Genomic characterization and evolution of SARS-CoV-2 of a Canadian population

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.

Fig 1. Sequence diversity of SARS-CoV-2 from different populations around world.

Sequence similarity was plotted according to viruses from the corresponding populations using Pluton implemented in EMBOSS. Red circle shows the result from Canadian population; arrow shows the result from Asian population.

Fig 2. Genomic variation of SARS-CoV-2 in a Canadian population.

Genomic variants were identified by referring to MN908947 using SNP-sites [10]. The locations and frequencies of the variants were plotted along genomic sequence of MN908947. The open reading frames of SARS-CoV-2 were shown as rectangles that were aligned with nucleotide positions of coronavirus.

Fig 3. Phylogenetic relationship of the SARS-Cov-2 sequences of a Canadian population with other reported sequences in the world.

Phylogenetic tree was built by an approximately maximum likelihood method on the full-genomes of novel coronaviruses worldwide from GISAID. The clades were defined by referring to the classification of Nextstrain (https://nextrain.org/). Canadian isolates were highlighted in green dots.

Fig 4. Phylogenetic tree of the SARS-Cov-2 sequences in Canada.

Phylogenetic tree was built by an approximately maximum likelihood method on the full-genomes of novel coronaviruses from a Canadian population. The three groups of lineages were classified into three clusters: cluster I, II, and III. MN908947 is the reference. Red dot indicates the reference.