Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.
Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.
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DOI：
10.1038/s41467-023-38188-z
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发表时间：
2023-05-11
影响因子：
16.6
通讯作者：
Nishiuchi, Tomoko
中科院分区：
文献类型：
--
作者：
Ito, Jumpei;Suzuki, Rigel;Uriu, Keiya;Itakura, Yukari;Zahradnik, Jiri;Kimura, Kanako Terakado;Deguchi, Sayaka;Wang, Lei;Lytras, Spyros;Tamura, Tomokazu;Kida, Izumi;Nasser, Hesham;Shofa, Maya;Begum, Mst Monira;Tsuda, Masumi;Oda, Yoshitaka;Suzuki, Tateki;Sasaki, Jiei;Sasaki-Tabata, Kaori;Fujita, Shigeru;Yoshimatsu, Kumiko;Ito, Hayato;Nao, Naganori;Asakura, Hiroyuki;Nagashima, Mami;Sadamasu, Kenji;Yoshimura, Kazuhisa;Yamamoto, Yuki;Nagamoto, Tetsuharu;Kuramochi, Jin;Schreiber, Gideon;Saito, Akatsuki;Matsuno, Keita;Takayama, Kazuo;Hashiguchi, Takao;Tanaka, Shinya;Fukuhara, Takasuke;Ikeda, Terumasa;Sato, Kei;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 P.;Strange, Adam;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
在2022年末，各种Omicron亚变体出现并在全球范围内共同传播。这些变体在刺突蛋白中的关键残基（包括残基R346、K444、L452、N460和F486）处会聚地获得氨基酸取代。在这里，我们的特点是收敛演化的Omicron子变量和属性的一个最近的血统的关注，BQ.1.1。我们的系统发育分析表明，这五个取代是经常收购，特别是在年轻的Omicron血统。流行动力学模型表明，这五个取代增加病毒的健身，并在Omicron谱系内的健身变化的很大一部分可以解释这些取代。与BA.5相比，BQ.1.1更有效地逃避BA.2和BA.5感染血清的突破，如中和试验所示。BQ.1.1对仓鼠的致病性低于BA.5。我们的多尺度调查阐明了截至2022年已知Omicron谱系的趋同进化的进化规则。最近Omicron SARS-CoV-2亚变体独立获得5个关键刺突突变。在这里，作者评估了5个突变的进化重要性，并描述了携带所有5个突变的变体BQ.1.1的病毒学特性。
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. Recent Omicron SARS-CoV-2 subvariants independently acquire 5 key Spike mutations. Here, the authors evaluate the evolutionary importance of the 5 mutations and characterize the virological properties of variant BQ.1.1 harboring all 5 mutations.
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DOI：
10.1093/infdis/jiab368
发表时间：
2021-09-17
期刊：
The Journal of infectious diseases
影响因子：
--
作者：
Ferreira IATM;Kemp SA;Datir R;Saito A;Meng B;Rakshit P;Takaori-Kondo A;Kosugi Y;Uriu K;Kimura I;Shirakawa K;Abdullahi A;Agarwal A;Ozono S;Tokunaga K;Sato K;Gupta RK;CITIID-NIHR BioResource COVID-19 Collaboration, Indian SARS-CoV-2 Genomics Consortium;Genotype to Phenotype Japan (G2P-Japan) Consortium
通讯作者：
Genotype to Phenotype Japan (G2P-Japan) Consortium
影响因子：
7.3
作者：
Deshpande A;Harris BD;Martinez-Sobrido L;Kobie JJ;Walter MR
通讯作者：
Walter MR
DOI：
10.1107/s0907444904019158
发表时间：
2004-12-01
影响因子：
2.2
作者：
Emsley, P;Cowtan, K
通讯作者：
Cowtan, K
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
64.8
作者：
Cao, Yunlong;Yisimayi, Ayijiang;Jian, Fanchong;Song, Weiliang;Xiao, Tianhe;Wang, Lei;Du, Shuo;Wang, Jing;Li, Qianqian;Chen, Xiaosu;Yu, Yuanling;Wang, Peng;Zhang, Zhiying;Liu, Pulan;An, Ran;Hao, Xiaohua;Wang, Yao;Feng, Rui;Sun, Haiyan;Zhao, Lijuan;Zhang, Wen;Zhao, Dong;Zheng, Jiang;Yu, Lingling;Li, Can;Zhang, Na;Wang, Rui;Niu, Xiao;Yang, Sijie;Song, Xuetao;Chai, Yangyang;Hu, Ye;Shi, Yansong;Zheng, Linlin;Li, Zhiqiang;Gu, Qingqing;Shao, Fei;Huang, Weijin;Jin, Ronghua;Shen, Zhongyang;Wang, Youchun;Wang, Xiangxi;Xiao, Junyu;Xie, Xiaoliang Sunney
通讯作者：
Xie, Xiaoliang Sunney