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 deletion

SUBMITTER: Koyama T 

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

REPOSITORIES: biostudies-literature