Published on 05/13/2021
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
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Association Between Vaccination With BNT162b2 and Incidence of Symptomatic and Asymptomatic SARS-CoV-2 Infections Among Health Care Workers.
Angel Yoel et al. JAMA 2021 5In this retrospective cohort study conducted in Tel Aviv, Israel, that included 6710 health care workers who underwent periodic testing for SARS-CoV-2 infection, vaccination with the BNT162b2 vaccine was associated with an adjusted incidence rate ratio of 0.03 for symptomatic infection and 0.14 for asymptomatic infection more than 7 days after the second dose. Both incidence rate ratios were statistically significant. -
Asymptomatic and Symptomatic SARS-CoV-2 Infections After BNT162b2 Vaccination in a Routinely Screened Workforce.
Tang Li et al. JAMA 2021 5This study found an association between vaccination with BNT162b2 in hospital employees and a decreased risk of symptomatic and asymptomatic infections with SARS-CoV-2. -
Antibody Response to 2-Dose SARS-CoV-2 mRNA Vaccine Series in Solid Organ Transplant Recipients.
Boyarsky Brian J et al. JAMA 2021 5In this study of the humoral response to 2 doses of mRNA SARS-CoV-2 vaccine among solid organ transplant recipients, the majority had detectable antibody responses after the second dose, although participants without a response after dose 1 had generally low antibody levels. Poor humoral response was persistently associated with use of antimetabolite immunosuppression. -
Precision Health Diagnostic and Surveillance Network uses S Gene Target Failure (SGTF) combined with sequencing technologies to identify emerging SARS-CoV-2 variants.
RG Preston et al, MEDRXIV, May 7, 2021Several genomic epidemiology tools have been developed to track the public and population health impact of SARS-CoV-2 community spread worldwide. A SARS-CoV-2 Variant of Concern (VOC) B.1.1.7, known as 501Y.V1, which shows increased transmissibility, has rapidly become the dominant VOC in the United States (US). Our objective was to develop an evidenced-based genomic surveillance algorithm that combines RT-PCR and sequencing technologies to identify VOCs. -
Multi-site Evaluation of SARS-CoV-2 Spike Mutation Detection Using a Multiplex Real-time RT-PCR Assay
C Bier et al, MEDRXIV, May 7, 2021We developed a multiplex, real-time RT-PCR assay (cobas SARS-CoV-2 Variant Set 1) for the qualitative detection and differentiation of three key SARS-CoV-2 mutations in the viral spike protein: del 69-70, E484K and N501Y. Data collected at three independent laboratories indicates excellent performance and concordance of cobas SARS-CoV-2 Variant Set 1 with sequencing. -
Association between ACE2 and TMPRSS2 nasopharyngeal expression and COVID-19 respiratory distress.
Rossi Átila Duque et al. Scientific reports 2021 5 (1) 9658ACE2 and TMPRSS2 levels positively correlated with age, which was also strongly associated with respiratory distress. Increased nasopharyngeal ACE2 levels showed a protective effect against this outcome (adjOR = 0.30; 95% CI 0.09-0.91), while TMPRSS2/ACE2 ratio was associated with risk (adjOR = 4.28; 95% CI 1.36-13.48). -
RT-qPCR-based tests for SARS-CoV-2 detection in pooled saliva samples for massive population screening to monitor epidemics.
M Rosanski et al, MEDRXIV, May 9, 3031Testing of 1475 individual clinical samples pooled in 374 pools of 4 revealed 0.8% false positive pools and no false negative pools. In weekly prophylactic testing of 113 people within 6 months, a two-tier testing approach enabled the detection of 18 infected individuals, including several asymptomatic individuals, with a fraction of the costs of individual RT-PCR testing. -
Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe
G Dudas et al, MEDRXIV, May 8, 2021Over a year into the pandemic following unprecedented reductions in worldwide human mobility, distinct introduced lineages of SARS-CoV-2 without sequenced antecedents are increasingly discovered in high-income countries as a result of ongoing SARS-CoV-2 genomic surveillance initiatives. We here describe one such SARS-CoV-2 lineage, carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69del, Y144del, and LLA241/243del. -
"It seems like COVID-19 now is the only disease present on Earth": living with a rare or undiagnosed disease during the COVID-19 pandemic.
