Dynamics of severe acute respiratory syndrome coronavirus 2 genome variants in the feces during convalescence

Yi Xu; Lu Kang; Zijie Shen; Xufang Li; Weili Wu; Wentai Ma; Chunxiao Fang; Fengxia Yang; Xuan Jiang; Sitang Gong; Li Zhang; Mingkun Li

doi:10.1016/j.jgg.2020.10.002

Volume 47 Issue 10

Oct. 2020

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Dynamics of severe acute respiratory syndrome coronavirus 2 genome variants in the feces during convalescence

doi: 10.1016/j.jgg.2020.10.002

Yi Xu^{a, 1},
Lu Kang^{b, c, 1},
Zijie Shen^{b, c, 1},
Xufang Li^{a, 1},
Weili Wu^b,
Wentai Ma^{b, c},
Chunxiao Fang^a,
Fengxia Yang^a,
Xuan Jiang^b,
Sitang Gong^{a, 1},
Li Zhang^{b, 1},
Mingkun Li^{b, c, d, 1}

a
Department of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
b
Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 101300, China
c
University of Chinese Academy of Sciences, Beijing, 100049, China
d
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China

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Corresponding author: E-mail address: sitangg@126.com (Sitang Gong); E-mail address: zhangl@big.ac.cn (Li Zhang); E-mail address: limk@big.ac.cn (Mingkun Li)
Publish Date: 2020-10-25

Abstract

Abstract

In response to the current coronavirus disease 2019 (COVID-19) pandemic, it is crucial to understand the origin, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which relies on close surveillance of genomic diversity in clinical samples. Although the mutation at the population level had been extensively investigated, how the mutations evolve at the individual level is largely unknown. Eighteen time-series fecal samples were collected from nine patients with COVID-19 during the convalescent phase. The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method. First, we demonstrated the outstanding performance of the hybrid capture method in detecting intra-host variants. We identified 229 intra-host variants at 182 sites in 18 fecal samples. Among them, nineteen variants presented frequency changes > 0.3 within 1–5 days, reflecting highly dynamic intra-host viral populations. Moreover, the evolution of the viral genome demonstrated that the virus was probably viable in the gastrointestinal tract during the convalescent period. Meanwhile, we also found that the same mutation showed a distinct pattern of frequency changes in different individuals, indicating a strong random drift. In summary, dramatic changes of the SARS-CoV-2 genome were detected in fecal samples during the convalescent period; whether the viral load in feces is sufficient to establish an infection warranted further investigation.
- SARS-CoV-2,
- Intra-host variant,
- Dynamics,
- Mutation,
- Hybrid capture

Author S.G., L.Z., and M.L. contributed equally to this manuscript.

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References(31)

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