T cell epitopes in SARS-CoV-2 proteins are substantially conserved in the Omicron variant.
T cell epitopes in SARS-CoV-2 proteins are substantially conserved in the Omicron variant.
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DOI：
10.1038/s41423-022-00838-5
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发表时间：
2022-03
影响因子：
24.1
通讯作者：
Shin EC
中科院分区：
文献类型：
--
作者：
Choi SJ;Kim DU;Noh JY;Kim S;Park SH;Jeong HW;Shin EC
2021年11月，奥密克隆变种（B. 1.1. 529)出现并被世界卫生组织指定为关注变体（VOC）。最近，据报道，Omicron广泛逃避COVID-19疫苗接种或自然感染引起的中和抗体[1-3]。然而，Omicron是否逃避了COVID-19疫苗接种或自然感染引发的T细胞免疫仍有待阐明。为了解决这个问题，我们分析了从原始SARS-CoV-2毒株（武汉-胡-1）中鉴定的Omicron变体（hCoV-19/South Africa/CERI-KRISP-K 032284/2021）的T细胞表位的氨基酸序列。首先，我们检查了454个主要组织相容性复合体（MHC）I类限制性CD 8 + T细胞表位，这些表位先前通过活化诱导标记物（AIM）测定鉴定[4]。在Omicron变体中，来自刺突蛋白的88.4%（137/155）的表位和来自非刺突蛋白的98.3%（294/299）的表位是完全保守的（图1A），并且94.9%（431/454）的CD 8 + T细胞表位是完全保守的。我们对122个CD 8 + T细胞表位进行了类似的分析，这些表位先前通过使用肽-MHC I类复合物多聚体的系统分析鉴定[5]。在Omicron变异体中，来自刺突蛋白和非刺突蛋白的表位分别为88.9%（16/18）和98.1%（102/104），并且96.7%（118/122）的CD 8 + T细胞表位完全保守。我们通过对来自18项研究的852名COVID-19康复者的CD 8 + T细胞表位数据进行荟萃分析，确定了19个优势表位[6]，所有19个CD 8 + T细胞表位在Omicron变体中完全保守。我们还检查了280个MHC II类限制性CD 4 + T细胞表位，这些表位先前通过AIM测定法鉴定[4]。在Omicron变异体中，来自刺突蛋白和非刺突蛋白的表位分别有80.4%（74/92）和94.7%（178/188）是完全保守的，并且90.0%（252/280）的CD 4 + T细胞表位是完全保守的。这些结果表明大多数T细胞表位在Omicron变体中相当保守。
In November 2021, the Omicron variant (B. 1.1. 529) emerged and was designated a variant of concern (VOC) by the World Health Organization. Recently, Omicron was reported to extensively escape neutralizing antibodies elicited by COVID-19 vaccination or natural infection [1-3]. However, whether Omicron evades the T cell immunity elicited by COVID-19 vaccination or natural infection remains to be elucidated. To address this issue, we analyzed the amino acid sequences of T cell epitopes identified from the original SARS-CoV-2 strain (Wuhan-Hu-1) in the Omicron variant (hCoV-19/South Africa/CERI-KRISP-K032284/2021). First, we examined 454 major histocompatibility complex (MHC) class I-restricted CD8+ T cell epitopes that were previously identified by activation-induced marker (AIM) assays [4]. In the Omicron variant, 88.4%(137/155) of epitopes from the spike protein and 98.3%(294/299) of epitopes from nonspike proteins were fully conserved (Fig. 1 A), and 94.9%(431/454) of CD8+ T cell epitopes were completely conserved. We performed a similar analysis with 122 CD8+ T cell epitopes that were previously identified by a systematic analysis using peptide-MHC class I complex multimers [5]. In the Omicron variant, 88.9%(16/18) and 98.1%(102/104) of epitopes from the spike and nonspike proteins, respectively, were fully conserved, and 96.7%(118/122) of CD8+ T cell epitopes were completely conserved. We identified 19 dominant epitopes by a meta-analysis of CD8+ T cell epitope data from 18 studies with 852 COVID-19 convalescents [6], and all 19 CD8+ T cell epitopes were completely conserved in the Omicron variant. We also examined 280 MHC class II-restricted CD4+ T cell epitopes that were previously identified by AIM assays [4]. In the Omicron variant, 80.4%(74/92) and 94.7%(178/188) of epitopes from the spike and nonspike proteins, respectively, were fully conserved, and 90.0%(252/280) of CD4+ T cell epitopes were completely conserved. These results indicate that the majority of T cell epitopes are considerably conserved in the Omicron variant.
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影响因子：
24.8
作者：
Saini SK;Hersby DS;Tamhane T;Povlsen HR;Amaya Hernandez SP;Nielsen M;Gang AO;Hadrup SR
通讯作者：
Hadrup SR
DOI：
10.1038/s41577-021-00625-9
发表时间：
2021-11
期刊：
Nature reviews. Immunology
影响因子：
--
作者：
Noh JY;Jeong HW;Kim JH;Shin EC
通讯作者：
Shin EC
DOI：
10.1016/j.xcrm.2021.100312
发表时间：
2021-06-15
期刊：
Cell reports. Medicine
影响因子：
--
作者：
Quadeer AA;Ahmed SF;McKay MR
通讯作者：
McKay MR
影响因子：
64.8
作者：
Planas, Delphine;Veyer, David;Schwartz, Olivier
通讯作者：
Schwartz, Olivier
DOI：
10.1016/j.xcrm.2021.100204
发表时间：
2021-02-16
期刊：
Cell reports. Medicine
影响因子：
--
作者：
Tarke A;Sidney J;Kidd CK;Dan JM;Ramirez SI;Yu ED;Mateus J;da Silva Antunes R;Moore E;Rubiro P;Methot N;Phillips E;Mallal S;Frazier A;Rawlings SA;Greenbaum JA;Peters B;Smith DM;Crotty S;Weiskopf D;Grifoni A;Sette A
通讯作者：
Sette A