Published on 06/03/2021
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
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COVID-19 mass testing: harnessing the power of wastewater epidemiology
SF Fitzgerald et al, MEDRXIV, May 26, 2021In Scotland, wastewater testing has been expanded to cover 75% of the population, with sub-catchment sampling being used to focus surge testing. SARS-CoV-2 variant detection, assessment of vaccination on community transmission and surveillance for other infectious diseases represent promising future applications. -
COVID-19 associated risks of myocardial infarction in persons with familial hypercholesterolemia with or without ASCVD
KD Myers et al, AJPM, May 25, 2021Our analyses confirm that pre-existing ASCVD is associated with increased risk of acute myocardial infarction in the setting of COVID-19. Additionally, we establish that both diagnosed and probable FH are associated with increased risk for AMI in the setting of COVID-19. Critically, our data indicate that those with both ASCVD and FH are at very high risk of AMI if they contract COVID-19. -
Genetics of symptom remission in outpatients with COVID-19.
Dubé Marie-Pierre et al. Scientific reports 2021 5 (1) 10847We conducted a genome-wide association study of time to remission of COVID-19 symptoms in 1723 outpatients with at least one risk factor for disease severity from the COLCORONA clinical trial. We found a significant association at 5p13.3 (rs1173773; P = 4.94 × 10-8) near the natriuretic peptide receptor 3 gene (NPR3). By day 15 of the study, 44%, 54% and 59% of participants with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. -
SARS-CoV-2 variants of concern partially escape humoral but not T-cell responses in COVID-19 convalescent donors and vaccinees.
Geers Daryl et al. Science immunology 2021 5 (59)this study shows that some variants can partially escape humoral immunity induced by SARS-CoV-2 infection or BNT162b2 vaccination, but S-specific CD4+ T-cell activation is not affected by the mutations in the B.1.1.7 and B.1.351 variants. -
Immune response to SARS-CoV-2 variants of concern in vaccinated individuals.
Becker Matthias et al. Nature communications 2021 5 (1) 3109 -
Blood DNA methylation and COVID-19 outcomes.
Balnis Joseph et al. Clinical epigenetics 2021 5 (1) 118Among COVID-19-positive patients, worse outcomes were associated with a prevailing hyper-methylated status. Recursive feature elimination identified 77 differentially methylated positions predictive of COVID-19 severity measured by the GRAM-risk score. -
Minor allele of Intercellular adhesion molecule-1 (ICAM-1) polymorphism (rs5498 1462A>G) is associated with SARS-CoV-2 infection and related mortality.
Padhi Sunali et al. The Journal of infectious diseases 2021 5 -
BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans.
Sahin Ugur et al. Nature 2021 5We extend our previous phase 1/2 trial report2 and present BNT162b2 prime/boost induced immune response data from a second phase 1/2 trial in healthy adults (18-55 years of age). BNT162b2 elicited strong antibody responses, with SARS-CoV-2 serum 50% neutralizing geometric mean titers up to 3.3-fold above those observed in COVID-19 human convalescent samples (HCS) one week post-boost. -
TMEM41B is a host factor required for the replication of diverse coronaviruses including SARS-CoV-2.
Trimarco Joseph D et al. PLoS pathogens 2021 5 (5) e1009599We report the identification and validation of an ER-resident host protein, TMEM41B, as an essential host factor for not only HCoV-229E but also genetically distinct coronaviruses including the pandemic beta-coronavirus SARS-CoV-2. We show that the protein is required at an early, but post-receptor engagement, stage of the viral lifecycle. -
The UGT2A1/UGT2A2 locus is associated with COVID-19-related anosmia
JF Shelton et al, MEDRXIV, May 31, 2021We ran a trans-ethnic genome-wide association study (GWAS) comparing loss of smell or taste (n=47,298) with no loss of smell or taste (n=22,543) among those with a positive SARS-CoV-2 test result. We identified an association (rs7688383) in the vicinity of the UGT2A1 and UGT2A2 genes (OR=1.115, p-value=4x10-15), which have been linked to olfactory function. These results may shed light on the biological mechanisms underlying COVID-19 related anosmia. -
Serum neutralising activity against SARS-CoV-2 variants elicited by CoronaVac.
