Published on 12/03/2020
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
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Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2
Popa A, et al. Sci Transl Med, 2020 Nov 23;eabe2555."Phylogenetic-epidemiological analysis enabled the reconstruction of superspreading events and charts a map of tourism-related viral spread originating from Austria in spring 2020.... Time-resolved virus sequencing unveiled viral mutation dynamics within individuals with COVID-19, and epidemiologically validated infector-infectee pairs enabled us to determine an average transmission bottleneck size of 103 SARS-CoV-2 particles. In conclusion, this study illustrates the power of combining epidemiological analysis with deep viral genome sequencing to unravel the spread of SARS-CoV-2, and to gain fundamental insights into mutational dynamics and transmission properties." -
Mining a GWAS of Severe Covid-19
DH Katz et al, NEJM, November 24, 2020The COVID-19 genetic risk variant rs657152-A at the ABO locus is strongly associated with increased levels of the CD209 antigen. This dendritic cell-surface protein has been found to facilitate infection by SARS-CoV-2 and other viruses. -
Association of Toll-like receptor 7 variants with life-threatening COVID-19 disease in males
C Fallerini et al, MEDRXIV, November 27, 2020Recently, two families in which COVID-19 segregates like an X-linked recessive monogenic disorder have been reported leading to identification of variants in TLR7. We sought to determine whether the two families represent the tip of the iceberg of a subset of COVID-19 male patients. In 1178 SARS-CoV-2-infected subjects (<60y, 79 severe cases versus 77 control cases). Missense mutations in TLR7 disorder may contribute to disease susceptibility in up to 4% of severe COVID-19. -
Clonal hematopoiesis is associated with risk of severe Covid-19
KL Bolton et al, MEDRXIV, NOvember 27, 2020Among 515 individuals with Covid-19 we found that CH was associated with severe Covid-19 outcomes (OR=1.9, 95%=1.2-2.9, p=0.01). We further explored the relationship between CH and risk of other infections in 14,211 solid tumor patients at MSK. CH was significantly associated with risk of Clostridium Difficile and Streptococcus/Enterococcus infections. These findings suggest a relationship between CH and risk of severe infections that warrants further investigation. -
Virus genomics as a clinical and epidemiological tool.
Petrone Mary et al. EBioMedicine 2020 Nov 103141A recent article presents an apt case study on the role of virus genomics in epidemiology and clinical practice. The D614G substitution is one example of how SARS-CoV-2 is evolving. Continuing to use whole genome sequencing as an epidemiological tool will facilitate the rapid detection and monitoring of new SARS-CoV-2 variants when they emerge. -
Computational Immune Proteomics Approach to Target COVID-19.
Tilocca Bruno et al. Journal of proteome research 2020 11 (11) 4233-4241
Non-Genomics Precision Health Studies
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Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2
Popa A, et al. Sci Transl Med, 2020 Nov 23;eabe2555."Phylogenetic-epidemiological analysis enabled the reconstruction of superspreading events and charts a map of tourism-related viral spread originating from Austria in spring 2020.... Time-resolved virus sequencing unveiled viral mutation dynamics within individuals with COVID-19, and epidemiologically validated infector-infectee pairs enabled us to determine an average transmission bottleneck size of 103 SARS-CoV-2 particles. In conclusion, this study illustrates the power of combining epidemiological analysis with deep viral genome sequencing to unravel the spread of SARS-CoV-2, and to gain fundamental insights into mutational dynamics and transmission properties." -
Mining a GWAS of Severe Covid-19
DH Katz et al, NEJM, November 24, 2020The COVID-19 genetic risk variant rs657152-A at the ABO locus is strongly associated with increased levels of the CD209 antigen. This dendritic cell-surface protein has been found to facilitate infection by SARS-CoV-2 and other viruses. -
Association of Toll-like receptor 7 variants with life-threatening COVID-19 disease in males
C Fallerini et al, MEDRXIV, November 27, 2020Recently, two families in which COVID-19 segregates like an X-linked recessive monogenic disorder have been reported leading to identification of variants in TLR7. We sought to determine whether the two families represent the tip of the iceberg of a subset of COVID-19 male patients. In 1178 SARS-CoV-2-infected subjects (<60y, 79 severe cases versus 77 control cases). Missense mutations in TLR7 disorder may contribute to disease susceptibility in up to 4% of severe COVID-19. -
Clonal hematopoiesis is associated with risk of severe Covid-19
KL Bolton et al, MEDRXIV, NOvember 27, 2020Among 515 individuals with Covid-19 we found that CH was associated with severe Covid-19 outcomes (OR=1.9, 95%=1.2-2.9, p=0.01). We further explored the relationship between CH and risk of other infections in 14,211 solid tumor patients at MSK. CH was significantly associated with risk of Clostridium Difficile and Streptococcus/Enterococcus infections. These findings suggest a relationship between CH and risk of severe infections that warrants further investigation. -
Virus genomics as a clinical and epidemiological tool.
