Published on 11/24/2020
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
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Safety and immunogenicity of ChAdOx1 nCoV-19 vaccine administered in a prime-boost regimen in young and old adults (COV002): a single-blind, randomised, controlled, phase 2/3 trial
NN Ramasamy et al, The Lancet, November 18, 2020This is the fifth published clinical trial of a vaccine against SARS-CoV-2 tested in an older adult population (aged 18–55 years, 56–69 years, and =70 years). The vaccine was safe and well tolerated, with reduced reactogenicity in older adults. Antibody responses against the SARS-CoV-2 spike protein were induced in all age groups and were boosted and maintained at 28 days after booster vaccination, including in the 70 years and older group. -
coronapp: A Web Application to Annotate and Monitor SARS-CoV-2 Mutations.
Mercatelli Daniele et al. Journal of medical virology 2020 NovWe present a webtool, coronapp, dedicated to easily processing user-provided SARS-CoV-2 genomic sequences and visualizing current worldwide status of SARS-CoV-2 mutations. The webtool allows users to highlight mutations and categorize them by frequency, country, genomic location and effect on protein sequences, and to monitor their presence in populations over time. -
Stability of SARS-CoV-2 phylogenies.
Turakhia Yatish et al. PLoS genetics 2020 Nov (11) e1009175SARS-CoV-2 genome sequences have been produced by hundreds of labs across the world. Idiosyncratic data generation or processing has the potential to inject non-random errors into genome sequences provided by individual lab groups. Here we show that these sites can be detected and removed by identifying variants that appear to reoccur many times across a phylogeny and are associated with specific lab groups. -
A simple direct RT-LAMP SARS-CoV-2 saliva diagnostic
MJ Flynn et al, MEDRXIV, November 22, 2020We report an optimized RT-LAMP-based SARS-CoV-2 diagnostic protocol for saliva and swab samples. When tested on clinical swab and saliva samples, this assay achieves a limit of detection of 105 viral genomes per ml, with sensitivity close to 90% and specificity close to 100%, and takes 45 minutes from sample collection to result, making it well suited for a COVID-19 surveillance program. -
Coagulation factors and COVID-19 severity: Mendelian randomization analyses and supporting evidence
Y Zhou et al, MEDRXIV, November 23, 2020We assessed causal relationship between 12 coagulation factors and severe COVID-19 illness based on Mendelian randomization (MR) analyses. We then curated clinical evidence supporting causal associations between COVID-19 severity and particular coagulation factors which showed significant results in MR analyses. We validated our results in an independent cohort from UK Biobank (UKBB) using polygenic risk score (PRS) analysis and logistic regression model. -
Flight-Associated Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Corroborated by Whole-Genome Sequencing.
Speake Hollie et al. Emerging infectious diseases 2020 Dec (12) 2872-2880To investigate potential transmission of SARS-CoV-2 during a domestic flight, we performed epidemiologic analyses with whole-genome sequencing. Eleven passengers with PCR-confirmed infection and symptom onset within 48 hours of the flight were considered infectious during travel; 9 had recently disembarked from a cruise ship with a retrospectively identified outbreak. The virus strain of those on the cruise and the flight was linked (A2-RP) and had not been previously identified in Australia. For 11 passengers, none of whom had traveled on the cruise ship, PCR-confirmed SARS-CoV-2 illness developed between 48 hours and 14 days after the flight. Eight cases were considered flight associated with the distinct SARS-CoV-2 A2-RP strain; the remaining 3 cases (1 with A2-RP) were possibly flight associated. All 11 passengers had been in the same cabin with symptomatic persons who had culture-positive A2-RP virus strain. -
On-site rapid molecular testing, mobile sampling teams and eHealth to support primary care physicians during the COVID-19 pandemic
NN Cheung et al, MedRXIV, November 23, 2020The combination of rapid molecular testing and eHealth reduced the time between referral and results sent back to the GP to less than four hours. In addition, mobile sampling teams helped in reaching non-mobile, elderly patient populations with a higher prevalence of COVID-19.