Chen Yuxin et al. The Lancet. Infectious diseases 2021 5
Non-Genomics Precision Health Studies
-
COVID-19 mass testing: harnessing the power of wastewater epidemiology
SF Fitzgerald et al, MEDRXIV, May 26, 2021In Scotland, wastewater testing has been expanded to cover 75% of the population, with sub-catchment sampling being used to focus surge testing. SARS-CoV-2 variant detection, assessment of vaccination on community transmission and surveillance for other infectious diseases represent promising future applications. -
COVID-19 associated risks of myocardial infarction in persons with familial hypercholesterolemia with or without ASCVD
KD Myers et al, AJPM, May 25, 2021Our analyses confirm that pre-existing ASCVD is associated with increased risk of acute myocardial infarction in the setting of COVID-19. Additionally, we establish that both diagnosed and probable FH are associated with increased risk for AMI in the setting of COVID-19. Critically, our data indicate that those with both ASCVD and FH are at very high risk of AMI if they contract COVID-19. -
Genetics of symptom remission in outpatients with COVID-19.
Dubé Marie-Pierre et al. Scientific reports 2021 5 (1) 10847We conducted a genome-wide association study of time to remission of COVID-19 symptoms in 1723 outpatients with at least one risk factor for disease severity from the COLCORONA clinical trial. We found a significant association at 5p13.3 (rs1173773; P = 4.94 × 10-8) near the natriuretic peptide receptor 3 gene (NPR3). By day 15 of the study, 44%, 54% and 59% of participants with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. -
SARS-CoV-2 variants of concern partially escape humoral but not T-cell responses in COVID-19 convalescent donors and vaccinees.
Geers Daryl et al. Science immunology 2021 5 (59)this study shows that some variants can partially escape humoral immunity induced by SARS-CoV-2 infection or BNT162b2 vaccination, but S-specific CD4+ T-cell activation is not affected by the mutations in the B.1.1.7 and B.1.351 variants. -
Immune response to SARS-CoV-2 variants of concern in vaccinated individuals.
Becker Matthias et al. Nature communications 2021 5 (1) 3109 -
Blood DNA methylation and COVID-19 outcomes.
Balnis Joseph et al. Clinical epigenetics 2021 5 (1) 118Among COVID-19-positive patients, worse outcomes were associated with a prevailing hyper-methylated status. Recursive feature elimination identified 77 differentially methylated positions predictive of COVID-19 severity measured by the GRAM-risk score. -
Minor allele of Intercellular adhesion molecule-1 (ICAM-1) polymorphism (rs5498 1462A>G) is associated with SARS-CoV-2 infection and related mortality.
Padhi Sunali et al. The Journal of infectious diseases 2021 5 -
BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans.
Sahin Ugur et al. Nature 2021 5We extend our previous phase 1/2 trial report2 and present BNT162b2 prime/boost induced immune response data from a second phase 1/2 trial in healthy adults (18-55 years of age). BNT162b2 elicited strong antibody responses, with SARS-CoV-2 serum 50% neutralizing geometric mean titers up to 3.3-fold above those observed in COVID-19 human convalescent samples (HCS) one week post-boost. -
TMEM41B is a host factor required for the replication of diverse coronaviruses including SARS-CoV-2.
Trimarco Joseph D et al. PLoS pathogens 2021 5 (5) e1009599We report the identification and validation of an ER-resident host protein, TMEM41B, as an essential host factor for not only HCoV-229E but also genetically distinct coronaviruses including the pandemic beta-coronavirus SARS-CoV-2. We show that the protein is required at an early, but post-receptor engagement, stage of the viral lifecycle. -
The UGT2A1/UGT2A2 locus is associated with COVID-19-related anosmia
JF Shelton et al, MEDRXIV, May 31, 2021We ran a trans-ethnic genome-wide association study (GWAS) comparing loss of smell or taste (n=47,298) with no loss of smell or taste (n=22,543) among those with a positive SARS-CoV-2 test result. We identified an association (rs7688383) in the vicinity of the UGT2A1 and UGT2A2 genes (OR=1.115, p-value=4x10-15), which have been linked to olfactory function. These results may shed light on the biological mechanisms underlying COVID-19 related anosmia. -
Serum neutralising activity against SARS-CoV-2 variants elicited by CoronaVac.
