Published on 08/04/2022
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
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Modelling the impact of Omicron and emerging variants on SARS-CoV-2 transmission and public health burden
EA Le Rutte et al, Comm Medicine, July 25, 2022We show that, with first-generation SARS-CoV-2 vaccines and limited physical distancing in place, a VOC’s potential future dominance is primarily driven by its infectivity, which does not always lead to an increased public health burden. However, we also show that highly immune-evading variants that become dominant, even in the case of reduced variant severity, would likely require alternative measures to avoid strain on health systems, such as strengthened physical distancing measures, novel treatments, and second-generation vaccines. Expanded vaccination, that includes a booster dose for adults and child vaccination strategies, is projected to have the biggest public health benefit for a highly infective, highly severe VOC with low immune-evading capacity. -
An analysis of 45 large-scale wastewater sites in England to estimate SARS-CoV-2 community prevalence.
Morvan Mario et al. Nature communications 2022 7 (1) 4313Accurate surveillance of the COVID-19 pandemic can be weakened by under-reporting of cases, particularly due to asymptomatic or pre-symptomatic infections, resulting in bias. Quantification of SARS-CoV-2 RNA in wastewater can be used to infer infection prevalence, but uncertainty in sensitivity and considerable variability has meant that accurate measurement remains elusive. Here, we use data from 45 sewage sites in England, covering 31% of the population, and estimate SARS-CoV-2 prevalence to within 1.1% of estimates from representative prevalence surveys . -
Risk of BA.5 infection in individuals exposed to prior SARS-CoV-2 variants
J Malato et al, MEDRXIV, July 28, 2022 -
Correlates of protection for booster doses of the BNT162b2 vaccine
T Hertz et al, MEDRXIV, July 28, 2022 -
Comparative effectiveness of BNT162b2 versus mRNA-1273 boosting in England: a cohort study in OpenSAFELY-TPP
WJ Hulme et al, MEDRXIV, July 30, 2022 -
Development of Resistance-Associated Mutations After Sotrovimab Administration in High-risk Individuals Infected With the SARS-CoV-2 Omicron Variant
E Birnie et al, JAMA, August 1, 2022The SARS-CoV-2 Omicron variant of concern is currently the dominant variant circulating globally. Sotrovimab is among the few monoclonal antibodies that has retained its neutralizing activity against Omicron/BA.1 and received Emergency Use Authorization for treatment of patients at risk for progression to severe disease. This study found rapid development of sotrovimab resistance–associated mutations at positions S:E340 and S:P337 in a large proportion of high-risk patients infected with the Omicron variant after treatment with sotrovimab, which was associated with a delay in viral clearance. -
Postmarketing active surveillance of myocarditis and pericarditis following vaccination with COVID-19 mRNA vaccines in persons aged 12 to 39 years in Italy: A multi-database, self-controlled case series study.
Massari Marco et al. PLoS medicine 2022 7 (7) e1004056This population-based study of about 3 millions of residents in Italy suggested that mRNA vaccines were associated with myocarditis/pericarditis in the population younger than 40 years. According to our results, increased risk of myocarditis/pericarditis was associated with the second dose of BNT162b2 and both doses of mRNA-1273. The highest risks were observed in males of 12 to 39 years and in males and females 18 to 29 years vaccinated with mRNA-1273. -
Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform
BJ Stanhope et al, MEDRXIV, August 2, 2022We have created a panel of four triplex RT-qPCR assays targeting 12 mutations to detect and differentiate all five variants of concern: Alpha, Beta, Gamma, Delta and Omicron. We also developed an expanded pentaplex assay that can reliably distinguish among the major sublineages (BA.1-BA.5) of Omicron. In silico, analytical and clinical testing of the variant panel indicate the assays have a sensitivity and specificity of >95%. This variant panel can be used as a Research Use Only screening tool for triaging SARS-CoV-2 positive samples prior to whole genome sequencing. -
Association of SARS-CoV-2 BA.4/BA.5 Omicron lineages with immune escape and clinical outcome
JA Lewnard et al, MEDRXIV, August 2, 2022 -
Coronaviruses exploit a host cysteine-aspartic protease for replication
H Chu et al, Nature, August 3, 2022We show that a cysteine-aspartic protease of the apoptosis cascade, caspase-6, serves as an important host factor for efficient coronavirus replication. We demonstrate that caspase-6 cleaves coronavirus nucleocapsid (N) proteins, generating N fragments that serve as interferon (IFN) antagonists, thus facilitating virus replication. -
Neutralization of SARS-CoV-2 Omicron sublineages by 4 doses of mRNA vaccine
X Xie et al, BIORXIV, July 29, 2022In sera from 2- 3- and 4-dose vaccinees in the US with and without BA.1 breakthrough, vaccine plus prior BA.1 better neutralized Omicron VOCs than 4-doses with no infection. Neutralization titers were similar for 2- and 3-doses post breakthrough and were 1.4, 4.8, 3.1, 4.1, 4.9, and 3.9x higher for WA1/2020, BA.1-, BA.2-, BA.212.1-, BA.3-, and BA.4/5, respectively, for 2-dose and breakthroughs vs 4 doses only. -
Association of Receiving a Fourth Dose of the BNT162b Vaccine With SARS-CoV-2 Infection Among Health Care Workers in Israel.
