Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses.
Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses.
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DOI：
10.1016/j.jaut.2021.102715
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发表时间：
2021-11
影响因子：
12.8
通讯作者：
Singh K
中科院分区：
文献类型：
--
作者：
Kannan SR;Spratt AN;Cohen AR;Naqvi SH;Chand HS;Quinn TP;Lorson CL;Byrareddy SN;Singh K
严重急性呼吸道综合征冠状病毒2型（SARS-CoV-2）以新变体的形式迅速演变。至少有11种已知的变种被报道。本研究的目的是描述Delta和Delta Plus变异体突变谱的差异。Delta（B.1.617.2）和Delta Plus（AY.1或B.1.617.2.1）变体的高质量序列（n = 1756）用于确定整个SARS-CoV-2基因组中突变（≥ 20%）的流行率、它们的共存以及一段时间内流行率的变化。进行结构分析以深入了解突变对抗体结合的影响。使用系统发育分析结合序列采集日期生成Sankey图，以推断Delta Plus变体的迁移及其在美国的存在。Delta Plus变体的高流行率突变（≥ 20%）数量显著高于Delta变体。Spike中的签名突变（G142 D、A222 V和T95 I）在Delta Plus变体中比Delta变体中以更显著的百分比存在。Spike中的三个突变（K417 N、V70 F和W258 L）仅存在于Delta Plus变体中。在ORF 1a（A1146 T）中发现了一种新的突变，该突变仅存在于Delta Plus变体中，患病率约为58%。此外，5个关键突变（T95 I、A222 V、G142 D、R158 G和K417 N）在Delta Plus中的发生率显著高于Delta变体。结构分析表明，突变改变了侧链构象，削弱了与抗体的相互作用。Delta Plus首先出现在印度，通过英国和日本到达美国，随后传播到20多个美国。根据本文提供的结果，很明显Delta和Delta Plus变体具有独特的突变谱，Delta Plus变体不仅仅是将K417 N简单添加到Delta变体中。高度相关的突变可能已经出现，以保持病毒的结构完整性。
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been rapidly evolving in the form of new variants. At least eleven known variants have been reported. The objective of this study was to delineate the differences in the mutational profile of Delta and Delta Plus variants. High-quality sequences (n = 1756) of Delta (B.1.617.2) and Delta Plus (AY.1 or B.1.617.2.1) variants were used to determine the prevalence of mutations (≥20 %) in the entire SARS-CoV-2 genome, their co-existence, and change in prevalence over a period of time. Structural analysis was conducted to get insights into the impact of mutations on antibody binding. A Sankey diagram was generated using phylogenetic analysis coupled with sequence-acquisition dates to infer the migration of the Delta Plus variant and its presence in the United States. The Delta Plus variant had a significant number of high-prevalence mutations (≥20 %) than in the Delta variant. Signature mutations in Spike (G142D, A222V, and T95I) existed at a more significant percentage in the Delta Plus variant than the Delta variant. Three mutations in Spike (K417N, V70F, and W258L) were exclusively present in the Delta Plus variant. A new mutation was identified in ORF1a (A1146T), which was only present in the Delta Plus variant with ~58 % prevalence. Furthermore, five key mutations (T95I, A222V, G142D, R158G, and K417N) were significantly more prevalent in the Delta Plus than in the Delta variant. Structural analyses revealed that mutations alter the sidechain conformation to weaken the interactions with antibodies. Delta Plus, which first emerged in India, reached the United States through England and Japan, followed by its spread to more than 20 the United States. Based on the results presented here, it is clear that the Delta and Delta Plus variants have unique mutation profiles, and the Delta Plus variant is not just a simple addition of K417N to the Delta variant. Highly correlated mutations may have emerged to keep the structural integrity of the virus.
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影响因子：
64.8
作者：
Plante JA;Liu Y;Liu J;Xia H;Johnson BA;Lokugamage KG;Zhang X;Muruato AE;Zou J;Fontes-Garfias CR;Mirchandani D;Scharton D;Bilello JP;Ku Z;An Z;Kalveram B;Freiberg AN;Menachery VD;Xie X;Plante KS;Weaver SC;Shi PY
通讯作者：
Shi PY
影响因子：
64.5
作者：
Liu C;Ginn HM;Dejnirattisai W;Supasa P;Wang B;Tuekprakhon A;Nutalai R;Zhou D;Mentzer AJ;Zhao Y;Duyvesteyn HME;López-Camacho C;Slon-Campos J;Walter TS;Skelly D;Johnson SA;Ritter TG;Mason C;Costa Clemens SA;Gomes Naveca F;Nascimento V;Nascimento F;Fernandes da Costa C;Resende PC;Pauvolid-Correa A;Siqueira MM;Dold C;Temperton N;Dong T;Pollard AJ;Knight JC;Crook D;Lambe T;Clutterbuck E;Bibi S;Flaxman A;Bittaye M;Belij-Rammerstorfer S;Gilbert SC;Malik T;Carroll MW;Klenerman P;Barnes E;Dunachie SJ;Baillie V;Serafin N;Ditse Z;Da Silva K;Paterson NG;Williams MA;Hall DR;Madhi S;Nunes MC;Goulder P;Fry EE;Mongkolsapaya J;Ren J;Stuart DI;Screaton GR
通讯作者：
Screaton GR
影响因子：
64.5
作者：
Korber, Bette;Fischer, Will M.;Montefiori, David C.
通讯作者：
Montefiori, David C.
DOI：
10.2807/1560-7917.es.2021.26.24.2100509
发表时间：
2021-06
期刊：
Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
影响因子：
--
作者：
Campbell F;Archer B;Laurenson-Schafer H;Jinnai Y;Konings F;Batra N;Pavlin B;Vandemaele K;Van Kerkhove MD;Jombart T;Morgan O;le Polain de Waroux O
通讯作者：
le Polain de Waroux O
影响因子：
5.8
作者：
Hadfield, James;Megill, Colin;Neher, Richard A.
通讯作者：
Neher, Richard A.