@article{Ito_J-2023_135337,
title = {Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant},
author = {Ito, J. and Suzuki, R. and Itakura, Y. and Zahradnik, J. and Kimura, K. and Deguchi, S. and Lytras, S. and Tamura, T. and Kida, I. and Nasser, H. and Shofa, M. and Begum, M. and Tsuda, M. and Oda, Y. and Suzuki, T. and Sasaki, J. and Sasaki-Tabata, K. and Fujita, S. and Yoshimatsu, K. and Ito, H. and Nao, N. and Asakura, H. and Nagashima, M. and Sadamasu, K. and Yoshimura, K. and Yamamoto, Y. and Nagamoto, T. and Kuramochi, J. and Schreiber, G. and Saito, A. and Matsuno, K. and Takayama, K. and Hashiguchi, T. and Tanaka, S. and Fukuhara, T. and Ikeda, T. and Uriu, K. and Wang, L. and Sato, K. and Genotype to Phenotype Japan (G2P-Japan) Consortium},
month = {may},
year = {2023},
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.},
volume = {14},
journal = {Nature Communications},
publisher = {Springer Nature},
url = {https://doi.org/10.1038/s41467-023-38188-z},
}