Cohen Matan J et al. JAMA network open 2022 8 (8) e2224657Was there a benefit of vaccinating health care workers with a fourth dose of BNT162b2 vaccine during the Omicron variant outbreak of the COVID-19 pandemic? In this multicenter cohort study of 29?611 health care workers in Israel, the breakthrough infection rate among those who received 4 doses was 6.9% compared with 19.8% in those who received 3 doses. -
Longitudinal analyses after COVID-19 recovery or prolonged infection reveal unique immunological signatures after repeated vaccinations
D Hismatsu et al, MEDRXIV, August 3, 2022 -
Non-Genomics Precision Health Studies
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Modelling the impact of Omicron and emerging variants on SARS-CoV-2 transmission and public health burden
EA Le Rutte et al, Comm Medicine, July 25, 2022We show that, with first-generation SARS-CoV-2 vaccines and limited physical distancing in place, a VOC’s potential future dominance is primarily driven by its infectivity, which does not always lead to an increased public health burden. However, we also show that highly immune-evading variants that become dominant, even in the case of reduced variant severity, would likely require alternative measures to avoid strain on health systems, such as strengthened physical distancing measures, novel treatments, and second-generation vaccines. Expanded vaccination, that includes a booster dose for adults and child vaccination strategies, is projected to have the biggest public health benefit for a highly infective, highly severe VOC with low immune-evading capacity. -
An analysis of 45 large-scale wastewater sites in England to estimate SARS-CoV-2 community prevalence.
Morvan Mario et al. Nature communications 2022 7 (1) 4313Accurate surveillance of the COVID-19 pandemic can be weakened by under-reporting of cases, particularly due to asymptomatic or pre-symptomatic infections, resulting in bias. Quantification of SARS-CoV-2 RNA in wastewater can be used to infer infection prevalence, but uncertainty in sensitivity and considerable variability has meant that accurate measurement remains elusive. Here, we use data from 45 sewage sites in England, covering 31% of the population, and estimate SARS-CoV-2 prevalence to within 1.1% of estimates from representative prevalence surveys . -
Risk of BA.5 infection in individuals exposed to prior SARS-CoV-2 variants
J Malato et al, MEDRXIV, July 28, 2022 -
Correlates of protection for booster doses of the BNT162b2 vaccine
T Hertz et al, MEDRXIV, July 28, 2022 -
Comparative effectiveness of BNT162b2 versus mRNA-1273 boosting in England: a cohort study in OpenSAFELY-TPP
WJ Hulme et al, MEDRXIV, July 30, 2022 -
Development of Resistance-Associated Mutations After Sotrovimab Administration in High-risk Individuals Infected With the SARS-CoV-2 Omicron Variant
E Birnie et al, JAMA, August 1, 2022The SARS-CoV-2 Omicron variant of concern is currently the dominant variant circulating globally. Sotrovimab is among the few monoclonal antibodies that has retained its neutralizing activity against Omicron/BA.1 and received Emergency Use Authorization for treatment of patients at risk for progression to severe disease. This study found rapid development of sotrovimab resistance–associated mutations at positions S:E340 and S:P337 in a large proportion of high-risk patients infected with the Omicron variant after treatment with sotrovimab, which was associated with a delay in viral clearance. -
Postmarketing active surveillance of myocarditis and pericarditis following vaccination with COVID-19 mRNA vaccines in persons aged 12 to 39 years in Italy: A multi-database, self-controlled case series study.
