Medical Virology & Parasistology

Unit 1:
Diagnostic virology-Cultivation Of pathogenic Viruses in lab Animals &

Tissue Culture:
Cultivation of pathogenic viruses in laboratory animals and tissue culture is a critical aspect of
virology research, vaccine development, and diagnostics. Here’s a detailed overview of both
approaches:
1. Cultivation in Lab Animals:
 Purpose: Animal models are used to study the pathogenesis, immune response, and
transmission of viruses. They are also essential for the development of vaccines and antiviral
drugs.
 Commonly Used Animals: Mice, rats, guinea pigs, rabbits, and primates are often used
depending on the virus being studied. Chick embryos are also widely used, especially for
influenza virus cultivation.
 Procedure:
o Inoculation: The virus is introduced into the animal via different routes
(intracerebral, intranasal, intraperitoneal, etc.) depending on the research objective.
o Observation: After inoculation, animals are observed for signs of infection, and
samples (blood, tissues) are collected at various stages.
o Harvesting: Once the virus has replicated sufficiently, it is harvested from the
infected tissue or fluids for further study.
 Ethical Considerations: Animal research must adhere to ethical guidelines, ensuring minimal
suffering and humane treatment.
2. Cultivation in Tissue Culture:
 Purpose: Tissue culture allows for the controlled study of viral infection, replication, and
cytopathic effects in a laboratory environment, providing a more refined model than whole
animals.
 Types of Cultures:
o Primary Cell Cultures: Derived directly from animal tissues (e.g., kidney, liver
cells). These cells have a limited lifespan but maintain the characteristics of the
original tissue.
o Continuous Cell Lines: Immortalized cells that can divide indefinitely (e.g., HeLa,
Vero cells). These are commonly used due to their ease of maintenance.
o Organ Cultures: Involve maintaining a whole organ or part of it in culture, providing

a more complex environment than isolated cells.
 Procedure:
o Inoculation: The virus is added to the cultured cells, which are then incubated under
controlled conditions (temperature, CO₂ levels).
o Observation: The effects of viral replication are monitored, often by observing

cytopathic effects (CPE) like cell rounding, detachment, or death.
o Harvesting: After sufficient replication, the virus is harvested from the culture
medium or cells.
 Applications: Tissue cultures are used for vaccine production, studying viral life cycles, drug
screening, and diagnostic assays.
3. Comparison:
 Control: Tissue culture offers greater control over experimental conditions, reducing
variability.
 Ethics: Tissue cultures minimize the need for animal use, aligning with the 3Rs principle
(Replacement, Reduction, Refinement) in animal research.
 Relevance: Animal models are often necessary for studying the full scope of a virus's
pathogenicity, immune response, and transmission in a living organism.
4. Safety and Containment:
 Cultivating pathogenic viruses requires strict biosafety protocols to prevent accidental release
or infection of lab personnel. Depending on the virus, work is done in biosafety level (BSL) 2,
3, or 4 facilities.
This process is essential for advancing our understanding of viral diseases and developing treatments
and preventive measures.
Identification of Pathogenic Viruses and Establishment of Viral Etiology:

Identification of Pathogenic Viruses and Establishment of Viral Etiology
Introduction
The identification of pathogenic viruses and the establishment of viral etiology are critical
components of virology and infectious disease management. Understanding the causative viruses
behind diseases enables the development of effective treatments, vaccines, and public health
strategies. This process involves a multi-step approach, integrating various diagnostic techniques to
confirm viral infections and establish their role in disease. This document provides an in-depth
exploration of methods used to identify pathogenic viruses, the principles behind these methods, and
the approach to establish viral etiology.
1. Principles of Viral Identification
Identification of viruses typically involves:
1. Isolation and Cultivation: Culturing viruses in appropriate host cells or systems.

2. Detection and Identification: Using methods to detect viral presence and characterize the
virus.
3. Establishment of Etiology: Correlating the presence of the virus with clinical disease.
2. Isolation and Cultivation
2.1. Viral Isolation
Isolation involves growing the virus from a clinical specimen to study its properties. This is often
done using cell culture techniques. The choice of cell line depends on the virus; for example:
 Embryonated Eggs: Used for influenza and certain other viruses.
 Animal Models: Sometimes necessary for viruses that do not grow well in cell cultures.
2.2. Cell Culture Techniques
 Primary Cell Cultures: Directly derived from tissues. They have a limited lifespan but are
useful for isolating viruses that require specific host cells.
 Continuous Cell Lines: Immortalized cell lines that can grow indefinitely. These are often
used for routine virus cultivation and characterization.
2.3. Growth Characteristics
Observing viral growth characteristics in cultures can provide preliminary identification. This
includes:
 Cytopathic Effects (CPE): Changes in host cells (e.g., cell rounding, lysis).
 Plaque Assay: Measures viral infectivity by counting the number of plaques formed in a
monolayer of cells.
3. Detection and Identification Methods
3.1. Traditional Methods
 Microscopy: Electron microscopy can visualize viruses directly, although it's less commonly
used due to cost and complexity.
 Hemagglutination Assay: Used for viruses like influenza that agglutinate red blood cells.
3.2. Molecular Techniques
 Polymerase Chain Reaction (PCR): Detects viral nucleic acids with high sensitivity and
specificity. Variants include:
o Reverse Transcription PCR (RT-PCR): For detecting RNA viruses.
o Real-Time PCR (qPCR): Provides quantitative information about the viral load.
 Nucleic Acid Amplification Tests (NAATs): Includes PCR and other techniques like loop-
mediated isothermal amplification (LAMP).
3.3. Serological Techniques

 Enzyme-Linked Immunosorbent Assay (ELISA): Detects viral antigens or antibodies
against the virus.
 Immunofluorescence Assays: Uses fluorescently labeled antibodies to detect viral proteins in

infected cells.
3.4. Protein and Antigen Detection
 Western Blotting: Detects specific viral proteins in a sample.
 Immunoassays: Various formats, including lateral flow assays, can provide rapid results.
3.5. Next-Generation Sequencing (NGS)
 Whole Genome Sequencing (WGS): Provides detailed information about the viral genome,
useful for identifying novel viruses and tracking mutations.
 Metagenomics: Allows for the identification of viruses in complex samples without prior
knowledge of the virus.
4. Establishing Viral Etiology
4.1. Correlation with Clinical Disease
Establishing a virus as the etiological agent involves demonstrating a link between the presence of the
virus and disease symptoms. This includes:
 Epidemiological Studies: Analyzing patterns and incidence of disease in populations.
 Clinical Correlation: Observing consistent clinical presentations in infected individuals.
4.2. Causation Studies
 Animal Models: Inoculating animals with the virus and observing disease development.
 Koch's Postulates: Traditional criteria for proving causation, though modern approaches may
not always strictly follow these steps.
4.3. Molecular Koch's Postulates
For some viruses, traditional postulates are adapted to molecular techniques:
 Presence of Viral DNA/RNA: Correlates with disease symptoms.
 Specificity: Demonstration that viral genetic material or proteins are only present in diseased
tissues.
 Reproducibility: Ability to reproduce the disease by introducing the virus into a susceptible
host.
4.4. Genetic and Phenotypic Analysis
 Phylogenetic Analysis: Determines evolutionary relationships and helps identify viral strains.
 Phenotypic Characterization: Assesses viral properties like infectivity, replication rate, and
virulence factors.
5. Diagnostic Challenges
5.1. Virus Variability
 Genetic Diversity: High mutation rates in some viruses (e.g., influenza, HIV) complicate
diagnosis and treatment.
 Co-infections: Presence of multiple viruses in a single host can obscure identification.
5.2. Sample Quality
 Specimen Handling: Improper handling or storage can degrade viral RNA/DNA or proteins.
 Contamination: Risk of contamination during collection or processing can lead to false

results.
5.3. Technical Limitations
 Sensitivity and Specificity: Balancing sensitivity (detecting low levels of virus) and
specificity (avoiding false positives) is crucial.
 Cost and Accessibility: Advanced techniques like NGS can be expensive and may not be
available in all settings.
6. Emerging Trends and Future Directions
6.1. Integrated Diagnostics
Combining multiple diagnostic methods (e.g., molecular and serological) for comprehensive viral
identification.
6.2. Point-of-Care Testing
Developing rapid, user-friendly tests for use in remote or resource-limited settings.
6.3. Personalized Medicine
Using genetic and viral information to tailor treatments to individual patients.
6.4. Artificial Intelligence and Machine Learning
Applying AI and ML to analyze diagnostic data, improve accuracy, and predict outcomes.
6.5. Global Surveillance Networks
Enhancing global collaboration to monitor emerging viruses and facilitate rapid response.
Conclusion
The identification of pathogenic viruses and the establishment of viral etiology are complex processes
that require a multi-faceted approach. By integrating traditional and modern diagnostic techniques,
researchers and clinicians can accurately identify viral pathogens, understand their role in disease, and
develop effective interventions. Continued advancements in technology and global collaboration will
further enhance our ability to combat viral infections and protect public health.
Structure, Cultivation, Pathogenicity, lab diagnostics, prevention & control
of Influenza Virus:
The influenza virus is a significant human pathogen responsible for seasonal flu epidemics and
occasional pandemics. Understanding its structure, cultivation, pathogenicity, laboratory diagnostics,
and methods for prevention and control is crucial in managing its impact on public health.
1. Structure of the Influenza

Virus:
The influenza virus belongs to

the Orthomyxoviridae family
and is an enveloped, single-
stranded RNA virus. There are
three main types: Influenza A,
B, and C, with Influenza A and
B being the most clinically
relevant.
 Genome: The virus has

a segmented RNA
genome consisting of 7-
8 segments, depending on the type. Influenza A and B have 8 segments, while Influenza C has
7.
 Envelope: The viral envelope is derived from the host cell membrane and contains two main
glycoproteins:
o Hemagglutinin (HA): A trimeric protein responsible for binding the virus to sialic
acid receptors on the host cell surface, facilitating viral entry.
o Neuraminidase (NA): A tetrameric protein that helps release new virions from the
host cell by cleaving sialic acid residues.
 Matrix Protein (M1): Lines the inside of the viral envelope, providing structural integrity.
 M2 Ion Channel: Involved in the uncoating of the virus after entry into the host cell.
 Ribonucleoprotein (RNP): Composed of RNA segments, nucleoproteins, and polymerase

proteins (PB1, PB2, PA) that facilitate viral replication.
2. Cultivation of the Influenza Virus
A. In Cell Culture
 Madin-Darby Canine Kidney (MDCK) Cells: These are commonly used to cultivate
influenza viruses due to their susceptibility to infection.
 Procedure:
o The virus is inoculated into a monolayer of MDCK cells and incubated at 35-37°C.
o After several days, the culture is monitored for cytopathic effects (CPE), such as cell
rounding and detachment.
 Advantages: Allows for large-scale production of viruses, used in vaccine development.
B. In Embryonated Chicken Eggs
 Allantoic/Inoculation: The virus is injected into the allantoic cavity of 9-11-day-old

embryonated chicken eggs.
 Incubation: The eggs are incubated at 33-37°C for 2-3 days.
 Harvesting: Allantoic fluid, which contains high titers of the virus, is harvested.
 Applications: Widely used in vaccine production and diagnostic assays.
3. Pathogenicity of the Influenza Virus:
Flowchart
Inhalation Entry into Virus
Virus Enters Release of
of Influenza Respiratory Attaches to
Cells Viral RNA
Virus Tract Cells
Viral RNA New Virus New Virus Infection

Virus
Goes to Particles Particles Spreads to
Replicates
Nucleus Assembled Released Nearby Cells
Immune
Immune Inflammation Recovery or
System
Response and Symptoms Complication
Fights
Triggered Develop s
Infection
A. Transmission
 Respiratory Droplets: The primary mode of transmission is through inhalation of droplets

expelled by coughing, sneezing, or talking.
 Contact Transmission: Can also spread via direct contact with contaminated surfaces,
followed by touching the face.
B. Viral Replication and Pathogenesis
 Attachment and Entry: The virus binds to sialic acid receptors on epithelial cells in the
respiratory tract via HA. It is then internalized through endocytosis.
 Uncoating: Acidification within the endosome triggers the M2 ion channel, leading to the
release of viral RNA into the cytoplasm.
 Replication: Viral RNA is transcribed and replicated in the nucleus, followed by assembly in
the cytoplasm.
 Release: Newly formed virions are released from the host cell by the action of NA, leading to
the spread of infection to adjacent cells.
 Immune Response: The virus induces a robust immune response, including cytokine release,
which contributes to the symptoms of fever, malaise, and myalgia.
C. Clinical Manifestations
 Symptoms: Fever, cough, sore throat, nasal congestion, body aches, fatigue, and headache.
Severe cases can lead to pneumonia, acute respiratory distress syndrome (ARDS), and death,
particularly in high-risk groups (e.g., elderly, immunocompromised).
4. Laboratory Diagnostics for Influenza
A. Specimen Collection
 Respiratory Specimens: Nasopharyngeal swabs, throat swabs, nasal aspirates, or

bronchoalveolar lavage fluid are collected for testing.
B. Diagnostic Tests
 Rapid Influenza Diagnostic Tests (RIDTs):
o Detect viral antigens in respiratory specimens.
o Provide results within 15-30 minutes but have variable sensitivity.
 Reverse Transcription Polymerase Chain Reaction (RT-PCR):
o The gold standard for influenza diagnosis.
o Highly sensitive and specific; can differentiate between influenza types and subtypes.
 Viral Culture:
o Involves inoculating specimens into cell cultures or embryonated eggs.
o Takes several days and is used for strain characterization and vaccine production.
 Immunofluorescence Assays:
o Detect viral antigens in infected cells using fluorescent-labeled antibodies.
 Serology:
o Detects antibodies against the influenza virus in blood samples, useful for
epidemiological studies.
5. Prevention and Control of Influenza
A. Vaccination
 Seasonal Influenza Vaccines:
o Inactivated Influenza Vaccine (IIV): The most common type, administered via
injection. Contains inactivated viruses or viral proteins.
o Live Attenuated Influenza Vaccine (LAIV): Administered via nasal spray,

containing live, weakened viruses.
 Vaccine Composition:
o Updated annually to match circulating strains, based on WHO recommendations.

o Typically contains two influenza A subtypes (H1N1 and H3N2) and one or two
influenza B strains (trivalent or quadrivalent vaccines).
 Target Groups: Recommended for everyone over six months of age, especially high-risk
groups (e.g., elderly, healthcare workers, pregnant women).
B. Antiviral Medications
 Neuraminidase Inhibitors:
o Oseltamivir (Tamiflu) and Zanamivir (Relenza): Block the release of new virions,
reducing the severity and duration of symptoms if administered early.
 M2 Ion Channel Inhibitors:
o Amantadine and Rimantadine: Effective against some strains of influenza A, but

resistance has limited their use.
 Baloxavir Marboxil (Xofluza): A newer antiviral that inhibits viral RNA polymerase.
C. Non-Pharmaceutical Interventions
 Hygiene Measures:
o Frequent handwashing, using alcohol-based hand sanitizers, and avoiding touching

the face.
o Respiratory hygiene, such as covering the mouth and nose with a tissue or elbow
when coughing or sneezing.
 Social Distancing:
o Staying home when sick, avoiding close contact with infected individuals, and using
masks to reduce transmission.
 Isolation and Quarantine:
o Isolating infected individuals and quarantining exposed contacts to prevent further

spread.
D. Public Health Measures
 Surveillance:
o Global and national surveillance programs monitor circulating influenza strains, track
outbreaks, and guide vaccine formulation.
 Education Campaigns:
o Public health campaigns to promote vaccination, hygiene practices, and awareness of

influenza symptoms.
E. Pandemic Preparedness
 Stockpiling Vaccines and Antivirals: Ensuring adequate supplies for potential pandemics.
 Emergency Response Plans: Developing and updating plans for managing large-scale
outbreaks, including resource allocation and healthcare system readiness.
Effective management of influenza relies on a combination of vaccination, antiviral treatment, public
health interventions, and ongoing research to monitor and respond to evolving viral strains.
Structure, Cultivation, Pathogenicity, lab diagnostics, prevention & control of

