Published on 10/08/2020
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
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The major genetic risk factor for severe COVID-19 is inherited from Neanderthals.
Zeberg Hugo et al. Nature 2020 SepA recent genetic association study1 identified a gene cluster on chromosome 3 as a risk locus for respiratory failure upon SARS-CoV-2 infection. A new study2 comprising 3,199 hospitalized COVID-19 patients and controls finds that this is the major genetic risk factor for severe SARS-CoV-2 infection and hospitalization (COVID-19 Host Genetics Initiative). Here, we show that the risk is conferred by a genomic segment of ~50 kb that is inherited from Neanderthals and is carried by ~50% of people in South Asia and ~16% of people in Europe today. -
A Comparison of Five SARS-CoV-2 Molecular Assays With Clinical Correlations.
Procop Gary W et al. American journal of clinical pathology 2020 OctWe compared five SARS-CoV-2 assays using nasopharyngeal and nasal swab specimens submitted in transport media; we enriched this cohort for positive specimens, since we were particularly interested in the sensitivity and false-negative rate. Performance of each test was compared with a composite standard. The sensitivities and false-negative rates of the 239 specimens that met inclusion criteria were, respectively, as follows: Centers for Disease Control and Prevention 2019 nCoV Real-Time RT-PCR Diagnostic Panel, 100% and 0%; TIB MOLBIOL/Roche z 480 Assay, 96.5% and 3.5%; Xpert Xpress SARS-CoV-2 (Cepheid), 97.6% and 2.4%; Simplexa COVID-19 Direct Kit (DiaSorin), 88.1% and 11.9%; and ID Now COVID-19 (Abbott), 83.3% and 16.7%. -
Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic
W Zang et al, JAMA Network Open, October 7, 2020This case series of 192 patients found that 82% of SARS-CoV-2 isolates from Los Angeles shared closest similarity to those originating in Europe vs those from Asia (15%). Using the variation signature of the viral genomes, 2 main clusters were identified, with the top variants sharing genomic features from European SARS-CoV-2 isolates, and several subclusters of SARS-CoV-2 outbreaks represented trackable community spread in Los Angeles. -
Comprehensive Genome Analysis of 6,000 USA SARS-CoV-2 Isolates Reveals Haplotype Signatures and Localized Transmission Patterns by State and by Country.
Shen Lishuang et al. Frontiers in microbiology 2020 573430Genomic analysis of SARS-CoV-2 sequences is crucial in determining the effectiveness of prudent safer at home measures in the United States (US). By haplotype analysis of 6,356 US isolates, we identified a pattern of strongly localized outbreaks at the city-, state-, and country-levels, and temporal transmissions.
Non-Genomics Precision Health Studies
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The major genetic risk factor for severe COVID-19 is inherited from Neanderthals.
Zeberg Hugo et al. Nature 2020 SepA recent genetic association study1 identified a gene cluster on chromosome 3 as a risk locus for respiratory failure upon SARS-CoV-2 infection. A new study2 comprising 3,199 hospitalized COVID-19 patients and controls finds that this is the major genetic risk factor for severe SARS-CoV-2 infection and hospitalization (COVID-19 Host Genetics Initiative). Here, we show that the risk is conferred by a genomic segment of ~50 kb that is inherited from Neanderthals and is carried by ~50% of people in South Asia and ~16% of people in Europe today. -
A Comparison of Five SARS-CoV-2 Molecular Assays With Clinical Correlations.
