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Manoj Pohare

The University of Sheffield, Department of Infection, Immunity & Cardiovascular Disease, Post-Doc

Ehime University, Applied Bioresources, Faculty of Agriculture, Alumnus

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A highly skilled molecular microbiologist with strong expertise in protein biochemistry. Currently working as a postdoctoral research associate in the Department of Infection, Immunity and Cardiovascular Diseases at The University of Sheffield, UK.

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Papers by Manoj Pohare

Efficient overexpression and purification of SARS-CoV-2 Nucleocapsid proteins in Escherichia coli

The fundamental biology of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) nucleocap... more The fundamental biology of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (Ncap), its use in diagnostic assays and its potential application as a vaccine component have received considerable attention since the outbreak of the Covid19 pandemic in late 2019. Here we report the scalable expression and purification of soluble, immunologically active, SARS-CoV-2 Ncap in Escherichia coli. Codon-optimised synthetic genes encoding the original Ncap sequence and four common variants with an N-terminal 6His affinity tag (sequence MHHHHHHG) were cloned into an inducible expression vector carrying a regulated bacteriophage T5 synthetic promoter controlled by lac operator binding sites. The constructs were used to express Ncap proteins and protocols developed which allow efficient production of purified Ncap with yields of over 200 mg per litre of culture media. These proteins were deployed in ELISA assays to allow comparison of their responses to human sera. Our results suggest that there was no detectable difference between the 6His-tagged and untagged original Ncap proteins but there may be a slight loss of sensitivity of sera to other Ncap isolates.

Efficient overexpression and purification of SARS-CoV-2 Nucleocapsid proteins in <i>Escherichia coli</i>

Biochemical journal, May 7, 2024

Bacillus thuringiensis as Potential Biocontrol Agent for Sustainable Agriculture

Environmental and microbial biotechnology, Nov 11, 2020

Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections

Communications biology, Jul 5, 2022

B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results... more B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions in antibody neutralization. Subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome. Applying our tool (periscope) to ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 SARS-CoV-2 positive clinical samples, we show that normalised sgRNA is significantly increased in B.1.1.7 (alpha) infections (n = 879). This increase is seen over the previous dominant lineage in the UK, B.1.177 (n = 943), which is independent of genomic reads, E cycle threshold and days since symptom onset at sampling. A noncanonical sgRNA which could represent ORF9b is found in 98.4% of B.1.1.7 SARS-CoV-2 infections compared with only 13.8% of other lineages, with a 16-fold increase in median sgRNA abundance. We demonstrate that ORF9b protein levels are increased 6-fold in B.1.1.7 compared to a B lineage virus in vitro. We hypothesise that increased ORF9b in B.1.1.7 is a direct consequence of a triple nucleotide mutation in nucleocapsid (28280:GAT > CAT, D3L) creating a transcription regulatory-like sequence complementary to a region 3' of the genomic leader. These findings provide a unique insight into the biology of B.1.1.7 and support monitoring of sgRNA profiles to evaluate emerging potential variants of concern.

A Rapid and Simple, Recombination-based Cloning Method in Escherichia coli

Biosciences, Biotechnology Research Asia, Mar 25, 2017

Cloning is indispensable in molecular biology. Here we developed an in vivo homologous recombinat... more Cloning is indispensable in molecular biology. Here we developed an in vivo homologous recombination-based cloning procedure and determined the optimal conditions. This procedure required two PCR products to be amplified from a gene of interest and desired plasmid vector. The 5' ends of both primers that amplified one product had nucleotide sequences complementary to that used to amplify the other product. Once the mixture of those PCR products was introduced into Escherichia coli DH5á competent cells, transformants carried plasmids in which the gene of interest had been properly cloned. Optimizing the cloning conditions, at least 12-nucleotides overlaps between the terminal ends of two fragments were required to generate desired plasmids. This value was much shorter than the length of overlaps required for the same procedure employed in the yeast system. Therefore, this procedure is expected to be an attractive alternative for cloning in the E. coli system.

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Journal of Hospital Infection

Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Nature Microbiology

jointly supervised the work, as now indicated in the HTML and PDF versions of the article.

Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

Scientific Reports

Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploite... more Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living conditions within residential halls, and high social contact rates. Here we analysed SARS-CoV-2 whole genome sequences in combination with epidemiological data to investigate a large cluster of student cases associated with University of Glasgow accommodation in autumn 2020, Scotland. We identified 519 student cases of SARS-CoV-2 infection associated with this large cluster through contact tracing data, with 30% sequencing coverage for further analysis. We estimated at least 11 independent introductions of SARS-CoV-2 into the student population, with four comprising the majority of detected cases and consistent with separate outbreaks. These fou...

Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections

Communications Biology

B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results... more B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions in antibody neutralization. Subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome. Applying our tool (periscope) to ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 SARS-CoV-2 positive clinical samples, we show that normalised sgRNA is significantly increased in B.1.1.7 (alpha) infections (n = 879). This increase is seen over the previous dominant lineage in the UK, B.1.177 (n = 943), which is independent of genomic reads, E cycle threshold and days since symptom onset at sampling. A noncanonical sgRNA which could represent ORF9b is found in 98.4% of B.1.1.7 SARS-CoV-2 infections compared with only 13.8% of other lineages, with a 16-fold increase in median sgRNA abundance. We demonstrate that ORF9b protein levels are increased 6-fold in B.1.1.7 compared to a B lineage virus in vitro. We hypothesise tha...

COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study

Scientific Reports

The Delta (B.1.617.2) variant was the predominant UK circulating SARS-CoV-2 strain between May an... more The Delta (B.1.617.2) variant was the predominant UK circulating SARS-CoV-2 strain between May and December 2021. How Delta infection compares with previous variants is unknown. This prospective observational cohort study assessed symptomatic adults participating in the app-based COVID Symptom Study who tested positive for SARS-CoV-2 from May 26 to July 1, 2021 (Delta overwhelmingly the predominant circulating UK variant), compared (1:1, age- and sex-matched) with individuals presenting from December 28, 2020 to May 6, 2021 (Alpha (B.1.1.7) the predominant variant). We assessed illness (symptoms, duration, presentation to hospital) during Alpha- and Delta-predominant timeframes; and transmission, reinfection, and vaccine effectiveness during the Delta-predominant period. 3581 individuals (aged 18 to 100 years) from each timeframe were assessed. The seven most frequent symptoms were common to both variants. Within the first 28 days of illness, some symptoms were more common with Delt...

Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England

Nature

PhD Dissertation Abstract: Application of precursor proteins with steric hindrance for blocking the process of protein import into chloroplasts in vitro ( 立体障害を有する前駆体蛋白質が葉緑体への蛋白質輸送に及ぼす影響)

Summary PhD Dissertation: Application of precursor proteins with steric hindrance for blocking the process of protein import into chloroplasts in vitro

SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2

Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transm... more Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Here we present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. From 9 to 27 September 2021 (round 14) and 19 October to 5 November 2021 (round 15), all lineages sequenced within REACT-1 were Delta or a Delta sub-lineage with 44 unique lineages identified. The proportion of the original Delta variant (B.1.617.2) was found to be increasing between September and November 2021, which may reflect an increasing number of sub-lineages which have yet to be ident...

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Nature Microbiology

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response... more Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the ...

Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

Nature Communications, 2022

Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare servi... more Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181 patients and healthcare workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March to 25th July 2020) and Wave 2 (30th November 2020 to 24th January 2021). We show that staff-to-staff transmissions reduced from 31.6% to 12.9% of all infections. Patient-to-patient transmissions increased from 27.1% to 52.1%. 40%-50% of hospital-onset patient cases resulted in onward transmission compared to 4% of community-acquired cases. Control measures introduced during the pandemic likely reduced transmissions between healthcare workers but were insufficient to prevent increasing numbers of patient-to-patient transmissions. As hospital-acquired cases drive most onwar...

Publisher Correction: Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

Nature Communications, 2022

Sugarcane for Economical Bioplastic Production

Plastics are the petroleum-based products and their demand in the market is continuously increasi... more Plastics are the petroleum-based products and their demand in the market is continuously increasing. This increase in demand coupled with the depletion of existing oil resources, and a decline in the rate of their replacement has led to increases in the costs of fossil resources and energy. Despite of the several other disadvantages, plastic remains the most commonly used material in daily life. In order to avoid the hazardous effects of non-biodegradable plastic, an alternative ecofriendly and renewable bioplastic can be used. Sugarcane accounts for the largest value of production and holds an enviable position among all the commercial crops in India. By taking an advantage of Sugarcane as a resource for bioplastic production, we suggested the genetic modification of sugarcane with bacterial polyester, polyhydroxybutyrate (PHB). Here we proposed the possible strategy for economical, renewable and environment friendly bioplastic production in India.

