerase (RdRp)-associated nucleotidyltransferase (NiRAN), RdRp, zinc-
binding domain (ZBD) and HEL1), the Coronaviridae Study Group of the
International Committee on Taxonomy of Viruses estimated the pairwise
patristic distances between SARS-CoV-2 and known coronaviruses, and
assigned SARS-CoV-2 to the existing species SARSr-CoV17. Although
phyloge- netically related, SARS-CoV-2 is distinct from all other coronaviruses
from bats and pangolins in this species.
The SARS-CoV-2 S protein has a full size of 1,273 amino acids, longer than
that of SARS-CoV (1,255 amino acids) and known bat SARSr-CoVs (1,245-
1,269 amino acids). It is distinct from the S proteins of most members in the
subgenus Sarbecovirus, sharing amino acid sequence similarities of 76.7-
77.0% with SARS-CoVs from civets and humans,
possible origin of SARS-CoV-2 and the first mode of disease transmission are
not yet identified (70). Analysis of the initial cluster of infections suggests that
the infected individuals had a common exposure point, a seafood market in
Wuhan, Hubei Province, China (Fig. 6). The restaurants of this market are well-
known for providing different types of wild animals for human consumption
(71). The Huanan South China Seafood Market also sells live animals, such as
poultry, bats, snakes, and marmots (72). This might be the point where
zoonotic (animal-to- human) transmission occurred (71). Although SARS-CoV-
2 is alleged to have originated from an animal host (zoonotic origin) with
further human-to- human transmission (Fig. 6), the likelihood of foodborne
transmission should be ruled out with further investigations, since it is a latent
possibility (1). Additionally, other potential and expected routes would be
associated with transmission, as in other respiratory viruses, by direct contact,
such as shaking contaminated hands, or by direct contact with contaminated
surfaces (Fig. 6). Still, whether blood transfusion and organ transplantation
(276), as well as transplacental and perinatal routes, are possible routes for
SARS-CoV-2 transmission needs to be determined (Fig. 6).
the initial stages of the outbreak, only mild symptoms were noticed in those
patients that are infected by human-to-human transmission (14).
The initial trends suggested that the mortality associated with COVID-19 was
less than that of previous outbreaks of SARS (101). The updates obtained
from countries like China, Japan, Thailand, and South Korea indicated that the
COVID-19 patients had relatively mild manifestations compared to those with
SARS and MERS (4). Regardless of the coronavirus type, immune cells, like
mast cells, that are present in the submucosa of the respiratory tract and
nasal cavity are considered the primary barrier against this virus (92).
Advanced in-depth analysis of the genome has identified 380 amino acid
substitutions between the amino acid sequences of SARS-CoV-2 and the
SARS/SARS-like
coronaviruses. These differences in the amino acid sequences might have
contributed to the difference in the pathogenic divergence of SARS-CoV-2
(16). Further research is required to evaluate the possible differences in
tropism, pathogenesis, and transmission of this novel agent associated with
this change in the amino acid sequence. With the current outbreak of COVID-
19, there is an expectancy of a significant increase in the number of published
studies about this emerging coronavirus, as occurred
and ritonavir had little therapeutic benefit in patients with COVID-19, but
appeared more effective when used in combination with other drugs, including
ribavirin and interferon beta-1b143,144. The Randomized Evaluation of COVID-
19 Therapy (RECOVERY) trial, a national clinical trial programme in the UK,
has stopped treatment with lopinavir and ritonavir as no significant beneficial
effect was observed in a randomized trial established in March 2020 with a
total of 1,596 patients145. Nevertheless,
that remdesivir has to be further evaluated for its efficacy in the treatment of
COVID-19 infection in humans. The broad-spectrum activity exhibited by
remdesivir will help control the spread of disease in the event of a new
coronavirus outbreak.
Chloroquine is an antimalarial drug known to possess antiviral activity due to
its ability to block virus-cell fusion by raising the endosomal pH necessary for
fusion. It also interferes with virus- receptor binding by interfering with the
terminal glycosylation of SARS-CoV cellular receptors, such as ACE2 (196). In
a recent multicenter clinical trial that was conducted in China, chloroquine
phosphate was found to exhibit both efficacy and safety in the therapeutic
management of SARS-CoV-2-associated pneumonia (197). This drug is
already included in the treatment guidelines issued by the National Health
Commission of the People's Republic of China. The preliminary clinical trials
using hydroxychloroquine, another aminoquinoline drug, gave promising
results. The COVID-19 patients received 600 mg of hydroxychloroquine daily
along with azithromycin as a single-arm protocol. This protocol was found to
be associated with a noteworthy reduction in viral load. Finally, it resulted in a
complete cure (271); however, the study comprised a small population and,
hence, the
primary anti-genic epitopes mainly those recognised by neutralising

antibodies. The spike S-protein being in a spike form is subjected to a
structural rearrangement process so that fusing the outer membrane of the
virus with the host- cell membrane becomes easier. 19, 20 Recent SARS-COV
work has also shown that the membrane exopeptidase ACE enzyme
(angiotensin-converting enzyme) functions as a COVID-19 receptor to enter
the human cell.21
Repurposed broad-spectrum antiviral drugs having proven uses against other