Massari Marco et al. PLoS medicine 2022 7 (7) e1004056This population-based study of about 3 millions of residents in Italy suggested that mRNA vaccines were associated with myocarditis/pericarditis in the population younger than 40 years. According to our results, increased risk of myocarditis/pericarditis was associated with the second dose of BNT162b2 and both doses of mRNA-1273. The highest risks were observed in males of 12 to 39 years and in males and females 18 to 29 years vaccinated with mRNA-1273. -
Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform
BJ Stanhope et al, MEDRXIV, August 2, 2022We have created a panel of four triplex RT-qPCR assays targeting 12 mutations to detect and differentiate all five variants of concern: Alpha, Beta, Gamma, Delta and Omicron. We also developed an expanded pentaplex assay that can reliably distinguish among the major sublineages (BA.1-BA.5) of Omicron. In silico, analytical and clinical testing of the variant panel indicate the assays have a sensitivity and specificity of >95%. This variant panel can be used as a Research Use Only screening tool for triaging SARS-CoV-2 positive samples prior to whole genome sequencing. -
Association of SARS-CoV-2 BA.4/BA.5 Omicron lineages with immune escape and clinical outcome
JA Lewnard et al, MEDRXIV, August 2, 2022 -
Coronaviruses exploit a host cysteine-aspartic protease for replication
H Chu et al, Nature, August 3, 2022We show that a cysteine-aspartic protease of the apoptosis cascade, caspase-6, serves as an important host factor for efficient coronavirus replication. We demonstrate that caspase-6 cleaves coronavirus nucleocapsid (N) proteins, generating N fragments that serve as interferon (IFN) antagonists, thus facilitating virus replication. -
Neutralization of SARS-CoV-2 Omicron sublineages by 4 doses of mRNA vaccine
X Xie et al, BIORXIV, July 29, 2022In sera from 2- 3- and 4-dose vaccinees in the US with and without BA.1 breakthrough, vaccine plus prior BA.1 better neutralized Omicron VOCs than 4-doses with no infection. Neutralization titers were similar for 2- and 3-doses post breakthrough and were 1.4, 4.8, 3.1, 4.1, 4.9, and 3.9x higher for WA1/2020, BA.1-, BA.2-, BA.212.1-, BA.3-, and BA.4/5, respectively, for 2-dose and breakthroughs vs 4 doses only. -
Association of Receiving a Fourth Dose of the BNT162b Vaccine With SARS-CoV-2 Infection Among Health Care Workers in Israel.
Cohen Matan J et al. JAMA network open 2022 8 (8) e2224657Was there a benefit of vaccinating health care workers with a fourth dose of BNT162b2 vaccine during the Omicron variant outbreak of the COVID-19 pandemic? In this multicenter cohort study of 29?611 health care workers in Israel, the breakthrough infection rate among those who received 4 doses was 6.9% compared with 19.8% in those who received 3 doses. -
Longitudinal analyses after COVID-19 recovery or prolonged infection reveal unique immunological signatures after repeated vaccinations
D Hismatsu et al, MEDRXIV, August 3, 2022 -
News, Reviews and Commentaries
-
Modelling the impact of Omicron and emerging variants on SARS-CoV-2 transmission and public health burden
EA Le Rutte et al, Comm Medicine, July 25, 2022We show that, with first-generation SARS-CoV-2 vaccines and limited physical distancing in place, a VOC’s potential future dominance is primarily driven by its infectivity, which does not always lead to an increased public health burden. However, we also show that highly immune-evading variants that become dominant, even in the case of reduced variant severity, would likely require alternative measures to avoid strain on health systems, such as strengthened physical distancing measures, novel treatments, and second-generation vaccines. Expanded vaccination, that includes a booster dose for adults and child vaccination strategies, is projected to have the biggest public health benefit for a highly infective, highly severe VOC with low immune-evading capacity. -
An analysis of 45 large-scale wastewater sites in England to estimate SARS-CoV-2 community prevalence.
