Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic

Ahmad Alkhansa; Ghayas Lakkis; Loubna El Zein

doi:10.1016/j.genrep.2021.101024

Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic

Gene Rep. 2021 Jun:23:101024. doi: 10.1016/j.genrep.2021.101024. Epub 2021 Jan 17.

Authors

Ahmad Alkhansa¹, Ghayas Lakkis², Loubna El Zein²

Affiliations

¹ Bologna University, Faculty of Pharmacy, Bio-computation Laboratory, Via San Giacomo 9, Bologna 40126, Emilia-Romagna, Italy.
² Lebanese University, Faculty of Sciences I, Biology Department, Rafic Hariri Campus, P.O. Box: 14 - 6573, Beirut, Lebanon.

Abstract

SARS-CoV-2, the causal agent of COVID 19, is a new human pathogen that appeared in Wuhan, late December 2019. SARS-CoV-2 is a positive sense RNA virus, having four structural and six accessory proteins including that encoded by ORF8 gene known to be one of the most hypervariable and rapidly evolving genes. Thus, global characterization of mutations in this gene is important for pathogenicity and diagnostics. 240 different nonsynonymous mutations and 2 deletions were identified in 45,400 ORF8 nucleotide sequences during six months pandemic with about half of these variants were deleterious for ORF8, and the quarter of them were located in conserved amino acids. Genetic diversity analysis showed two main regions that harbor L84S and S24L. L84S is by far the most predominant mutation, followed by S24L that appeared first in USA. Phylogenetic analysis of ORF8 variants revealed the appearance of small clades with that of L84S being closer to bats. This is the first study that revealed the global nonsynonymous mutations in ORF8 from January to June 2020.

Keywords: COVID-19; Deletions; Nonsynonymous mutations; ORF8; Phylogenetic analysis; SARS-CoV-2; Single nucleotide variations.