Rhinovirus
Rhinovirus Overview
Rhinovirus is a major cause of the common cold, especially prevalent during the fall and spring. It is
a member of the Picornaviridae family and is primarily transmitted via respiratory droplets or
contaminated surfaces.
1. Structure of Rhinovirus
 Capsid: The virus has a non-

enveloped icosahedral capsid,
composed of 60 protomers.
Each protomer consists of four
proteins (VP1, VP2, VP3, and
VP4) that form a protective
shell around the viral RNA.
 Genome: The genome is a

single-stranded RNA of positive
polarity. It encodes for a single
polyprotein that is cleaved into
structural and non-structural
proteins.
 Surface Features: The capsid

proteins are involved in receptor
binding and entry into host
cells.
2. Cultivation of Rhinovirus
A. In Cell Culture
 Cell Lines: Commonly cultured in human epithelial cell lines such as HeLa or human
rhabdomyosarcoma (RD) cells.
 Procedure:
o Inoculation: The virus is added to a monolayer of susceptible cells.
o Incubation: Cells are incubated at 33-35°C, which is optimal for rhinovirus

replication.
o Monitoring: Cytopathic effects (CPE) such as cell rounding, and detachment are
observed.
o Harvesting: After sufficient viral replication, the virus is harvested from the cell
culture supernatant.
B. In Animal Models
 Limited Use: Rhinoviruses are less commonly cultivated in animals due to their specific
tropism for human cells. However, some research uses transgenic mice or other modified
models.
3. Pathogenicity of Rhinovirus
Flowchart
Attachment to
Entry into
Inhalation of Nasal Endocytosis of
Respiratory
Rhinovirus Epithelial Virus
Tract
Cells
Viral Uncoating Viral RNA

Synthesis of Assembly of New
and Release of Replication in
Viral Proteins Virions
RNA Cytoplasm
Inflammation
Release of
Spread to Immune Response and Symptoms:
Virions and
Adjacent Cells Activation Runny Nose,
Cell Lysis
Cough, Sneezing
Resolution of
Infection OR
Exacerbation of
Existing
Conditions
A. Entry and Infection
 Transmission: Spread via respiratory droplets, contact with contaminated surfaces, or hand-
to-face contact.
 Attachment: The virus binds to the ICAM-1 receptor on nasal epithelial cells using surface
proteins.
 Endocytosis: The virus is internalized into the host cell via endocytosis.
B. Replication
 Uncoating: Viral RNA is released into the cytoplasm.
 Replication: The RNA is translated into a polyprotein, which is cleaved into functional viral
proteins. The viral RNA is replicated in the cytoplasm.
 Assembly: New virions are assembled in the cytoplasm.
 Release: Newly formed virions are released from the host cell, often leading to cell lysis and
further spread of the virus.
C. Immune Response and Symptoms
 Immune Response: The immune system responds with inflammation, cytokine release, and
recruitment of immune cells.
 Symptoms: Common cold symptoms include runny nose, sore throat, cough, sneezing, and
congestion.
D. Complications
 Secondary Infections: Can lead to secondary bacterial infections or exacerbate asthma and
other respiratory conditions.
4. Laboratory Diagnostics for Rhinovirus
 Samples: Nasal swabs, throat swabs, or aspirates.
B. Diagnostic Tests
 RT-PCR: Detects viral RNA with high sensitivity and specificity.
 Viral Culture: Culturing in cell lines can confirm the presence of the virus.
 Rapid Antigen Tests: Detects viral proteins; less sensitive than RT-PCR but provides rapid
results.
 Serology: Detects antibodies in response to rhinovirus infection; less commonly used for
acute diagnosis.
5. Prevention and Control of Rhinovirus
A. Hygiene Measures
 Hand Hygiene: Frequent hand washing or use of alcohol-based hand sanitizers.
 Avoiding Touching Face: Reduces the risk of transferring the virus from contaminated
surfaces to mucosal surfaces.
 Respiratory Etiquette: Covering coughs and sneezes with a tissue or elbow.
B. Environmental Cleaning
 Disinfection: Regularly disinfecting commonly touched surfaces to reduce virus viability.
C. Public Health Measures
 Awareness Campaigns: Educating the public on hygiene practices and symptom

management.
D. Vaccination
 No Vaccine: Currently, there is no vaccine for rhinovirus due to its high variability and
numerous serotypes.
of Coronavirus
Coronaviruses are a group of RNA viruses that can cause diseases in mammals and birds, including
humans. In humans, they can cause respiratory infections that range from mild colds to severe
diseases like COVID-19.
1. Structure of Coronavirus Envelope: Coronaviruses are

enveloped viruses, meaning they have a lipid bilayer derived
from the host cell membrane.
 Spike Glycoprotein (S): Protruding from the

envelope are spike (S) glycoproteins, which give the
virus its characteristic crown-like appearance. These
spikes are crucial for binding to host cell receptors
and mediating entry into the host cell.
 Nucleocapsid (N): The virus contains a

nucleocapsid protein that binds to the RNA genome,
forming a helical structure inside the envelope.
 Membrane (M) Protein: The most abundant

structural protein, involved in virus assembly and shaping the virion.
 Envelope (E) Protein: A small protein that plays a role in virus assembly and release.
2. Cultivation of Coronavirus
A. In Cell Culture
 Cell Lines: Coronaviruses are commonly cultured in human epithelial cell lines such as Vero
E6 cells (derived from African green monkey kidney cells).
 Procedure:
o Inoculation: The virus is inoculated onto a monolayer of susceptible cells.
o Incubation: The cells are incubated at 37°C, allowing the virus to replicate.
o Monitoring: Cytopathic effects (CPE), such as cell rounding and syncytia formation,
are observed.
o Harvesting: The virus can be harvested from the cell culture supernatant for further
analysis.
B. In Animal Models
 Transgenic Models: Mouse models genetically modified to express human ACE2 receptors
are used for studying the pathogenesis of SARS-CoV-2 (the virus responsible for COVID-19).
3. Pathogenicity of Coronavirus
Flowchart
Attachment to Virus Enters

Inhalation of Entry into
Host Cells via Cells and
Coronavirus Respiratory Tract
Spike (S) Protein Releases RNA
Viral RNA Release of

Assembly of New Spread to
Replication and Virions from Host
Virions Adjacent Cells
Protein Synthesis Cell
Resolution of
Inflammation and Infection OR
Immune Response Symptoms: Cough, Complications
Activation Fever, Shortness (e.g., ARDS,
of Breath Multi-organ
Failure)
 Transmission: Spread primarily via respiratory droplets, though contact with contaminated
surfaces can also lead to transmission.
 Attachment: The spike (S) protein binds to the angiotensin-converting enzyme 2 (ACE2)
receptor on the surface of host cells, particularly in the respiratory tract.
 Fusion and Entry: After binding, the virus fuses with the host cell membrane, allowing entry
into the cell.
B. Replication
 Uncoating: The viral RNA genome is released into the host cell cytoplasm.
 Translation and Replication: The viral RNA is translated into viral proteins and replicates in
the host cell’s cytoplasm.
 Assembly: New virions are assembled in the host cell, where viral RNA is packaged into new
nucleocapsids.
C. Release and Spread
 Budding: New virions bud from the host cell membrane, acquiring an envelope in the
process.
 Spread: The virus can infect nearby cells, spreading the infection within the host.
D. Immune Response and Symptoms
 Immune Response: The body’s immune response includes the release of cytokines and
recruitment of immune cells, leading to inflammation.
 Symptoms: Symptoms range from mild respiratory symptoms to severe pneumonia,
depending on the viral load and host immune response.
E. Complications
 Severe Disease: In severe cases, particularly in older adults or those with underlying
conditions, the infection can lead to acute respiratory distress syndrome (ARDS), multi-organ
failure, and death.
4. Laboratory Diagnostics for Coronavirus
 Samples: Nasopharyngeal swabs, oropharyngeal swabs, or lower respiratory specimens like

sputum or bronchoalveolar lavage.
B. Diagnostic Tests
 RT-PCR: The gold standard for detecting viral RNA with high sensitivity and specificity.
 Antigen Tests: Detect viral proteins; these are faster but generally less sensitive than RT-
PCR.
 Serology: Detects antibodies in response to infection; useful for understanding past exposure
and immune response.
 Viral Culture: Less commonly used for diagnosis due to biosafety concerns, but can be
performed in specialized laboratories.
5. Prevention and Control of Coronavirus
A. Personal Protective Measures
 Face Masks: Wearing masks to prevent the spread of respiratory droplets.
 Hand Hygiene: Frequent hand washing or use of alcohol-based hand sanitizers.
 Physical Distancing: Maintaining distance from others to reduce the spread of the virus.
 Disinfection: Regular cleaning and disinfection of surfaces, especially in public spaces.
C. Vaccination
 Vaccines: Several vaccines have been developed to prevent COVID-19, which induce
immunity and reduce the severity of the disease.
 Testing and Contact Tracing: Identifying and isolating infected individuals to prevent the
spread of the virus.
 Quarantine and Isolation: Implementing quarantine for exposed individuals and isolation
for confirmed cases to contain outbreaks.
of rubella virus
Rubella Virus, also known as the German measles virus, is a single-stranded RNA virus that causes
rubella, a typically mild illness characterized by a rash and fever. However, if contracted during
pregnancy, rubella can cause severe congenital defects, known as congenital rubella syndrome (CRS).
1. Structure of Rubella Virus
 Envelope: Rubella virus is an enveloped virus, with a lipid bilayer derived from the host cell
membrane.
 Glycoproteins: The envelope contains two glycoproteins, E1 and E2, which are responsible
for binding to host cell receptors and facilitating viral entry.
 Capsid: Inside the envelope is the

nucleocapsid, which is icosahedral in
shape and composed of the capsid
protein.
 Genome: The virus has a single-

stranded, positive-sense RNA genome
that encodes for non-structural proteins
involved in replication, as well as
structural proteins.
2. Cultivation of Rubella Virus
A. In Cell Culture
 Cell Lines: Rubella virus can be cultured in various human and animal cell lines, including
Vero cells (derived from African green monkey kidney) and RK13 cells (rabbit kidney cells).
 Procedure:
o Incubation: Cells are incubated at 35-37°C.
o Monitoring: Cytopathic effects (CPE) are generally mild but can include cell
rounding and detachment.
o Harvesting: After sufficient replication, the virus is harvested from the cell culture
supernatant.
B. In Animal Models
 Limited Use: Animal models are not commonly used for rubella virus cultivation due to its
specific human tropism. However, some research uses transgenic animals or humanized
models.
3. Pathogenicity of Rubella Virus
Flowchart
Attachment to Virus Enters

Inhalation of Entry into
Host Cells via E1 Cells and
Rubella Virus Respiratory Tract
Glycoprotein Releases RNA
Viral RNA Release of

Assembly of New Spread to Skin
Replication and Virions and
Virions and Other Tissues
Protein Synthesis Viremia
Resolution of
Symptoms: Fever, Infection OR
Immune Response
Rash, Swollen Complications
Activation
Lymph Nodes (e.g., Congenital
Rubella Syndrome)
A. Entry and Initial Infection
 Transmission: Rubella is transmitted via respiratory droplets from an infected person.
 Attachment: The virus attaches to host cells in the respiratory tract using the E1
glycoprotein, which binds to cellular receptors.
B. Replication
 Fusion and Entry: The virus enters the host cell by endocytosis, followed by fusion with the
endosomal membrane.
 Uncoating: Viral RNA is released into the cytoplasm.
 Translation and Replication: The RNA is translated into viral proteins, and the genome is
replicated within the host cell.
 Assembly: New virions are assembled in the cytoplasm, where the RNA is packaged into the
nucleocapsid.
 Budding: New virions bud from the host cell membrane, acquiring their envelope.
 Viremia: The virus enters the bloodstream (viremia), spreading to other tissues, including the
skin, where it causes the characteristic rubella rash.

 Immune Response: The body’s immune response involves the production of antibodies and
activation of T cells, leading to the clearance of the virus.
 Symptoms: Rubella typically presents with a mild fever, rash, and swollen lymph nodes. In
pregnant women, the virus can cross the placenta and infect the fetus, leading to congenital
rubella syndrome.
E. Complications
 Congenital Rubella Syndrome (CRS): If a pregnant woman contracts rubella, the virus can
cause severe fetal abnormalities, including deafness, cataracts, heart defects, and
developmental delays.
4. Laboratory Diagnostics for Rubella Virus
 Samples: Blood samples, nasopharyngeal swabs, or amniotic fluid in the case of suspected
congenital infection.
B. Diagnostic Tests
 Serology: Detects rubella-specific IgM antibodies in acute infection or IgG antibodies for
immunity status.
 RT-PCR: Detects viral RNA in blood or other samples, particularly useful for confirming
congenital rubella.
 Viral Culture: Can be performed in cell culture but is less commonly used due to the
availability of faster diagnostic methods.
5. Prevention and Control of Rubella Virus
A. Vaccination
 MMR Vaccine: The most effective method of prevention is vaccination with the MMR
(measles, mumps, rubella) vaccine, which is highly effective in preventing rubella.
 Herd Immunity: High vaccination coverage in the population helps protect those who are not
vaccinated, such as newborns and individuals with certain medical conditions.
B. Public Health Measures
 Screening and Vaccination of Women of Childbearing Age: Ensuring that women are
immune to rubella before pregnancy is crucial to prevent congenital rubella syndrome.
 Outbreak Control: Rapid identification and isolation of rubella cases, along with vaccination
of susceptible contacts, can help control outbreaks.
C. Infection Control
 Isolation: Infected individuals should be isolated to prevent the spread of the virus,
particularly in healthcare settings and among pregnant women.
of adenovirus (Type2)
Adenoviruses are a group of common viruses that infect the lining of the eyes, airways, lungs,
intestines, urinary tract, and nervous system. Adenovirus type 2 is one of the many serotypes that can
cause respiratory illnesses, conjunctivitis, gastroenteritis, and other infections.
1. Structure of Adenovirus (Type 2)
 Capsid: Adenovirus type 2 has a

non-enveloped icosahedral
capsid, made up of 252
capsomeres (240 hexons and 12
pentons).
 Fibers: The capsid has fibers

protruding from each vertex
(penton base), which are
involved in binding to host cell
receptors.
 Genome: The virus contains a linear, double-stranded DNA genome. The genome is
approximately 36,000 base pairs long and is associated with core proteins within the capsid.
 Protein Composition: The viral capsid is composed of several structural proteins, including
hexon, penton base, and fiber proteins, which play key roles in the virus's ability to infect host
cells.
2. Cultivation of Adenovirus (Type 2)
A. In Cell Culture
 Cell Lines: Adenovirus type 2 is typically cultured in human epithelial cells, such as HEp-2
(human laryngeal carcinoma) or A549 cells (human lung carcinoma).
 Procedure:
o Incubation: Cells are incubated at 37°C in an atmosphere with 5% CO2.
o Monitoring: Cytopathic effects (CPE) such as rounding, and detachment of cells are
observed within 2-5 days post-infection.
o Harvesting: Once CPE is observed, the virus can be harvested from the cell culture
supernatant.
B. In Animal Models
 Animal Models: Adenovirus type 2 can be studied in animal models, including mice, for
understanding viral pathogenesis and immune response.
3. Pathogenicity of Adenovirus (Type 2)
Flowchart
Inhalation or Attachment to Endocytosis and Transport of

