Published on 11/17/2022
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
-
The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants.
McMillen Tracy et al. Scientific reports 2022 11 (1) 18968We evaluated the accuracy of the SGTF signature in identifying these two variants through analysis of all positive SARS-CoV-2 samples tested on the TaqPath RT-PCR and sequenced by next generation sequencing between December 2020 to July 2022. 2324 samples were successfully sequenced including 914 SGTF positive samples. The sensitivity and specificity of the SGTF signature was 99.6% (95% CI 96.1-99.9%) and 98.6% (95% CI 99.2-99.8%) for the Alpha variant and 99.6% (95% CI 98.9-99.9%) and 99.8% (95% CI 99.4-99.9%) for the Omicron variant. At the peak of their corresponding wave, the positive predictive value of the SGTF was 98% for Alpha and 100% for Omicron. -
Clinical accuracy of SARS-CoV-2 rapid antigen testing in screening children and adolescents in comparison to RT-qPCR, November 2020 to September 2022
M Krone et al, MEDRXIV, November 10, 2022This single centre prospective diagnostic study evaluates three RDT (NADAL®, Panbio™, MEDsan®) in comparison to quantitative reverse transcription polymerase chain reaction (RT-qPCR). 9,760 oropharyngeal screening samples regarding SARS-CoV-2 VOC and COVID-19 vaccination in paediatric hospitalised patients aged younger than 18 years were enrolled. Findings RDT sensitivity was 44·7% (157/351, 95% CI 39·6%-50·0%) compared to the reference standard RT-qPCR, specificity 99·8% (9,392/9,409, 95% CI 99·7%-99·9%). Most SARS-CoV-2 infections considered were caused by Omicron VOC. -
COVID-19-Associated Hospitalizations Among U.S. Infants Aged <6 Months - COVID-NET, 13 States, June 2021-August 2022.
Hamid Sarah et al. MMWR. Morbidity and mortality weekly report 2022 11 (45) 1442-1448Infants aged <6 months, who are ineligible for vaccination, have high COVID-19–associated hospitalization rates compared with other pediatric age groups. Although population-based COVID-19–associated hospitalization rates among infants aged <6 months increased in the Omicron variant–predominant periods compared with the Delta variant–predominant period, indicators of the most severe disease among hospitalized infants aged <6 months did not. -
High–temporal resolution profiling reveals distinct immune trajectories following the first and second doses of COVID-19 mRNA vaccines
D Rinchai et al, Science, November 11, 2022We investigated responses to COVID-19 mRNA vaccination via high–temporal resolution blood transcriptome profiling. The first vaccine dose elicited modest interferon and adaptive immune responses, which peaked on days 2 and 5, respectively. The second vaccine dose, in contrast, elicited sharp day 1 interferon, inflammation, and erythroid cell responses, followed by a day 5 plasmablast response. Both post-first and post-second dose interferon signatures were associated with the subsequent development of antibody responses. Yet, we observed distinct interferon response patterns after each of the doses that may reflect quantitative or qualitative differences in interferon induction. -
Health, socioeconomic and genetic predictors of COVID-19 vaccination uptake: a nationwide machine-learning study
T Hartonen et al, MEDRXIV, November 11, 2022 -
Shared genetic influences between blood analyte levels and risk of severe COVID-19
HM Tanha et al, Cell Reports, November 6, 2022Here we utilise GWAS summary statistics to study the shared genetic influences (pleiotropy) between severe COVID-19 and 344 blood analytes at the genome, gene and single nucleotide polymorphism levels. Our pleiotropy analyses genetically link blood levels of 71 analytes to severe COVID-19 in at least one of the three levels of investigation—suggesting shared biological mechanisms or causal relationships. Six analytes (alanine aminotransferase, alkaline phosphatase, apolipoprotein B, C-reactive protein, triglycerides, and urate) display evidence of pleiotropy with severe COVID-19 at all three levels. -
Protection from previous natural infection compared with mRNA vaccination against SARS-CoV-2 infection and severe COVID-19 in Qatar: a retrospective cohort study
H Chemaitelly et al, The Lancet Microbe, November 11, 2022Understanding protection conferred by natural SARS-CoV-2 infection versus COVID-19 vaccination is important for informing vaccine mandate decisions. We compared protection conferred by natural infection versus that from the BNT162b2 (Pfizer–BioNTech) and mRNA-1273 (Moderna) vaccines in Qatar. We found that previous natural infection was associated with lower incidence of SARS-CoV-2 infection, regardless of the variant, than mRNA primary-series vaccination. -
Variant-specific symptoms of COVID-19 in a study of 1,542,510 adults in England.