Non-Genomics Precision Health Studies
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Safety and immunogenicity of ChAdOx1 nCoV-19 vaccine administered in a prime-boost regimen in young and old adults (COV002): a single-blind, randomised, controlled, phase 2/3 trial
NN Ramasamy et al, The Lancet, November 18, 2020This is the fifth published clinical trial of a vaccine against SARS-CoV-2 tested in an older adult population (aged 18–55 years, 56–69 years, and =70 years). The vaccine was safe and well tolerated, with reduced reactogenicity in older adults. Antibody responses against the SARS-CoV-2 spike protein were induced in all age groups and were boosted and maintained at 28 days after booster vaccination, including in the 70 years and older group. -
coronapp: A Web Application to Annotate and Monitor SARS-CoV-2 Mutations.
Mercatelli Daniele et al. Journal of medical virology 2020 NovWe present a webtool, coronapp, dedicated to easily processing user-provided SARS-CoV-2 genomic sequences and visualizing current worldwide status of SARS-CoV-2 mutations. The webtool allows users to highlight mutations and categorize them by frequency, country, genomic location and effect on protein sequences, and to monitor their presence in populations over time. -
Stability of SARS-CoV-2 phylogenies.
Turakhia Yatish et al. PLoS genetics 2020 Nov (11) e1009175SARS-CoV-2 genome sequences have been produced by hundreds of labs across the world. Idiosyncratic data generation or processing has the potential to inject non-random errors into genome sequences provided by individual lab groups. Here we show that these sites can be detected and removed by identifying variants that appear to reoccur many times across a phylogeny and are associated with specific lab groups. -
A simple direct RT-LAMP SARS-CoV-2 saliva diagnostic
MJ Flynn et al, MEDRXIV, November 22, 2020We report an optimized RT-LAMP-based SARS-CoV-2 diagnostic protocol for saliva and swab samples. When tested on clinical swab and saliva samples, this assay achieves a limit of detection of 105 viral genomes per ml, with sensitivity close to 90% and specificity close to 100%, and takes 45 minutes from sample collection to result, making it well suited for a COVID-19 surveillance program. -
Coagulation factors and COVID-19 severity: Mendelian randomization analyses and supporting evidence
Y Zhou et al, MEDRXIV, November 23, 2020We assessed causal relationship between 12 coagulation factors and severe COVID-19 illness based on Mendelian randomization (MR) analyses. We then curated clinical evidence supporting causal associations between COVID-19 severity and particular coagulation factors which showed significant results in MR analyses. We validated our results in an independent cohort from UK Biobank (UKBB) using polygenic risk score (PRS) analysis and logistic regression model. -
Flight-Associated Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Corroborated by Whole-Genome Sequencing.
Speake Hollie et al. Emerging infectious diseases 2020 Dec (12) 2872-2880To investigate potential transmission of SARS-CoV-2 during a domestic flight, we performed epidemiologic analyses with whole-genome sequencing. Eleven passengers with PCR-confirmed infection and symptom onset within 48 hours of the flight were considered infectious during travel; 9 had recently disembarked from a cruise ship with a retrospectively identified outbreak. The virus strain of those on the cruise and the flight was linked (A2-RP) and had not been previously identified in Australia. For 11 passengers, none of whom had traveled on the cruise ship, PCR-confirmed SARS-CoV-2 illness developed between 48 hours and 14 days after the flight. Eight cases were considered flight associated with the distinct SARS-CoV-2 A2-RP strain; the remaining 3 cases (1 with A2-RP) were possibly flight associated. All 11 passengers had been in the same cabin with symptomatic persons who had culture-positive A2-RP virus strain. -
On-site rapid molecular testing, mobile sampling teams and eHealth to support primary care physicians during the COVID-19 pandemic
NN Cheung et al, MedRXIV, November 23, 2020The combination of rapid molecular testing and eHealth reduced the time between referral and results sent back to the GP to less than four hours. In addition, mobile sampling teams helped in reaching non-mobile, elderly patient populations with a higher prevalence of COVID-19.