Morvan Mario et al. Nature communications 2022 7 (1) 4313Accurate surveillance of the COVID-19 pandemic can be weakened by under-reporting of cases, particularly due to asymptomatic or pre-symptomatic infections, resulting in bias. Quantification of SARS-CoV-2 RNA in wastewater can be used to infer infection prevalence, but uncertainty in sensitivity and considerable variability has meant that accurate measurement remains elusive. Here, we use data from 45 sewage sites in England, covering 31% of the population, and estimate SARS-CoV-2 prevalence to within 1.1% of estimates from representative prevalence surveys . -
Risk of BA.5 infection in individuals exposed to prior SARS-CoV-2 variants
J Malato et al, MEDRXIV, July 28, 2022 -
Correlates of protection for booster doses of the BNT162b2 vaccine
T Hertz et al, MEDRXIV, July 28, 2022 -
Comparative effectiveness of BNT162b2 versus mRNA-1273 boosting in England: a cohort study in OpenSAFELY-TPP
WJ Hulme et al, MEDRXIV, July 30, 2022 -
Development of Resistance-Associated Mutations After Sotrovimab Administration in High-risk Individuals Infected With the SARS-CoV-2 Omicron Variant
E Birnie et al, JAMA, August 1, 2022The SARS-CoV-2 Omicron variant of concern is currently the dominant variant circulating globally. Sotrovimab is among the few monoclonal antibodies that has retained its neutralizing activity against Omicron/BA.1 and received Emergency Use Authorization for treatment of patients at risk for progression to severe disease. This study found rapid development of sotrovimab resistance–associated mutations at positions S:E340 and S:P337 in a large proportion of high-risk patients infected with the Omicron variant after treatment with sotrovimab, which was associated with a delay in viral clearance. -
Postmarketing active surveillance of myocarditis and pericarditis following vaccination with COVID-19 mRNA vaccines in persons aged 12 to 39 years in Italy: A multi-database, self-controlled case series study.
Massari Marco et al. PLoS medicine 2022 7 (7) e1004056This population-based study of about 3 millions of residents in Italy suggested that mRNA vaccines were associated with myocarditis/pericarditis in the population younger than 40 years. According to our results, increased risk of myocarditis/pericarditis was associated with the second dose of BNT162b2 and both doses of mRNA-1273. The highest risks were observed in males of 12 to 39 years and in males and females 18 to 29 years vaccinated with mRNA-1273. -
Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform
BJ Stanhope et al, MEDRXIV, August 2, 2022We have created a panel of four triplex RT-qPCR assays targeting 12 mutations to detect and differentiate all five variants of concern: Alpha, Beta, Gamma, Delta and Omicron. We also developed an expanded pentaplex assay that can reliably distinguish among the major sublineages (BA.1-BA.5) of Omicron. In silico, analytical and clinical testing of the variant panel indicate the assays have a sensitivity and specificity of >95%. This variant panel can be used as a Research Use Only screening tool for triaging SARS-CoV-2 positive samples prior to whole genome sequencing. -
Association of SARS-CoV-2 BA.4/BA.5 Omicron lineages with immune escape and clinical outcome
JA Lewnard et al, MEDRXIV, August 2, 2022 -
Coronaviruses exploit a host cysteine-aspartic protease for replication
H Chu et al, Nature, August 3, 2022We show that a cysteine-aspartic protease of the apoptosis cascade, caspase-6, serves as an important host factor for efficient coronavirus replication. We demonstrate that caspase-6 cleaves coronavirus nucleocapsid (N) proteins, generating N fragments that serve as interferon (IFN) antagonists, thus facilitating virus replication. -
Neutralization of SARS-CoV-2 Omicron sublineages by 4 doses of mRNA vaccine
X Xie et al, BIORXIV, July 29, 2022In sera from 2- 3- and 4-dose vaccinees in the US with and without BA.1 breakthrough, vaccine plus prior BA.1 better neutralized Omicron VOCs than 4-doses with no infection. Neutralization titers were similar for 2- and 3-doses post breakthrough and were 1.4, 4.8, 3.1, 4.1, 4.9, and 3.9x higher for WA1/2020, BA.1-, BA.2-, BA.212.1-, BA.3-, and BA.4/5, respectively, for 2-dose and breakthroughs vs 4 doses only. -
Association of Receiving a Fourth Dose of the BNT162b Vaccine With SARS-CoV-2 Infection Among Health Care Workers in Israel.
Cohen Matan J et al. JAMA network open 2022 8 (8) e2224657Was there a benefit of vaccinating health care workers with a fourth dose of BNT162b2 vaccine during the Omicron variant outbreak of the COVID-19 pandemic? In this multicenter cohort study of 29?611 health care workers in Israel, the breakthrough infection rate among those who received 4 doses was 6.9% compared with 19.8% in those who received 3 doses. -
Longitudinal analyses after COVID-19 recovery or prolonged infection reveal unique immunological signatures after repeated vaccinations
D Hismatsu et al, MEDRXIV, August 3, 2022 -
- Page last reviewed:Feb 1, 2024
- Page last updated:May 01, 2024
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