Biosafety and Health (Feb 2023)
Temporal dynamics of SARS-CoV-2 genome mutations that occurred in vivo on an aircraft
- Yaqing He,
- Shengyuan Dang,
- Wentai Ma,
- Long Chen,
- Renli Zhang,
- Shujiang Mei,
- Xinyi Wei,
- Qiuying Lv,
- Bo Peng,
- Ying Sun,
- Dongfeng Kong,
- Jiancheng Chen,
- Shimin Li,
- Xiujuan Tang,
- Qingju Lu,
- Can Zhu,
- Zhigao Chen,
- Jia Wan,
- Xuan Zou,
- Mingkun Li,
- Tiejiang Feng,
- Lili Ren,
- Jianwei Wang
Affiliations
- Yaqing He
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Shengyuan Dang
- 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 100730, China
- Wentai Ma
- University of Chinese Academy of Sciences, Beijing 100190, China; Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- Long Chen
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Renli Zhang
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Shujiang Mei
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Xinyi Wei
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Qiuying Lv
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Bo Peng
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Ying Sun
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Dongfeng Kong
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Jiancheng Chen
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Shimin Li
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Xiujuan Tang
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Qingju Lu
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Can Zhu
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Zhigao Chen
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Jia Wan
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Xuan Zou
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China
- Mingkun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Corresponding authors: No.9 Dong Dan San Tiao, Dongcheng District, Beijing 100730, China (L. Ren); Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China (M. Li). Center for Disease Control and Prevention, Shenzhen 518055, China (T. Feng).
- Tiejiang Feng
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China; Center for Disease Control and Prevention, Shenzhen 518055, China; Corresponding authors: No.9 Dong Dan San Tiao, Dongcheng District, Beijing 100730, China (L. Ren); Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China (M. Li). Center for Disease Control and Prevention, Shenzhen 518055, China (T. Feng).
- Lili Ren
- 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 100730, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; Corresponding authors: No.9 Dong Dan San Tiao, Dongcheng District, Beijing 100730, China (L. Ren); Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China (M. Li). Center for Disease Control and Prevention, Shenzhen 518055, China (T. Feng).
- Jianwei Wang
- 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 100730, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Journal volume & issue
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Vol. 5,
no. 1
pp. 62 – 67
Abstract
We analyzed variations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome during a flight-related cluster outbreak of coronavirus disease 2019 (COVID-19) in Shenzhen, China, to explore the characteristics of SARS-CoV-2 transmission and intra-host single nucleotide variations (iSNVs) in a confined space. Thirty-three patients with COVID-19 were sampled, and 14 were resampled 3–31 days later. All 47 nasopharyngeal swabs were deep-sequenced. iSNVs and similarities in the consensus genome sequence were analyzed. Three SARS-CoV-2 variants of concern, Delta (n = 31), Beta (n = 1), and C.1.2 (n = 1), were detected among the 33 patients. The viral genome sequences from 30 Delta-positive patients had similar SNVs; 14 of these patients provided two successive samples. Overall, the 47 sequenced genomes contained 164 iSNVs. Of the 14 paired (successive) samples, the second samples (T2) contained more iSNVs (median: 3; 95% confidence interval [95% CI]: 2.77–10.22) than did the first samples (T1; median: 2; 95% CI: 1.63–3.74; Wilcoxon test, P = 0.021). 38 iSNVs were detected in T1 samples, and only seven were also detectable in T2 samples. Notably, T2 samples from two of the 14 paired samples had additional mutations than the T1 samples. The iSNVs of the SARS-CoV-2 genome exhibited rapid dynamic changes during a flight-related cluster outbreak event. Intra-host diversity increased gradually with time, and new site mutations occurred in vivo without a population transmission bottleneck. Therefore, we could not determine the generational relationship from the mutation site changes alone.