Ingestion of Host Cells via Entry into Host Viral DNA to
Adenovirus CAR Receptor Cell Nucleus
Spread to
Viral DNA Assembly of New Host Cell Lysis
Adjacent Cells
Replication and Virions in and Release of
and Possible
Protein Synthesis Nucleus Virions
Viremia
Resolution of
Symptoms: Fever,
Infection OR
Immune Response Respiratory
Complications
Activation Symptoms,
(e.g., Pneumonia,
Conjunctivitis
Hepatitis)
 Transmission: Adenovirus type 2 spreads via respiratory droplets, fecal-oral route, or direct
contact with contaminated surfaces.
 Attachment: The virus binds to the coxsackievirus and adenovirus receptor (CAR) on host
cells via the fiber protein.
 Endocytosis: After attachment, the virus is internalized into the host cell through receptor-
mediated endocytosis.
B. Replication
 Uncoating: The viral capsid is dismantled, and the viral DNA is transported to the nucleus.
 Transcription: Early viral genes are transcribed in the nucleus by the host's RNA
polymerase, leading to the production of early proteins involved in DNA replication and
immune evasion.
 Replication: The viral DNA genome is replicated in the nucleus.
 Late Gene Expression: Late viral proteins, including structural proteins, are produced.
 Assembly: New virions are assembled in the nucleus by packaging the replicated DNA into
newly synthesized capsid proteins.
 Lysis: The host cell undergoes lysis, releasing new virions, which can then infect adjacent
cells.
 Viremia: In severe cases, the virus may enter the bloodstream, spreading to other organs.
 Immune Response: The host immune response includes the activation of T cells and the
production of antibodies, which help to control the infection.
 Symptoms: Depending on the site of infection, symptoms may include fever, sore throat,
conjunctivitis (pink eye), bronchitis, pneumonia, diarrhea, or gastroenteritis.
E. Complications
 Severe Disease: In immunocompromised individuals, adenovirus infection can lead to severe

complications such as pneumonia, hepatitis, or multi-organ failure.
4. Laboratory Diagnostics for Adenovirus (Type 2)
 Samples: Respiratory secretions, stool samples, urine, or conjunctival swabs depending on

the site of infection.
B. Diagnostic Tests
 PCR: Polymerase chain reaction (PCR) to detect adenovirus DNA in clinical specimens is the
most sensitive and specific method.
 Viral Culture: The virus can be isolated in cell culture, but this method is slower and less
commonly used for routine diagnosis.
 Antigen Detection: Immunofluorescence or enzyme immunoassays can be used to detect

adenovirus antigens in clinical specimens.
 Serology: Detection of antibodies specific to adenovirus can be used to diagnose past

infections or in epidemiological studies.
5. Prevention and Control of Adenovirus (Type 2)
 Hand Hygiene: Frequent hand washing or use of hand sanitizers can help prevent
transmission.
 Avoiding Close Contact: Staying away from infected individuals can reduce the risk of
transmission, especially in crowded environments like schools or military barracks.
 Disinfection: Regular cleaning and disinfection of surfaces, especially in healthcare settings

and childcare facilities, are essential to control the spread.
C. Vaccination
 Military Use: Adenovirus vaccines are available for military personnel in the United States to
prevent outbreaks of respiratory illness caused by adenovirus types 4 and 7. However, no
vaccine is widely available for the general public.
D. Infection Control
 Isolation: Infected individuals, particularly those with respiratory symptoms, should be
isolated to prevent the spread of the virus, especially in hospitals and long-term care facilities.
Structure, Cultivation, Pathogenicity, lab diagnostics, prevention &

control of Mumps Virus
Mumps Virus is a member of the Paramyxoviridae family and is the causative agent of mumps, a
contagious viral infection that typically causes swelling of the parotid glands (a condition known
as parotitis). The virus primarily affects children but can also infect adults.
1. Structure of Mumps Virus
 Envelope: Mumps virus is an

enveloped virus with a lipid bilayer
derived from the host cell
membrane.
 Glycoproteins:
o Hemagglutinin-
Neuraminidase (HN): This
glycoprotein plays a dual
role in attaching the virus to
sialic acid-containing
receptors on host cells and
in cleaving sialic acid
residues to facilitate the release of new virions.
o Fusion (F) Protein: Facilitates the fusion of the viral envelope with the host cell
membrane, allowing the viral RNA to enter the cell.
 Nucleocapsid: Inside the envelope, the virus contains a helical nucleocapsid made of the
nucleoprotein (NP) bound to the viral RNA.
 Genome: The mumps virus has a single-stranded, negative-sense RNA genome

approximately 15,384 nucleotides in length, encoding several structural and non-structural
proteins.
2. Cultivation of Mumps Virus
A. In Cell Culture
 Cell Lines: Mumps virus can be cultured in various cell lines, including Vero cells (African
green monkey kidney cells) and primary human amnion cells.
 Procedure:
o Monitoring: Cytopathic effects (CPE), such as cell rounding and syncytia formation
(fusion of infected cells), are observed within a few days post-infection.
o Harvesting: The virus is harvested from the cell culture supernatant after sufficient
replication.
B. In Animal Models
 Animal Models: Mumps virus can be studied in animal models, such as mice and ferrets, to
understand pathogenesis and immune response.
3. Pathogenicity of Mumps Virus
Flowchart
Attachment to Fusion of Viral

Respiratory Envelope with Release of
Inhalation of Viral RNA into
Mumps Virus Tract Cells via Host Cell
HN Protein Membrane Cytoplasm
Viral RNA Spread to

Replication and Assembly of New Release of Parotid Glands
Virions in Virions and
Protein and Other
Synthesis Cytoplasm Viremia Organs
Resolution of
Symptoms: Infection OR
Immune Response Fever, Complications
Activation Headache, (e.g.,
Parotitis Orchitis,
Meningitis)
 Transmission: Mumps is spread through respiratory droplets, direct contact with infected
saliva, or fomites.
 Attachment: The virus attaches to host cells in the respiratory tract using the hemagglutinin-
neuraminidase (HN) protein, which binds to sialic acid-containing receptors on the cell
surface.
 Fusion and Entry: The fusion (F) protein facilitates the fusion of the viral envelope with the
host cell membrane, allowing the viral RNA to enter the cytoplasm.
B. Replication
 Uncoating: The viral RNA is released into the cytoplasm after the envelope fuses with the
host cell membrane.
 Transcription and Replication: The viral RNA is transcribed into mRNA by the viral RNA-
dependent RNA polymerase and then translated into viral proteins. The negative-sense RNA
genome is replicated via a positive-sense RNA intermediate.
 Assembly: New virions are assembled in the cytoplasm, where viral RNA is packaged into
nucleocapsids and enveloped with host-derived membranes.
C. Spread and Pathogenesis
 Viremia: The virus enters the bloodstream (viremia), spreading to other tissues, including the
salivary glands, CNS, and other organs.
 Parotitis: The virus commonly targets the parotid glands, leading to inflammation and
swelling, which is the hallmark of mumps.
 Immune Response: The body's immune response includes the production of neutralizing
antibodies and activation of T cells, leading to viral clearance.
 Symptoms: Mumps typically presents with fever, headache, muscle aches, fatigue, and
swelling of the parotid glands. Other complications can include orchitis (inflammation of the
testes), oophoritis (inflammation of the ovaries), meningitis, and pancreatitis.
E. Complications
 Severe Disease: Although rare, mumps can lead to complications such as aseptic meningitis,
encephalitis, permanent deafness, and infertility in males.
4. Laboratory Diagnostics for Mumps Virus
 Samples: Buccal swabs (from the inside of the cheek), throat swabs, saliva, cerebrospinal
fluid (in cases of suspected meningitis), or blood samples for serology.
B. Diagnostic Tests
 RT-PCR: Reverse transcription-polymerase chain reaction (RT-PCR) is used to detect viral

RNA in clinical specimens and is the preferred method for diagnosis.
 Viral Culture: The virus can be isolated from clinical samples and cultured in susceptible cell
lines, although this method is less commonly used due to the availability of faster molecular
diagnostics.
 Serology: Detection of mumps-specific IgM antibodies in acute infection or IgG antibodies

for immunity status.
 Enzyme-Linked Immunosorbent Assay (ELISA): Used to detect specific antibodies against

the mumps virus in serum samples.
5. Prevention and Control of Mumps Virus
A. Vaccination
 MMR Vaccine: The most effective prevention method is vaccination with the MMR
(measles, mumps, rubella) vaccine, which is highly effective in preventing mumps.
 Herd Immunity: High vaccination coverage helps prevent outbreaks by reducing the number
of susceptible individuals in the population.
B. Personal Protective Measures

 Hand Hygiene: Frequent hand washing with soap and water or use of alcohol-based hand
sanitizers.
 Avoiding Contact: Avoiding close contact with infected individuals, especially during
outbreaks.
 Outbreak Control: Rapid identification and isolation of mumps cases, along with
vaccination of susceptible contacts, can help control outbreaks.
 School Exclusion: Infected individuals, especially children, should be excluded from school
or daycare for at least five days after the onset of parotitis to prevent further transmission

control of MeaslesVirus
Measles Virus is a highly contagious virus that causes measles, a severe respiratory disease
characterized by fever, cough, runny nose, conjunctivitis, and a widespread skin rash. The virus
can lead to serious complications, especially in young children, pregnant women, and
immunocompromised individuals.
1. Structure of Measles Virus
 Envelope: The measles virus is an

enveloped virus, with a lipid bilayer
derived from the host cell membrane.
 Glycoproteins: The envelope contains

two key glycoproteins:
o Hemagglutinin (H) Protein:

Responsible for binding to the
host cell receptors, facilitating
viral entry.
o Fusion (F) Protein: Mediates

the fusion of the viral envelope
with the host cell membrane,
allowing the viral genome to enter the cell.
 Capsid: Inside the envelope is the nucleocapsid, which is helical and composed of the
nucleocapsid (N) protein.
 Genome: The virus has a single-stranded, negative-sense RNA genome, which is

approximately 15,894 nucleotides long and encodes for six structural proteins and two non-
structural proteins.
2. Cultivation of Measles Virus
A. In Cell Culture
 Cell Lines: Measles virus can be cultured in several human and primate cell lines, such as
Vero cells (derived from African green monkey kidney cells), B95a cells (marmoset B
lymphocytes), and human epithelial cells.
 Procedure:
o Incubation: Cells are incubated at 35-37°C in a CO2 incubator.
o Monitoring: Cytopathic effects (CPE), such as syncytia formation (multinucleated

giant cells), are observed within 3-7 days post-infection.
o Harvesting: The virus can be harvested from the cell culture supernatant when CPE
is evident.
B. In Animal Models
 Animal Models: The measles virus can be studied in small animal models, such as mice and
ferrets, which have been genetically modified to express human receptors.
3. Pathogenicity of Measles Virus
Flowchart
Attachment to
Fusion and Entry Viral RNA
Inhalation of Host Cells via
of Viral RNA into Transcription and
Measles Virus CD46/SLAM/Nectin-
Host Cell Protein Synthesis
4 Receptors
Release of
Assembly of New Infection of
Virions and Immune Response
Virions in the Respiratory
Spread via Activation
Cytoplasm Tract, Skin, CNS
Viremia
Resolution of
Symptoms: Fever, Infection OR
Cough, Rash, Complications
Conjunctivitis (e.g., Pneumonia,
Encephalitis)
 Transmission: The virus is primarily spread through respiratory droplets when an infected
person coughs or sneezes. It can also be transmitted through direct contact with contaminated
surfaces.
 Attachment: The virus attaches to the CD46, SLAM (signaling lymphocyte activation
molecule), or Nectin-4 receptors on host cells via the hemagglutinin (H) protein.
 Fusion and Entry: The fusion (F) protein facilitates the fusion of the viral envelope with the
host cell membrane, allowing the viral RNA to enter the cytoplasm.
B. Replication
 Uncoating: The viral RNA is released into the cytoplasm.
 Transcription and Replication: The viral RNA-dependent RNA polymerase transcribes the
negative-sense RNA genome into positive-sense mRNA, which is translated into viral
proteins. The genome is also replicated to produce new viral RNA.
 Assembly: New nucleocapsids are assembled in the cytoplasm, and the viral envelope is
acquired by budding from the host cell membrane.
C. Spread and Systemic Infection
 Viremia: The virus enters the bloodstream (primary viremia), spreading to various organs,
including the respiratory tract, skin, and the central nervous system (CNS).
 Rash Formation: The characteristic measles rash is due to the immune response to infected
endothelial cells in the skin.
 Immune Response: The body's immune response involves the activation of T cells and the
production of neutralizing antibodies.
 Symptoms: Initial symptoms include high fever, cough, runny nose, and conjunctivitis. This
is followed by the appearance of Koplik spots in the mouth and a widespread red rash that
typically starts on the face and spreads downward.
E. Complications
 Severe Disease: Complications can include pneumonia, encephalitis, and subacute sclerosing
panencephalitis (SSPE), a rare but fatal degenerative disease of the CNS that can occur years
after infection.
4. Laboratory Diagnostics for Measles Virus
 Samples: Throat swabs, nasopharyngeal swabs, urine samples, and blood samples (for
serology) can be collected for diagnosis.
B. Diagnostic Tests
 RT-PCR: Reverse transcription-polymerase chain reaction (RT-PCR) is used to detect viral

RNA in clinical specimens.
 Serology: Detection of measles-specific IgM antibodies in blood samples confirms acute

infection. IgG antibodies can be used to assess immunity or past infection.
 Viral Culture: Although less commonly used, the virus can be isolated from clinical
specimens and grown in cell culture.
 Immunofluorescence: Direct fluorescent antibody (DFA) testing can detect viral antigens in
clinical specimens.
5. Prevention and Control of Measles Virus
A. Vaccination
 MMR Vaccine: The measles, mumps, and rubella (MMR) vaccine is highly effective in
preventing measles. Two doses of the vaccine are recommended for children, with the first
dose given at 12-15 months and the second dose at 4-6 years.
 Herd Immunity: High vaccination coverage in the population helps to protect those who
cannot be vaccinated, such as infants and immunocompromised individuals.
B. Infection Control
 Isolation: Infected individuals should be isolated, particularly in healthcare settings, to

prevent the spread of the virus.
 Quarantine: Close contacts of infected individuals should be monitored and quarantined if

necessary.
 Outbreak Response: Rapid identification and isolation of cases, along with vaccination of
susceptible individuals, are critical in controlling outbreaks.
 Surveillance: Ongoing surveillance for measles cases and vaccination coverage is essential
for measles elimination efforts.
UNIT 2
control of Hepatitis virus (HAV)
Hepatitis A Virus (HAV) is a small, non-enveloped RNA virus that causes hepatitis A, a liver
infection. HAV is primarily transmitted through the fecal-oral route, often via contaminated food
or water. While HAV infection is usually self-limiting and does not cause chronic liver disease, it
can lead to severe illness in some cases.
1. Structure of Hepatitis A Virus (HAV)

 Capsid: HAV has a non-enveloped,
icosahedral capsid composed of 60 copies
each of four viral proteins (VP1, VP2, VP3,
and VP4). The capsid protects the viral RNA
and facilitates its entry into host cells.
 Genome: The virus contains a single-

stranded, positive-sense RNA genome of
approximately 7.5 kilobases. The genome
encodes a single polyprotein that is cleaved
into structural and non-structural proteins
necessary for viral replication and assembly.
 Proteins: The viral proteins, particularly

VP1 and VP3, are involved in receptor binding and immune response.
2. Cultivation of Hepatitis A Virus (HAV)
A. In Cell Culture
 Cell Lines: HAV is difficult to cultivate in cell culture compared to other viruses. It can be
grown in certain human and primate cell lines, such as FRhK-4 (fetal rhesus monkey kidney)
and PLC/PRF/5 (human hepatoma) cells.
 Procedure:
o Incubation: The cells are incubated at 37°C in an atmosphere with 5% CO2.
o Monitoring: HAV replicates slowly in culture, and cytopathic effects (CPE) are often
not visible. Instead, viral replication is typically monitored using molecular
techniques like RT-PCR or immunofluorescence assays.
B. In Animal Models
 Limited Use: Animal models, such as chimpanzees, have been used in research to study HAV
pathogenesis, but their use is limited due to ethical concerns and the availability of alternative
methods.
2. Pathogenicity of Hepatitis A Virus (HAV)
Flowchart
Ingestion of
HAV via Attachment to Virus Enters
Entry into Intestinal Cells and
Contaminated Small Intestine
Food/Water Cells Releases RNA
Viral RNA Viral RNA

Translation and Replication and Exocytosis and
Release of Spread to Liver
Protein Assembly of New via Bloodstream
Processing Virions Virions
Resolution of
Inflammation Infection OR
Infection of and Symptoms:
Hepatocytes and Immune Response Complications
Activation Jaundice, (e.g.,
Kupffer Cells Fatigue, Fulminant
Abdominal Pain Hepatitis)
 Transmission: HAV is primarily transmitted via the fecal-oral route, often through
consumption of contaminated food or water.
 Attachment: After ingestion, HAV reaches the small intestine and binds to its target cells
using the viral proteins VP1 and VP3, although the exact receptors are not fully identified.
 Entry: The virus enters the host cells via receptor-mediated endocytosis.
B. Replication
 Uncoating: After entry, the viral RNA is released into the cytoplasm.
 Translation: The RNA is directly translated into a polyprotein by the host’s ribosomes.
 Processing: The polyprotein is cleaved into individual viral proteins, including enzymes
necessary for RNA replication.
 RNA Replication: The viral RNA is replicated in the host cell's cytoplasm.
 Assembly: New virions are assembled in the cytoplasm, where the RNA is packaged into the
capsid proteins.
 Exocytosis: The assembled virions are released from the host cell via exocytosis, without
causing cell lysis.
 Spread: The virus spreads to the liver via the bloodstream, where it infects hepatocytes (liver
cells) and Kupffer cells (liver macrophages).

