Comparative Analysis of SARS-CoV-2 Variants of Concern, Including Omicron, Highlights Their Common and Distinctive Amino Acid Substitution Patterns, Especially at the Spike ORF.

Authors
Nikolaidis, Marios 
Papakyriakou, Athanasios  ORCID logo  https://orcid.org/0000-0003-3931-6232
Chlichlia, Katerina  ORCID logo  https://orcid.org/0000-0003-4952-0675
Markoulatos, Panayotis 

Loading...
Thumbnail Image
Type
Article
Change log
Abstract

In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant of concern (VoC), a study of amino acid substitution (AAS) patterns was performed and compared with those of the other four successful variants of concern (Alpha, Beta, Gamma, Delta) and one closely related variant of interest (VoI-Lambda). The Spike ORF consistently emerges as an AAS hotspot in all six lineages, but in Omicron this enrichment is significantly higher. The progenitors of each of these VoC/VoI lineages underwent positive selection in the Spike ORF. However, once they were established, their Spike ORFs have been undergoing purifying selection, despite the application of global vaccination schemes from 2021 onwards. Our analyses reject the hypothesis that the heavily mutated receptor binding domain (RBD) of the Omicron Spike was introduced via recombination from another closely related Sarbecovirus. Thus, successive point mutations appear as the most parsimonious scenario. Intriguingly, in each of the six lineages, we observed a significant number of AAS wherein the new residue is not present at any homologous site among the other known Sarbecoviruses. Such AAS should be further investigated as potential adaptations to the human host. By studying the phylogenetic distribution of AAS shared between the six lineages, we observed that the Omicron (BA.1) lineage had the highest number (8/10) of recurrent mutations.

Publication Date
2022-03-29
Online Publication Date
2022-03-29
Acceptance Date
2022-03-27
Keywords
COVID-19, Omicron, SARS-CoV-2, amino acid substitutions, dN/dS, evolution, recurrent mutations, spike, variants of concern, Amino Acid Substitution, COVID-19, Humans, Phylogeny, SARS-CoV-2, Spike Glycoprotein, Coronavirus
Journal Title
Viruses
Journal ISSN
1999-4915
1999-4915
Volume Title
14
Publisher
MDPI AG