Whitaker Matthew et al. Nature communications 2022 11 (1) 6856We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell or taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. -
Protection conferred by Delta and BA.1/BA.2 infection against BA.4/BA.5 infection and hospitalization: A Retrospective Cohort Study
N Winchester et al, MEDSCAPE, November 14, 2022 -
Bivalent BNT162b2mRNA original/Omicron BA.4-5 booster vaccination: adverse reactions and inability to work compared to the monovalent COVID-19 booster
I Wagenhauser et al, MEDRXIV, November 2022Among healthcare workers who received a 4th COVID-19 vaccine dose (n=76, Germany, Aug 2021–Oct 2022), rate of adverse reactions was significantly higher among recipients of BA.4-5 adapted bivalent vaccine (33/39=84.6%) compared with recipients of monovalent BNT162b2 vaccine (19/37=51.4%). Also, more recipients reported taking post-vaccination medication in the bivalent (13/39=33.3%) vs monovalent (8/37=21.6%) groups, and more reported inability to work in the bivalent (9/39=23.1%) vs monovalent (5/37=13.5%) groups, although these differences were not significant. -
Using Genome Sequence Data to Predict SARS-CoV-2 Detection Cycle Threshold Values
L Duesterwald et al, MEDRXIV, November 15, 2022 -
Effectiveness of a third BNT162b2 mRNA COVID-19 vaccination during pregnancy: a national observational study in Israel.
Guedalia Joshua et al. Nature communications 2022 11 (1) 6961Compared with the second dose, the third dose effectively prevents overall hospitalizations with SARS-CoV-2 infections, with estimated effectiveness of 92% (95% CI 83–96%) during Delta, and enhances protection against significant disease during Omicron, with effectiveness of 92% (95% CI 26–99%), and 48% (95% CI 37–57%) effectiveness against hospitalization overall. A third dose of the BNT162b2 mRNA COVID-19 vaccine during pregnancy, given at least 5 months after the second vaccine dose, enhances protection against adverse COVID-19-related outcomes. -
In Vitro Efficacy of Antiviral Agents against Omicron Subvariant BA.4.6
E Takashita et al, NEJM, November 16, 2022Our data suggest that remdesivir, molnupiravir, and nirmatrelvir and the monoclonal antibodies bebtelovimab and imdevimab retain effectiveness against BA.4.6 in vitro. Our findings also indicate that monoclonal antibodies casirivimab, sotrovimab, tixagevimab, and cilgavimab may not be effective against BA.4.6.
Non-Genomics Precision Health Studies
-
The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants.
McMillen Tracy et al. Scientific reports 2022 11 (1) 18968We evaluated the accuracy of the SGTF signature in identifying these two variants through analysis of all positive SARS-CoV-2 samples tested on the TaqPath RT-PCR and sequenced by next generation sequencing between December 2020 to July 2022. 2324 samples were successfully sequenced including 914 SGTF positive samples. The sensitivity and specificity of the SGTF signature was 99.6% (95% CI 96.1-99.9%) and 98.6% (95% CI 99.2-99.8%) for the Alpha variant and 99.6% (95% CI 98.9-99.9%) and 99.8% (95% CI 99.4-99.9%) for the Omicron variant. At the peak of their corresponding wave, the positive predictive value of the SGTF was 98% for Alpha and 100% for Omicron. -
Clinical accuracy of SARS-CoV-2 rapid antigen testing in screening children and adolescents in comparison to RT-qPCR, November 2020 to September 2022
M Krone et al, MEDRXIV, November 10, 2022This single centre prospective diagnostic study evaluates three RDT (NADAL®, Panbio™, MEDsan®) in comparison to quantitative reverse transcription polymerase chain reaction (RT-qPCR). 9,760 oropharyngeal screening samples regarding SARS-CoV-2 VOC and COVID-19 vaccination in paediatric hospitalised patients aged younger than 18 years were enrolled. Findings RDT sensitivity was 44·7% (157/351, 95% CI 39·6%-50·0%) compared to the reference standard RT-qPCR, specificity 99·8% (9,392/9,409, 95% CI 99·7%-99·9%). Most SARS-CoV-2 infections considered were caused by Omicron VOC. -
COVID-19-Associated Hospitalizations Among U.S. Infants Aged <6 Months - COVID-NET, 13 States, June 2021-August 2022.