 Immune Response: The immune system recognizes and attacks the infected liver cells,
leading to liver inflammation (hepatitis).
 Symptoms: Symptoms of hepatitis A include jaundice (yellowing of the skin and eyes),
fatigue, abdominal pain, loss of appetite, nausea, and dark urine. The severity of the disease
varies, with most cases being mild and self-limiting.
E. Complications
 Fulminant Hepatitis: In rare cases, HAV infection can lead to fulminant hepatitis, a severe
and life-threatening form of liver failure.
4. Laboratory Diagnostics for Hepatitis A Virus (HAV)
 Samples: Blood samples are the primary specimen used for diagnosing hepatitis A.
B. Diagnostic Tests
 Serology:
o IgM Anti-HAV: The presence of IgM antibodies against HAV in the blood indicates
acute or recent infection.
o IgG Anti-HAV: The presence of IgG antibodies indicates past infection or immunity
(due to vaccination or previous infection).
 RT-PCR: Detection of HAV RNA in blood or stool samples can confirm an acute infection,
especially in early stages before antibodies are detectable.
 Liver Function Tests: Elevated levels of liver enzymes (ALT, AST) indicate liver damage
and are commonly seen in HAV infection.
5. Prevention and Control of Hepatitis A Virus (HAV)
A. Vaccination
 HAV Vaccine: The most effective method of prevention is vaccination against HAV. The
vaccine is highly effective and provides long-term protection against the virus.
 Herd Immunity: Widespread vaccination can help achieve herd immunity, protecting those
who are unvaccinated or at higher risk.
 Hand Hygiene: Frequent hand washing, especially after using the bathroom and before
handling food, can prevent transmission.
 Safe Food and Water Practices: Avoiding consumption of contaminated food and water is
crucial, especially in areas with poor sanitation.
 Outbreak Control: In the event of an outbreak, public health measures such as vaccination
campaigns and public education on hygiene practices are essential.
 Isolation: Infected individuals should be isolated to prevent the spread of the virus,
particularly in settings like schools, daycare centers, and food service establishments.

control of poliomyelitis virus
Poliovirus is the causative agent of poliomyelitis, a highly infectious disease that primarily
affects children under five years of age. The virus can invade the nervous system and cause
irreversible paralysis in some cases. Poliovirus is a member of
the genus Enterovirus in the family Picornaviridae.
1. Structure of Poliovirus
 Capsid: Poliovirus has a small, non-enveloped,
icosahedral capsid, which is about 30 nm in diameter. The
capsid is composed of 60 copies each of four viral proteins
(VP1, VP2, VP3, and VP4).
 Genome: The virus has a single-stranded, positive-sense

RNA genome, approximately 7,500 nucleotides long. The
RNA genome serves as both the genetic material and the
messenger RNA (mRNA) for protein synthesis.
 Surface Features: The capsid has depressions or

"canyons" around the five-fold axes, which are involved in
binding to the poliovirus receptor on host cells.
2. Cultivation of Poliovirus
A. In Cell Culture
 Cell Lines: Poliovirus is commonly cultured in human and monkey kidney cell lines, such as
HeLa cells (human cervical cancer cells) and Vero cells (African green monkey kidney cells).
 Procedure:
o Incubation: Cells are incubated at 37°C.
o Monitoring: Cytopathic effects (CPE), including cell rounding and detachment, are
observed within 2-3 days post-infection.
o Harvesting: Once CPE is observed, the virus can be harvested from the cell culture
supernatant.
B. In Animal Models
 Animal Models: Poliovirus can be studied in transgenic mice expressing the human
poliovirus receptor (CD155). These models are used for research on viral pathogenesis and
vaccine development.
2. Pathogenicity of Poliovirus
Flowchart
Attachment to
Intestinal Virus Entry Release of
Ingestion of through Viral RNA into
Poliovirus Epithelial
Cells via CD155 Endocytosis Cytoplasm
Receptor
Viral RNA Viral RNA

Translation and Replication and Release of
Virions and Spread to CNS
Polyprotein Assembly of New via Bloodstream
Synthesis Virions Primary Viremia
Resolution of
Invasion of Cytopathic Symptoms: Infection OR
Motor Neurons Effects Leading Fever, Fatigue,
Permanent
in Spinal Cord to Neuron Paralysis (in Paralysis (in
and Brainstem Damage Severe Cases) Severe Cases)
 Transmission: Poliovirus spreads via the fecal-oral route, often through contaminated food or
water.
 Attachment: The virus binds to the poliovirus receptor (PVR, also known as CD155) on the
surface of intestinal epithelial cells.
 Endocytosis: After attachment, the virus enters the host cell through receptor-mediated
endocytosis.
B. Replication
 Uncoating: The viral RNA is released into the cytoplasm, where it serves as mRNA for the
translation of viral proteins.
 Translation: The viral RNA is translated into a single polyprotein, which is then cleaved into
functional viral proteins.
 Replication: The viral RNA genome is replicated in the cytoplasm using the host cell's
machinery.
 Assembly: New virions are assembled in the cytoplasm by packaging the replicated RNA into
newly synthesized capsid proteins.
C. Spread and Nervous System Invasion
 Primary Viremia: The virus enters the bloodstream (viremia) and spreads to various tissues,
including the central nervous system (CNS).
 Invasion of CNS: The virus can cross the blood-brain barrier and infect motor neurons in the
spinal cord and brainstem, leading to paralysis in severe cases.
 Cytopathic Effects: Infection of neurons leads to cell death and inflammation, which causes
the characteristic neurological symptoms of poliomyelitis.
 Immune Response: The body mounts an immune response, producing antibodies that
neutralize the virus and prevent further infection.
 Symptoms: Most infections are asymptomatic, but some cases present with fever, fatigue,
headache, vomiting, neck stiffness, and limb pain. In severe cases, paralysis occurs.
E. Complications
 Paralysis: In a small percentage of cases, poliovirus infection leads to permanent paralysis,

most often affecting the legs. Respiratory muscles may also be paralyzed, leading to death if
left untreated.
4. Laboratory Diagnostics for Poliovirus
 Samples: Stool samples, throat swabs, cerebrospinal fluid (CSF), and blood samples are
commonly collected for diagnosis.
B. Diagnostic Tests
 Virus Isolation: The virus can be isolated from stool or throat swabs using cell culture
techniques. This remains the gold standard for poliovirus detection.
 PCR: Polymerase chain reaction (PCR) is used to detect poliovirus RNA in clinical
specimens, providing rapid and sensitive diagnosis.
 Serology: Detection of antibodies to poliovirus in blood samples can confirm past infection or
vaccination.
 Intratypic Differentiation: Molecular methods such as sequencing are used to differentiate

wild poliovirus strains from vaccine-derived strains.
5. Prevention and Control of Poliovirus
A. Vaccination
 Oral Polio Vaccine (OPV): A live attenuated vaccine administered orally. It provides strong
immunity in the intestines, preventing virus shedding and transmission. OPV is used in mass
vaccination campaigns in polio-endemic areas.
 Inactivated Polio Vaccine (IPV): A killed virus vaccine administered via injection. It induces
systemic immunity, protecting against paralysis but does not prevent intestinal infection and
virus shedding. IPV is used in many countries for routine immunization.
B. Public Health Measures
 Mass Vaccination Campaigns: These are critical in eradicating polio, especially in endemic
regions.
 Surveillance: Monitoring for cases of acute flaccid paralysis (AFP) helps detect and respond
to poliovirus transmission.
C. Environmental Measures
 Sanitation and Hygiene: Improved sanitation, clean water, and hygiene practices reduce the
spread of poliovirus.

control of Rabies virus
Rabies virus is a neurotropic virus belonging to the Lyssavirus genus in the Rhabdoviridae
family. It is the causative agent of rabies, a fatal viral encephalitis that affects mammals, including
humans. Transmission typically occurs through the bite of an infected animal.
1. Structure of Rabies Virus
 Shape: The rabies virus has a bullet-shaped,

enveloped structure, approximately 180 nm long
and 75 nm in diameter.
 Envelope: The virus is enveloped by a lipid

bilayer derived from the host cell membrane. The
envelope is studded with glycoprotein spikes (G
protein) that are crucial for binding to host cell
receptors.
 Capsid: Inside the envelope, the virus has a

helical nucleocapsid composed of the
nucleoprotein (N), which encapsulates the viral
RNA genome.
 Genome: The rabies virus contains a single-stranded, negative-sense RNA genome of about
12,000 nucleotides. The genome encodes five viral proteins:
o Glycoprotein (G): Involved in receptor binding and membrane fusion.
o Nucleoprotein (N): Encapsidates the RNA genome.
o Phosphoprotein (P): Functions as a cofactor for the RNA polymerase.
o Matrix protein (M): Plays a role in virus assembly and budding.
o RNA-dependent RNA polymerase (L): Responsible for viral RNA synthesis.
2. Cultivation of Rabies Virus
A. In Cell Culture
 Cell Lines: Rabies virus can be cultured in several types of cell lines, including baby hamster
kidney (BHK-21) cells and mouse neuroblastoma cells (NA cells).
 Procedure:
o Inoculation: The virus is introduced to a monolayer of susceptible cells.

o Incubation: The cells are incubated at 35-37°C.
o Monitoring: Cytopathic effects (CPE), such as cell rounding and syncytia formation,
are observed over several days.
o Harvesting: Once sufficient viral replication occurs, the virus is harvested from the
cell culture supernatant.
B. In Animal Models
 Animal Models: Rabies virus can be studied in animal models, particularly in mice, for
understanding its pathogenesis and for vaccine development.
3. Pathogenicity of Rabies Virus

Flowchart
Entry of
Attachment to
Virus into Endocytosis
Bite by Rabid Host Cells
Peripheral and Viral
Animal via G
Nerves or Entry
Muscle Cells Glycoprotein
Retrograde
Spread to
Replication Axonal Extensive
Transport to Other Organs
of Viral RNA Replication (e.g.,
in Cytoplasm Central in the CNS
Nervous Salivary
Glands)
System (CNS)
Clinical
Symptoms: Encephalitis
Death (if
Fever, and Neuronal
Damage untreated)
Hydrophobia,
Paralysis
 Transmission: Rabies is primarily transmitted through the bite of an infected animal, with the
virus present in the saliva. The virus can also enter through scratches, open wounds, or
mucous membranes.
 Attachment: The virus enters peripheral nerves or directly infects muscle cells at the site of
the bite. The glycoprotein (G) binds to nicotinic acetylcholine receptors (nAChRs) or neural
cell adhesion molecules (NCAMs) on host cells.
 Entry: After attachment, the virus enters the host cell via receptor-mediated endocytosis.
B. Replication and Spread
 Replication: The viral RNA genome is transcribed into mRNA in the cytoplasm using the
viral RNA polymerase (L protein). The mRNA is translated into viral proteins.
 Neuronal Spread: The virus hijacks the host cell’s machinery and travels retrogradely along
the peripheral nerves to the central nervous system (CNS), where it replicates extensively.
 Dissemination: The virus then spreads centrifugally from the CNS to other tissues, including
salivary glands, facilitating transmission to other hosts.
C. Clinical Symptoms and Immune Response
 Incubation Period: The incubation period of rabies can vary from days to months, depending
on the site of entry and the amount of virus.
 Symptoms: Initial symptoms include fever, headache, and general malaise, followed by
neurological symptoms such as hydrophobia, agitation, hallucinations, paralysis, and coma.
 Immune Response: The immune response is usually delayed, which allows the virus to reach
the CNS before an effective immune response can be mounted.
D. Complications
 Fatal Outcome: Once clinical symptoms appear, rabies is almost invariably fatal due to
encephalitis and extensive neuronal damage.
4. Laboratory Diagnostics for Rabies Virus
 Samples: Samples include saliva, cerebrospinal fluid (CSF), skin biopsy from the nape of the
neck, and brain tissue (post-mortem).
B. Diagnostic Tests
 Direct Fluorescent Antibody Test (dFA): The gold standard for diagnosing rabies. It detects
viral antigens in brain tissue or skin biopsies using fluorescently labeled antibodies.
 RT-PCR: Used to detect viral RNA in saliva, CSF, or brain tissue. It is highly sensitive and
specific.
 Virus Isolation: The virus can be isolated in cell culture, but this method is less commonly
used due to time constraints.
 Serology: Detection of rabies-specific antibodies in serum or CSF can confirm diagnosis,

particularly in vaccinated individuals.
5. Prevention and Control of Rabies Virus
A. Vaccination
 Pre-exposure Prophylaxis: Rabies vaccination is recommended for individuals at high risk

of exposure, such as veterinarians, animal handlers, and travelers to endemic areas.
 Post-exposure Prophylaxis (PEP): Rabies vaccination combined with rabies

immunoglobulin (RIG) is administered after potential exposure to the virus. PEP is nearly
100% effective if given promptly and correctly.
B. Animal Control and Public Health Measures
 Vaccination of Animals: Mass vaccination of domestic animals, particularly dogs, is the most
effective way to control rabies in humans.
 Wildlife Management: Oral rabies vaccines for wildlife can help control rabies in animal
reservoirs.
 Quarantine and Surveillance: Strict quarantine measures and surveillance systems help
prevent the spread of rabies.
C. Education and Awareness
 Public Awareness: Educating the public about rabies, safe animal handling, and the
importance of seeking medical attention after potential exposure is crucial for prevention.

control of Dengue Virus
Dengue virus (DENV) is a mosquito-borne flavivirus that causes dengue fever, a potentially
severe disease characterized by high fever, severe headache, pain behind the eyes, joint and
muscle pain, rash, and in some cases, severe bleeding and organ damage (dengue hemorrhagic
fever or dengue shock syndrome). Dengue is primarily transmitted by the Aedes aegypti
mosquito.
1. Structure of Dengue Virus
 Envelope: Dengue virus is an enveloped

virus with a lipid bilayer derived from the
host cell membrane.
 Glycoproteins: The envelope contains two

major glycoproteins, E (envelope) and M
(membrane), which are crucial for viral
entry into host cells. The E protein
facilitates binding to host cell receptors
and membrane fusion.
 Capsid: Inside the envelope is the

nucleocapsid, which is composed of the
capsid (C) protein and the viral RNA
genome.
 Genome: Dengue virus has a single-stranded, positive-sense RNA genome approximately

11,000 nucleotides long, which encodes a single polyprotein that is processed into structural
and non-structural proteins.
2. Cultivation of Dengue Virus
A. In Cell Culture
 Cell Lines: Dengue virus can be cultured in various cell lines, including C6/36 cells (derived
from Aedes albopictus mosquito), Vero cells (African green monkey kidney), and human
hepatoma cells.
 Procedure:

o Incubation: The cells are incubated at 28-37°C, depending on the cell line used.
o Monitoring: Cytopathic effects (CPE) such as cell rounding, detachment, and

syncytium formation are observed.
o Harvesting: The virus can be harvested from the cell culture supernatant for further
studies.
B. In Animal Models
 Animal Models: Dengue virus research often involves mouse models, including
immunocompromised mice or humanized mice, to study viral pathogenesis and immune
responses.
4. Pathogenicity of Dengue Virus