Effect of Gamma Radiations on the Morphological Characters in in vitro Regenerated Polianthes tuberosa

In the present study, induction of genetic variability in in vitro regenerated Polianthes tuberos... more In the present study, induction of genetic variability in in vitro regenerated Polianthes tuberosa was observed in the local cultivar, with five different doses of gamma radiations (10, 20, 30, 40 and 50 Gy). No significant differences were observed in the survival rates among the untreated (control) and treated plants with different doses of gamma irradiation. But significant differences were recorded in the plant morphological characters upon gamma radiation treatment of 30 Gy in terms of plant height, number of leaves, leaf size and colour as compared to the control plant.

In vitro Micro Propagation of Blue Passion Flower (Passiflora caerulea L.)

A successful in vitro culture establishment has been achieved from the leaves of blue passion flo... more A successful in vitro culture establishment has been achieved from the leaves of blue passion flower (Passiflora caerulea L) and the regeneration of shoots was observed with and without callus development. Leaf segment of Passiflora caerulea L. formed callus when cultured on modified Murashige and Skoog (MS) medium supplemented with 0.5 mg/l NAA, 0.5 mg/l IAA, 0.5 mg/l 2-4-D, 0.5 mg/l Kinetin and 1 mg/l BAP. Direct shoot regeneration without a callus phase has also been achieved from the leaf segment in presence of 2 mg/l BAP and 1 mg/l kinetin. According to our study, a complete plant of blue passion flower along with shoots and roots was developed in around 54 days, which may take near about two seasons or sometimes a year for a seed of blue passion flower to germinate.

Efficient overexpression and purification of SARS-CoV-2 Nucleocapsid proteins in Escherichia coli

The fundamental biology of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) nucleocap... more The fundamental biology of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (Ncap), its use in diagnostic assays and its potential application as a vaccine component have received considerable attention since the outbreak of the Covid19 pandemic in late 2019. Here we report the scalable expression and purification of soluble, immunologically active, SARS-CoV-2 Ncap in Escherichia coli. Codon-optimised synthetic genes encoding the original Ncap sequence and four common variants with an N-terminal 6His affinity tag (sequence MHHHHHHG) were cloned into an inducible expression vector carrying a regulated bacteriophage T5 synthetic promoter controlled by lac operator binding sites. The constructs were used to express Ncap proteins and protocols developed which allow efficient production of purified Ncap with yields of over 200 mg per litre of culture media. These proteins were deployed in ELISA assays to allow comparison of their responses to human sera. Our results suggest that there was no detectable difference between the 6His-tagged and untagged original Ncap proteins but there may be a slight loss of sensitivity of sera to other Ncap isolates.

Efficient overexpression and purification of SARS-CoV-2 Nucleocapsid proteins in <i>Escherichia coli</i>

Biochemical journal, May 7, 2024

Bacillus thuringiensis as Potential Biocontrol Agent for Sustainable Agriculture

Environmental and microbial biotechnology, Nov 11, 2020

Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections

Communications biology, Jul 5, 2022

B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results... more B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions in antibody neutralization. Subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome. Applying our tool (periscope) to ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 SARS-CoV-2 positive clinical samples, we show that normalised sgRNA is significantly increased in B.1.1.7 (alpha) infections (n = 879). This increase is seen over the previous dominant lineage in the UK, B.1.177 (n = 943), which is independent of genomic reads, E cycle threshold and days since symptom onset at sampling. A noncanonical sgRNA which could represent ORF9b is found in 98.4% of B.1.1.7 SARS-CoV-2 infections compared with only 13.8% of other lineages, with a 16-fold increase in median sgRNA abundance. We demonstrate that ORF9b protein levels are increased 6-fold in B.1.1.7 compared to a B lineage virus in vitro. We hypothesise that increased ORF9b in B.1.1.7 is a direct consequence of a triple nucleotide mutation in nucleocapsid (28280:GAT > CAT, D3L) creating a transcription regulatory-like sequence complementary to a region 3' of the genomic leader. These findings provide a unique insight into the biology of B.1.1.7 and support monitoring of sgRNA profiles to evaluate emerging potential variants of concern.