News, Reviews and Commentaries
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Safety and immunogenicity of ChAdOx1 nCoV-19 vaccine administered in a prime-boost regimen in young and old adults (COV002): a single-blind, randomised, controlled, phase 2/3 trial
NN Ramasamy et al, The Lancet, November 18, 2020This is the fifth published clinical trial of a vaccine against SARS-CoV-2 tested in an older adult population (aged 18–55 years, 56–69 years, and =70 years). The vaccine was safe and well tolerated, with reduced reactogenicity in older adults. Antibody responses against the SARS-CoV-2 spike protein were induced in all age groups and were boosted and maintained at 28 days after booster vaccination, including in the 70 years and older group. -
coronapp: A Web Application to Annotate and Monitor SARS-CoV-2 Mutations.
Mercatelli Daniele et al. Journal of medical virology 2020 NovWe present a webtool, coronapp, dedicated to easily processing user-provided SARS-CoV-2 genomic sequences and visualizing current worldwide status of SARS-CoV-2 mutations. The webtool allows users to highlight mutations and categorize them by frequency, country, genomic location and effect on protein sequences, and to monitor their presence in populations over time. -
Stability of SARS-CoV-2 phylogenies.
Turakhia Yatish et al. PLoS genetics 2020 Nov (11) e1009175SARS-CoV-2 genome sequences have been produced by hundreds of labs across the world. Idiosyncratic data generation or processing has the potential to inject non-random errors into genome sequences provided by individual lab groups. Here we show that these sites can be detected and removed by identifying variants that appear to reoccur many times across a phylogeny and are associated with specific lab groups. -
A simple direct RT-LAMP SARS-CoV-2 saliva diagnostic
MJ Flynn et al, MEDRXIV, November 22, 2020We report an optimized RT-LAMP-based SARS-CoV-2 diagnostic protocol for saliva and swab samples. When tested on clinical swab and saliva samples, this assay achieves a limit of detection of 105 viral genomes per ml, with sensitivity close to 90% and specificity close to 100%, and takes 45 minutes from sample collection to result, making it well suited for a COVID-19 surveillance program. -
Coagulation factors and COVID-19 severity: Mendelian randomization analyses and supporting evidence
Y Zhou et al, MEDRXIV, November 23, 2020We assessed causal relationship between 12 coagulation factors and severe COVID-19 illness based on Mendelian randomization (MR) analyses. We then curated clinical evidence supporting causal associations between COVID-19 severity and particular coagulation factors which showed significant results in MR analyses. We validated our results in an independent cohort from UK Biobank (UKBB) using polygenic risk score (PRS) analysis and logistic regression model. -
Flight-Associated Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Corroborated by Whole-Genome Sequencing.
Speake Hollie et al. Emerging infectious diseases 2020 Dec (12) 2872-2880To investigate potential transmission of SARS-CoV-2 during a domestic flight, we performed epidemiologic analyses with whole-genome sequencing. Eleven passengers with PCR-confirmed infection and symptom onset within 48 hours of the flight were considered infectious during travel; 9 had recently disembarked from a cruise ship with a retrospectively identified outbreak. The virus strain of those on the cruise and the flight was linked (A2-RP) and had not been previously identified in Australia. For 11 passengers, none of whom had traveled on the cruise ship, PCR-confirmed SARS-CoV-2 illness developed between 48 hours and 14 days after the flight. Eight cases were considered flight associated with the distinct SARS-CoV-2 A2-RP strain; the remaining 3 cases (1 with A2-RP) were possibly flight associated. All 11 passengers had been in the same cabin with symptomatic persons who had culture-positive A2-RP virus strain. -
On-site rapid molecular testing, mobile sampling teams and eHealth to support primary care physicians during the COVID-19 pandemic
NN Cheung et al, MedRXIV, November 23, 2020The combination of rapid molecular testing and eHealth reduced the time between referral and results sent back to the GP to less than four hours. In addition, mobile sampling teams helped in reaching non-mobile, elderly patient populations with a higher prevalence of COVID-19.
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- Page last updated:Mar 28, 2024
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