Flowchart
Infected
Virus Enters Replication in
Mosquito Bite
Transmits Dengue Skin and Infects Local Lymph
Dendritic Cells Nodes
Virus
Immune Response
Infection of
Virus Enters Activation (T
Various Organs cells,
Bloodstream (Liver, Spleen,
(Viremia) Antibodies,
Bone Marrow) Cytokines)
Potential
Symptoms: High Resolution of
Progression to
Fever, Severe Severe Dengue Infection OR
Headache, Joint Complications
(DHF/DSS) with
and Muscle Pain, Plasma Leakage, (e.g., Shock,
Rash Organ Failure)
Severe Bleeding
 Transmission: Dengue virus is transmitted to humans through the bite of an infected Aedes
mosquito, primarily Aedes aegypti.
 Attachment: The virus attaches to host cells, such as dendritic cells and monocytes, via
receptors including DC-SIGN (dendritic cell-specific intercellular adhesion molecule-3-
grabbing non-integrin).
B. Replication
 Uncoating: The viral RNA is released into the cytoplasm after fusion with the endosomal
membrane.
 Translation and Replication: The viral RNA is translated into a polyprotein, which is
cleaved into functional proteins. The viral RNA genome is replicated within membrane-bound
replication complexes in the cytoplasm.
 Assembly: New virions are assembled in the endoplasmic reticulum, where the viral RNA is
packaged into nucleocapsids and enveloped by the host-derived lipid bilayer.
 Budding and Release: The new virions bud off into the Golgi apparatus and are transported
to the cell surface, where they are released by exocytosis.
 Viremia: The virus enters the bloodstream (viremia) and spreads to other tissues, including
the liver, spleen, and bone marrow.
 Immune Response: The host immune response includes the activation of T cells, production
of antibodies, and release of cytokines, which contribute to both viral clearance and the
pathogenesis of severe dengue.
 Symptoms: Dengue fever is characterized by sudden high fever, severe headache, pain
behind the eyes, joint and muscle pain, rash, and mild bleeding. Severe cases can progress to
dengue hemorrhagic fever (DHF) or dengue shock syndrome (DSS), marked by plasma
leakage, severe bleeding, and organ impairment.
E. Complications
 Severe Disease: DHF/DSS can lead to severe complications, including shock, organ failure,
and death, particularly if not promptly managed.
4. Laboratory Diagnostics for Dengue Virus
 Samples: Blood samples are typically collected to diagnose dengue virus infection.
B. Diagnostic Tests
 NS1 Antigen Test: Detects the dengue non-structural protein 1 (NS1) antigen, which is
present during the early stages of infection.
 RT-PCR: Polymerase chain reaction (PCR) to detect dengue viral RNA is highly sensitive
and specific, particularly in the first week of infection.
 Serology: Detection of dengue-specific IgM and IgG antibodies. IgM is usually detectable
after the first week of illness, while IgG indicates past or secondary infection.
 Viral Culture: Dengue virus can be isolated in cell culture, but this method is less commonly
used in clinical settings due to the availability of more rapid diagnostic tests.
5. Prevention and Control of Dengue Virus
A. Mosquito Control
 Vector Control: The primary strategy for preventing dengue involves controlling the Aedes
mosquito population. This includes:
o Eliminating Breeding Sites: Removal or treatment of standing water where

mosquitoes lay their eggs.
o Insecticide Use: Spraying insecticides in areas with high mosquito populations.
o Biological Control: Introduction of natural predators of mosquitoes or use of

genetically modified mosquitoes to reduce the mosquito population.
 Avoiding Mosquito Bites: Use of insect repellent, wearing long sleeves and pants, and using
bed nets, especially during peak mosquito activity (early morning and late afternoon).
 Window and Door Screens: Ensuring that windows and doors have screens to keep
mosquitoes out.
C. Vaccination
 Dengue Vaccine: Dengvaxia, the first dengue vaccine, has been approved in some countries
for use in individuals who have had a previous dengue infection. However, its use is limited
due to concerns about its safety and efficacy in dengue-naive individuals.
 Surveillance and Early Warning: Monitoring and reporting dengue cases to detect
outbreaks early and implement control measures.
 Community Education: Raising awareness about dengue prevention, symptoms, and when
to seek medical care.

control of Japanese encephalitis
Japanese Encephalitis Virus (JEV) is a flavivirus that causes Japanese encephalitis (JE), a serious
disease that affects the central nervous system. JEV is transmitted to humans primarily through the
bite of infected Culex mosquitoes, particularly in rural areas of Asia and the Western Pacific.
1. Structure of Japanese Encephalitis Virus

(JEV)
 Envelope: JEV is an enveloped virus with a lipid
bilayer derived from the host cell membrane.
 Glycoproteins: The envelope contains two main

glycoproteins, the E (envelope) protein and the M
(membrane) protein.
o E Protein: The E protein is responsible

for receptor binding and membrane
fusion during viral entry into the host cell. It is also the major target for neutralizing
antibodies.
o M Protein: The M protein is involved in viral assembly and maturation.
 Capsid: Inside the envelope is the nucleocapsid, which is composed of the C (capsid) protein
and encases the viral RNA.
 Genome: The virus has a single-stranded, positive-sense RNA genome that is approximately
11 kb in length. The genome encodes three structural proteins (C, M, E) and several non-
structural proteins involved in viral replication.
2. Cultivation of Japanese Encephalitis Virus
A. In Cell Culture
 Cell Lines: JEV can be cultured in various cell lines, including Vero cells (African green
monkey kidney cells), BHK-21 cells (baby hamster kidney cells), and C6/36 mosquito cells.
 Procedure:
o Incubation: Cells are incubated at 37°C (or 28°C for mosquito cells).
o Monitoring: Cytopathic effects (CPE) such as cell rounding, detachment, and

syncytium formation are observed.
o Harvesting: Once significant CPE is observed, the virus can be harvested from the
cell culture supernatant.
B. In Animal Models
 Mouse Models: Mice, particularly suckling mice, are used for studying the pathogenesis of
JEV and for virus isolation from clinical specimens.
2. Pathogenicity of Japanese Encephalitis Virus

Flowchart
Bite from Virus Enters

Infected Introduction of Local Lymph
JEV into Skin
Mosquito Nodes
Primary Viremia Secondary Viral

and Spread to Viremia and Replication in
Organs Spread to CNS Neurons
Resolution of
Infection OR
Inflammation of Symptoms: Fever, Complications
the Brain Headache, Stiff (e.g., Coma,
(Encephalitis) Neck, Seizures Death,
Neurological
Sequelae)
 Transmission: JEV is transmitted to humans through the bite of infected Culex mosquitoes,
which acquire the virus from infected animals, particularly pigs and wading birds.
 Attachment: The virus attaches to specific receptors on host cells, likely via the E protein.
B. Replication
 Uncoating: The viral RNA is released into the host cell cytoplasm.
 Translation and Replication: The viral RNA is translated into viral proteins, and the genome
is replicated within the cytoplasm.
 Assembly: New virions are assembled in the endoplasmic reticulum (ER), where the viral
RNA is packaged into new nucleocapsids.
 Budding: New virions bud from the ER, acquiring their envelope, and are transported to the
Golgi apparatus for further processing.
 Exocytosis: The mature virions are then released from the host cell via exocytosis.
 Viremia: The virus enters the bloodstream (viremia) and spreads to various organs, including
the central nervous system (CNS).
 Immune Response: The immune response involves the activation of innate and adaptive
immunity, including the production of neutralizing antibodies.
 Symptoms: Most infections are asymptomatic or cause mild febrile illness. However, severe
cases can result in encephalitis, characterized by fever, headache, neck stiffness,
disorientation, seizures, and, in severe cases, coma and death.
E. Complications
 Neurological Sequelae: Survivors of severe JE often experience long-term neurological

complications, including cognitive impairment, motor deficits, and seizures.
4. Laboratory Diagnostics for Japanese Encephalitis Virus
 Samples: Blood, cerebrospinal fluid (CSF), or brain tissue (in fatal cases) are collected for
diagnostic testing.
B. Diagnostic Tests
 Serology: The detection of JEV-specific IgM antibodies in blood or CSF is the most common
method for diagnosing JE. The IgM antibody capture ELISA (MAC-ELISA) is widely used.
 PCR: Reverse transcription polymerase chain reaction (RT-PCR) can detect viral RNA in
blood or CSF, particularly in the early stages of infection.
 Virus Isolation: The virus can be isolated in cell culture or animal models, but this method is
less commonly used for routine diagnosis.
 Immunohistochemistry: Used in post-mortem analysis to detect viral antigens in brain

tissue.
5. Prevention and Control of Japanese Encephalitis Virus
A. Vaccination
 JE Vaccines: Vaccination is the most effective method of preventing JE. Several vaccines are
available, including live attenuated, inactivated, and recombinant vaccines.
o Routine Immunization: JE vaccination is part of routine immunization programs in

endemic countries.
o Travelers: JE vaccine is recommended for travelers to endemic areas, especially if

staying for extended periods or visiting rural areas.
B. Vector Control
 Mosquito Control: Reducing mosquito populations through insecticide spraying, elimination

of standing water, and use of larvicides.
 Personal Protection: Use of mosquito repellents, bed nets, and protective clothing to reduce
the risk of mosquito bites.
 Surveillance: Active surveillance for JE cases and monitoring of mosquito populations in

endemic areas.
 Public Education: Educating communities about the risks of JE and the importance of
vaccination and mosquito control measures.

control of Smallpox Virus
Smallpox is caused by the Variola virus, a member of the Orthopoxvirus genus. Smallpox was a
severe and contagious disease, characterized
by fever, malaise, and a distinctive
progressive skin rash. It was declared
eradicated by the World Health Organization
(WHO) in 1980, following a successful
global vaccination campaign.
1. Structure of the Smallpox Virus

(Variola Virus)
 Envelope: The virus is enveloped, with an outer membrane derived from the host cell.
 Brick-shaped Virion: The virus has a large, complex, brick-shaped structure, with a size of
approximately 200-300 nm in diameter.
 Lateral Bodies: Located on either side of the viral core, these structures contain enzymes and
proteins needed early in the infection.
 Core: The central structure is dumbbell-shaped and contains the viral genome and associated
proteins.
 Genome: The virus has a large, linear, double-stranded DNA genome, approximately 186,000
base pairs in length. The genome encodes over 200 proteins, including enzymes involved in
viral replication and immune evasion.
 Surface Proteins: The envelope contains several proteins involved in binding to host cells
and entry, including hemagglutinin.
2. Cultivation of the Smallpox Virus
Note: Due to the eradication of smallpox and the associated global biosecurity risks, live Variola
virus is only permitted to be held in two laboratories worldwide (CDC in the USA and VECTOR
Institute in Russia). Research is tightly regulated, and routine cultivation is not performed.
A. In Cell Culture (Historical Context)
 Cell Lines: Historically, the virus was grown in primary human and monkey kidney cells.
 Procedure:
o Inoculation: The virus was inoculated onto a monolayer of susceptible cells.
o Incubation: Cells were incubated at 37°C.
o Monitoring: Cytopathic effects (CPE), such as cell rounding and detachment, were
observed.
o Harvesting: The virus was harvested from the cell culture supernatant after sufficient
replication.
B. In Animal Models (Historical Context)
 Animal Models: Smallpox virus could infect non-human primates and rabbits, with infection
leading to disease manifestations similar to those seen in humans.
2. Pathogenicity of the Smallpox Virus

Flowchart
Entry into Attachment to Endocytosis and
Inhalation of Respiratory Host Cells via Entry into Host
Smallpox Virus
Tract Surface Proteins Cell
Viral DNA
Uncoating and Replication and Release of
Release of Viral Assembly of New Virions via Cell
Protein Virions in
DNA into Synthesis in Lysis or
Cytoplasm Cytoplasmic Cytoplasm Exocytosis
Factories
Resolution of
Infection OR
Spread to
Bloodstream Symptoms: Fever, Complications
Rash, Fatigue (e.g.,
(Viremia) and Hemorrhagic
Other Organs Smallpox,
Scarring)
 Transmission: Smallpox spread primarily through respiratory droplets during close face-to-
face contact. It could also be transmitted via fomites (contaminated objects) or direct contact
with bodily fluids.
 Attachment: The virus entered the respiratory tract and attached to host cells using surface
proteins.
 Endocytosis: The virus was taken into the host cell through endocytosis.
B. Replication
 Uncoating: The viral core was released into the cytoplasm, where the viral DNA was
uncoated.
 Early Transcription: The viral DNA was transcribed in the cytoplasm by viral RNA
polymerase, producing early proteins necessary for DNA replication.
 DNA Replication: The viral DNA was replicated in cytoplasmic "factories" within the host
cell.
 Late Transcription: Late viral proteins, including structural proteins, were produced.
 Assembly: New virions were assembled in the cytoplasm.
 Mature Virions: The virions were either released by cell lysis or wrapped in an additional
membrane and released by exocytosis.
 Viremia: The virus entered the bloodstream, spreading to other organs, including the skin,
leading to the characteristic rash.
 Immune Response: The host's immune system responded with both innate and adaptive
immunity, involving the activation of T cells, production of cytokines, and antibodies.
 Symptoms: Initial symptoms included high fever, fatigue, and body aches, followed by a
characteristic rash that progressed from macules to papules, vesicles, pustules, and scabs.
E. Complications
 Severe Disease: Complications included hemorrhagic smallpox, secondary bacterial

infections, and scarring. Mortality rates for smallpox could reach 30% in unvaccinated
individuals.
4. Laboratory Diagnostics for Smallpox Virus (Historical Context)
 Samples: Lesion material (e.g., scabs, vesicular fluid), blood samples.
B. Diagnostic Tests
 Electron Microscopy: Used to identify the virus based on its distinctive structure.
 Virus Isolation: Historically, the virus was isolated and grown in cell culture or on the
chorioallantoic membrane of embryonated eggs.
 Serology: Detection of antibodies against the virus in patients' blood.
 PCR: Polymerase chain reaction (PCR) could be used to detect viral DNA, though this
method became prominent after the virus's eradication.
5. Prevention and Control of Smallpox Virus
A. Vaccination
 Vaccinia Virus: Smallpox was eradicated through mass vaccination campaigns using the
vaccinia virus, a related but less pathogenic poxvirus.
 Ring Vaccination: This strategy involved vaccinating close contacts of an infected person to
prevent the spread of the virus.
 Vaccine Stockpiles: In the event of an outbreak, countries maintain vaccine stockpiles.
B. Quarantine and Isolation
 Infected Individuals: Patients were isolated to prevent transmission.
 Contact Tracing: Close contacts of infected individuals were identified, quarantined, and
vaccinated if necessary.
C. Environmental Control
 Disinfection: Infected materials and environments were thoroughly disinfected to prevent

transmission through fomites.
control of Smallpox Virus
Herpesviruses are a large family of DNA viruses that cause a variety of diseases in humans and
animals. The family is divided into three subfamilies: Alphaherpesvirinae (e.g., HSV-1, HSV-2),
Betaherpesvirinae (e.g., CMV), and Gammaherpesvirinae (e.g., EBV). Here, we'll focus on Herpes
Simplex Virus (HSV), a common member of the Alphaherpesvirinae subfamily.
1. Structure of Herpes Simplex Virus (HSV)
 Envelope: HSV is an enveloped virus with a lipid

 Glycoproteins: The envelope contains

several glycoproteins (e.g., gB, gC, gD, gE,
gG) that play crucial roles in attachment and
entry into host cells.
 Capsid: Inside the envelope is an icosahedral

capsid composed of 162 capsomers that house the
viral DNA.
 Tegument: Between the envelope and the capsid is the tegument, a protein layer that contains
viral proteins involved in the early stages of infection.
 Genome: HSV has a linear double-stranded DNA genome of approximately 152-155 kb. The
genome encodes for structural proteins, regulatory proteins, and enzymes necessary for
replication.
2. Cultivation of Herpes Simplex Virus (HSV)
A. In Cell Culture
 Cell Lines: HSV is cultured in human cell lines such as HEp-2 (human laryngeal carcinoma)
or Vero cells (African green monkey kidney cells).
 Procedure:
o Monitoring: Cytopathic effects (CPE) like cell rounding, syncytia formation

(multinucleated cells), and cell lysis are observed.
o Harvesting: After CPE is observed, the virus is harvested from the cell culture
supernatant.
B. In Animal Models
 Research Use: Animal models such as mice, rabbits, and guinea pigs are used for studying
HSV pathogenesis and evaluating vaccines and treatments.
3. Pathogenicity of Herpes Simplex Virus (HSV)

Flowchart
Contact with Attachment to Fusion with Uncoating and
Infected Host Cells Host Cell Release of
Secretions or via Membrane and Viral DNA
Lesions Glycoproteins Entry into Nucleus
Spread to
Viral DNA Budding of
Assembly of Adjacent
Replication New Virions Cells and
and Protein New Virions from Host
in Nucleus Possible
Synthesis Cell Viremia
Symptoms:
Resolution of
Immune Painful
Blisters, Infection OR
Response Latency and
Activation Itching,
Swelling Reactivation
 Transmission: HSV is transmitted through direct contact with infected bodily fluids or
lesions, including oral, genital, or eye secretions.
 Attachment: The virus binds to host cells via glycoproteins (e.g., gD) interacting with
cellular receptors (e.g., heparan sulfate, nectin-1).
 Fusion and Entry: The virus enters the host cell through fusion of the viral envelope with the
host cell membrane.
B. Replication
 Uncoating: The viral capsid is transported to the nucleus, where it releases the viral DNA.
 Transcription and Replication: Viral DNA is transcribed into mRNA and replicated within
the nucleus. Early proteins are produced first, followed by late structural proteins.
 Assembly: Newly synthesized capsid proteins and viral DNA are assembled into new virions
in the nucleus.
 Budding: New virions acquire their envelope by budding through the nuclear membrane and
then through the host cell membrane.
C. Latency and Reactivation
 Latency: After primary infection, HSV can establish latency in sensory nerve ganglia (e.g.,
trigeminal ganglion for HSV-1).
 Reactivation: The virus can reactivate from latency, leading to recurrent infections, often
triggered by stress, immunosuppression, or UV exposure.