viral pathogens can be employed for SARS-CoV-2-infected patients. These
possess benefits of easy accessibility and recognized pharmacokinetic and
pharmacodynamic activities, stability, doses, and side effects (9). Repurposed
drugs have been studied for treating CoV infections, like lopinavir/ritonavir,
and interferon-1ẞ revealed in vitro anti-MERS-CoV action. The in vivo
experiment carried out in the nonhuman primate model of common
marmosets treated with lopinavir/ritonavir and interferon beta showed
superior protective results in treated animals than in the untreated ones (190).
A combination of these drugs is being evaluated to treat MERS in humans
(MIRACLE trial) (191). These two protease inhibitors (lopinavir and ritonavir),
in combination with ribavirin, gave encouraging clinical outcomes in SARS
patients, suggesting their therapeutic values (165). However, in the current
scenario, due to the lack of specific therapeutic agents against SARS- CoV-2,
hospitalized patients confirmed for the disease are given supportive care, like
oxygen and fluid therapy, along with antibiotic therapy for managing
secondary bacterial infections (192). Patients with novel coronavirus or
COVID-19 pneumonia who are mechanically ventilated often require sedatives.
analgesics. and even muscle
Inhibition of virus entry. SARS-CoV-2 uses ACE2 as the receptor and human
proteases as entry activators; subsequently it fuses the viral membrane with
the cell membrane and achieves invasion. Thus, drugs that interfere with
entry may be a potential treatment for COVID-19. Umifenovir (Arbidol) is a
drug approved in Russia and China for the treatment of influenza and other
respiratory viral infections. It can target the interaction between the S protein
and ACE2 and inhibit membrane fusion (FIG. 5). In vitro experiments showed
that it has activity against SARS-CoV-2, and current clinical data revealed it
may be more effective than lopinavir and ritonavir in treating COVID-19
(REFS122,123). However, other clinical studies showed umifenovir might not
improve the prognosis of or accelerate SARS-CoV-2 clearance in patients
with mild to moderate COVID-19 (REFS124,125). Yet some ongoing clinical
trials are evaluating its efficacy for COVID-19 treatment. Camostat mesylate is
approved in Japan for the treatment of pancreatitis and postoper- ative reflux
oesophagitis. Previous studies showed that it can prevent SARS-CoV from
entering cells by blocking TMPRSS2 activity and protect mice from lethal
infection with SARS-CoV in a pathogenic mouse model (wild- type mice
infected with a mouse-adapted SARS-CoV strain) 126,127. Recently, a study
revealed that camostat mesylate blocks the entry of SARS-CoV-2 into human
lung cells. Thus, it can be a potential antiviral drug against SARS-CoV-2
infection, although so far there are not sufficient clinical data to support its
efficacy.
INTRODUCTION
Over the past 2 decades, coronaviruses (CoVs) have been associated with
significant disease outbreaks in East Asia and the Middle East. The severe
acute respiratory syndrome (SARS) and the Middle East respiratory syndrome
(MERS) began to emerge in 2002 and 2012, respectively. Recently, a novel
coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),
causing coronavirus disease 2019 (COVID-19), emerged in late 2019, and it
has posed a global health threat, causing an ongoing pandemic in many
countries and territories (1).
Health workers worldwide are currently making efforts to control further
disease outbreaks caused by the novel CoV (originally named 2019-nCoV),
which was first identified in Wuhan City, Hubei Province, China, on 12
December 2019. On 11 February 2020, the World Health Organization (WHO)
announced the official designation for the current CoV-associated disease to
be COVID-19, caused by SARS-CoV-2. The primary cluster of patients was
found to be connected with the Huanan South China Seafood Market in
Wuhan (2). CoVs belong to the family Coronaviridae (subfamily
Coronavirinae), the members of which infect a broad
residues for receptor binding (FIG. 3b). In comparison with the Guangdong
strains, pangolin coronaviruses reported from Guangxi are less similar to
SARS-CoV-2, with 85.5% genome sequence identity. The repeated occurrence
of SARS-CoV-2-related coronavirus infections in pangolins from different
smuggling events suggests that these animals are possible hosts of the
viruses. However, unlike bats, which carry coronaviruses healthily, the infected
pangolins showed clinical signs and histopathological changes, including
interstitial pneumonia and inflammatory cell infiltration in diverse organs 40.
These abnormalities suggest that pangolins are unlikely to be the reservoir of
these coronaviruses but more likely acquired the viruses after spillover from
the natural hosts.
An intermediate host usually plays an important role in the outbreak of bat-
derived emerging coronaviruses; for example, palm civets for SARS-CoV and
dromedary camels for MERS-CoV. The virus strains carried by these two
intermediate hosts were almost genetically identical to the corresponding
viruses in humans (more than 99% genome sequence identity)'. Despise an
RBD that is virtually identical to that of SARS-CoV-2, the pangolin
coronaviruses known to date have no more than 92% genome identity with
SARS-CoV-2 (REF.42). The available data are insufficient to interpret
pangolins as the intermediate host of SARS-CoV-2. So far, no evidence has
shown that pangolins were directly involved in the emergence of SARS-CoV-2.
DIAGNOSIS OF SARS-CoV-2 (COVID-

19)
RNA tests can confirm the diagnosis of SARS- CoV-2 (COVID-19) cases with
real-time RT-PCR or next-generation sequencing (148, 149, 245, 246). At
present, nucleic acid detection techniques, like RT- PCR, are considered an
effective method for confirming the diagnosis in clinical cases of COVID- 19
(148). Several companies across the world are currently focusing on
developing and marketing SARS-CoV-2-specific nucleic acid detection kits.
Multiple laboratories are also developing their own in-house RT-PCR. One of
them is the SARS-CoV-2 nucleic acid detection kit produced by Shuoshi
Biotechnology (double fluorescence PCR method) (150). Up to 30 March
2020, the U.S. Food and Drug Administration (FDA) had granted 22 in vitro
diagnostics Emergency Use Authorizations (EUAS), including for the RT-PCR
diagnostic panel for the universal detection of SARS-like betacoronaviruses
and specific detection of SARS-CoV-2, developed by the U.S. CDC (Table 1)
(258, 259).
pieces of evidence are available that link NSAID uses with the occurrence of
respiratory and cardiovascular adverse effects. Hence, as a cautionary
approach, it is better to recommend the use of NSAIDs as the first-line option
for managing COVID-19 symptoms The use of
(302).
corticosteroids in COVID-19 patients is still a matter of controversy and
requires further systematic clinical studies. The guidelines that were put
forward to manage critically ill adults suggest the use of systemic
corticosteroids in mechanically ventilated adults with ARDS (303). The
generalized use of corticosteroids is not indicated in COVID-19, since there
are some concerns associated with the use of corticosteroids in viral
pneumonia. Stem cell therapy using mesenchymal stem cells (MSCs) is
another hopeful strategy that can be used in clinical cases of COVID-19 owing
to its potential immunomodulatory capacity. It may have a beneficial role in
attenuating the cytokine storm that is observed in severe cases of SARS-CoV-
2 infection, thereby reducing mortality. Among the different types of MSCs,
expanded umbilical cord MSCs can be considered a potential therapeutic
agent that requires further validation for managing critically ill COVID-19
patients (304).
Repurposed broad-spectrum antiviral drugs
Coronaviruses in Humans-SARS, MERS,

