Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant-Reference-Cited by-同舟云学术

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

Published:2023-05-11 Issue:1 Volume:14 Page:
ISSN:2041-1723
Container-title:Nature Communications
language:en
Short-container-title:Nat Commun

Author:

Ito Jumpei^ORCID,Suzuki Rigel,Uriu Keiya,Itakura Yukari^ORCID,Zahradnik Jiri^ORCID,Kimura Kanako Terakado,Deguchi Sayaka,Wang Lei^ORCID,Lytras Spyros^ORCID,Tamura Tomokazu,Kida Izumi^ORCID,Nasser Hesham^ORCID,Shofa Maya,Begum Mst Monira,Tsuda Masumi^ORCID,Oda Yoshitaka,Suzuki Tateki^ORCID,Sasaki Jiei,Sasaki-Tabata Kaori,Fujita Shigeru^ORCID,Yoshimatsu Kumiko^ORCID,Ito Hayato,Nao Naganori,Asakura Hiroyuki,Nagashima Mami,Sadamasu Kenji,Yoshimura Kazuhisa,Yamamoto Yuki,Nagamoto Tetsuharu,Kuramochi Jin^ORCID,Schreiber Gideon^ORCID,Suzuki Saori,Kato Marie,Ferdous Zannatul,Mouri Hiromi,Shishido Kenji,Misawa Naoko,Kimura Izumi,Kosugi Yusuke,Lin Pan,Suganami Mai,Chiba Mika,Yoshimura Ryo,Yasuda Kyoko,Iida Keiko,Ohsumi Naomi,Strange Adam P.,Sauter Daniel,Nakagawa So,Wu Jiaqi,Watanabe Yukio,Sakamoto Ayaka,Yasuhara Naoko,Nakajima Yukari,Yajima Hisano,Shirakawa Kotaro,Takaori-Kondo Akifumi,Nagata Kayoko,Kazuma Yasuhiro,Nomura Ryosuke,Horisawa Yoshihito,Tashiro Yusuke,Kawa Yugo,Irie Takashi,Kawabata Ryoko,Shimizu Ryo,Takahashi Otowa,Ichihara Kimiko,Motozono Chihiro,Toyoda Mako,Ueno Takamasa,Shibatani Yuki,Nishiuchi Tomoko,Saito Akatsuki^ORCID,Matsuno Keita^ORCID,Takayama Kazuo,Hashiguchi Takao^ORCID,Tanaka Shinya^ORCID,Fukuhara Takasuke^ORCID,Ikeda Terumasa^ORCID,Sato Kei^ORCID,

Abstract

AbstractIn 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.

Funder

Japan Agency for Medical Research and Development

Publisher

Springer Science and Business Media LLC

Subject

General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary

Link

https://www.nature.com/articles/s41467-023-38188-z.pdf

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