 Immune Response: The immune response involves the production of antibodies, T cell
responses, and activation of innate immune mechanisms.
 Symptoms: HSV infections can cause oral herpes (cold sores), genital herpes (painful sores),
and herpes keratitis (eye infections). Symptoms include painful blisters, itching, and swelling.
E. Complications
 Severe Disease: In immunocompromised individuals, HSV can cause severe infections such
as encephalitis, disseminated disease, and esophagitis.
4. Laboratory Diagnostics for Herpes Simplex Virus (HSV)
 Samples: Lesion swabs, cerebrospinal fluid (CSF), blood, or other relevant fluids.
B. Diagnostic Tests
 PCR: Polymerase chain reaction (PCR) to detect HSV DNA in clinical specimens is highly
sensitive and specific.
 Viral Culture: HSV can be isolated from lesion samples or other fluids by culturing in cell
lines. This method is less commonly used due to the availability of faster tests.
 Direct Fluorescent Antibody (DFA): Detects HSV antigens in lesion samples using
fluorescently labeled antibodies.
 Serology: Detects antibodies against HSV (IgM for recent infection, IgG for past infection) in
blood samples.
5. Prevention and Control of Herpes Simplex Virus (HSV)
 Avoiding Contact: Avoid direct contact with active lesions or bodily fluids of an infected
person.
 Use of Condoms: Reduces the risk of genital herpes transmission, though it does not
eliminate the risk entirely.
B. Medication
 Antiviral Medications: Drugs such as acyclovir, valacyclovir, and famciclovir can reduce the
severity and frequency of outbreaks and are used for both treatment and prophylaxis.
C. Vaccination
 No Vaccine: Currently, there is no commercially available vaccine for HSV, though research
is ongoing to develop one.
 Avoiding Sharing: Do not share utensils, lip balms, or other personal items that may come
into contact with infectious secretions.
control of Hepatitis B Virus
Hepatitis B Virus (HBV) is a DNA virus that primarily affects the liver, causing inflammation and
potentially leading to chronic liver disease, cirrhosis, or liver cancer. It is transmitted through contact
with infectious body fluids.
1. Structure of Hepatitis B Virus
 Envelope: HBV is an enveloped virus, with a lipid

 Surface Antigens: The envelope contains surface

antigens, including the large (L), middle (M), and small
(S) proteins. These proteins form the outer coating and
are involved in receptor binding and immune response.
 Capsid: The core of the virus is an icosahedral capsid

composed of the core protein (HBcAg), which encases
the viral DNA and polymerase.
 Genome: HBV has a partially double-stranded circular

DNA genome. It is approximately 3.2 kilobases in length
and includes a pregenomic RNA intermediate during
replication.
2. Cultivation of Hepatitis B Virus
A. In Cell Culture
 Cell Lines: HBV is challenging to culture in traditional cell lines. However, certain cell lines,
like HepG2 (human liver cancer cells) or Huh7 (human hepatoma cells), can be used to study
HBV infection and replication.
 Procedure:
o Inoculation: The virus is added to a monolayer of susceptible liver cells.
o Monitoring: The production of viral surface antigens and the presence of core
antigens are monitored as indicators of viral replication.
o Harvesting: The virus can be harvested from the cell culture supernatant once
sufficient replication has occurred.
B. In Animal Models
 Transgenic Mice: Mice engineered to express human HBV receptors or transgenic mice with
human liver cells are used for studying HBV pathogenesis and testing antiviral therapies.
4. Pathogenicity of Hepatitis B Virus

Flowchart
Endocytosis and Viral DNA
Attachment to
Exposure to HBV Release of Viral Transported to
Hepatocytes
Core Nucleus
Formation of Reverse Budding and

Assembly of New
cccDNA and Transcription of Release of
Virions
Transcription Pregenomic RNA Virions
Resolution of
Spread to Other
Immune Response Jaundice, Chronic Infection
Hepatocytes and
Activation Fatigue, and Complications
Viremia
Abdominal Pain (e.g., Cirrhosis,
Liver Cancer)
 Transmission: HBV is transmitted through contact with infectious body fluids, including
blood, semen, and vaginal fluids. It can also be transmitted from mother to child during
childbirth.
 Attachment: The virus binds to hepatocytes (liver cells) via the viral surface antigens that
interact with cell surface receptors.
 Entry: The virus enters the host cell through endocytosis, and the envelope fuses with the
endosomal membrane to release the viral core into the cytoplasm.
B. Replication
 Uncoating: The viral core is transported to the nucleus, where the viral DNA genome is
released.
 DNA Replication: The viral DNA is converted into a covalently closed circular DNA
(cccDNA) in the nucleus, which serves as a template for transcription.
 RNA Production: The cccDNA is transcribed into pregenomic RNA (pgRNA) and various
mRNA species.
 Reverse Transcription: Pregenomic RNA is reverse transcribed into DNA by the viral
polymerase in the cytoplasm.
 Assembly: New virions are assembled in the cytoplasm and are enveloped before being
released from the cell.
 Budding: Newly formed virions bud from the cell membrane and are released into the
bloodstream.
 Viremia: HBV spreads through the bloodstream to other hepatocytes, continuing the infection
cycle.
 Immune Response: The host immune system responds with the production of antibodies and
activation of T cells. Chronic HBV infection may lead to liver inflammation and damage due
to an ongoing immune response.
 Symptoms: Acute HBV infection can cause jaundice, fatigue, abdominal pain, and dark urine.
Chronic infection may be asymptomatic initially but can lead to liver cirrhosis or
hepatocellular carcinoma over time.
E. Complications
 Chronic Hepatitis: Persistent HBV infection can lead to chronic hepatitis, cirrhosis, and an
increased risk of liver cancer.
4. Laboratory Diagnostics for Hepatitis B Virus
 Samples: Blood samples are collected for testing.
B. Diagnostic Tests
 Serological Tests:
o HBsAg (Hepatitis B Surface Antigen): Indicates active HBV infection.
o Anti-HBs (Antibody to Hepatitis B Surface Antigen): Indicates recovery from

HBV infection or vaccination.
o Anti-HBc (Antibody to Hepatitis B Core Antigen): Indicates past or ongoing

infection.
o IgM Anti-HBc: Indicates recent acute infection.
 Molecular Tests:
o HBV DNA: PCR tests detect and quantify viral DNA, assessing viral load.
o HBV Genotyping: Determines the HBV strain, useful for treatment decisions.
 Liver Function Tests: Assess liver damage and function (e.g., ALT, AST).
5. Prevention and Control of Hepatitis B Virus
A. Vaccination
 HBV Vaccine: The most effective method of prevention is vaccination with the HBV vaccine,
which is highly effective in preventing HBV infection. The vaccine is typically given as a
series of three or four doses.

 Safe Practices: Avoiding contact with potentially contaminated body fluids, using barrier
protection (e.g., condoms), and not sharing needles or personal items that may be
contaminated.
C. Screening and Diagnosis
 Screening Programs: Regular screening for at-risk populations, including pregnant women,
healthcare workers, and individuals with high-risk behaviors.
D. Treatment and Management
 Antiviral Therapy: Chronic HBV infection may be managed with antiviral medications such
as tenofovir or entecavir, which help reduce viral load and prevent liver damage.
E. Public Health Measures
 Education: Raising awareness about HBV transmission and prevention.
 Infection Control: Implementing infection control practices in healthcare settings to prevent

the spread of HBV.

AIDS (Acquired Immunodeficiency Syndrome) is caused by the Human Immunodeficiency Virus
(HIV), which is a retrovirus that attacks the immune system, specifically CD4+ T lymphocytes. The
progression of HIV infection leads to a gradual weakening of the immune system, making the body
vulnerable to opportunistic infections and certain cancers.
1. Structure of HIV
Envelope: HIV is an
enveloped virus with
a lipid bilayer derived
from the host cell
membrane.
 Glycoproteins: The
envelope contains two
major glycoproteins:
o gp120: Binds to
the CD4 receptor
on host cells.
o gp41: Facilitates
fusion of the viral
envelope with the
host cell
membrane.
 Capsid: Inside the envelope is a cone-shaped capsid composed of the protein p24. The capsid
contains the viral RNA genome and essential enzymes.
 Genome: HIV has two identical strands of single-stranded RNA, which encode various viral
proteins.
 Enzymes: The virus also contains three key enzymes:
o Reverse Transcriptase: Converts viral RNA into DNA.
o Integrase: Integrates viral DNA into the host cell’s genome.
o Protease: Cleaves viral polyproteins into functional proteins.
2. Cultivation of HIV
A. In Cell Culture
 Cell Lines: HIV is cultivated in various human cell lines such as MT-4 or Jurkat cells, and
primary T lymphocytes.
 Procedure:
o Inoculation: The virus is added to a culture of susceptible cells.
o Incubation: Cells are incubated at 37°C with 5% CO2.
o Monitoring: Changes in cell morphology and growth characteristics are monitored.
o Harvesting: Virus is harvested from the cell culture supernatant for further study.
B. In Animal Models
 Animal Models: HIV does not naturally infect non-human animals. However, simian
immunodeficiency virus (SIV) is used in non-human primates to study HIV-like infections.
2. Pathogenicity of HIV
Flowchart
Attachment to Reverse
Fusion and Entry
Exposure to HIV CD4+ T Cells via Transcription of
into Host Cell
gp120 Viral RNA to DNA
Integration of Replication and Budding and

Spread to Other
Viral DNA into Assembly of New Release of New
CD4+ T Cells
Host Genome Virions Virions
Progression to
Symptoms: Acute AIDS and
Retroviral Complications
Immune Response
Syndrome, (e.g.,
Activation
Chronic Immune Opportunistic
Suppression Infections,
Cancers)
 Transmission: HIV is transmitted through contact with infected bodily fluids, including
blood, semen, vaginal fluids, and breast milk.
 Attachment: The virus binds to the CD4 receptor on host T lymphocytes via the gp120
protein and the co-receptors (CCR5 or CXCR4).
 Fusion and Entry: The gp41 protein facilitates the fusion of the viral envelope with the host
cell membrane.
B. Replication
 Reverse Transcription: The viral RNA is reverse-transcribed into DNA by the reverse
transcriptase enzyme.
 Integration: The viral DNA is transported to the nucleus and integrated into the host cell’s
genome by the integrase enzyme.
 Transcription and Translation: The integrated viral DNA (provirus) is transcribed into
RNA, which is then translated into viral proteins.
 Assembly: New virions are assembled in the host cell’s cytoplasm.
 Budding: New virions are released from the host cell by budding, taking a portion of the host
cell membrane as their envelope.
 Spread: The virus spreads to other CD4+ T lymphocytes, leading to widespread infection and
immune system damage.
 Immune Response: The immune system mounts a response involving both innate and
adaptive immunity, including the production of antibodies and activation of cytotoxic T
lymphocytes.
 Symptoms: Initial HIV infection may cause acute retroviral syndrome (flu-like symptoms).
Chronic infection can lead to a gradual decline in CD4+ T cells, resulting in AIDS.
E. Complications
 Opportunistic Infections: Due to immune suppression, individuals with AIDS are

susceptible to opportunistic infections such as tuberculosis, pneumocystis pneumonia, and
candidiasis.
 AIDS-Related Cancers: Increased risk of cancers such as Kaposi’s sarcoma and non-
Hodgkin’s lymphoma.
4. Laboratory Diagnostics for HIV
 Samples: Blood samples are typically collected for diagnostic testing.
B. Diagnostic Tests
 HIV Antibody Tests: Detect antibodies against HIV in the blood. Examples include enzyme
immunoassays (EIAs) and rapid diagnostic tests.
 HIV RNA Tests: Detect viral RNA in the blood, used for early diagnosis and monitoring viral
load. Examples include quantitative PCR and nucleic acid tests.
 HIV Antigen Tests: Detect the p24 antigen, which is part of the viral core protein.
 CD4 Count: Measures the number of CD4+ T lymphocytes, indicating the level of immune
system compromise.
 HIV Drug Resistance Testing: Assesses resistance to antiretroviral drugs, which helps guide
treatment options.
5. Prevention and Control of HIV
 Safe Sex Practices: Using condoms consistently and correctly reduces the risk of HIV
transmission.
 Needle Exchange Programs: Providing access to clean needles for people who inject drugs
helps prevent transmission.
B. Medical Interventions
 Pre-Exposure Prophylaxis (PrEP): Antiretroviral medications taken by HIV-negative

individuals at high risk of infection to prevent HIV acquisition.
 Post-Exposure Prophylaxis (PEP): Antiretroviral treatment given within 72 hours of

potential HIV exposure to reduce the risk of infection.
C. Antiretroviral Therapy (ART)
 ART: Long-term treatment with a combination of antiretroviral drugs to suppress HIV

replication, maintain immune function, and reduce the risk of transmission.
 Testing and Counselling: Regular HIV testing and counseling for at-risk populations to
facilitate early diagnosis and treatment.
 Education and Awareness: Promoting awareness about HIV transmission and prevention
methods.
E. Infection Control
 Universal Precautions: Using protective measures to prevent HIV transmission in healthcare

settings, including the use of gloves and proper disposal of needles.
Unit 2:

Malaria is caused by protozoan parasites of the genus Plasmodium, with Plasmodium falciparum
being the most severe and prevalent species. It is transmitted to humans through the bites of infected
female Anopheles mosquitoes.
1. Structure of Plasmodium (Malaria Parasite)
Unlike viruses, Plasmodium is a protozoan parasite and does not have a viral structure. Here is an
overview of its lifecycle and morphology:
 Oocyst: After ingestion by the mosquito, Plasmodium sporozoites develop into oocysts in the
mosquito’s gut.
 Sporozoites: The infectious form of the parasite, which is injected into humans by the
mosquito.
 Trophozoite: The active feeding stage in the human liver and red blood cells.
 Schizont: A stage where the parasite undergoes asexual replication in red blood cells.
 Gametocytes: The sexual form of the parasite, which develops in the human blood and is
taken up by mosquitoes during a blood meal.
2. Cultivation of Plasmodium
A. In Cell Culture
 Cell Lines: Plasmodium species can be cultured in human red blood cells. For Plasmodium
falciparum, continuous culture can be maintained in vitro using human erythrocytes and
specific culture media.
 Procedure:
o Inoculation: Infected blood or cultured parasites are added to a culture of human red
blood cells.
o Incubation: Cultures are incubated at 37°C in a controlled environment with 5%