Hamid Sarah et al. MMWR. Morbidity and mortality weekly report 2022 11 (45) 1442-1448Infants aged <6 months, who are ineligible for vaccination, have high COVID-19–associated hospitalization rates compared with other pediatric age groups. Although population-based COVID-19–associated hospitalization rates among infants aged <6 months increased in the Omicron variant–predominant periods compared with the Delta variant–predominant period, indicators of the most severe disease among hospitalized infants aged <6 months did not. -
High–temporal resolution profiling reveals distinct immune trajectories following the first and second doses of COVID-19 mRNA vaccines
D Rinchai et al, Science, November 11, 2022We investigated responses to COVID-19 mRNA vaccination via high–temporal resolution blood transcriptome profiling. The first vaccine dose elicited modest interferon and adaptive immune responses, which peaked on days 2 and 5, respectively. The second vaccine dose, in contrast, elicited sharp day 1 interferon, inflammation, and erythroid cell responses, followed by a day 5 plasmablast response. Both post-first and post-second dose interferon signatures were associated with the subsequent development of antibody responses. Yet, we observed distinct interferon response patterns after each of the doses that may reflect quantitative or qualitative differences in interferon induction. -
Health, socioeconomic and genetic predictors of COVID-19 vaccination uptake: a nationwide machine-learning study
T Hartonen et al, MEDRXIV, November 11, 2022 -
Shared genetic influences between blood analyte levels and risk of severe COVID-19
HM Tanha et al, Cell Reports, November 6, 2022Here we utilise GWAS summary statistics to study the shared genetic influences (pleiotropy) between severe COVID-19 and 344 blood analytes at the genome, gene and single nucleotide polymorphism levels. Our pleiotropy analyses genetically link blood levels of 71 analytes to severe COVID-19 in at least one of the three levels of investigation—suggesting shared biological mechanisms or causal relationships. Six analytes (alanine aminotransferase, alkaline phosphatase, apolipoprotein B, C-reactive protein, triglycerides, and urate) display evidence of pleiotropy with severe COVID-19 at all three levels. -
Protection from previous natural infection compared with mRNA vaccination against SARS-CoV-2 infection and severe COVID-19 in Qatar: a retrospective cohort study
H Chemaitelly et al, The Lancet Microbe, November 11, 2022Understanding protection conferred by natural SARS-CoV-2 infection versus COVID-19 vaccination is important for informing vaccine mandate decisions. We compared protection conferred by natural infection versus that from the BNT162b2 (Pfizer–BioNTech) and mRNA-1273 (Moderna) vaccines in Qatar. We found that previous natural infection was associated with lower incidence of SARS-CoV-2 infection, regardless of the variant, than mRNA primary-series vaccination. -
Variant-specific symptoms of COVID-19 in a study of 1,542,510 adults in England.
Whitaker Matthew et al. Nature communications 2022 11 (1) 6856We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell or taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. -
Protection conferred by Delta and BA.1/BA.2 infection against BA.4/BA.5 infection and hospitalization: A Retrospective Cohort Study
N Winchester et al, MEDSCAPE, November 14, 2022 -
Bivalent BNT162b2mRNA original/Omicron BA.4-5 booster vaccination: adverse reactions and inability to work compared to the monovalent COVID-19 booster
I Wagenhauser et al, MEDRXIV, November 2022Among healthcare workers who received a 4th COVID-19 vaccine dose (n=76, Germany, Aug 2021–Oct 2022), rate of adverse reactions was significantly higher among recipients of BA.4-5 adapted bivalent vaccine (33/39=84.6%) compared with recipients of monovalent BNT162b2 vaccine (19/37=51.4%). Also, more recipients reported taking post-vaccination medication in the bivalent (13/39=33.3%) vs monovalent (8/37=21.6%) groups, and more reported inability to work in the bivalent (9/39=23.1%) vs monovalent (5/37=13.5%) groups, although these differences were not significant. -
Using Genome Sequence Data to Predict SARS-CoV-2 Detection Cycle Threshold Values
L Duesterwald et al, MEDRXIV, November 15, 2022 -
Effectiveness of a third BNT162b2 mRNA COVID-19 vaccination during pregnancy: a national observational study in Israel.