and COVID-19
Coronavirus infection in humans is commonly associated with mild to severe
respiratory diseases, with high fever, severe inflammation, cough, and internal
organ dysfunction that can even lead to death (92). Most of the identified
coronaviruses cause the common cold in humans. However, this changed
when SARS-CoV was identified, paving the way for severe forms of the
disease in humans (22). Our previous experience with the outbreaks of other
coronaviruses, like SARS and MERS, suggests that the mode of transmission
in COVID-19 as mainly human-to-human transmission via direct contact,
droplets, and fomites (25). Recent studies have demonstrated that the virus
could remain viable for hours in aerosols and up to days on surfaces; thus,
aerosol and fomite contamination could play potent roles in the transmission
of SARS-CoV-2 (257).
The immune response against coronavirus is vital to control and get rid of the
infection. However, maladjusted immune responses may contribute to the
immunopathology of the disease, resulting in impairment of pulmonary gas
exchange. Understanding the interaction between CoVs and host innate
immune systems could enlighten our
Recently, 95 full-length genomic sequences of

SARAS-COV-2 strains available in the National Center for Biotechnology
Information and GISAID databases were subjected to multiple-sequence
alignment and phylogenetic analyses for studying variations in the viral
genome (260). All the viral strains revealed high homology of 99.99% (99.91%
to 100%) at the nucleotide level and 99.99% (99.79% to 100%) at the amino
acid level. Overall variation was found to be low in ORF regions, with 13
variation sites recognized in 1a, 1b, S, 3a, M, 8, and N regions. Mutation rates
of 30.53% (29/95) and 29.47% (28/95) were observed at nt 28144 (ORF8) and
nt 8782 (ORF1a) positions, respectively. Owing to such selective mutations, a
few specific regions of SARS-CoV-2 should not be considered for designing
primers and probes. The SARS-CoV-2 reference sequence could pave the way
to study molecular biology and pathobiology, along with developing
diagnostics and appropriate prevention and control strategies for countering
SARS-CoV-2 (260).
Nucleic acids of SARS-CoV-2 can be detected from samples (64) such as
bronchoalveolar lavage fluid, sputum, nasal swabs, fiber bronchoscope brush
biopsy specimen, pharyngeal swabs, feces, blood, and urine, with different
levels of diagnostic performance (Table 2) (80, 245, 246). The viral loads
and deaths. The COVID-19 outbreak has also been associated with severe
economic impacts globally due to the sudden interruption of global trade and
supply chains that forced multinational companies to make decisions that led
to significant economic losses (66). The recent increase in the number of
confirmed critically ill patients with COVID-19 has already surpassed the
intensive care supplies, limiting intensive care services to only a small portion
of critically ill patients (67). This might also have contributed to the increased
case fatality rate observed in the COVID-19 outbreak.
Viewpoint on SARS-CoV-2 Transmission, Spread, and Emergence
The novel coronavirus was identified within 1 month (28 days) of the
outbreak. This is impressively fast compared to the time taken to identify
SARS- CoV reported in Foshan, Guangdong Province, China (125 days) (68).
Immediately after the confirmation of viral etiology, the Chinese virologists
rapidly released the genomic sequence of SARS-CoV-2, which played a crucial
role in controlling the spread of this newly emerged novel coronavirus to other
parts of the world (69). The possible origin of SARS-CoV-2 and the first mode
of
into the host cell. Heptad repeat 1 (HR1) and heptad repeat 2 (HR2) can
interact and form a six-helix bundle that brings the viral and cellular
membranes in close proximity, facilitating its fusion. The sequence alignment
study conducted between COVID-19 and SARS-CoV identified that the S2
subunits are highly conserved in these CoVs. The HR1 and HR2 domains
showed 92.6% and 100% overall identity, respectively (210). From these
findings, we can confirm the significance of COVID-19 HR1 and HR2 and their
vital role in host cell entry. Hence, fusion inhibitors target the HR1 domain of S
protein, thereby preventing viral fusion and entry into the host cell. This is
another potential therapeutic strategy that can be used in the management of
COVID-19. Other than the specific therapy directed against COVID-19, general
treatments play a vital role in the enhancement of host immune responses
against the viral agent. Inadequate nutrition is linked to the weakening of the
host immune response, making the individual more susceptible. The role
played by nutrition in disease susceptibility should be measured by evaluating
the nutritional status of patients with COVID-19 (205).
Sampic.
A suspected case of COVID-19 infection is said to be confirmed if the
respiratory tract aspirate or blood samples test positive for SARS-CoV-2
nucleic acid using RT-PCR or by the identification of SARS- CoV-2 genetic
sequence in respiratory tract aspirate or blood samples (80). The patient will
be confirmed as cured when two subsequent oral swab results are negative
(153). Recently, the live virus was detected in the self-collected saliva of
patients infected with COVID-19. These findings were confirmative of using
saliva as a noninvasive specimen for the diagnosis of COVID-19 infection in
suspected individuals (152). It has also been observed that the initial
screening of COVID-19 patients infected with RT-PCR may give negative
results even if they have chest CT findings that are suggestive of infection.
Hence, for the accurate diagnosis of COVID-19, a combination of repeated
swab tests using RT-PCR and CT scanning is required to prevent the possibility
of false-negative results during disease screening (154). RT-PCR is the most
widely used test for diagnosing COVID-19. However, it has some significant
limitations from the clinical perspective, since it will not give any clarity
regarding disease progression. Droplet digital PCR (ddPCR) can be used for
the quantification of viral load in the samples obtained from lower respiratory
tracts.
countries. Large-scale screening programs might help us to control the spread

of this virus. However, this is both challenging as well as time-consuming due
to the present extent of infection (226). The current scenario demands
effective implementation of vigorous prevention and control strategies owing
to the prospect of COVID-19 for nosocomial infections (68). Follow-ups of
infected patients by telephone on day 7 and day 14 are advised to avoid any
further unintentional spread or nosocomial transmission (312). The
availability of public data sets provided by independent analytical teams will
act as robust evidence that would guide us in designing interventions against
the COVID-19 outbreak. Newspaper reports and social media can be used to
analyze and reconstruct the progression of an outbreak. They can help us to
obtain detailed patient- level data in the early stages of an outbreak (227).
Immediate travel restrictions imposed by several countries might have
contributed significantly to preventing the spread of SARS-CoV-2 globally (89,
228). Following the outbreak, a temporary ban was imposed on the wildlife
trade, keeping in mind the possible role played by wild animal species in the
origin of SARS-CoV-2/COVID-19 (147). Making a permanent and bold decision
on the trade of wild animal species is necessary to prevent the possibility
by the University of Oxford. In a randomized controlled phase I/II trial, it