CO2.
o Monitoring: Regular microscopic examination is used to monitor the stages of the

parasite's lifecycle.
o Harvesting: Parasites can be harvested for research or diagnostic purposes once they
have reached a sufficient density.
B. In Animal Models
 Animal Models: Plasmodium parasites are generally not cultured in animals, but mice or
other rodent models are used to study malaria pathogenesis and test drugs.
3. Pathogenicity of Plasmodium (Malaria)
Flowchart
Travel to Development
Transmission Sporozoites
Liver and into
via Mosquito Enter Invasion of Merozoites in
Bite Bloodstream
Hepatocytes Liver
Release of
Release of Development
Invasion of New
Merozoites into Merozoites
into Red Blood Trophozoites
Cells and Cycle
Bloodstream and Schizonts Repeats
Immune
Ingestion by Response and
Formation of Resolution of
Mosquito and Symptoms:
Gametocytes Completion of Infection OR
in Blood Fever, Complications
Life Cycle Chills,
Anemia
A. Transmission and Infection
 Transmission: Occurs through the bite of an infected female Anopheles mosquito.
 Entry: Sporozoites enter the bloodstream from the mosquito's saliva and travel to the liver.
B. Liver Stage (Exoerythrocytic Cycle)
 Hepatic Infection: Sporozoites invade liver cells (hepatocytes) and develop into merozoites.
 Release: Merozoites are released into the bloodstream when liver cells rupture.
C. Blood Stage (Erythrocytic Cycle)
 Invasion of Red Blood Cells: Merozoites invade red blood cells and mature into
trophozoites.
 Replication: Trophozoites develop into schizonts, which burst to release new merozoites.
 Reinfection: Newly released merozoites invade more red blood cells, leading to cyclical fever
and anemia.
D. Gametocyte Formation
 Sexual Stage: Some merozoites develop into gametocytes, which are taken up by mosquitoes
during a blood meal.
 Fertilization: Inside the mosquito, gametocytes undergo fertilization to form oocysts,

completing the life cycle.
E. Immune Response and Symptoms
 Immune Response: The host’s immune system attempts to clear the infection, leading to
symptoms like fever, chills, and anemia.
 Symptoms: Include high fever, chills, headache, sweating, nausea, and, in severe cases,
complications like cerebral malaria, severe anemia, or organ failure.
4. Laboratory Diagnostics for Malaria
 Samples: Blood samples from patients, often collected using fingerstick or venipuncture.
B. Diagnostic Tests
 Microscopy: Examination of blood smears under a microscope to identify Plasmodium

species and determine the level of parasitemia.
 Rapid Diagnostic Tests (RDTs): Detect specific malaria antigens or antibodies with a quick
and simple procedure.
 PCR: Polymerase chain reaction (PCR) can detect Plasmodium DNA with high sensitivity
and specificity.
 Serology: Detection of antibodies against Plasmodium can be used for epidemiological

studies.
5. Prevention and Control of Malaria
 Insecticide-Treated Nets: Use of bed nets treated with insecticides to protect against
mosquito bites during the night.
 Repellents: Application of mosquito repellents to exposed skin.
B. Environmental Control
 Mosquito Control: Reducing mosquito breeding sites by eliminating standing water and
using larvicides.
 Indoor Residual Spraying: Spraying insecticides on indoor surfaces to kill mosquitoes.
C. Chemoprophylaxis
 Preventive Medication: Use of antimalarial drugs in individuals traveling to or living in

malaria-endemic areas.
D. Vaccination
 Vaccine Development: Efforts are ongoing to develop effective malaria vaccines. The
RTS,S/AS01 vaccine has shown some efficacy in preventing malaria in children.
E. Treatment
 Antimalarial Drugs: Treatment of malaria with antimalarial drugs such as artemisinin-based

combination therapies (ACTs) for Plasmodium falciparum infections, and chloroquine or
primaquine for other types.
of Amoebiasis B Virus
Entamoeba histolytica is an anaerobic protozoan parasite that causes amoebiasis. It primarily affects
the human intestine and can lead to conditions ranging from mild diarrhea to severe dysentery.
1. Structure of Entamoeba histolytica
 Trophozoite Stage:
o Shape: Irregular
and motile, with
pseudopodia
(temporary
projections of the
cell membrane) for
movement and
feeding.
o Nucleus: Typically
contains a single nucleus with a centrally located karyosome.
o Cytoplasm: Granular and may contain ingested red blood cells (in severe cases).
 Cyst Stage:
o Shape: Spherical with a thick cyst wall.
o Nucleus: Contains multiple nuclei (typically 4), which are visible in the mature cyst.
o Wall: A protective wall that allows the cyst to survive outside the host and be
transmitted via fecal-oral route.
2. Cultivation of Entamoeba histolytica
A. In Laboratory Cultures
 Media: Can be cultured in specialized media such as TYI-S-33 or Robinson's medium, which
supports the growth of E. histolytica.
 Procedure:
o Inoculation: The parasite is introduced into the culture medium containing human or
animal tissue cells.
o Incubation: The culture is maintained at 37°C, simulating body temperature.
o Monitoring: The growth of trophozoites and cysts is monitored under a microscope.
o Harvesting: Parasites can be collected from the culture for further study or testing.
B. In Animal Models
 Animal Models: Used for research purposes to study pathogenic mechanisms and test
treatments. For example, laboratory rodents can be infected with E. histolytica to study
disease progression and immunity.
4. Pathogenicity of Entamoeba histolytica

Flowchart
Excystation Trophozoites
Ingestion of
in Small Released into
Cysts
Intestine Intestine
Invasion and Local

Adhesion to
Damage to Symptoms:
Intestinal
Replication Diarrhea,
Mucosa
and Spread Dysentery
Possible
Extraintestin Immune Resolution of
al Spread Response Infection OR
(e.g., Liver Activation Complications
Abscesses)
 Transmission: E. histolytica is transmitted via the fecal-oral route, often through

contaminated food or water.
 Cyst Ingestion: The infection begins when cysts are ingested and pass through the stomach
into the intestine.
B. Trophozoite Stage
 Excystation: In the small intestine, cysts undergo excystation, releasing trophozoites.
 Adhesion and Invasion: Trophozoites adhere to the intestinal mucosa using surface lectins
and enzymes, leading to cell damage and ulceration.
C. Replication and Spread
 Local Damage: Trophozoites can invade the intestinal lining, causing dysentery (bloody
diarrhea) and abscesses.
 Systemic Spread: In severe cases, E. histolytica can spread to other organs, such as the liver,
causing amoebic liver abscesses.
 Immune Response: The host's immune response includes the activation of macrophages and
other immune cells to control the infection.
 Symptoms: Symptoms range from mild diarrhea to severe dysentery with abdominal pain,
fever, and weight loss. Extraintestinal manifestations include liver abscesses.
E. Complications
 Severe Complications: If untreated, can lead to severe complications such as liver abscesses,
perforation of the colon, and secondary bacterial infections.
4. Laboratory Diagnostics for Entamoeba histolytica
 Samples: Stool samples, aspirates from abscesses, or biopsies from the intestinal lining.
B. Diagnostic Tests
 Microscopy: Direct microscopic examination of stool samples for the presence of cysts or
trophozoites.
 Stool Antigen Tests: Enzyme immunoassays (EIAs) to detect specific antigens of E.

histolytica in stool.
 PCR: Polymerase chain reaction (PCR) for detecting E. histolytica DNA in clinical
specimens.
 Serology: Detection of antibodies against E. histolytica in blood, which may indicate past or
current infection.
5. Prevention and Control of Entamoeba histolytica
 Hand Hygiene: Regular hand washing with soap and water, especially after using the toilet or
handling food.
 Food and Water Safety: Ensuring that food is cooked properly and drinking water is treated
or boiled.
 Sanitation: Proper sanitation and disposal of human waste to prevent contamination of water
and food sources.
C. Medical Treatment
 Antiparasitic Drugs: Treatment with drugs such as metronidazole or tinidazole to eradicate

the parasite. For asymptomatic carriers, drugs like paromomycin may be used.
 Health Education: Educating communities about hygiene and sanitation practices.

 Screening and Treatment: Screening at-risk populations (e.g., travelers to endemic areas)
and providing treatment to prevent outbreaks.

control of Trichomoniasis Virus
Trichomoniasis is caused by the protozoan parasite Trichomonas vaginalis, not a virus. It is a
sexually transmitted infection (STI) that affects the urogenital tract in humans. Here’s a detailed
overview of Trichomonas vaginalis:
1. Structure of Trichomonas vaginalis

 Shape: T. vaginalis is a pear-shaped protozoan with a single nucleus and a characteristic
undulating membrane.
 Flagella: It has four anterior flagella and one

posterior flagellum that helps in motility.
 Undulating Membrane: A membrane that

extends along one side of the organism,
aiding in movement.
 Pellicle: The outer covering of the organism,

which is a flexible, proteinaceous layer.
2. Cultivation of Trichomonas vaginalis
A. In Laboratory Culture
 Medium: T. vaginalis can be cultivated in specialized liquid media such as Diamond’s

medium or other similar culture media.
 Procedure:
o Inoculation: The parasite is inoculated into the medium containing nutrients essential
for its growth.
o Incubation: Cultures are incubated at 37°C, which is close to the human body
temperature, and often under anaerobic conditions since T. vaginalis is an anaerobic
organism.
o Monitoring: Growth is monitored under a microscope, where the presence of motile

T. vaginalis is observed.
o Harvesting: The organism can be harvested from the culture for further analysis or
experimental use.
B. In Animal Models
 Limited Use: T. vaginalis is primarily studied in vitro. Animal models are not commonly
used due to the parasite's specific adaptation to the human urogenital tract.
2. Pathogenicity of Trichomonas vaginalis
Flowchart
Transmission
through Sexual Entry into Attachment to
Contact or
Urogenital Tract Mucosal Surfaces
Contaminated
Items\
Colonization and Inflammation and Immune Response

Replication Tissue Damage Activation
Symptoms:
Vaginal Treatment with
Discharge, Antiparasitic
Itching, Medications
Urethritis
 Transmission: T. vaginalis is transmitted primarily through sexual contact, but it can also be
spread through shared items like towels or bath equipment in some cases.
 Attachment: The parasite attaches to the mucosal surfaces of the urogenital tract using its
flagella and adhesive structures.
B. Replication and Pathogenesis
 Colonization: Once attached, T. vaginalis causes inflammation and irritation in the urogenital
mucosa.
 Replication: The parasite replicates by binary fission, leading to an increase in the number of
organisms present.
 Pathogenesis: The presence of T. vaginalis can cause local tissue damage and an
inflammatory response, leading to symptoms.
 Immune Response: The host's immune response includes the production of inflammatory
cytokines and the recruitment of immune cells to the infection site.
 Symptoms: In women, symptoms include vaginal discharge, itching, and discomfort. Men are
often asymptomatic but can experience urethritis or discharge.
D. Complications
 Reproductive Health Issues: Infections can increase susceptibility to other STIs and may
contribute to adverse pregnancy outcomes, such as preterm birth or low birth weight.
4. Laboratory Diagnostics for Trichomonas vaginalis

 Samples: Vaginal swabs, urethral swabs, or urine samples.
B. Diagnostic Tests
 Microscopy: Direct examination of wet mount preparations of discharge or swabs can reveal
motile T. vaginalis.
 Culture: Culturing T. vaginalis from clinical samples in specialized media.
 NAAT (Nucleic Acid Amplification Tests): PCR-based tests to detect T. vaginalis DNA with
high sensitivity.
 Rapid Antigen Tests: Detect specific antigens of T. vaginalis in clinical samples.
5. Prevention and Control of Trichomonas vaginalis
 Safe Sex Practices: Use of condoms to reduce the risk of transmission.
 Regular Screening: Regular screening for sexually active individuals, particularly those with
multiple partners or symptoms.
 Avoid Sharing Personal Items: Minimize sharing towels or other personal items that could
harbor the parasite.
C. Treatment
 Antiparasitic Medications: Treatment typically involves medications such as metronidazole

or tinidazole, which are effective in clearing the infection.
D. Education
 Public Health Campaigns: Education about the importance of safe sexual practices and
regular testing.

control of Round Warm
Roundworms, also known as nematodes, are a

diverse group of worms that can infect humans
and other animals. For this overview, we will
focus on Ascaris lumbricoides, a common
roundworm that causes ascariasis.
1. Structure of Roundworm (Ascaris

lumbricoides)
 Body Shape: Cylindrical and tapered at both ends, which is characteristic of roundworms.
 Cuticle: The body is covered with a tough, flexible outer layer called the cuticle, which
protects the worm from the host's digestive enzymes.
 Digestive System: Includes a mouth, esophagus, intestine, and anus. The digestive system is
simple, with the intestine running the length of the body.
 Reproductive System:
o Male: Contains two spicules and a cloaca for reproductive functions.
o Female: Larger than males, with a pair of ovaries and a uterus that can hold
thousands of eggs.
 Nervous System: Consists of a simple nerve ring around the esophagus and longitudinal
nerve cords running along the body.
2. Cultivation of Roundworm
A. In Laboratory Settings
 Cultivation:
o Eggs: Typically, eggs are collected from fecal samples of infected individuals. These
eggs can be incubated in controlled environments to induce hatching.
o Larvae: After hatching, larvae can be cultured in specialized media to study their
development.
o Adult Worms: Cultivating adult roundworms in the lab is complex and less common.
It usually involves using animal models or in vitro systems.
B. In Animal Models
 Animal Models: Rodents or other laboratory animals can be used to study the lifecycle and
pathogenicity of roundworms.
2. Pathogenicity of Roundworm (Ascaris lumbricoides)

Flowchart
Ingestion of Hatching of Eggs Larvae Penetrate
Ascaris Eggs in Intestines Intestinal Wall
Maturation in Swallowing and

Migration to
Lungs and Return to
Lungs Coughing Up Intestines
Resolution of
Infection OR
Immune Response Complications
Adult Worms in and Symptoms: (e.g.,
Intestines Abdominal Pain, Intestinal
Nausea, Diarrhea Obstruction,
Migration to
Other Organs)
A. Infection Cycle
 Transmission: Humans become infected by ingesting eggs from contaminated soil or food.
The eggs hatch into larvae in the intestines.
 Migration: The larvae penetrate the intestinal wall, enter the bloodstream, and migrate to the
lungs, where they mature into adults.
 Swallowing: The larvae are coughed up and swallowed, returning to the intestines to mature
into adult worms.
B. Symptoms
 Early Phase: Symptoms include cough, fever, and eosinophilia as the larvae migrate through
the lungs.
 Intestinal Phase: Adult worms in the intestines can cause abdominal pain, nausea, vomiting,
and diarrhea. Heavy infestations can lead to intestinal obstruction or malnutrition.
 Complications: In severe cases, worms can migrate to other organs, including the liver or
pancreas, causing additional health issues.
C. Immune Response
 Host Response: The immune system responds to the presence of the worms with
inflammation and eosinophilia. Antibody responses and cytokine release help in controlling
the infection.
4. Laboratory Diagnostics for Roundworm
 Samples: Fecal samples for egg identification or larvae, blood samples for serological tests.
B. Diagnostic Tests
 Microscopic Examination: Fecal samples are examined under a microscope for the presence
of Ascaris eggs.
 Immunoassays: ELISA or other serological tests can detect antibodies or antigens related to
Ascaris infection.
 Imaging: In severe cases, imaging techniques such as ultrasound or CT scans can help
identify the presence of adult worms or complications.
5. Prevention and Control of Roundworm
A. Hygiene and Sanitation
 Hand Hygiene: Regular hand washing with soap and water, especially after using the toilet
and before eating.
 Food and Water Safety: Ensuring food is properly cooked and drinking water is clean and
safe. Avoiding eating unwashed fruits and vegetables.
 Sanitation: Proper disposal of human waste and maintaining clean living environments to
prevent soil contamination.
 De-worming Programs: Regular de-worming of populations at risk, such as children in

endemic areas.
C. Medical Treatment
 Anthelmintic Medications: Drugs such as albendazole, mebendazole, or ivermectin are

effective in treating roundworm infections.

control of Hook Warm
Hookworms are parasitic worms that infect the intestines of humans. The most common species
affecting humans are Ancylostoma duodenale and Necator americanus. These parasites cause a
condition known as hookworm disease, which can lead to anemia and malnutrition.
1. Structure of Hookworm
 Adult Worms:
o Shape: Hookworms are small,

cylindrical, and have a slightly
curved or hook-like appearance,
hence the name.
o Size: Adults typically range from 5

to 11 mm in length.
o Mouth Parts: The anterior end has cutting plates or teeth that help the worm attach to
the host’s intestinal wall.
o Body: The body is covered with a cuticle that helps protect it from the host's digestive
enzymes.
 Larvae:
o Rhabditiform Larvae: Found in the soil, these larvae are non-infectious and develop
into filariform larvae.
o Filariform Larvae: These are the infectious stage of the hookworm that can
penetrate the skin.
2. Cultivation of Hookworm
A. In Laboratory Settings
 Soil Cultures: Hookworm larvae can be cultured from soil samples, which is useful for
studying their development and behavior.
 Infection Models: Hookworm eggs are incubated under controlled conditions to obtain
larvae, which can then be used to infect experimental animals or for further studies.
B. In Animal Models
 Experimental Infections: Animal models, such as rats or mice, are used to study the lifecycle
and pathology of hookworm infections. These models help in understanding disease
mechanisms and testing treatment options.
3. Pathogenicity of Hookworm
Flowchart
Penetration of Migration
Skin by through Coughed Up and Larvae Reach
Filariform Bloodstream to Swallowed Intestines
Larvae Lungs
Feeding on Host Eggs Pass in

Attachment to Blood and Egg Feces and Hatch Immune Response
Intestinal Wall Activation
Production in Soil
Resolution of
Abdominal Pain,
Complications
Diarrhea, (e.g., Chronic
Anemia Anemia)

