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Emerging Microbes & Infections Volume 11, 2022 - Issue 1
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Coronaviruses

Possible recombination between two variants of concern in a COVID-19 patient

Yaqing Hea Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Wentai Mac Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, People’s Republic of China;d University of Chinese Academy of Sciences, Beijing, People’s Republic of ChinaView further author information
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Shengyuan Dange 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, People’s Republic of ChinaView further author information
,
Long Chena Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Renli Zhanga Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Shujiang Meia Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaORCID Iconhttps://orcid.org/0000-0001-5976-9058View further author information
ORCID Icon,
Xinyi Weia Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Qiuying Lva Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Bo Penga Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Jiancheng Chena Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Dongfeng Konga Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Ying Suna Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Xiujuan Tanga Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Weihua Wua Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Zhigao Chena Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Shimin Lia Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Jia Wana Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Xuan Zoua Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaView further author information
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Mingkun Lic Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, People’s Republic of China;d University of Chinese Academy of Sciences, Beijing, People’s Republic of China;f Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, People’s Republic of ChinaCorrespondence[email protected]
View further author information
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Tiejian Fenga Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People’s Republic of China;b Center for Disease Control and Prevention, Shenzhen, People’s Republic of ChinaCorrespondence[email protected]
View further author information
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Lili Rene 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, People’s Republic of China;g Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of ChinaCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0002-6645-8183View further author information
ORCID Icon &
Jianwei Wange 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, People’s Republic of China;g Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of ChinaCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0002-1116-4559View further author information
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Pages 552-555 | Received 17 Dec 2021, Accepted 19 Jan 2022, Published online: 10 Feb 2022

Figures & data

Figure 1. Signals of recombination in Case 49H. (A) The frequency of the Beta and Delta-I alleles in Case 49H. Only sites differing between the Delta-I genome and the Beta genome are shown. The frequency distribution are shown for different time-ponts (T1, T2 and T3). The missing sites on T3 were caused by limited sequencing depth in these regions. (B) The summary of haplotypes identified through TA clonal sequencing. Alleles that were identical to the Delta-I and Beta strain were labelled in different colours. Gray stands for non-informative sites (same allele possessed by two strains). The number of clones detected for each haplotype is labelled at the end of the sequences and the inferred recombination breakpoints are marked with red triangles.

Figure 1. Signals of recombination in Case 49H. (A) The frequency of the Beta and Delta-I alleles in Case 49H. Only sites differing between the Delta-I genome and the Beta genome are shown. The frequency distribution are shown for different time-ponts (T1, T2 and T3). The missing sites on T3 were caused by limited sequencing depth in these regions. (B) The summary of haplotypes identified through TA clonal sequencing. Alleles that were identical to the Delta-I and Beta strain were labelled in different colours. Gray stands for non-informative sites (same allele possessed by two strains). The number of clones detected for each haplotype is labelled at the end of the sequences and the inferred recombination breakpoints are marked with red triangles.
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Possible recombination between two variants of concern in a COVID-19 patient
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