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Variant analysis of SARS-CoV-2 genomes.

ABSTRACT: Objective:To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Methods:Between 1 February and 1 May 2020, we downloaded 10?022 SARS CoV-2 genomes from four databases. The genomes were from infected patients in 68 countries. We identified variants by extracting pairwise alignment to the reference genome NC_045512, using the EMBOSS needle. Nucleotide variants in the coding regions were converted to corresponding encoded amino acid residues. For clade analysis, we used the open source software Bayesian evolutionary analysis by sampling trees, version 2.5. Findings:We identified 5775 distinct genome variants, including 2969 missense mutations, 1965 synonymous mutations, 484 mutations in the non-coding regions, 142 non-coding deletions, 100 in-frame deletions, 66 non-coding insertions, 36 stop-gained variants, 11 frameshift deletions and two in-frame insertions. The most common variants were the synonymous 3037C >?T (6334 samples), P4715L in the open reading frame 1ab (6319 samples) and D614G in the spike protein (6294 samples). We identified six major clades, (that is, basal, D614G, L84S, L3606F, D448del and G392D) and 14 subclades. Regarding the base changes, the C >?T mutation was the most common with 1670 distinct variants. Conclusion:We found that several variants of the SARS-CoV-2 genome exist and that the D614G clade has become the most common variant since December 2019. The evolutionary analysis indicated structured transmission, with the possibility of multiple introductions into the population.

SUBMITTER: Koyama T

PROVIDER: S-EPMC7375210 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Variant analysis of SARS-CoV-2 genomes.

Koyama Takahiko T Platt Daniel D Parida Laxmi L

Bulletin of the World Health Organization 20200602 7

<h4>Objective</h4>To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).<h4>Methods</h4>Between 1 February and 1 May 2020, we downloaded 10 022 SARS CoV-2 genomes from four databases. The genomes were from infected patients in 68 countries. We identified variants by extracting pairwise alignment to the reference genome NC_045512, using the EMBOSS needle. Nucleotide variants in the coding regions were converted to corresponding encoded amino acid residues. For ...[more]

PMID: 32742035

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Project description:BackgroundCoronavirus (COVID-19) was introduced into society in late 2019 and has now reached over 88 million cases and 1.9 million deaths. The Middle East has a death toll of ~80,000 and over 35000 of these are in Iran, which has over 1.2 million confirmed cases. We expect that Iranian cases caused outbreaks in the neighbouring countries and that variant mapping and phylogenetic analysis can be used to prove this. We also aim to analyse the variants of severe acute respiratory syndrome coronavirus-2 (SARS -CoV-2) to characterise the common genome variants and provide useful data in the global effort to prevent further spread of COVID-19.MethodsThe approach uses bioinformatics approaches including multiple sequence alignment, variant calling and annotation and phylogenetic analysis to identify the genomic variants found in the region. The approach uses 122 samples from the 13 countries of the Middle East sourced from the Global Initiative on Sharing All Influenza Data (GISAID).FindingsWe identified 2200 distinct genome variants including 129 downstream gene variants, 298 frame shift variants, 789 missense variants, 1 start lost, 13 start gained, 1 stop lost, 249 synonymous variants and 720 upstream gene variants. The most common, high impact variants were 10818delTinsG, 2772delCinsC, 14159delCinsC and 2789delAinsA. These high impact variant ultimately results in 36 number of mutations on spike glycoprotein. Variant alignment and phylogenetic tree generation indicates that samples from Iran likely introduced COVID-19 to the rest of the Middle East.InterpretationThe phylogenetic and variant analysis provides unique insight into mutation types in genomes. Initial introduction of COVID-19 was most likely due to Iranian transmission. Some countries show evidence of novel mutations and unique strains. Increased time in small populations is likely to contribute to more unique genomes. This study provides more in depth analysis of the variants affecting in the region than any other study.

Dataset Information

Variant analysis of SARS-CoV-2 genomes.

Publications

Variant analysis of SARS-CoV-2 genomes.

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