 Transmission: Infection occurs when filariform larvae penetrate the skin, often through bare
feet, while walking on contaminated soil.
 Migration: The larvae migrate through the bloodstream to the lungs, then are coughed up and
swallowed, reaching the intestines.
B. Adult Worms in the Intestine
 Attachment: Once in the intestines, the worms attach to the intestinal wall using their mouth
parts.
 Feeding: The worms feed on blood from the host’s tissues, causing blood loss and potential
anemia.
 Egg Production: Adult worms lay eggs in the intestine, which are passed in the feces to the
environment, where they can hatch into larvae.
 Immune Response: The body’s immune response includes inflammation at the site of larval
entry and the development of immune responses to adult worms.
 Symptoms: Symptoms of hookworm infection include abdominal pain, diarrhea, anemia, and
fatigue. Severe infections can lead to more serious health issues like chronic anemia and
protein malnutrition.
D. Complications
 Anemia: Chronic blood loss from the feeding of adult worms can lead to iron-deficiency
anemia.
 Malnutrition: Ongoing blood loss can result in protein malnutrition, particularly in children
and vulnerable populations.
4. Laboratory Diagnostics for Hookworm
 Samples: Stool samples are collected to identify hookworm eggs.
B. Diagnostic Tests
 Microscopy: Stool samples are examined under a microscope to identify hookworm eggs.
The eggs are oval and have thin shells.
 Kato-Katz Technique: A quantitative technique used to determine the number of eggs per
gram of stool, which helps assess the intensity of the infection.
 ELISA: Enzyme-linked immunosorbent assay (ELISA) can be used to detect antibodies or

antigens related to hookworm infection, though it is less commonly used.
5. Prevention and Control of Hookworm
 Footwear: Wearing shoes or sandals can prevent larvae from penetrating the skin.
 Hygiene: Good hygiene practices, including regular hand washing and avoiding walking
barefoot in areas where hookworm is common, help reduce the risk of infection.
 Sanitation: Improving sanitation and hygiene to prevent contamination of soil with feces.
Proper disposal of human waste reduces the spread of hookworm larvae.
 Soil Management: Regular de-worming of livestock and soil management practices can
reduce the environmental reservoir of hookworm larvae.
C. Treatment
 Anthelmintic Medications: Drugs such as albendazole or mebendazole are effective in

treating hookworm infections. These medications kill the worms and help alleviate symptoms.
 Mass Drug Administration: In areas with high prevalence, mass drug administration
programs may be implemented to reduce the burden of hookworm disease.
 Education: Public health education on hygiene, sanitation, and the importance of footwear
helps in preventing hookworm infections.
Medical Mycology- Dermatomycosis,systemic Mycosis, Types,pathogensis

& Diagnostics
Medical Mycology: Dermatomycosis, Systemic Mycosis, Types, Pathogenesis, and Diagnostics
1. Introduction to Medical Mycology
Medical mycology is a specialized branch of microbiology that focuses on the study of fungi that
cause diseases in humans. Fungi are a diverse group of organisms, and their interactions with
human hosts can lead to a range of conditions, from superficial skin infections to life-
threatening systemic diseases. This field is crucial for understanding the diagnosis, treatment,
and prevention of fungal infections.
2. Dermatomycosis, also referred to as dermatophytosis, encompasses a range of

fungal infections that affect the skin, hair, and nails. These infections are caused by
dermatophytes, a specific group of fungi that thrive on keratinized tissues, using
keratin as their primary nutrient source. Dermatomycosis is prevalent and can impact
individuals of all ages, manifesting in various forms depending on the site of infection
and the dermatophyte species involved.
Types of Dermatomycosis
1. Tinea Capitis
Tinea capitis primarily targets the scalp and is most common in children, though it
can affect adults as well. The infection can be categorized into several types based on
the fungal species and the pattern of invasion:
 Endothrix Type: In this type, dermatophytes invade and grow inside the hair
shaft. This leads to the hair becoming brittle and breaking off. The affected hair
may appear broken and stubbly.
 Ectothrix Type: Here, the fungi grow on the outside of the hair shaft, forming a
sheath around it. This type is often characterized by more visible fungal
elements around the hair and can lead to extensive hair loss.
Symptoms of tinea capitis include itching, hair loss, and scaly patches on the scalp.
The condition may present as a single patch or multiple patches of hair loss with
inflammation. In severe cases, it can lead to kerion, a large, swollen, and abscess-like
lesion that is painful and can cause scarring.
2. Tinea Corporis
Also known as ringworm, tinea corporis affects the body’s trunk and extremities. It is
characterized by:
 Ring-Shaped Rashes: The infection presents as red, itchy, ring-shaped rashes

with a clear central area. The edges of the rash are often raised and more
inflamed compared to the center.
 Spread and Transmission: Tinea corporis spreads through direct skin-to-skin

contact with an infected person or animal, and through contact with
contaminated surfaces such as gym mats or towels. It can also spread via
fomites, such as contaminated clothing or bedding.
3. Tinea Cruris
Commonly referred to as jock itch, tinea cruris affects the groin area, inner thighs,
and buttocks. Key features include:
 Red, Itchy Rash: The rash typically starts in the groin and may spread
outwards. It is often red, inflamed, and intensely itchy. The edges of the rash
may appear raised and well-defined, with the central area becoming less
inflamed.
 Contributing Factors: Tinea cruris is exacerbated by moisture and heat.

Wearing tight, non-breathable clothing can create an environment conducive to
fungal growth. The infection is often seen in individuals who sweat excessively
or who have been in close contact with infected individuals.
4. Tinea Pedis
Known as athlete’s foot, tinea pedis primarily affects the feet and is prevalent in areas
where people walk barefoot, such as public showers and swimming pools. Symptoms
include:
 Itching and Burning: Itchy, burning sensations between the toes or on the
soles of the feet are common. The skin may also become red, cracked, and
peeling.
 Moist Environments: The condition is exacerbated by tight, non-breathable
footwear and by walking barefoot in communal areas. The warm, moist
environment between the toes is ideal for fungal growth.
5. Tinea Unguium
Tinea unguium, also known as onychomycosis, affects the nails, leading to:
 Thickened, Discolored Nails: Infected nails may become thickened, discolored

(yellow, brown, or white), and brittle. They may also become crumbly and may
separate from the nail bed.
 Complications: Tinea unguium often develops as a complication of tinea pedis.

Treating onychomycosis can be challenging due to the slow growth of nails
and the depth of infection, which makes topical treatments less effective
compared to systemic antifungal therapies.
2.2. Pathogenesis
Dermatophytes invade the stratum corneum, the outermost layer of the skin, where they secrete
keratinase to break down keratin. The fungi are transmitted through direct contact with
infected individuals or contaminated surfaces. Once established, they can spread locally or
through autoinoculation (self-infection) from one part of the body to another.
2.3. Diagnosis
 Clinical Examination: The appearance of the lesions is often characteristic, but a

definitive diagnosis requires laboratory confirmation.
 KOH Preparation: Skin scrapings are treated with potassium hydroxide (KOH) to clear
non-fungal material and then examined under a microscope for fungal hyphae and
spores.
 Fungal Culture: Samples from infected areas are cultured on Sabouraud dextrose agar
to isolate and identify the dermatophytes.
 Wood’s Lamp Examination: Some dermatophytes fluoresce under ultraviolet light,

aiding in diagnosis.
2.4. Treatment
Treatment typically involves topical antifungals like terbinafine or clotrimazole for localized
infections. For extensive or recurrent cases, systemic antifungals such as itraconazole or
fluconazole may be required.
3. Systemic Mycosis
Systemic mycoses are infections caused by fungi that can affect internal organs and systems,
and they are often more serious than superficial infections. These diseases are typically seen in
immunocompromised individuals but can also occur in otherwise healthy people.
3.1. Types of Systemic Mycosis
1. Histoplasmosis: Caused by Histoplasma capsulatum. It often affects the lungs but can
disseminate to other organs. Common in regions with bat or bird droppings.
2. Coccidioidomycosis: Caused by Coccidioides immitis or Coccidioides posadasii. Known as
Valley fever, it primarily affects the lungs and can disseminate to the skin, bones, and
joints.
3. Blastomycosis: Caused by Blastomyces dermatitidis. It primarily affects the lungs but can
also disseminate to the skin, bones, and genitourinary tract.
4. Paracoccidioidomycosis: Caused by Paracoccidioides brasiliensis. Predominantly found

in Latin America, it affects the lungs and can disseminate to the skin and mucous
membranes.
5. Cryptococcosis: Caused by Cryptococcus neoformans. It often affects the central nervous

system, leading to cryptococcal meningitis, and can also affect the lungs.
3.2. Pathogenesis
Systemic mycoses typically begin with inhalation of fungal spores or conidia. The fungi are then
engulfed by alveolar macrophages but can survive and proliferate within these cells, leading to
dissemination through the bloodstream. The ability to evade host immune responses and the
production of virulence factors contribute to the pathogenicity of these fungi.
3.3. Diagnosis
 Clinical Examination: Symptoms can be non-specific, such as fever and cough, and
require a detailed history of exposure or travel.
 Microscopy and Staining: Direct examination of clinical specimens (e.g., sputum, tissue
biopsies) with special stains like methenamine silver or mucicarmine can reveal the
fungi.
 Fungal Culture: Culturing clinical specimens on appropriate media to isolate the

causative fungi. This can be time-consuming and may take several weeks.
 Serological Tests: Detection of antibodies or antigens in the blood can aid in diagnosis.
Tests such as the cryptococcal antigen test for cryptococcosis are highly specific.
 Molecular Methods: PCR and other nucleic acid-based assays can provide rapid and
specific diagnosis of systemic mycoses.
3.4. Treatment
Treatment often involves systemic antifungals. Options include:
 Azoles (e.g., itraconazole, fluconazole): Effective against various systemic fungi.
 Echinocandins (e.g., caspofungin, micafungin): Useful for infections like Candida and
Aspergillus.
 Amphotericin B: Often used for severe or life-threatening infections, although it has

significant side effects.
4. Conclusion
Medical mycology encompasses a broad range of fungal infections with varying presentations,
pathogenesis, and diagnostic approaches. Dermatomycosis, although generally less severe, can
cause significant discomfort and requires accurate diagnosis and treatment. Systemic mycosis,
on the other hand, poses serious health risks, especially in immunocompromised individuals,
and requires prompt and effective treatment to manage.
Understanding the different types of mycotic infections, their pathogenesis, and the diagnostic
tools available is crucial for effective management and treatment. Ongoing research and
advancements in diagnostic techniques continue to improve our ability to address these
challenging infections.
Fungal infections associated with COVID19, precautions & Management
Fungal infections associated with COVID-19 have gained attention due to their impact on patient
outcomes, particularly in severe cases or those with underlying conditions. Two notable types of
fungal infections observed in COVID-19 patients are mucormycosis and candidiasis.
Fungal Infections Associated with COVID-19
1. Mucormycosis (Black Fungus)
Mucormycosis is a serious, often rapidly progressing fungal infection caused by molds from the
Mucoraceae family. It has been reported in COVID-19 patients, especially those with uncontrolled
diabetes or those who have received prolonged corticosteroid therapy.
 Pathogens: Rhizopus species, Mucor species, Absidia species.
 Symptoms: Nasal congestion, facial pain, swelling around the eyes, black lesions on the nasal
bridge or palate, and in severe cases, sinusitis, or pulmonary involvement.
 Risk Factors: Diabetes, immunosuppression, prolonged use of corticosteroids, high iron

levels, and severe COVID-19.
2. Candidiasis
Candidiasis is an infection caused by yeasts of the Candida genus. It can range from superficial
infections to invasive systemic infections, particularly in critically ill COVID-19 patients.
 Pathogens: Candida albicans, Candida auris, Candida glabrata.
 Symptoms: Oral thrush, esophageal candidiasis, or systemic infections with symptoms like
fever, chills, and signs of organ dysfunction.
 Risk Factors: Use of broad-spectrum antibiotics, central venous catheters,

immunosuppression, and severe illness.
Precautions to Prevent Fungal Infections in COVID-19 Patients
1. Infection Control Measures:
o Hand Hygiene: Regular handwashing and use of hand sanitizers.
o Protective Equipment: Use personal protective equipment (PPE) like masks and
gloves in healthcare settings to prevent fungal spore exposure.
o Environmental Cleaning: Regular disinfection of hospital environments, especially
in areas with high humidity.
2. Monitoring and Management of Risk Factors:
o Blood Sugar Control: For diabetic patients, maintain tight glycemic control to
reduce the risk of mucormycosis.
o Corticosteroid Use: Use corticosteroids judiciously and only when necessary.

Minimize the dose and duration of corticosteroid therapy.
3. Appropriate Use of Antibiotics:
o Antifungal Stewardship: Avoid unnecessary use of broad-spectrum antibiotics that

can disrupt normal flora and increase the risk of candidiasis.
4. Monitoring and Early Detection:
o Regular Monitoring: For patients at high risk, including those on

immunosuppressive therapy, regularly monitor for signs of fungal infections.
o Prompt Diagnosis: Be vigilant for symptoms of fungal infections and use

appropriate diagnostic tests early to initiate treatment.
Management of Fungal Infections in COVID-19 Patients
1. Diagnosis:
o Clinical Assessment: Evaluate symptoms and history for possible fungal infections.
o Laboratory Tests:
 Mucormycosis: Direct microscopy of tissue samples, fungal culture, and

imaging (CT/MRI) to assess sinus or orbital involvement.
 Candidiasis: Blood cultures, urine cultures, and tissue biopsies for invasive
candidiasis. Oral swabs for superficial infections.
2. Treatment:
o Mucormycosis:
 Antifungal Therapy: Administer high-dose intravenous amphotericin B.

Newer options like posaconazole or isavuconazole may also be considered.
 Surgical Intervention: Surgical debridement of necrotic tissue is often

necessary to control the spread of infection.
o Candidiasis:
 Antifungal Therapy: Use antifungal agents such as fluconazole,

echinocandins (caspofungin, micafungin), or amphotericin B depending on
the severity and Candida species.
 Address Underlying Conditions: Remove or replace infected central lines

or catheters, and correct other predisposing factors.
3. Supportive Care:
o Manage Symptoms: Provide supportive care to manage symptoms and improve

overall health.
o Nutritional Support: Ensure adequate nutrition to support immune function and

recovery.

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Unit 1:

Diagnostic virology-Cultivation Of pathogenic Viruses in lab Animals &

1. Cultivation in Lab Animals:

2. Cultivation in Tissue Culture:

o Organ Cultures: Involve maintaining a whole organ or part of it in culture, providing

o Observation: The effects of viral replication are monitored, often by observing

4. Safety and Containment:

Identification of Pathogenic Viruses and Establishment of Viral Etiology:

1. Principles of Viral Identification

Identification of viruses typically involves:

1. Isolation and Cultivation: Culturing viruses in appropriate host cells or systems.

2. Isolation and Cultivation

2.1. Viral Isolation

 Embryonated Eggs: Used for influenza and certain other viruses.

2.2. Cell Culture Techniques

2.3. Growth Characteristics

3. Detection and Identification Methods

3.1. Traditional Methods

3.2. Molecular Techniques

o Reverse Transcription PCR (RT-PCR): For detecting RNA viruses.

3.3. Serological Techniques

 Immunofluorescence Assays: Uses fluorescently labeled antibodies to detect viral proteins in

3.4. Protein and Antigen Detection

 Western Blotting: Detects specific viral proteins in a sample.

3.5. Next-Generation Sequencing (NGS)

4. Establishing Viral Etiology

4.1. Correlation with Clinical Disease

 Epidemiological Studies: Analyzing patterns and incidence of disease in populations.

 Clinical Correlation: Observing consistent clinical presentations in infected individuals.

4.2. Causation Studies

4.3. Molecular Koch's Postulates

For some viruses, traditional postulates are adapted to molecular techniques:

 Presence of Viral DNA/RNA: Correlates with disease symptoms.

4.4. Genetic and Phenotypic Analysis

 Co-infections: Presence of multiple viruses in a single host can obscure identification.

5.2. Sample Quality

 Contamination: Risk of contamination during collection or processing can lead to false

5.3. Technical Limitations

6. Emerging Trends and Future Directions

6.1. Integrated Diagnostics

6.2. Point-of-Care Testing

Developing rapid, user-friendly tests for use in remote or resource-limited settings.

6.3. Personalized Medicine

Using genetic and viral information to tailor treatments to individual patients.

6.4. Artificial Intelligence and Machine Learning

6.5. Global Surveillance Networks

1. Structure of the Influenza

The influenza virus belongs to

 Genome: The virus has

 Ribonucleoprotein (RNP): Composed of RNA segments, nucleoproteins, and polymerase

2. Cultivation of the Influenza Virus

 Advantages: Allows for large-scale production of viruses, used in vaccine development.

B. In Embryonated Chicken Eggs

 Allantoic/Inoculation: The virus is injected into the allantoic cavity of 9-11-day-old

 Incubation: The eggs are incubated at 33-37°C for 2-3 days.

 Applications: Widely used in vaccine production and diagnostic assays.

3. Pathogenicity of the Influenza Virus:

Viral RNA New Virus New Virus Infection

 Respiratory Droplets: The primary mode of transmission is through inhalation of droplets