induced neutralizing antibodies against SARS-COV-2 in all 1,077 participants
after a second vaccine dose, while its safety profile was acceptable as
well163. The NIAID and Moderna co-manufactured mRNA-1273, a lipid
nanoparticle-formulated mRNA vaccine candidate that encodes the stabilized
prefusion SARS-COV-2 S protein. Its immunogenicity has been confirmed by a
phase I trial in which robust neutralizing antibody responses were induced in a
dose-dependent manner and increased after a second dose164. . Regarding
inactivated vaccines, a successful phase I/II trial involving 320 participants
has been reported in China. The whole-virus COVID-19 vaccine had a low rate
of adverse reactions and effectively induced neutralizing antibody production
165. The verified safety and immunogenicity support advancement of these
vaccine candidates to phase III clinical trials, which will evaluate their efficacy
in protecting healthy populations from SARS-CoV-2 infection.
Future perspectives
COVID-19 is the third highly pathogenic human coronavirus disease to date.
Although less deadly than SARS and MERS, the rapid spreading of this highly
contagious disease has posed the severest threat to global health in this
century. The SARS-CoV-2 outbreak has lasted for more than half a year now,
and it is likely that
CONCLUDING REMARKS
to
Several years after the global SARS epidemic, the current SARS-CoV-2/COVID-
19 pandemic has served as a reminder of how novel pathogens can rapidly
emerge and spread through the human population and eventually cause
severe public health crises. Further research should be conducted to establish
animal models for SARS-CoV-2 investigate replication, transmission
dynamics, and pathogenesis in humans. This may help develop and evaluate
potential therapeutic strategies against zoonotic CoV epidemics. Present
trends suggest the occurrence of future outbreaks of CoVs due to changes in
the climate, and ecological conditions may be associated with human-animal
contact. Live- animal markets, such as the Huanan South China Seafood
Market, represent ideal conditions for interspecies contact of wildlife with
domestic birds, pigs, and mammals, which substantially increases the
probability of interspecies transmission of CoV infections and could result in
high risks to humans due to adaptive genetic recombination in these viruses
(323-325).
The COVID-19-associated symptoms are fever, cough, expectoration,
headache, and myalgia or fatigue. Individuals with asymptomatic and atypical
weeks, and the typical symptom occurrence from incubation period to

infection takes an average of 12.5 days.29
6 CLINICAL DIAGNOSIS
The symptoms of COVID-19 remain very similar to those of the other
respiratory epidemics in the past, which include SARS and MERS, but here the
range of symptoms includes mild rhinitis to septic shock. Some intestinal
disturbances were reported with the other epidemics, but COVID-19 was
devoid of such symptoms. When examined, unilateral or bilateral involvement
compatible with viral pneumonia is observed in the patients, and bilateral
multiple lobular and sub-segmental consolidation areas were observed in
patients hospitalised in the intensive care unit. Comorbid patients showed a
more severe clinical course than predicted from previous epidemics.
Diagnosis of COVID-19 includes the complete history of travel and touch, with
laboratory testing. It is more preferable to choose serological screening, which
can help to analyse even the asymptomatic infections; several serological
tests are in progress for SARS-COV-2.14, 30
We also predict the possibility of another outbreak, as predicted by Fan et al.

(6). Indeed, the present outbreak caused by SARS-CoV-2 (COVID- 19) was
expected. Similar to previous outbreaks, the current outbreak also will be
contained shortly. However, the real issue is how we are planning to counter
the next zoonotic CoV epidemic that is likely to occur within the next 5 to 10
years or even sooner (Fig. 7).
encircled with an
envelope containing viral nucleocapsid. The nucleocapsids in CoVs are
arranged in helical symmetry, which reflects an atypical attribute in positive-
sense RNA viruses (30). The electron micrographs of SARS-CoV-2 revealed a
diverging spherical outline with some degree of pleomorphism, virion
diameters varying from 60 to 140 nm, and distinct spikes of 9 to 12 nm, giving
the virus the appearance of a solar corona (3). The CoV genome is arranged
linearly as 5'-leader-UTR- replicase-structural genes (S-E-M-N)-3'
UTR-
poly(A) (32). Accessory genes, such as 3a/b, 4a/b, and the hemagglutinin-
esterase gene (HE), are also seen intermingled with the structural genes (30).
SARS-COV-2 has also been found to be arranged similarly and encodes
several accessory proteins, although it lacks the HE, which is characteristic of
some betacoronaviruses (31). The positive-sense genome of CoVs serves as
the mRNA and is translated to polyprotein 1a/lab (ppla/lab) (33). A replication-
transcription complex (RTC) is formed in double-membrane vesicles (DMVs)
by nonstructural proteins (nsps), encoded by the polyprotein gene (34).
Subsequently, the RTC synthesizes a nested set of subgenomic RNAs
(sgRNAs) via discontinuous transcription (35).
countries have a fragile health system that can be crippled in the event of an
outbreak. Effective management of COVID-19 would be difficult for low-
income countries due to their inability to respond rapidly due to the lack of an
efficient health care system (65). Controlling the imported cases is critical in
preventing the spread of COVID-19 to other countries that have not reported
the disease until now. The possibility of an imported case of COVID-19 leading
to sustained human-to-human transmission was estimated to be 0.41. This
can be reduced to a value of 0.012 by decreasing the mean time from the
onset of symptoms to hospitalization and can only be made possible by using
intense disease surveillance systems (235). The silent importations of
infected individuals (before the manifestation of clinical signs) also
contributed significantly to the spread of disease across the major cities of
the world. Even though the travel ban was implemented in Wuhan (89),
infected persons who traveled out of the city just before the imposition of the
ban might have remained undetected and resulted in local outbreaks (236).
Emerging novel diseases like COVID-19 are difficult to contain within the
country of origin, since globalization has led to a world without borders.
Hence, international collaboration plays a vital role
length to the corresponding proteins in SARS-CoV. Of the four structural

