Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients

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Abstract

Background

A novel coronavirus (SARS-CoV-2) has infected more than 75,000 individuals and spread to over 20 countries. It is still unclear how fast the virus evolved and how the virus interacts with other microorganisms in the lung.

Methods

We have conducted metatranscriptome sequencing for the bronchoalveolar lavage fluid of eight SARS-CoV-2 patients, 25 community-acquired pneumonia (CAP) patients, and 20 healthy controls.

Results

The median number of intra-host variants was 1-4 in SARS-CoV-2 infected patients, which ranged between 0 and 51 in different samples. The distribution of variants on genes was similar to those observed in the population data (110 sequences). However, very few intra-host variants were observed in the population as polymorphism, implying either a bottleneck or purifying selection involved in the transmission of the virus, or a consequence of the limited diversity represented in the current polymorphism data. Although current evidence did not support the transmission of intra-host variants in a person-to-person spread, the risk should not be overlooked. The microbiota in SARS-CoV-2 infected patients was similar to those in CAP, either dominated by the pathogens or with elevated levels of oral and upper respiratory commensal bacteria.

Conclusion

SARS-CoV-2 evolves in vivo after infection, which may affect its virulence, infectivity, and transmissibility. Although how the intra-host variant spreads in the population is still elusive, it is necessary to strengthen the surveillance of the viral evolution in the population and associated clinical changes.

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Author and article information

Journal

Journal ID (nlm-ta): Clin Infect Dis

Journal ID (iso-abbrev): Clin. Infect. Dis

Journal ID (publisher-id): cid

Title: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America

Publisher: Oxford University Press (US )

ISSN (Print): 1058-4838

ISSN (Electronic): 1537-6591

Publication date (Electronic): 09 March 2020

Electronic Location Identifier: ciaa203

Affiliations

[1 ] Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation , Beijing, China

[2 ] University of Chinese Academy of Sciences , Beijing, China

[3 ] National Health Commission of the People’s Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing, China

[4 ] Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University , Beijing, China

[5 ] Department of Respiratory and Critical Care Medicine, Peking University People's Hospital , Beijing, China

[6 ] National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory for Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology , Shenzhen, China

[7 ] Fujian Provincial Hospital , Fujian, PR China

[8 ] Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi'an Jiaotong University , Shaanxi Province, P.R. China

[9 ] Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming, China

Author notes

Corresponding author: Mingkun Li E-mail: limk@ 123456big.ac.cn Beijing Institute of Genomics, Chinese Academy of Sciences No. 1-104, Beichen West Road, Chaoyang District, Beijing, 100101, China Tel/Fax: 86-10-84097716

Alternate corresponding author: Lili Ren E-mail: renliliipb@ 123456163.com Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College Building 7, Di Sheng Bei Jie Street 1, Yizhuang District, Beijing 100730, China; Tel/Fax: 86-10-67837321

Author Z.S., Y.X., L.K., and W.M. contributed equally to this manuscript

Author L.R. and M.L. contributed equally to this manuscript

Article

Publisher ID: ciaa203

DOI: 10.1093/cid/ciaa203

PMC ID: 7108196

PubMed ID: 32129843

SO-VID: 6d2e6c02-a5d0-4c73-a1d8-16275b3b8cfe

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