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Li B, Deng A, Li K, Hu Y, Li Z, Shi Y, Xiong Q, Liu Z, Guo Q, Zou L, Zhang H, Zhang M, Ouyang F, Su J, Su W, Xu J, Lin H, Sun J, Peng J, Jiang H, Zhou P, Hu T, Luo M, Zhang Y, Zheng H, Xiao J, Liu T, Tan M, Che R, Zeng H, Zheng Z, Huang Y, Yu J, Yi L, Wu J, Chen J, Zhong H, Deng X, Kang M, Pybus OG, Hall M, Lythgoe KA, Li Y, Yuan J, He J, Lu J. Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant. Nat Commun 2022; 13:460. [PMID: 35075154 PMCID: PMC8786931 DOI: 10.1038/s41467-022-28089-y] [Citation(s) in RCA: 184] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/04/2022] [Indexed: 12/30/2022] Open
Abstract
The SARS-CoV-2 Delta variant has spread rapidly worldwide. To provide data on its virological profile, we here report the first local transmission of Delta in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of quarantined individuals indicated that the viral loads of Delta infections, when they first become PCR-positive, were on average ~1000 times greater compared to lineage A/B infections during the first epidemic wave in China in early 2020, suggesting potentially faster viral replication and greater infectiousness of Delta during early infection. The estimated transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in 29 donor-recipient transmission pairs. However, the transmission of minor iSNVs resulted in at least 3 of the 34 substitutions that were identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.
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Affiliation(s)
- Baisheng Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Aiping Deng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Kuibiao Li
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Yao Hu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhencui Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yaling Shi
- Guangzhou 8th People's Hospital, Guangzhou, Guangdong, China
| | - Qianling Xiong
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Zhe Liu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Qianfang Guo
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lirong Zou
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huan Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Meng Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Fangzhu Ouyang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Juan Su
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Wenzhe Su
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Jing Xu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huifang Lin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jing Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jinju Peng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Huiming Jiang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Pingping Zhou
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Ting Hu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Min Luo
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yingtao Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huanying Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jianpeng Xiao
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Tao Liu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Mingkai Tan
- Guangzhou 8th People's Hospital, Guangzhou, Guangdong, China
| | - Rongfei Che
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Hanri Zeng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhonghua Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yushi Huang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jianxiang Yu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lina Yi
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jie Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jingdiao Chen
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Haojie Zhong
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaoling Deng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Min Kang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Katrina A Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Yan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China. .,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
| | - Jun Yuan
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
| | - Jianfeng He
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China. .,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
| | - Jing Lu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China. .,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China. .,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China.
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