genes, SARS-CoV-2 shares more than 90% amino acid identity with SARS-CoV
except for the S gene, which diverges11,24. The replicase gene covers two
thirds of the 5' genome, and encodes a large polyprotein (pplab), which is
proteolytically cleaved into 16 non-structural proteins that are involved in
transcription and virus replication. Most of these SARS-COV-2 non-structural
proteins have greater than 85% amino acid sequence identity with SARS-
CoV25.
The phylogenetic analysis for the whole genome shows that SARS-CoV-2 is
clustered with SARS-COV and SARS-related coronaviruses (SARSr-CoVs)
found in bats, placing it in the subgenus Sarbecovirus of the genus
Betacoronavirus. Within this clade, SARS-COV-2 is grouped in a distinct
lineage together with four horseshoe bat coronavirus isolates (RaTG13,
RmYN02, ZC45 and ZXC21) as well as novel coronaviruses recently identified
in pangolins, which group parallel to SARS-CoV
Therapeutics and Drugs

There is no currently licensed specific antiviral treatment for MERS- and SARS-
CoV infections, and the main focus in clinical settings remains on lessening
clinical signs and providing supportive care (183-186). Effective drugs to
manage COVID- 19 patients include remdesivir, lopinavir/ritonavir alone or in a
blend with interferon beta, convalescent plasma, and monoclonal antibodies
antibodies (MAbs);
hospitalized
however, efficacy and safety issues of these drugs require additional clinical
trials (187, 281). A controlled trial of ritonavir-boosted lopinavir and interferon
alpha 2b treatment was performed on COVID-19 patients
(ChiCTR2000029308) (188). In addition, the use of hydroxychloroquine and
tocilizumab for their for potential role in modulating inflammatory responses
in the lungs and antiviral effect has been proposed and discussed in many
research articles. Still, no fool-proof clinical trials have been published (194,
196, 197, 261-272). Recently, a clinical trial conducted on adult patients
suffering from severe COVID-19 revealed no benefit of lopinavir-ritonavir
treatment over standard care (273).
The efforts to control SARS-CoV-2 infection utilize defined strategies as
followed against MERS and SARS, along with adopting and strengthening a
Based on molecular characterization, SARS-

CoV-2 is considered
a new Betacoronavirus
belonging to the subgenus Sarbecovirus (3). A few other critical zoonotic
viruses (MERS-related CoV and SARS-related CoV) belong to the same genus.
However, SARS-CoV-2 was identified as a distinct virus based on the percent
identity with other Betacoronavirus; conserved open reading frame 1a/b
(ORF1a/b) is below 90% identity (3). An overall 80% nucleotide identity was
observed between SARS-CoV-2 and the original SARS-CoV, along with 89%
identity with ZC45 and ZXC21 SARS- related CoVs of bats (2, 31, 36). In
addition, 82% identity has been observed between SARS-CoV-2 and human
SARS-CoV Tor2 and human SARS-CoV BJ01 2003 (31). A sequence identity of
only 51.8% was observed between MERS-related CoV and the recently
emerged SARS-CoV-2 (37). Phylogenetic analysis of the structural genes also
revealed that SARS-CoV-2 is closer to bat SARS-related CoV. Therefore, SARS-
CoV-2 might have originated from bats, while other amplifier hosts might have
played a role in disease transmission to humans (31). Of note, the other two
zoonotic CoVS (MERS-related CoV and SARS-related CoV) also originated
from bats (38, 39). Nevertheless, for SARS and MERS, civet
areas. For example, a cohort study in London revea 44% of the frontline
health-care workers from a hosp were infected with SARS-CoV-2 (REF.94).
The high transmissibility of SARS-CoV-2 may be attributed to the unique
virological features of SARS-CoV-2. Transmission of SARS-CoV occurred
mainly after illness onset and peaked following disease severity95. However,
the SARS-CoV-2 viral load in upper respiratory tract samples was already high-
est during the first week of symptoms, and thus the risk of pharyngeal virus
shedding was very high at the beginning of infection 96,97. It was postulated
that undocumented infections might account for 79% of documented cases
owing to the high transmissibility of the virus during mild disease or the
asymptomatic period. A patient with COVID-19 spreads viruses in liquid
droplets during speech. However, smaller and much more numerous particles
known as aerosol particles can also be visualized, which could linger in the
air for a long time and then penetrate deep into the lungs when inhaled by
someone else98-100. Airborne transmission was also observed in the ferret
experiments mentioned above. SARS-CoV-2-infected ferrets shed
wrought havoc in China and caused a pandemic situation in the worldwide

population, leading to disease outbreaks that have not been controlled to date,
although extensive efforts are being put in place to counter this virus (25).
This virus has been proposed to be designated/named severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International
Committee on Taxonomy of Viruses (ICTV), which determined the virus
belongs to the Severe acute respiratory syndrome-related coronavirus
category and found this virus is related to SARS-CoVs (26). SARS-CoV-2 is a
member of the order Nidovirales, family Coronaviridae, subfamily
Orthocoronavirinae, which is subdivided into four genera,
Betacoronavirus,
viz.,
Alphacoronavirus,
Gammacoronavirus,
and
Deltacoronavirus (3, 27). The genera Alphacoronavirus and Betacoronavirus
originate from bats. while Gammacoronavirus and Deltacoronavirus have
evolved from bird and swine gene pools (24, 28, 29, 275).
Coronaviruses possess an unsegmented, single- stranded, positive-sense RNA
genome of around 30 kb, enclosed by a 5'-cap and 3'-poly(A) tail (30). The
genome of SARS-CoV-2 is 29,891 bp long, with a G+C content of 38% (31).
These viruses are encircled with an envelope containing viral
4.2 Viral replication