Petrone Mary et al. EBioMedicine 2020 Nov 103141A recent article presents an apt case study on the role of virus genomics in epidemiology and clinical practice. The D614G substitution is one example of how SARS-CoV-2 is evolving. Continuing to use whole genome sequencing as an epidemiological tool will facilitate the rapid detection and monitoring of new SARS-CoV-2 variants when they emerge. -
Computational Immune Proteomics Approach to Target COVID-19.
Tilocca Bruno et al. Journal of proteome research 2020 11 (11) 4233-4241
News, Reviews and Commentaries
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Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2
Popa A, et al. Sci Transl Med, 2020 Nov 23;eabe2555."Phylogenetic-epidemiological analysis enabled the reconstruction of superspreading events and charts a map of tourism-related viral spread originating from Austria in spring 2020.... Time-resolved virus sequencing unveiled viral mutation dynamics within individuals with COVID-19, and epidemiologically validated infector-infectee pairs enabled us to determine an average transmission bottleneck size of 103 SARS-CoV-2 particles. In conclusion, this study illustrates the power of combining epidemiological analysis with deep viral genome sequencing to unravel the spread of SARS-CoV-2, and to gain fundamental insights into mutational dynamics and transmission properties." -
Mining a GWAS of Severe Covid-19
DH Katz et al, NEJM, November 24, 2020The COVID-19 genetic risk variant rs657152-A at the ABO locus is strongly associated with increased levels of the CD209 antigen. This dendritic cell-surface protein has been found to facilitate infection by SARS-CoV-2 and other viruses. -
Association of Toll-like receptor 7 variants with life-threatening COVID-19 disease in males
C Fallerini et al, MEDRXIV, November 27, 2020Recently, two families in which COVID-19 segregates like an X-linked recessive monogenic disorder have been reported leading to identification of variants in TLR7. We sought to determine whether the two families represent the tip of the iceberg of a subset of COVID-19 male patients. In 1178 SARS-CoV-2-infected subjects (<60y, 79 severe cases versus 77 control cases). Missense mutations in TLR7 disorder may contribute to disease susceptibility in up to 4% of severe COVID-19. -
Clonal hematopoiesis is associated with risk of severe Covid-19
KL Bolton et al, MEDRXIV, NOvember 27, 2020Among 515 individuals with Covid-19 we found that CH was associated with severe Covid-19 outcomes (OR=1.9, 95%=1.2-2.9, p=0.01). We further explored the relationship between CH and risk of other infections in 14,211 solid tumor patients at MSK. CH was significantly associated with risk of Clostridium Difficile and Streptococcus/Enterococcus infections. These findings suggest a relationship between CH and risk of severe infections that warrants further investigation. -
Virus genomics as a clinical and epidemiological tool.
Petrone Mary et al. EBioMedicine 2020 Nov 103141A recent article presents an apt case study on the role of virus genomics in epidemiology and clinical practice. The D614G substitution is one example of how SARS-CoV-2 is evolving. Continuing to use whole genome sequencing as an epidemiological tool will facilitate the rapid detection and monitoring of new SARS-CoV-2 variants when they emerge. -
Computational Immune Proteomics Approach to Target COVID-19.
Tilocca Bruno et al. Journal of proteome research 2020 11 (11) 4233-4241
- Page last reviewed:Feb 1, 2024
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