Published on 12/23/2020
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
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One Year of SARS-CoV-2: How Much Has the Virus Changed?
S Vilar et al, BIORXIV, December 16, 2020We collected and computationally profiled ~223,000 full SARS-CoV-2 proteome sequences from GISAID over one year for emergent nonsynonymous mutations. Our analysis shows that SARS-CoV-2 proteins are mutating at substantially different rates, with most viral proteins exhibiting little mutational variability. -
Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka.
Pattabiraman Chitra et al. PloS one 2020 (12) e0243412 -
Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy.
Di Giallonardo Francesca et al. Viruses 2020 12 (12) -
Common variants at 21q22.3 locus influence MX1 gene expression and susceptibility to severe COVID-19
I Andolfo et al, MEDRXIV, December 20, 2020We performed a genetic analysis of chromosome 21 exploiting the genome-wide association study data including 6,406 individuals hospitalized for COVID-19 and 902,088 controls with European genetic ancestry. We found that five single nucleotide polymorphisms within TMPRSS2 and near MX1 gene show suggestive associations (P=1x10-5) with severe COVID-19. -
Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion ?H69/V70
S Kemp et al, BIORXIV, December 21, 2020SARS-CoV-2 Spike amino acid replacements in the receptor binding domain (RBD) occur relatively frequently and some have a consequence for immune recognition. Here we report recurrent emergence and significant onward transmission of a six-nucleotide deletion in the S gene, which results in loss of two amino acids: H69 and V70. -
Phylogenetic supertree reveals detailed evolution of SARS-CoV-2
T Li et al, Scientific Reports, December 22, 2020we applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2. The MRP pseudo-sequence supertree analysis firmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS-CoV-2, which was implied by other phylogenetic tree analysis based on viral genome sequences.
Non-Genomics Precision Health Studies
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One Year of SARS-CoV-2: How Much Has the Virus Changed?
S Vilar et al, BIORXIV, December 16, 2020We collected and computationally profiled ~223,000 full SARS-CoV-2 proteome sequences from GISAID over one year for emergent nonsynonymous mutations. Our analysis shows that SARS-CoV-2 proteins are mutating at substantially different rates, with most viral proteins exhibiting little mutational variability. -
Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka.
Pattabiraman Chitra et al. PloS one 2020 (12) e0243412 -
Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy.
Di Giallonardo Francesca et al. Viruses 2020 12 (12) -
Common variants at 21q22.3 locus influence MX1 gene expression and susceptibility to severe COVID-19
I Andolfo et al, MEDRXIV, December 20, 2020We performed a genetic analysis of chromosome 21 exploiting the genome-wide association study data including 6,406 individuals hospitalized for COVID-19 and 902,088 controls with European genetic ancestry. We found that five single nucleotide polymorphisms within TMPRSS2 and near MX1 gene show suggestive associations (P=1x10-5) with severe COVID-19. -
Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion ?H69/V70
S Kemp et al, BIORXIV, December 21, 2020SARS-CoV-2 Spike amino acid replacements in the receptor binding domain (RBD) occur relatively frequently and some have a consequence for immune recognition. Here we report recurrent emergence and significant onward transmission of a six-nucleotide deletion in the S gene, which results in loss of two amino acids: H69 and V70. -
Phylogenetic supertree reveals detailed evolution of SARS-CoV-2
T Li et al, Scientific Reports, December 22, 2020we applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2. The MRP pseudo-sequence supertree analysis firmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS-CoV-2, which was implied by other phylogenetic tree analysis based on viral genome sequences.
News, Reviews and Commentaries
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One Year of SARS-CoV-2: How Much Has the Virus Changed?
S Vilar et al, BIORXIV, December 16, 2020We collected and computationally profiled ~223,000 full SARS-CoV-2 proteome sequences from GISAID over one year for emergent nonsynonymous mutations. Our analysis shows that SARS-CoV-2 proteins are mutating at substantially different rates, with most viral proteins exhibiting little mutational variability. -
Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka.
Pattabiraman Chitra et al. PloS one 2020 (12) e0243412 -
Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy.
Di Giallonardo Francesca et al. Viruses 2020 12 (12) -
Common variants at 21q22.3 locus influence MX1 gene expression and susceptibility to severe COVID-19
I Andolfo et al, MEDRXIV, December 20, 2020We performed a genetic analysis of chromosome 21 exploiting the genome-wide association study data including 6,406 individuals hospitalized for COVID-19 and 902,088 controls with European genetic ancestry. We found that five single nucleotide polymorphisms within TMPRSS2 and near MX1 gene show suggestive associations (P=1x10-5) with severe COVID-19. -
Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion ?H69/V70
S Kemp et al, BIORXIV, December 21, 2020SARS-CoV-2 Spike amino acid replacements in the receptor binding domain (RBD) occur relatively frequently and some have a consequence for immune recognition. Here we report recurrent emergence and significant onward transmission of a six-nucleotide deletion in the S gene, which results in loss of two amino acids: H69 and V70. -
Phylogenetic supertree reveals detailed evolution of SARS-CoV-2
T Li et al, Scientific Reports, December 22, 2020we applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2. The MRP pseudo-sequence supertree analysis firmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS-CoV-2, which was implied by other phylogenetic tree analysis based on viral genome sequences.
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- Page last updated:Apr 18, 2024
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