Usually replication of coronavirus occurs within the cytoplasm and is closely
associated with endoplasmic reticulum and other cellular membrane
organelles. Human coronaviruses are thought to invade cells, primarily
through different receptors. For 229E and OC43, amino peptidase-N (AP-N)
and a sialic acid containing receptor, respectively, were known to function in
this role. After the virus enters the host cell and uncoating process occurs, the
genome is transcribed, and then, translated. A characteristic feature of
replication is that all mRNAs form an enclosed group of typical 3' ends; only
the special portions of the 5' ends are translated. In total, about 7 mRNAs are
produced. The shortest mRNA codes and the others can express the
synthesis of another genome segment for nucleoprotein. At the cell
membrane, these proteins are collected and genomic RNA is initiated as a
mature particle type by burgeoning from internal cell membranes. 22, 23
5 PATHOGENESIS
Coronaviruses are tremendously precise and mature in most of the airway
epithelial cells as observed through both in vivo and in vitro
8 PREVENTION
The WHO and other agencies such as the CDC have published protective
measures to mitigate the spread of COVID-19. This involves frequent hand
washing with handwash containing 60% of alcohol and soap for at least 20
seconds. Another important measure is avoiding close contact with sick
people and keeping a social distance of 1 metre always to everyone who is
coughing and sneezing. Not touching the nose, eyes and mouth was also
suggested. While coughing or sneezing, covering the mouth and nose with a
cloth/tissue or the bent elbow is advised. Staying at home is recommended
for those who are sick, and wearing a facial mask is advised when going out
among people. Furthermore, it is recommended to clean and sterilise
frequently touched surfaces such as phones and doorknobs on a daily basis.
51, 52 Staying at home as much as possible is
advisable for those who are at higher risk for severe illness, to minimise the
risk of exposure to COVID-19 during outbreaks.53
6.5 Specimen collection and storage

A Nasopharyngeal and oropharyngeal swab should be collected using Dacron
or polyester flocked swabs. It should be transported to the laboratory at a
temperature of 4°C and stored in the laboratory between 4 and -70°C on the
basis of the number of days and, in order to increase the viral load, both
nasopharyngeal and oropharyngeal swabs should be placed in the same tube.
Bronchoalveolar lavage and nasopharyngeal aspirate should be collected in a
sterile container and transported similarly to the laboratory by maintain a
temperature of 4°C.
Sputum samples, especially from the lower respiratory tract, should be
collected with the help of a sterile container and stored, whereas tissue from a
biopsy or autopsy should be collected using a sterile container along with
saline. However, both should be stored in the laboratory at a temperature that
ranges
between 4 and -70°C. Whole blood for detecting the antigen, particularly in the
first week of illness, should be collected in a collecting tube and stored in the
laboratory between 4 and -70°C. Urine samples must also be collected using a
sterile container and stored
between 4 and -70°C. Urine samples must also be collected using a sterile
container and stored in the laboratory at a temperature that ranges between 4
and -70°C,32
7 PREGNANCY
Currently, there is a paucity of knowledge and data related to the
consequences of COVID-19 during pregnancy. However, pregnant
40-42
women seem to have a high risk of developing severe infection and
complications during the recent 2019-nCoV outbreak.41-43 This speculation
was based on previous available scientific reports on coronaviruses during
pregnancy (SARS-CoV and MERS-CoV) as well as the limited number of
COVID-19 cases. 41-43 Analysing the clinical features and outcomes of 10
newborns (including two sets of twins) in China, whose mothers are
confirmed cases of COVID-19, revealed that perinatal infection with 2019-
nCoV may lead to adverse outcomes for the neonates, for example, premature
labour, respiratory distress, thrombocytopenia with 44 abnormal liver function
and even death. It is still unclear whether or not the COVID-19 infection can be
transmitted during pregnancy to the foetus through the transplacental
route.42
A recent case series report, which assessed intrauterine vertical transmission
of
turtles, ducks, fish, Siamese crocodiles, and other animal meats without any
fear of COVID-19. The Chinese government is encouraging people to feel they
can return to normalcy. However, this could be a risk, as it has been
mentioned in advisories that people should avoid contact with live-dead
animals as much as possible, as SARS-CoV-2 has shown zoonotic spillover.
Additionally, we cannot rule out the possibility of new mutations in the same
virus being closely related to contact with both animals and humans at the
market (284). In January 2020, China imposed a temporary ban on the sale of
live- dead animals in wet markets. However, now hundreds of such wet
markets have been reopened without optimizing standard food safety and
sanitation practices (286).
With China being the most populated country in the world and due to its
domestic and international food exportation policies, the whole world is now
facing the menace of COVID-19, including China itself. Wet markets of live-
dead animals do not maintain strict food hygienic practices. Fresh blood
splashes are present everywhere, on the floor and tabletops, and such food
customs could encourage many pathogens to adapt, mutate, and jump the
species barrier. As a result, the whole world is suffering from novel SARS-CoV-
2, with more than
differs from that in SARS-CoV in the five residues critical for ACE2 binding,
namely Y455L, L486F, N493Q, D494S and T501N52 (FIG. 3b,c). Owing to these
residue changes, interaction of SARS-CoV-2 with its receptor stabilizes the
two virus-binding hotspots on the surface of hACE2 (REF.5) (FIG. 3d).
Moreover, a four-residue motif in the RBM of SARS-CoV-2 (amino acids 482-
485: G-V-E-G) results in a more compact conformation of its hACE2-binding
ridge than in SARS-CoV and enables better contact with the N-terminal helix
of hACE2 (REF.50). Biochemical data confirmed that the structural features of
the SARS-CoV-2 RBD has strengthened its hACE2 binding affinity compared
with that of SARS-CoV 50,52,53
Similarly to other coronaviruses, SARS-CoV-2 needs proteolytic processing of
the S protein to activate the endocytic route. It has been shown that host
proteases participate in the cleavage of the S protein and activate the entry of
SARS-CoV-2, including transmembrane protease serine protease 2
(TMPRSS2), cathepsin L and furin47,54,55. Single-cell RNA sequencing data
showed that TMPRSS2 is highly expressed in several tissues and body sites
and is co-expressed with ACE2 in nasal epithelial cells, lungs and bronchial
branches, which explains some of the tissue tropism of SARS-CoV-2 (REFS
56,57). SARS-CoV-2 pseudovirus entry assays revealed that TMPRSS2 and
cathepsin L have cumu- lative effects with furin on activating virus entry55.
Analysis of the cryo-electron microscopy structure of SARS-CoV-2 S protein
revealed that its RBD is mostly in the lying-down state, whereas the SARS-CoV
S protein assumes equally standing-up and lying-down conforma- tional
states50,51,58,59. A lying-down conformation of the SARS-CoV-2 S protein
may not be in favour of receptor binding but is helpful for immune evasion55.
on
significance of frequent and good hand hygiene and sanitation practices
needs to be given due emphasis (249–252). Future explorative research
needs to be conducted with regard to the fecal-oral transmission of SARS-
CoV-2, along with focusing environmental investigations to find out if this
virus could stay viable in situations and atmospheres facilitating such potent
routes of transmission. The correlation of fecal concentrations of viral RNA
with disease severity needs to be determined, along with assessing the
gastrointestinal symptoms and the possibility of fecal SARS-CoV-2 RNA
detection during the COVID-19 incubation period or convalescence phases of
the disease (249–252).
The lower respiratory tract sampling techniques, like bronchoalveolar lavage
fluid aspirate, are considered the ideal clinical materials, rather than the throat
swab, due to their higher positive rate on the nucleic acid test (148). The
diagnosis of COVID- 19 can be made by using upper-respiratory-tract
specimens collected using nasopharyngeal and oropharyngeal swabs.
However, these techniques are associated with unnecessary risks to health
care workers due to close contact with patients (152). Similarly, a single
patient with a high viral load was reported to contaminate an entire endoscopy
room by shedding the virus, which may remain viable for at
visible signs of infection, making it challenging to identify animals actively

excreting MERS-CoV that has the potential to infect humans. However, they
may shed MERS-CoV through milk, urine, feces, and nasal and eye discharge
and can also be found in the raw organs (108). In a study conducted to
evaluate the susceptibility of animal species to MERS-CoV infection, llamas
and pigs were found to be susceptible, indicating the possibility of MERS- CoV
circulation in animal species other than dromedary camels (109).
Following the outbreak of SARS in China, SARS-CoV-like viruses were isolated
from Himalayan palm civets (Paguma larvata) and raccoon dogs (Nyctereutes
procyonoides) found in a live-animal market in Guangdong, China. The animal
isolates obtained from the live-animal market retained a 29-nucleotide
sequence that was not present in most of the human isolates (78). These
findings were critical in identifying the possibility of interspecies transmission
in SARS-CoV. The higher diversity and prevalence of bat coronaviruses in this
region compared to those in previous reports indicate a host/pathogen
coevolution. SARS-like coronaviruses also have been found circulating in the
Chinese horseshoe bat (Rhinolophus sinicus) populations. The in vitro and in
vivo studies carried
susceptible individuals. Hence, hand hygiene is equally as important as the

use of appropriate PPE, like face masks, to break the transmission cycle of the
virus; both hand hygiene and face masks help to lessen the risk of COVID-19
transmission (315).
Medical staff are in the group of individuals most at risk of getting COVID-19
infection. This is because they are exposed directly to infected patients.
Hence, proper training must be given to all hospital staff on methods of
prevention and protection so that they become competent enough to protect
themselves and others from this deadly disease (316). As a preventive
measure, health care workers caring for infected patients should take extreme
precautions against both contact and airborne transmission. They should use
PPE such as face masks (N95 or FFP3), eye protection (goggles), gowns, and
gloves to nullify the risk of infection (299).
The human-to-human transmission reported in SARS-CoV-2 infection occurs
mainly through droplet or direct contact. Due to this finding, frontline health
care workers should follow stringent infection control and preventive
measures, such as the use of PPE, to prevent infection (110). The mental
health of the medical/health workers who are involved in the COVID-19
outbreak is of great
Word
IS
Species barrier. AS a result, the WHOIC suffering from novel SARS-CoV-2, with
more than 4,170,424 cases and 287,399 deaths across the globe. There is an
urgent need for a rational international campaign against the unhealthy food
practices of China to encourage the sellers to increase hygienic food practices
or close the crude live-dead animal wet markets. There is a need to modify
food policies at national and international levels to avoid further life threats
and economic consequences from any emerging or reemerging pandemic due
to close animal-human interaction (285).
Even though individuals of all ages and sexes are susceptible to COVID-19,
older people with an underlying chronic disease are more likely to become
severely infected (80). Recently, individuals with asymptomatic infection were
also found to act as a source of infection to susceptible individuals (81). Both
the asymptomatic and symptomatic patients secrete similar viral loads, which
indicates that the transmission capacity of asymptomatic or minimally
symptomatic patients is very high. Thus, SARS-CoV-2 transmission can
happen early in the course of infection (82). Atypical clinical manifestations
have also been reported in COVID-19 in which the only reporting symptom
was fatigue. Such patients may lack respiratory signs, such as fever, cough,
and sputum (83). Hence, the clinicians
animal species is necessary to prevent the possibility of virus spread and

initiation of an outbreak due to zoonotic spillover (1).
Personal protective equipment (PPE), like face masks, will help to prevent the
spread of respiratory infections like COVID-19. Face masks not only protect
from infectious aerosols but also prevent the transmission of disease to other
susceptible individuals while traveling through public transport systems (313).
Another critical practice that can reduce the transmission of respiratory
diseases is the maintenance of hand hygiene. However, the efficacy of this
practice in reducing the transmission of respiratory viruses like SARS-CoV-2 is
much dependent upon the size of droplets produced. Hand hygiene will
reduce disease transmission only if the virus is transmitted through the
formation of large droplets (314). Hence, (314). Hence, it is better not to
overemphasize that hand hygiene will prevent the transmission of SARS-CoV-
2, since it may produce a false sense of safety among the general public that
further contributes to the spread of COVID-19. Even though airborne spread
has not been reported in SARS-CoV-2 infection, transmission can Occur
through droplets and fomites, especially when there is close, unprotected
contact between infected and susceptible individuals. Hence, hand hygiene is
COVID-19 patients showing severe signs are treated symptomatically along

with oxygen therapy. In such cases where the patients progress toward
respiratory failure and become refractory to oxygen therapy, mechanical
ventilation is necessitated. The COVID-19-induced septic shock can be
managed by providing adequate hemodynamic support (299). Several classes
of drugs are currently being evaluated for their potential therapeutic action
against SARS-CoV-2. Therapeutic agents that have anti-SARS-CoV-2 activity
can be broadly classified into three categories: drugs that block virus entry
into the host cell, drugs that block viral replication as well as its survival within
the host cell, and drugs that attenuate the exaggerated host immune response
(300). An inflammatory cytokine storm is commonly seen in critically ill
COVID-19 patients. Hence, they may benefit from the use of timely anti-
inflammation treatment. Anti-inflammatory therapy using drugs like
glucocorticoids, cytokine inhibitors, JAK inhibitors, and
chloroquine/hydroxychloroquine
should be done only after analyzing the risk/benefit ratio in COVID-19 patients
(301). There have not been any studies concerning the application of
nonsteroidal anti-inflammatory drugs (NSAID) to COVID-19-infected patients.
However, reasonable pieces of evidence are available that link NSAID
Animal Models and Cell Cultures