Chen Yuxin et al. The Lancet. Infectious diseases 2021 5
News, Reviews and Commentaries
-
COVID-19 mass testing: harnessing the power of wastewater epidemiology
SF Fitzgerald et al, MEDRXIV, May 26, 2021In Scotland, wastewater testing has been expanded to cover 75% of the population, with sub-catchment sampling being used to focus surge testing. SARS-CoV-2 variant detection, assessment of vaccination on community transmission and surveillance for other infectious diseases represent promising future applications. -
COVID-19 associated risks of myocardial infarction in persons with familial hypercholesterolemia with or without ASCVD
KD Myers et al, AJPM, May 25, 2021Our analyses confirm that pre-existing ASCVD is associated with increased risk of acute myocardial infarction in the setting of COVID-19. Additionally, we establish that both diagnosed and probable FH are associated with increased risk for AMI in the setting of COVID-19. Critically, our data indicate that those with both ASCVD and FH are at very high risk of AMI if they contract COVID-19. -
Genetics of symptom remission in outpatients with COVID-19.
Dubé Marie-Pierre et al. Scientific reports 2021 5 (1) 10847We conducted a genome-wide association study of time to remission of COVID-19 symptoms in 1723 outpatients with at least one risk factor for disease severity from the COLCORONA clinical trial. We found a significant association at 5p13.3 (rs1173773; P = 4.94 × 10-8) near the natriuretic peptide receptor 3 gene (NPR3). By day 15 of the study, 44%, 54% and 59% of participants with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. -
SARS-CoV-2 variants of concern partially escape humoral but not T-cell responses in COVID-19 convalescent donors and vaccinees.
Geers Daryl et al. Science immunology 2021 5 (59)this study shows that some variants can partially escape humoral immunity induced by SARS-CoV-2 infection or BNT162b2 vaccination, but S-specific CD4+ T-cell activation is not affected by the mutations in the B.1.1.7 and B.1.351 variants. -
Immune response to SARS-CoV-2 variants of concern in vaccinated individuals.
Becker Matthias et al. Nature communications 2021 5 (1) 3109 -
Blood DNA methylation and COVID-19 outcomes.
Balnis Joseph et al. Clinical epigenetics 2021 5 (1) 118Among COVID-19-positive patients, worse outcomes were associated with a prevailing hyper-methylated status. Recursive feature elimination identified 77 differentially methylated positions predictive of COVID-19 severity measured by the GRAM-risk score. -
Minor allele of Intercellular adhesion molecule-1 (ICAM-1) polymorphism (rs5498 1462A>G) is associated with SARS-CoV-2 infection and related mortality.
Padhi Sunali et al. The Journal of infectious diseases 2021 5 -
BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans.
Sahin Ugur et al. Nature 2021 5We extend our previous phase 1/2 trial report2 and present BNT162b2 prime/boost induced immune response data from a second phase 1/2 trial in healthy adults (18-55 years of age). BNT162b2 elicited strong antibody responses, with SARS-CoV-2 serum 50% neutralizing geometric mean titers up to 3.3-fold above those observed in COVID-19 human convalescent samples (HCS) one week post-boost. -
TMEM41B is a host factor required for the replication of diverse coronaviruses including SARS-CoV-2.
Trimarco Joseph D et al. PLoS pathogens 2021 5 (5) e1009599We report the identification and validation of an ER-resident host protein, TMEM41B, as an essential host factor for not only HCoV-229E but also genetically distinct coronaviruses including the pandemic beta-coronavirus SARS-CoV-2. We show that the protein is required at an early, but post-receptor engagement, stage of the viral lifecycle. -
The UGT2A1/UGT2A2 locus is associated with COVID-19-related anosmia
JF Shelton et al, MEDRXIV, May 31, 2021We ran a trans-ethnic genome-wide association study (GWAS) comparing loss of smell or taste (n=47,298) with no loss of smell or taste (n=22,543) among those with a positive SARS-CoV-2 test result. We identified an association (rs7688383) in the vicinity of the UGT2A1 and UGT2A2 genes (OR=1.115, p-value=4x10-15), which have been linked to olfactory function. These results may shed light on the biological mechanisms underlying COVID-19 related anosmia. -
Serum neutralising activity against SARS-CoV-2 variants elicited by CoronaVac.
Chen Yuxin et al. The Lancet. Infectious diseases 2021 5
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- Page last updated:Mar 28, 2024
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