Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant

Ito, J. et al. (2023) Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant. Nature Communications, 14, 2671. (doi: 10.1038/s41467-023-38188-z) (PMID:37169744) (PMCID:PMC10175283)

Abstract

In late 2022, various Omicron subvariants emerged and cocirculated worldwide. These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. Here, we characterize the convergent evolution of Omicron subvariants and the properties of one recent lineage of concern, BQ.1.1. Our phylogenetic analysis suggests that these five substitutions are recurrently acquired, particularly in younger Omicron lineages. Epidemic dynamics modelling suggests that the five substitutions increase viral fitness, and a large proportion of the fitness variation within Omicron lineages can be explained by these substitutions. Compared to BA.5, BQ.1.1 evades breakthrough BA.2 and BA.5 infection sera more efficiently, as demonstrated by neutralization assays. The pathogenicity of BQ.1.1 in hamsters is lower than that of BA.5. Our multiscale investigations illuminate the evolutionary rules governing the convergent evolution for known Omicron lineages as of 2022.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Lytras, Spyros
• Authors: Ito, J., Suzuki, R., Uriu, K., Itakura, Y., Zahradnik, J., Kimura, K. T., Deguchi, S., Wang, L., Lytras, S., Tamura, T., Kida, I., Nasser, H., Shofa, M., Begum, M. M., Tsuda, M., Oda, Y., Suzuki, T., Sasaki, J., Sasaki-Tabata, K., Fujita, S., Yoshimatsu, K., Ito, H., Nao, N., Asakura, H., Nagashima, M., Sadamasu, K., Yoshimura, K., Yamamoto, Y., Nagamoto, T., Kuramochi, J., Schreiber, G., Saito, A., Matsuno, K., Takayama, K., Hashiguchi, T., Tanaka, S., Fukuhara, T., Ikeda, T., and Sato, K.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Nature Communications
• Publisher: Nature Research
• ISSN: 2041-1723
• ISSN (Online): 2041-1723
• Copyright Holders: Copyright © 2023 The Authors
• First Published: First published in Nature Communications 14: 2671
• Publisher Policy: Reproduced under a Creative Commons License