Abstract
COVID-19 has greatly affected public health and world economy. In this study, we analyzed 129 full-length genomes of SARS-CoV-2 viruses of a Canadian population during early phase of the pandemic. Phylogenetic analysis revealed three major paths of transmission of SARS-CoV-2 viruses into Canada. Twenty-one substitutions that have frequencies greater than 3% of viral population were identified. Analysis of these substitutions indicated that P1427I (ORF1b), Y1464C (ORF1b), and Q57H (ORF3a) might affect functions of the corresponding SARS-CoV-2 encoded proteins. Additionally, we found the evidence of positive selection on the ORF3a and codon 614 of Spike protein, suggesting the viral components responsible for host entry and activation of inflammation response were targeted by host immune responses. The study showed genomic variation and evolution of SARS-CoV-2 in a Canadian population. These information may help develop preventive strategies and be used for further study of SARS-CoV-2 pathogenesis and therapeutics development.
Highlights
The unknown pneumonia case was first reported on December 31st, 2019 in Wuhan, China, and a novel coronavirus, named 2019-nCoV, was later identified to be the etiological agent of the pneumonia [1, 2]
The full-genome sequences with an average length of more than 29000 base pairs, high coverage, metadata, and annotations of SARS-CoV-2 were obtained from the Global Initiative on Sharing Avian Influenza Database—GISAID [14] and NCBI nucleotide sequence database— GenBank [15] on April 9th, 2020
The SARS-CoV-2 sequences in Asian (Fig 1G) populations have the lowest degree of similarity across the entire regions of SARS-CoV-2 genomes, indicating that SARS-CoV-2 sequences are very diverse in Asian populations
Summary
The unknown pneumonia case was first reported on December 31st, 2019 in Wuhan, China, and a novel coronavirus, named 2019-nCoV (lately SARS-CoV-2), was later identified to be the etiological agent of the pneumonia [1, 2]. Within a month, this coronavirus disease (COVID-19) swept China and rapidly spread across the globe. No therapeutic interventions or vaccines have been proven effective against SARS-CoV-2 infection. Viral-host interactions will likely determine the outcome of SARS-CoV-2 infection. It is important to analy2ze viral mutations driven by host immune responses to understand how host immune response influence viral mutations
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