Halley Meghan C et al. Genetics in medicine : official journal of the American College of Medical Genetics 2021 1 (5) 837-844Respondents (n?=?413), including 274 RUD patients and 139 family members, were predominantly female and white, though income varied. Impacts of the pandemic included (1) barriers to accessing essential health care, (2) specific impacts of restrictive COVID-19 visitation policies on ability to advocate in health-care settings, (3) uncertainty and fear regarding COVID-19 risk, (4) exacerbated physical and mental health challenges, (5) magnified impacts of reduced educational and therapeutic services, and (6) unexpected positive changes due to the pandemic. -
BNT162b2-Elicited Neutralization against New SARS-CoV-2 Spike Variants.
Liu Yang et al. The New England journal of medicine 2021 5To determine whether variants that have emerged more recently are also susceptible to BNT162b2-elicited neutralization, we engineered the complete S genes of the variant viruses into the genetic background of USA-WA1/2020 (isolated in January 2020). Our results suggest that, as compared with the previously reported neutralization of B.1.1.7-spike, the additional E484K mutation, which is also found in the B.1.351 and B.1.526 lineages, caused little compromise to neutralization
Non-Genomics Precision Health Studies
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Association Between Vaccination With BNT162b2 and Incidence of Symptomatic and Asymptomatic SARS-CoV-2 Infections Among Health Care Workers.
Angel Yoel et al. JAMA 2021 5In this retrospective cohort study conducted in Tel Aviv, Israel, that included 6710 health care workers who underwent periodic testing for SARS-CoV-2 infection, vaccination with the BNT162b2 vaccine was associated with an adjusted incidence rate ratio of 0.03 for symptomatic infection and 0.14 for asymptomatic infection more than 7 days after the second dose. Both incidence rate ratios were statistically significant. -
Asymptomatic and Symptomatic SARS-CoV-2 Infections After BNT162b2 Vaccination in a Routinely Screened Workforce.
Tang Li et al. JAMA 2021 5This study found an association between vaccination with BNT162b2 in hospital employees and a decreased risk of symptomatic and asymptomatic infections with SARS-CoV-2. -
Antibody Response to 2-Dose SARS-CoV-2 mRNA Vaccine Series in Solid Organ Transplant Recipients.
Boyarsky Brian J et al. JAMA 2021 5In this study of the humoral response to 2 doses of mRNA SARS-CoV-2 vaccine among solid organ transplant recipients, the majority had detectable antibody responses after the second dose, although participants without a response after dose 1 had generally low antibody levels. Poor humoral response was persistently associated with use of antimetabolite immunosuppression. -
Precision Health Diagnostic and Surveillance Network uses S Gene Target Failure (SGTF) combined with sequencing technologies to identify emerging SARS-CoV-2 variants.
RG Preston et al, MEDRXIV, May 7, 2021Several genomic epidemiology tools have been developed to track the public and population health impact of SARS-CoV-2 community spread worldwide. A SARS-CoV-2 Variant of Concern (VOC) B.1.1.7, known as 501Y.V1, which shows increased transmissibility, has rapidly become the dominant VOC in the United States (US). Our objective was to develop an evidenced-based genomic surveillance algorithm that combines RT-PCR and sequencing technologies to identify VOCs. -
Multi-site Evaluation of SARS-CoV-2 Spike Mutation Detection Using a Multiplex Real-time RT-PCR Assay
C Bier et al, MEDRXIV, May 7, 2021We developed a multiplex, real-time RT-PCR assay (cobas SARS-CoV-2 Variant Set 1) for the qualitative detection and differentiation of three key SARS-CoV-2 mutations in the viral spike protein: del 69-70, E484K and N501Y. Data collected at three independent laboratories indicates excellent performance and concordance of cobas SARS-CoV-2 Variant Set 1 with sequencing. -
Association between ACE2 and TMPRSS2 nasopharyngeal expression and COVID-19 respiratory distress.
