Evidence map›Paper›PMID 33618765›Full record

ArticleGenome medicine2021

Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients.

Yanqun Wang, Daxi Wang, Lu Zhang, Wanying Sun, Zhaoyong Zhang, Weijun Chen, Airu Zhu, Yongbo Huang, Fei Xiao, Jinxiu Yao and 24 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.

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101citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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3 · Its place in the literature

Who cites it

101 citing papers in PubMed.

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  11. SARS-CoV-2 mutant spectrum complexity is an epidemiologically evolvable trait.Proceedings of the National Academy of Sciences of the United States of America · 2025
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41 more citing papers are in PubMed but not listed here.

4 · The record

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5 · Who and what money

Authors and funding

34 authors.

Yanqun Wang *State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Daxi Wang *BGI-Shenzhen, Shenzhen, 518083, China.
Lu Zhang *Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, 510060, Guangdong, China.
Wanying Sun *BGI-Shenzhen, Shenzhen, 518083, China.
Zhaoyong Zhang *State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Weijun Chen *BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.
Airu Zhu *State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Yongbo Huang *State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Fei XiaoDepartment of Infectious Diseases, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong, China.
Jinxiu YaoYangjiang People's Hospital, Yangjiang, Guangdong, China.
Mian GanState Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Fang LiState Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Ling LuoState Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Xiaofang HuangState Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Yanjun ZhangState Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Sook-San WongState Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Xinyi ChengBGI-Shenzhen, Shenzhen, 518083, China.
Jingkai JiBGI-Shenzhen, Shenzhen, 518083, China.
Zhihua OuBGI-Shenzhen, Shenzhen, 518083, China.
Minfeng XiaoBGI-Shenzhen, Shenzhen, 518083, China.
Min LiBGI-Shenzhen, Shenzhen, 518083, China.
Jiandong LiBGI-Shenzhen, Shenzhen, 518083, China.
Peidi RenBGI-Shenzhen, Shenzhen, 518083, China.
Ziqing DengBGI-Shenzhen, Shenzhen, 518083, China.
Huanzi ZhongBGI-Shenzhen, Shenzhen, 518083, China.
Xun XuBGI-Shenzhen, Shenzhen, 518083, China.
Tie SongGuangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, Guangdong, China.
Chris Ka Pun MokState Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Malik PeirisState Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Nanshan ZhongState Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
Jingxian ZhaoState Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China. zhaojingxian@gird.cn.
Yimin LiState Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China. dryiminli@vip.163.com.
Junhua LiBGI-Shenzhen, Shenzhen, 518083, China. lijunhua@genomics.cn.
Jincun ZhaoState Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China. zhaojincun@gird.cn.

Funding

Guangdong Provincial Key Laboratory of Genome Read and Write 2017B030301011Guangdong Science and Technology Foundation 2019B030316028Guangzhou Medical University High-level University Innovation Team Training Program [2017] No.159National Natural Science Foundation of China 81702047, 81772191, 91842106 and 8181101118State Key Laboratory of Respiratory Disease SKLRD-QN-201715, SKLRD-QN-201912 and SKLRD-Z-202007the emergency grants for prevention and control of SARS-CoV-2 of Guangdong province 2020B1111320003, 2020B111108001, 2018B020207013, 2020B111112003the emergency grants for prevention and control of SARS-CoV-2 of Ministry of Science and Technology 2020YFC0841400the Guangdong Province Basic and Applied Basic Research Fund 2020A1515010911The National Key Research and Development Program of China 2018YFC1200100, 2018ZX10301403, 2018YFC1311900
6 · The paper itself

Abstract

backgroundSince early February 2021, the causative agent of COVID-19, SARS-CoV-2, has infected over 104 million people with more than 2 million deaths according to official reports. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown.

methodsUsing high-throughput sequencing of metatranscriptomic and hybrid captured libraries, we characterized consensus genomes and intra-host single nucleotide variations (iSNVs) of serial samples collected from eight patients with COVID-19. The distribution of iSNVs along the SARS-CoV-2 genome was analyzed and co-occurring iSNVs among COVID-19 patients were identified. We also compared the evolutionary dynamics of SARS-CoV-2 population in the respiratory tract (RT) and gastrointestinal tract (GIT).

resultsThe 32 consensus genomes revealed the co-existence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in a single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparing allele frequencies of the iSNVs revealed a clear genetic differentiation between intra-host populations from the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events during intra-host migrations. Compared to RT populations, the GIT populations showed a better maintenance and rapid development of viral genetic diversity following the suspected intra-host bottlenecks.

conclusionsOur findings here illustrate the intra-host bottlenecks and evolutionary dynamics of SARS-CoV-2 in different anatomic sites and may provide new insights to understand the virus-host interactions of coronaviruses and other RNA viruses.

Indexed as

Polymorphism, Single NucleotideCOVID-19Gene FrequencyGenome, ViralGenotypeHaplotypesHigh-Throughput Nucleotide SequencingHost-Pathogen InteractionsHumansPhylogenySARS-CoV-2COVID-19DynamicsIntra-hostSARS-CoV-2Variation

Identifiers

PMID33618765
PMCPMC7898256

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.