For evaluating the potential of vaccines and therapeutics against CoVs,
including SARS-CoV, MERS-CoVs, and the presently emerging SARS- CoV-2,
suitable animal models that can mimic the clinical disease are needed (211,
212). Various animal models were assessed for SARS- and MERS- CoVs, such
as mice, guinea pigs, golden Syrian hamsters, ferrets, rabbits, nonhuman
primates like rhesus macaques and marmosets, and cats (185, 213-218). The
specificity of the virus to hACE2 (receptor of SARS-CoV) was found to be a
significant barrier in developing animal models. Consequently, a SARS-CoV
transgenic mouse model has been developed by inserting the hACE2 gene
into the mouse genome (219). The inability of MERS-CoV to replicate in the
respiratory tracts of animals (mice, hamsters, and ferrets) is another limiting
factor. However, with genetic engineering, a 288-330+/+ MERS-CoV
genetically modified mouse model was developed and now is in use for the
assessment of novel drugs and vaccines against MERS-CoV (220). In the past,
small animals (mice or hamsters) have been targeted for being closer to a
humanized structure, such as mouse DPP4 altered with human DPP4
(hDPP4), hDPP4-transduced mice, and hDPP4-Tg mice (transgenic for
expressing
health emergency on 31 January 2020; subsequently, on 11 March 2020, they

declared it a pandemic situation. At present, we are not in a position to
effectively treat COVID-19, since neither approved vaccines nor specific
antiviral drugs for treating human CoV infections are available (7-9). Most
nations are currently making efforts to prevent the further spreading of this
potentially deadly virus by implementing preventive and control strategies.
In domestic animals, infections with CoVs are associated with a broad
spectrum of pathological conditions. Apart from infectious bronchitis virus,
canine respiratory CoV, and mouse hepatitis virus, CoVs are predominantly
associated with gastrointestinal diseases (10). The emergence of novel CoVs
may have become possible because of multiple CoVs being maintained in
their natural host, which could have favored the probability of genetic
recombination (10). High genetic diversity and the ability to infect multiple
host species are a result of high-frequency mutations in CoVs, which occur
due to the instability of RNA-dependent RNA polymerases along with higher
rates of homologous RNA recombination (10, 11). Identifying the origin of
SARS-CoV-2 and the pathogen's evolution will be helpful for disease
surveillance (12), development of

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• All clinicians should keep

category A agents (cholera, plague). Patients should be placed in separate

considerable protection in mice against a MERS- CoV lethal challenge. Such

other clinical trials in different phases are still ongoing elsewhere.

another study, the average reproductive number of COVID-19 was found to be

extended to other cities of Hupel

been used based on the experience

Epidemiology and Pathogenesis

13 CONVALESCENT PLASMA THERAPY

Prevention [21, 30]

absence of this protein is related to the altered virulence of coronaviruses due

including IL2, IL7, IL10, GCSF, IP10,

Interestingly, disease in patients outside Hubei province has been reported to

uroplets can spread 1-2 il ditu deposit

Cases continued to increase

SARS- or MERS-CoV outbreak (120). However, there has been concern

comprised a small population and, hence, the possibility of misinterpretation

of persistent local transmission or contact with patients with similar travel

was linked to a family member and 26

identified angiotensin receptor 2 (ACE2) as the receptor through which

Origin and Spread of COVID-19 [1, 2, 6]

with COVID-19 showed typical features on initial CT, including bilateral

infections clinically or through routine lab tests. Therefore travel history

epidemic progresses, commercial tests

comorbidities), it may progress to

such instance was in 2002-2003 when a

[median 17 d]. In the case series of

exponentially in other countries including South Korea, Italy and Iran.

(entertainment parks etc). China is also

article gives a bird's eye view about

mask and practice cough hygiene. Caregivers should be asked to wear a

risk regions. It is derived from a live attenuated strain of Mycobacterium

exponentially in other countries including South Korea, Italy and Iran.

other emerging viral diseases. Several therapeutic and preventive strategies,

Splits Tree phylogeny analysis.

Practice Points from an Indian

themselves while examining such

specimens, like bronchoalveolar lavage fluid, sputum, nasal swabs,

the SARS-COV. Environmental samples

respiratory infection (SARI) and respiratory distress, shock or hypoxaemia.

consolidation. It is also abnormal in

variant group. The receptor-binding gene region appears to be very similar to

glass opacities and sub segmental consolidation. It is also abnormal in

(using suitable animal models) should be conducted to evaluate the risk of

Inhibition of virus replication. Replication inhibitors include remdesivir (GS-

might be lower. Further genetic analysis is required between SARS-CoV-2 and

there, there is an increase in the outbreak of this virus through human-to-

prevailing chronic medical conditions such as lung disease, heart failure,

prevent further spread of disease at mass gatherings, functions remain

vaccine that can produce cross-reactive antibodies. However, the success of

specifically in the respiratory tract will help to reduce virus-triggered immune

polymorphism at nucleotide position 28,144, which results in amino acid

in asymptomatic patients. These abnormalities progress from the initial focal

vitro antiviral potential of FAD-approved drugs, viz., ribavirin, penciclovir,

nsps and Accessory Proteins

All of these therapeutic approaches have revealed

respiratory syncytial virus, rhinovirus, human metapneumovirus and SARS

severe illness, to minimise the risk of exposure to COVID-19 during

of plasma cytokines, which suggests an immunopatho- logical process