PMID- 36505092
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20221221
IS  - 2057-1577 (Print)
IS  - 2057-1577 (Electronic)
IS  - 2057-1577 (Linking)
VI  - 8
IP  - 2
DP  - 2022
TI  - SARS-CoV-2 intra-host single-nucleotide variants associated with disease 
      severity.
PG  - veac106
LID - 10.1093/ve/veac106 [doi]
LID - veac106
AB  - Variants of severe acute respiratory syndrome coronavirus 2 frequently arise 
      within infected individuals. Here, we explored the level and pattern of 
      intra-host viral diversity in association with disease severity. Then, we 
      analyzed information underlying these nucleotide changes to infer the impetus 
      including mutational signatures and immune selection from neutralizing antibody 
      or T-cell recognition. From 23 January to 31 March 2020, a set of cross-sectional 
      samples were collected from individuals with homogeneous founder virus regardless 
      of disease severity. Intra-host single-nucleotide variants (iSNVs) were 
      enumerated using deep sequencing. Human leukocyte antigen (HLA) alleles were 
      genotyped by Sanger sequencing. Medical records were collected and reviewed by 
      attending physicians. A total of 836 iSNVs (3-106 per sample) were identified and 
      distributed in a highly individualized pattern. The number of iSNVs paced with 
      infection duration peaked within days and declined thereafter. These iSNVs did 
      not stochastically arise due to a strong bias toward C > U/G > A and U > C/A > G 
      substitutions in reciprocal proportion with escalating disease severity. Eight 
      nonsynonymous iSNVs in the receptor-binding domain could escape from 
      neutralization, and eighteen iSNVs were significantly associated with specific 
      HLA alleles. The level and pattern of iSNVs reflect the in vivo viral-host 
      interaction and the disease pathogenesis.
CI  - (c) The Author(s) 2022. Published by Oxford University Press.
FAU - Zhang, Yi
AU  - Zhang Y
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Jiang, Ning
AU  - Jiang N
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
AD  - State Key Laboratory of Genetic Engineering and Institute of Biostatistics, 
      School of Life Sciences, Fudan University, Shanghai, China.
FAU - Qi, Weiqiang
AU  - Qi W
AD  - Shanghai Public Health Clinical Center, Shanghai 200051, China.
FAU - Li, Tao
AU  - Li T
AD  - Shanghai Public Health Clinical Center, Shanghai 200051, China.
FAU - Zhang, Yumeng
AU  - Zhang Y
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Wu, Jing
AU  - Wu J
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Zhang, Haocheng
AU  - Zhang H
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Zhou, Mingzhe
AU  - Zhou M
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Cui, Peng
AU  - Cui P
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Yu, Tong
AU  - Yu T
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Fu, Zhangfan
AU  - Fu Z
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Zhou, Yang
AU  - Zhou Y
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Lin, Ke
AU  - Lin K
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Wang, Hongyu
AU  - Wang H
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Wei, Tongqing
AU  - Wei T
AD  - State Key Laboratory of Genetic Engineering and Institute of Biostatistics, 
      School of Life Sciences, Fudan University, Shanghai, China.
FAU - Zhu, Zhaoqin
AU  - Zhu Z
AD  - Shanghai Public Health Clinical Center, Shanghai 200051, China.
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Ai, Jingwen
AU  - Ai J
AUID- ORCID: 0000-0002-5152-1557
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Qiu, Chao
AU  - Qiu C
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
FAU - Zhang, Wenhong
AU  - Zhang W
AUID- ORCID: 0000-0002-9165-3212
AD  - Department of Infectious Diseases, National Clinical Research Center for Aging 
      and Medicine, Shanghai Key Laboratory of Infectious Diseases and Biosafety 
      Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China.
AD  - State Key Laboratory of Genetic Engineering and Institute of Biostatistics, 
      School of Life Sciences, Fudan University, Shanghai, China.
LA  - eng
PT  - Journal Article
DEP - 20221129
PL  - England
TA  - Virus Evol
JT  - Virus evolution
JID - 101664675
PMC - PMC9728387
OTO - NOTNLM
OT  - COVID-19
OT  - HLA
OT  - SARS-CoV-2 variants
OT  - immune response
OT  - intra-host
OT  - neutralization antibody
EDAT- 2022/12/13 06:00
MHDA- 2022/12/13 06:01
PMCR- 2022/11/29
CRDT- 2022/12/12 10:54
PHST- 2022/04/19 00:00 [received]
PHST- 2022/10/24 00:00 [revised]
PHST- 2022/11/26 00:00 [accepted]
PHST- 2022/12/12 10:54 [entrez]
PHST- 2022/12/13 06:00 [pubmed]
PHST- 2022/12/13 06:01 [medline]
PHST- 2022/11/29 00:00 [pmc-release]
AID - veac106 [pii]
AID - 10.1093/ve/veac106 [doi]
PST - epublish
SO  - Virus Evol. 2022 Nov 29;8(2):veac106. doi: 10.1093/ve/veac106. eCollection 2022.