Guedalia Joshua et al. Nature communications 2022 11 (1) 6961Compared with the second dose, the third dose effectively prevents overall hospitalizations with SARS-CoV-2 infections, with estimated effectiveness of 92% (95% CI 83–96%) during Delta, and enhances protection against significant disease during Omicron, with effectiveness of 92% (95% CI 26–99%), and 48% (95% CI 37–57%) effectiveness against hospitalization overall. A third dose of the BNT162b2 mRNA COVID-19 vaccine during pregnancy, given at least 5 months after the second vaccine dose, enhances protection against adverse COVID-19-related outcomes. -
In Vitro Efficacy of Antiviral Agents against Omicron Subvariant BA.4.6
E Takashita et al, NEJM, November 16, 2022Our data suggest that remdesivir, molnupiravir, and nirmatrelvir and the monoclonal antibodies bebtelovimab and imdevimab retain effectiveness against BA.4.6 in vitro. Our findings also indicate that monoclonal antibodies casirivimab, sotrovimab, tixagevimab, and cilgavimab may not be effective against BA.4.6.
News, Reviews and Commentaries
-
The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants.
McMillen Tracy et al. Scientific reports 2022 11 (1) 18968We evaluated the accuracy of the SGTF signature in identifying these two variants through analysis of all positive SARS-CoV-2 samples tested on the TaqPath RT-PCR and sequenced by next generation sequencing between December 2020 to July 2022. 2324 samples were successfully sequenced including 914 SGTF positive samples. The sensitivity and specificity of the SGTF signature was 99.6% (95% CI 96.1-99.9%) and 98.6% (95% CI 99.2-99.8%) for the Alpha variant and 99.6% (95% CI 98.9-99.9%) and 99.8% (95% CI 99.4-99.9%) for the Omicron variant. At the peak of their corresponding wave, the positive predictive value of the SGTF was 98% for Alpha and 100% for Omicron. -
Clinical accuracy of SARS-CoV-2 rapid antigen testing in screening children and adolescents in comparison to RT-qPCR, November 2020 to September 2022
M Krone et al, MEDRXIV, November 10, 2022This single centre prospective diagnostic study evaluates three RDT (NADAL®, Panbio™, MEDsan®) in comparison to quantitative reverse transcription polymerase chain reaction (RT-qPCR). 9,760 oropharyngeal screening samples regarding SARS-CoV-2 VOC and COVID-19 vaccination in paediatric hospitalised patients aged younger than 18 years were enrolled. Findings RDT sensitivity was 44·7% (157/351, 95% CI 39·6%-50·0%) compared to the reference standard RT-qPCR, specificity 99·8% (9,392/9,409, 95% CI 99·7%-99·9%). Most SARS-CoV-2 infections considered were caused by Omicron VOC. -
COVID-19-Associated Hospitalizations Among U.S. Infants Aged <6 Months - COVID-NET, 13 States, June 2021-August 2022.
