TY - JOUR
T1 - Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant
AU - The Genotype to Phenotype Japan (G2P-Japan) Consortium
AU - Ito, Jumpei
AU - Suzuki, Rigel
AU - Uriu, Keiya
AU - Itakura, Yukari
AU - Zahradnik, Jiri
AU - Kimura, Kanako Terakado
AU - Deguchi, Sayaka
AU - Wang, Lei
AU - Lytras, Spyros
AU - Tamura, Tomokazu
AU - Kida, Izumi
AU - Nasser, Hesham
AU - Shofa, Maya
AU - Begum, Mst Monira
AU - Tsuda, Masumi
AU - Oda, Yoshitaka
AU - Suzuki, Tateki
AU - Sasaki, Jiei
AU - Sasaki-Tabata, Kaori
AU - Fujita, Shigeru
AU - Yoshimatsu, Kumiko
AU - Ito, Hayato
AU - Nao, Naganori
AU - Asakura, Hiroyuki
AU - Nagashima, Mami
AU - Sadamasu, Kenji
AU - Yoshimura, Kazuhisa
AU - Yamamoto, Yuki
AU - Nagamoto, Tetsuharu
AU - Kuramochi, Jin
AU - Schreiber, Gideon
AU - Suzuki, Saori
AU - Kato, Marie
AU - Ferdous, Zannatul
AU - Mouri, Hiromi
AU - Shishido, Kenji
AU - Misawa, Naoko
AU - Kimura, Izumi
AU - Kosugi, Yusuke
AU - Lin, Pan
AU - Suganami, Mai
AU - Chiba, Mika
AU - Yoshimura, Ryo
AU - Yasuda, Kyoko
AU - Iida, Keiko
AU - Ohsumi, Naomi
AU - Strange, Adam P.
AU - Motozono, Chihiro
AU - Hashiguchi, Takao
AU - Fukuhara, Takasuke
N1 - Publisher Copyright:
© 2023, The Author(s).
PY - 2023/12
Y1 - 2023/12
N2 - 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.
AB - 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.
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U2 - 10.1038/s41467-023-38188-z
DO - 10.1038/s41467-023-38188-z
M3 - Article
C2 - 37169744
AN - SCOPUS:85159215163
SN - 2041-1723
VL - 14
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 2671
ER -