Rossi Átila Duque et al. Scientific reports 2021 5 (1) 9658ACE2 and TMPRSS2 levels positively correlated with age, which was also strongly associated with respiratory distress. Increased nasopharyngeal ACE2 levels showed a protective effect against this outcome (adjOR = 0.30; 95% CI 0.09-0.91), while TMPRSS2/ACE2 ratio was associated with risk (adjOR = 4.28; 95% CI 1.36-13.48). -
RT-qPCR-based tests for SARS-CoV-2 detection in pooled saliva samples for massive population screening to monitor epidemics.
M Rosanski et al, MEDRXIV, May 9, 3031Testing of 1475 individual clinical samples pooled in 374 pools of 4 revealed 0.8% false positive pools and no false negative pools. In weekly prophylactic testing of 113 people within 6 months, a two-tier testing approach enabled the detection of 18 infected individuals, including several asymptomatic individuals, with a fraction of the costs of individual RT-PCR testing. -
Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe
G Dudas et al, MEDRXIV, May 8, 2021Over a year into the pandemic following unprecedented reductions in worldwide human mobility, distinct introduced lineages of SARS-CoV-2 without sequenced antecedents are increasingly discovered in high-income countries as a result of ongoing SARS-CoV-2 genomic surveillance initiatives. We here describe one such SARS-CoV-2 lineage, carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69del, Y144del, and LLA241/243del. -
"It seems like COVID-19 now is the only disease present on Earth": living with a rare or undiagnosed disease during the COVID-19 pandemic.
Halley Meghan C et al. Genetics in medicine : official journal of the American College of Medical Genetics 2021 1 (5) 837-844Respondents (n?=?413), including 274 RUD patients and 139 family members, were predominantly female and white, though income varied. Impacts of the pandemic included (1) barriers to accessing essential health care, (2) specific impacts of restrictive COVID-19 visitation policies on ability to advocate in health-care settings, (3) uncertainty and fear regarding COVID-19 risk, (4) exacerbated physical and mental health challenges, (5) magnified impacts of reduced educational and therapeutic services, and (6) unexpected positive changes due to the pandemic. -
BNT162b2-Elicited Neutralization against New SARS-CoV-2 Spike Variants.
Liu Yang et al. The New England journal of medicine 2021 5To determine whether variants that have emerged more recently are also susceptible to BNT162b2-elicited neutralization, we engineered the complete S genes of the variant viruses into the genetic background of USA-WA1/2020 (isolated in January 2020). Our results suggest that, as compared with the previously reported neutralization of B.1.1.7-spike, the additional E484K mutation, which is also found in the B.1.351 and B.1.526 lineages, caused little compromise to neutralization
News, Reviews and Commentaries
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Association Between Vaccination With BNT162b2 and Incidence of Symptomatic and Asymptomatic SARS-CoV-2 Infections Among Health Care Workers.
Angel Yoel et al. JAMA 2021 5In this retrospective cohort study conducted in Tel Aviv, Israel, that included 6710 health care workers who underwent periodic testing for SARS-CoV-2 infection, vaccination with the BNT162b2 vaccine was associated with an adjusted incidence rate ratio of 0.03 for symptomatic infection and 0.14 for asymptomatic infection more than 7 days after the second dose. Both incidence rate ratios were statistically significant. -
Asymptomatic and Symptomatic SARS-CoV-2 Infections After BNT162b2 Vaccination in a Routinely Screened Workforce.
Tang Li et al. JAMA 2021 5This study found an association between vaccination with BNT162b2 in hospital employees and a decreased risk of symptomatic and asymptomatic infections with SARS-CoV-2. -
Antibody Response to 2-Dose SARS-CoV-2 mRNA Vaccine Series in Solid Organ Transplant Recipients.
Boyarsky Brian J et al. JAMA 2021 5In this study of the humoral response to 2 doses of mRNA SARS-CoV-2 vaccine among solid organ transplant recipients, the majority had detectable antibody responses after the second dose, although participants without a response after dose 1 had generally low antibody levels. Poor humoral response was persistently associated with use of antimetabolite immunosuppression. -
Precision Health Diagnostic and Surveillance Network uses S Gene Target Failure (SGTF) combined with sequencing technologies to identify emerging SARS-CoV-2 variants.