A Rapid and Simple, Recombination-based Cloning Method in Escherichia coli

Biosciences, Biotechnology Research Asia, Mar 25, 2017

Cloning is indispensable in molecular biology. Here we developed an in vivo homologous recombinat... more Cloning is indispensable in molecular biology. Here we developed an in vivo homologous recombination-based cloning procedure and determined the optimal conditions. This procedure required two PCR products to be amplified from a gene of interest and desired plasmid vector. The 5' ends of both primers that amplified one product had nucleotide sequences complementary to that used to amplify the other product. Once the mixture of those PCR products was introduced into Escherichia coli DH5á competent cells, transformants carried plasmids in which the gene of interest had been properly cloned. Optimizing the cloning conditions, at least 12-nucleotides overlaps between the terminal ends of two fragments were required to generate desired plasmids. This value was much shorter than the length of overlaps required for the same procedure employed in the yeast system. Therefore, this procedure is expected to be an attractive alternative for cloning in the E. coli system.

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Journal of Hospital Infection

Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Nature Microbiology

jointly supervised the work, as now indicated in the HTML and PDF versions of the article.

Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

Scientific Reports

Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploite... more Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living conditions within residential halls, and high social contact rates. Here we analysed SARS-CoV-2 whole genome sequences in combination with epidemiological data to investigate a large cluster of student cases associated with University of Glasgow accommodation in autumn 2020, Scotland. We identified 519 student cases of SARS-CoV-2 infection associated with this large cluster through contact tracing data, with 30% sequencing coverage for further analysis. We estimated at least 11 independent introductions of SARS-CoV-2 into the student population, with four comprising the majority of detected cases and consistent with separate outbreaks. These fou...

Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections

Communications Biology

B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results... more B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions in antibody neutralization. Subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome. Applying our tool (periscope) to ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 SARS-CoV-2 positive clinical samples, we show that normalised sgRNA is significantly increased in B.1.1.7 (alpha) infections (n = 879). This increase is seen over the previous dominant lineage in the UK, B.1.177 (n = 943), which is independent of genomic reads, E cycle threshold and days since symptom onset at sampling. A noncanonical sgRNA which could represent ORF9b is found in 98.4% of B.1.1.7 SARS-CoV-2 infections compared with only 13.8% of other lineages, with a 16-fold increase in median sgRNA abundance. We demonstrate that ORF9b protein levels are increased 6-fold in B.1.1.7 compared to a B lineage virus in vitro. We hypothesise tha...

COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study

Scientific Reports

The Delta (B.1.617.2) variant was the predominant UK circulating SARS-CoV-2 strain between May an... more The Delta (B.1.617.2) variant was the predominant UK circulating SARS-CoV-2 strain between May and December 2021. How Delta infection compares with previous variants is unknown. This prospective observational cohort study assessed symptomatic adults participating in the app-based COVID Symptom Study who tested positive for SARS-CoV-2 from May 26 to July 1, 2021 (Delta overwhelmingly the predominant circulating UK variant), compared (1:1, age- and sex-matched) with individuals presenting from December 28, 2020 to May 6, 2021 (Alpha (B.1.1.7) the predominant variant). We assessed illness (symptoms, duration, presentation to hospital) during Alpha- and Delta-predominant timeframes; and transmission, reinfection, and vaccine effectiveness during the Delta-predominant period. 3581 individuals (aged 18 to 100 years) from each timeframe were assessed. The seven most frequent symptoms were common to both variants. Within the first 28 days of illness, some symptoms were more common with Delt...

Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England

Nature

PhD Dissertation Abstract: Application of precursor proteins with steric hindrance for blocking the process of protein import into chloroplasts in vitro ( 立体障害を有する前駆体蛋白質が葉緑体への蛋白質輸送に及ぼす影響)

Summary PhD Dissertation: Application of precursor proteins with steric hindrance for blocking the process of protein import into chloroplasts in vitro

SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2

Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transm... more Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Here we present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. From 9 to 27 September 2021 (round 14) and 19 October to 5 November 2021 (round 15), all lineages sequenced within REACT-1 were Delta or a Delta sub-lineage with 44 unique lineages identified. The proportion of the original Delta variant (B.1.617.2) was found to be increasing between September and November 2021, which may reflect an increasing number of sub-lineages which have yet to be ident...