Procop Gary W et al. American journal of clinical pathology 2020 OctWe compared five SARS-CoV-2 assays using nasopharyngeal and nasal swab specimens submitted in transport media; we enriched this cohort for positive specimens, since we were particularly interested in the sensitivity and false-negative rate. Performance of each test was compared with a composite standard. The sensitivities and false-negative rates of the 239 specimens that met inclusion criteria were, respectively, as follows: Centers for Disease Control and Prevention 2019 nCoV Real-Time RT-PCR Diagnostic Panel, 100% and 0%; TIB MOLBIOL/Roche z 480 Assay, 96.5% and 3.5%; Xpert Xpress SARS-CoV-2 (Cepheid), 97.6% and 2.4%; Simplexa COVID-19 Direct Kit (DiaSorin), 88.1% and 11.9%; and ID Now COVID-19 (Abbott), 83.3% and 16.7%. -
Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic
W Zang et al, JAMA Network Open, October 7, 2020This case series of 192 patients found that 82% of SARS-CoV-2 isolates from Los Angeles shared closest similarity to those originating in Europe vs those from Asia (15%). Using the variation signature of the viral genomes, 2 main clusters were identified, with the top variants sharing genomic features from European SARS-CoV-2 isolates, and several subclusters of SARS-CoV-2 outbreaks represented trackable community spread in Los Angeles. -
Comprehensive Genome Analysis of 6,000 USA SARS-CoV-2 Isolates Reveals Haplotype Signatures and Localized Transmission Patterns by State and by Country.
Shen Lishuang et al. Frontiers in microbiology 2020 573430Genomic analysis of SARS-CoV-2 sequences is crucial in determining the effectiveness of prudent safer at home measures in the United States (US). By haplotype analysis of 6,356 US isolates, we identified a pattern of strongly localized outbreaks at the city-, state-, and country-levels, and temporal transmissions.
News, Reviews and Commentaries
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The major genetic risk factor for severe COVID-19 is inherited from Neanderthals.
Zeberg Hugo et al. Nature 2020 SepA recent genetic association study1 identified a gene cluster on chromosome 3 as a risk locus for respiratory failure upon SARS-CoV-2 infection. A new study2 comprising 3,199 hospitalized COVID-19 patients and controls finds that this is the major genetic risk factor for severe SARS-CoV-2 infection and hospitalization (COVID-19 Host Genetics Initiative). Here, we show that the risk is conferred by a genomic segment of ~50 kb that is inherited from Neanderthals and is carried by ~50% of people in South Asia and ~16% of people in Europe today. -
A Comparison of Five SARS-CoV-2 Molecular Assays With Clinical Correlations.
Procop Gary W et al. American journal of clinical pathology 2020 OctWe compared five SARS-CoV-2 assays using nasopharyngeal and nasal swab specimens submitted in transport media; we enriched this cohort for positive specimens, since we were particularly interested in the sensitivity and false-negative rate. Performance of each test was compared with a composite standard. The sensitivities and false-negative rates of the 239 specimens that met inclusion criteria were, respectively, as follows: Centers for Disease Control and Prevention 2019 nCoV Real-Time RT-PCR Diagnostic Panel, 100% and 0%; TIB MOLBIOL/Roche z 480 Assay, 96.5% and 3.5%; Xpert Xpress SARS-CoV-2 (Cepheid), 97.6% and 2.4%; Simplexa COVID-19 Direct Kit (DiaSorin), 88.1% and 11.9%; and ID Now COVID-19 (Abbott), 83.3% and 16.7%. -
Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic
W Zang et al, JAMA Network Open, October 7, 2020This case series of 192 patients found that 82% of SARS-CoV-2 isolates from Los Angeles shared closest similarity to those originating in Europe vs those from Asia (15%). Using the variation signature of the viral genomes, 2 main clusters were identified, with the top variants sharing genomic features from European SARS-CoV-2 isolates, and several subclusters of SARS-CoV-2 outbreaks represented trackable community spread in Los Angeles. -
Comprehensive Genome Analysis of 6,000 USA SARS-CoV-2 Isolates Reveals Haplotype Signatures and Localized Transmission Patterns by State and by Country.
Shen Lishuang et al. Frontiers in microbiology 2020 573430Genomic analysis of SARS-CoV-2 sequences is crucial in determining the effectiveness of prudent safer at home measures in the United States (US). By haplotype analysis of 6,356 US isolates, we identified a pattern of strongly localized outbreaks at the city-, state-, and country-levels, and temporal transmissions.
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- Page last updated:May 07, 2024
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