RG Preston et al, MEDRXIV, May 7, 2021Several genomic epidemiology tools have been developed to track the public and population health impact of SARS-CoV-2 community spread worldwide. A SARS-CoV-2 Variant of Concern (VOC) B.1.1.7, known as 501Y.V1, which shows increased transmissibility, has rapidly become the dominant VOC in the United States (US). Our objective was to develop an evidenced-based genomic surveillance algorithm that combines RT-PCR and sequencing technologies to identify VOCs. -
Multi-site Evaluation of SARS-CoV-2 Spike Mutation Detection Using a Multiplex Real-time RT-PCR Assay
C Bier et al, MEDRXIV, May 7, 2021We developed a multiplex, real-time RT-PCR assay (cobas SARS-CoV-2 Variant Set 1) for the qualitative detection and differentiation of three key SARS-CoV-2 mutations in the viral spike protein: del 69-70, E484K and N501Y. Data collected at three independent laboratories indicates excellent performance and concordance of cobas SARS-CoV-2 Variant Set 1 with sequencing. -
Association between ACE2 and TMPRSS2 nasopharyngeal expression and COVID-19 respiratory distress.
Rossi Átila Duque et al. Scientific reports 2021 5 (1) 9658ACE2 and TMPRSS2 levels positively correlated with age, which was also strongly associated with respiratory distress. Increased nasopharyngeal ACE2 levels showed a protective effect against this outcome (adjOR = 0.30; 95% CI 0.09-0.91), while TMPRSS2/ACE2 ratio was associated with risk (adjOR = 4.28; 95% CI 1.36-13.48). -
RT-qPCR-based tests for SARS-CoV-2 detection in pooled saliva samples for massive population screening to monitor epidemics.
M Rosanski et al, MEDRXIV, May 9, 3031Testing of 1475 individual clinical samples pooled in 374 pools of 4 revealed 0.8% false positive pools and no false negative pools. In weekly prophylactic testing of 113 people within 6 months, a two-tier testing approach enabled the detection of 18 infected individuals, including several asymptomatic individuals, with a fraction of the costs of individual RT-PCR testing. -
Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe
G Dudas et al, MEDRXIV, May 8, 2021Over a year into the pandemic following unprecedented reductions in worldwide human mobility, distinct introduced lineages of SARS-CoV-2 without sequenced antecedents are increasingly discovered in high-income countries as a result of ongoing SARS-CoV-2 genomic surveillance initiatives. We here describe one such SARS-CoV-2 lineage, carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69del, Y144del, and LLA241/243del. -
"It seems like COVID-19 now is the only disease present on Earth": living with a rare or undiagnosed disease during the COVID-19 pandemic.
Halley Meghan C et al. Genetics in medicine : official journal of the American College of Medical Genetics 2021 1 (5) 837-844Respondents (n?=?413), including 274 RUD patients and 139 family members, were predominantly female and white, though income varied. Impacts of the pandemic included (1) barriers to accessing essential health care, (2) specific impacts of restrictive COVID-19 visitation policies on ability to advocate in health-care settings, (3) uncertainty and fear regarding COVID-19 risk, (4) exacerbated physical and mental health challenges, (5) magnified impacts of reduced educational and therapeutic services, and (6) unexpected positive changes due to the pandemic. -
BNT162b2-Elicited Neutralization against New SARS-CoV-2 Spike Variants.
Liu Yang et al. The New England journal of medicine 2021 5To determine whether variants that have emerged more recently are also susceptible to BNT162b2-elicited neutralization, we engineered the complete S genes of the variant viruses into the genetic background of USA-WA1/2020 (isolated in January 2020). Our results suggest that, as compared with the previously reported neutralization of B.1.1.7-spike, the additional E484K mutation, which is also found in the B.1.351 and B.1.526 lineages, caused little compromise to neutralization
- Page last reviewed:Feb 1, 2024
- Page last updated:Apr 23, 2024
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