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Nature Microbiology

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response... more Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the ...

Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

Nature Communications, 2022

Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare servi... more Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181 patients and healthcare workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March to 25th July 2020) and Wave 2 (30th November 2020 to 24th January 2021). We show that staff-to-staff transmissions reduced from 31.6% to 12.9% of all infections. Patient-to-patient transmissions increased from 27.1% to 52.1%. 40%-50% of hospital-onset patient cases resulted in onward transmission compared to 4% of community-acquired cases. Control measures introduced during the pandemic likely reduced transmissions between healthcare workers but were insufficient to prevent increasing numbers of patient-to-patient transmissions. As hospital-acquired cases drive most onwar...

Publisher Correction: Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

Nature Communications, 2022

Sugarcane for Economical Bioplastic Production

Plastics are the petroleum-based products and their demand in the market is continuously increasi... more Plastics are the petroleum-based products and their demand in the market is continuously increasing. This increase in demand coupled with the depletion of existing oil resources, and a decline in the rate of their replacement has led to increases in the costs of fossil resources and energy. Despite of the several other disadvantages, plastic remains the most commonly used material in daily life. In order to avoid the hazardous effects of non-biodegradable plastic, an alternative ecofriendly and renewable bioplastic can be used. Sugarcane accounts for the largest value of production and holds an enviable position among all the commercial crops in India. By taking an advantage of Sugarcane as a resource for bioplastic production, we suggested the genetic modification of sugarcane with bacterial polyester, polyhydroxybutyrate (PHB). Here we proposed the possible strategy for economical, renewable and environment friendly bioplastic production in India.

Effect of Gamma Radiations on the Morphological Characters in in vitro Regenerated Polianthes tuberosa

In the present study, induction of genetic variability in in vitro regenerated Polianthes tuberos... more In the present study, induction of genetic variability in in vitro regenerated Polianthes tuberosa was observed in the local cultivar, with five different doses of gamma radiations (10, 20, 30, 40 and 50 Gy). No significant differences were observed in the survival rates among the untreated (control) and treated plants with different doses of gamma irradiation. But significant differences were recorded in the plant morphological characters upon gamma radiation treatment of 30 Gy in terms of plant height, number of leaves, leaf size and colour as compared to the control plant.

In vitro Micro Propagation of Blue Passion Flower (Passiflora caerulea L.)

A successful in vitro culture establishment has been achieved from the leaves of blue passion flo... more A successful in vitro culture establishment has been achieved from the leaves of blue passion flower (Passiflora caerulea L) and the regeneration of shoots was observed with and without callus development. Leaf segment of Passiflora caerulea L. formed callus when cultured on modified Murashige and Skoog (MS) medium supplemented with 0.5 mg/l NAA, 0.5 mg/l IAA, 0.5 mg/l 2-4-D, 0.5 mg/l Kinetin and 1 mg/l BAP. Direct shoot regeneration without a callus phase has also been achieved from the leaf segment in presence of 2 mg/l BAP and 1 mg/l kinetin. According to our study, a complete plant of blue passion flower along with shoots and roots was developed in around 54 days, which may take near about two seasons or sometimes a year for a seed of blue passion flower to germinate.

CRISPR/Cas9 genome editing and its medical potential

AkiNik Publications, 2019

Crisper/Cas9 is one of the latest and most efficient genome editing tools which is in fact is the... more Crisper/Cas9 is one of the latest and most efficient genome editing tools which is in fact is the part of bacteria and archaea adaptive immunity. Crisper/Cas9 comprises of the guide RNA for targeted binding and Cas9 (endonuclease) for cleavage which attack sequences adjacent to PAM. Adeno associated viruses are mostly used to of deliver CRISPER/Cas9. Several researches targeted the undesirable sequences to manipulate gene expression in different organisms (zebrafish, mouse, etc.) and induced pluripotent cells (iPSCs). This simple mechanism has been applied in understanding and treatment of several complex diseases. Recent advances have expanded its potential which are discussed in detail in this paper. The biggest challenge is off-targeting. It has many ethical considerations as well. Despite the limitations, CRISPER/Cas9 has revolutionised the medical field with its wide applications. This paper 1st discusses how does the crisper/cas9 works in bacteria and as a gene manipulation tool. It then discusses how it is designed and delivered most effectively; followed by its applications and challenges.