Whole-genome comparison of representatives of all variants of SARS-CoV-2, including subvariant BA.2 and the GKA clade

Abstract

Since its discovery at the end of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly evolved into many variants, including subvariant BA.2 and the GKA clade. Genomic clarification is needed for better management of the current pandemic as well as the possible re-emergence of novel variants. The sequence of the original strain Wuhan-Hu-1 and approximately 20 representatives of each variant were downloaded from GenBank and GISAID. Two representatives with no track of un-definitive nucleotides were selected. The sequences were aligned using Muscle. The location of insertion/deletion (indel) in the genome was mapped following the open reading frame (ORF) of Wuhan-Hu-1. Amino acid substitutions in all ORFs were analysed separately. Evolutionary analysis was inferred using maximum likelihood. There are two indel sites in ORF1AB, eight in spike, and one each in ORF3A, Matrix (MA), Nucleoprotein (NP), and the 3’-untranslated regions (3’UTR). Some indel sites are not unique, and some are variant specific. There are 10 residues shared by the Omicron, BA2, and GKA lineages. Three deletions in NP are unique to Omicron and BA.2; two substitutions in ORF1AB, four in spike, three in NP, and two in ORF7A and ORF8 were exclusive to the Delta and GPA clades. Delta, Omicron, and BA.2 share the same single residue spike. Three insertions in spike are unique for Omicron and GKA. Phylogenetic analysis shows that the Omicron, BA.2, and GKA clades share a common cluster that emerged from Delta. In conclusion, whole-genome comparison reveals indels and polymorphic amino acids specific to variants or sub-variants. We propose that the GKA clade is an Omicron subvariant. Finally, the higher transmissibility of BA.2 might be attributed to a 48-nucleotide deletion in the 3’UTR.

Consensus insertion/deletions and amino acid variations of all coding and noncoding regions of the SARS-CoV-2 Omicron clades, including the XBB and BQ.1 lineages

“…All Omicron clades and lineages contained del-11260-11268 in ORF1AB and del-28346-28354 in NC. However, the del-11260-11268 is not unique, as it is present in the Alpha, Beta, and Gamma variants [15].…”