Hamid Sarah et al. MMWR. Morbidity and mortality weekly report 2022 11 (45) 1442-1448Infants aged <6 months, who are ineligible for vaccination, have high COVID-19–associated hospitalization rates compared with other pediatric age groups. Although population-based COVID-19–associated hospitalization rates among infants aged <6 months increased in the Omicron variant–predominant periods compared with the Delta variant–predominant period, indicators of the most severe disease among hospitalized infants aged <6 months did not. -
High–temporal resolution profiling reveals distinct immune trajectories following the first and second doses of COVID-19 mRNA vaccines
D Rinchai et al, Science, November 11, 2022We investigated responses to COVID-19 mRNA vaccination via high–temporal resolution blood transcriptome profiling. The first vaccine dose elicited modest interferon and adaptive immune responses, which peaked on days 2 and 5, respectively. The second vaccine dose, in contrast, elicited sharp day 1 interferon, inflammation, and erythroid cell responses, followed by a day 5 plasmablast response. Both post-first and post-second dose interferon signatures were associated with the subsequent development of antibody responses. Yet, we observed distinct interferon response patterns after each of the doses that may reflect quantitative or qualitative differences in interferon induction. -
Health, socioeconomic and genetic predictors of COVID-19 vaccination uptake: a nationwide machine-learning study
T Hartonen et al, MEDRXIV, November 11, 2022 -
Shared genetic influences between blood analyte levels and risk of severe COVID-19
HM Tanha et al, Cell Reports, November 6, 2022Here we utilise GWAS summary statistics to study the shared genetic influences (pleiotropy) between severe COVID-19 and 344 blood analytes at the genome, gene and single nucleotide polymorphism levels. Our pleiotropy analyses genetically link blood levels of 71 analytes to severe COVID-19 in at least one of the three levels of investigation—suggesting shared biological mechanisms or causal relationships. Six analytes (alanine aminotransferase, alkaline phosphatase, apolipoprotein B, C-reactive protein, triglycerides, and urate) display evidence of pleiotropy with severe COVID-19 at all three levels. -
Protection from previous natural infection compared with mRNA vaccination against SARS-CoV-2 infection and severe COVID-19 in Qatar: a retrospective cohort study
H Chemaitelly et al, The Lancet Microbe, November 11, 2022Understanding protection conferred by natural SARS-CoV-2 infection versus COVID-19 vaccination is important for informing vaccine mandate decisions. We compared protection conferred by natural infection versus that from the BNT162b2 (Pfizer–BioNTech) and mRNA-1273 (Moderna) vaccines in Qatar. We found that previous natural infection was associated with lower incidence of SARS-CoV-2 infection, regardless of the variant, than mRNA primary-series vaccination. -
Variant-specific symptoms of COVID-19 in a study of 1,542,510 adults in England.
Whitaker Matthew et al. Nature communications 2022 11 (1) 6856We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell or taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. -
Protection conferred by Delta and BA.1/BA.2 infection against BA.4/BA.5 infection and hospitalization: A Retrospective Cohort Study
N Winchester et al, MEDSCAPE, November 14, 2022 -
Bivalent BNT162b2mRNA original/Omicron BA.4-5 booster vaccination: adverse reactions and inability to work compared to the monovalent COVID-19 booster
I Wagenhauser et al, MEDRXIV, November 2022Among healthcare workers who received a 4th COVID-19 vaccine dose (n=76, Germany, Aug 2021–Oct 2022), rate of adverse reactions was significantly higher among recipients of BA.4-5 adapted bivalent vaccine (33/39=84.6%) compared with recipients of monovalent BNT162b2 vaccine (19/37=51.4%). Also, more recipients reported taking post-vaccination medication in the bivalent (13/39=33.3%) vs monovalent (8/37=21.6%) groups, and more reported inability to work in the bivalent (9/39=23.1%) vs monovalent (5/37=13.5%) groups, although these differences were not significant. -
Using Genome Sequence Data to Predict SARS-CoV-2 Detection Cycle Threshold Values
L Duesterwald et al, MEDRXIV, November 15, 2022 -
Effectiveness of a third BNT162b2 mRNA COVID-19 vaccination during pregnancy: a national observational study in Israel.
Guedalia Joshua et al. Nature communications 2022 11 (1) 6961Compared with the second dose, the third dose effectively prevents overall hospitalizations with SARS-CoV-2 infections, with estimated effectiveness of 92% (95% CI 83–96%) during Delta, and enhances protection against significant disease during Omicron, with effectiveness of 92% (95% CI 26–99%), and 48% (95% CI 37–57%) effectiveness against hospitalization overall. A third dose of the BNT162b2 mRNA COVID-19 vaccine during pregnancy, given at least 5 months after the second vaccine dose, enhances protection against adverse COVID-19-related outcomes. -
In Vitro Efficacy of Antiviral Agents against Omicron Subvariant BA.4.6
E Takashita et al, NEJM, November 16, 2022Our data suggest that remdesivir, molnupiravir, and nirmatrelvir and the monoclonal antibodies bebtelovimab and imdevimab retain effectiveness against BA.4.6 in vitro. Our findings also indicate that monoclonal antibodies casirivimab, sotrovimab, tixagevimab, and cilgavimab may not be effective against BA.4.6.
- Page last reviewed:Feb 1, 2024
- Page last updated:Apr 25, 2024
- Content source: