Omicron variant receptor-binding domain phylogenetics and molecular dynamics.

ABSTRACT:

Background

We investigated the evolutionary relationships, mutations, antigenic epitopes, and structural dynamics of the receptor-binding domain (RBD) of SARS-CoV-2, Omicron and other recently evolved variants.

Methods

The RBD of SARS-CoV-2 and its Omicron, Alpha, Beta, Gamma, Delta, and Mu variants were subjected to pairwise sequence matrix evaluation, antigenic epitope prediction, and phylogenetic relationship and structural dynamics analyses.

Results

The Omicron RBD contained 13-15 amino acid mutations, of which 12 were new and three conserved with other variants. In addition, two mutations found in the Alpha, Beta, Gamma, and Mu variants were not found in the Omicron RBD. The ultrametric clustering unweighted pair group method with arithmetic mean identified Omicr

SUBMITTER: Kandeel M 

PROVIDER: S-EPMC9110309 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature