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Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant

Author

Listed:
  • Baisheng Li

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Aiping Deng

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Kuibiao Li

    (Guangzhou Center for Disease Control and Prevention)

  • Yao Hu

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Zhencui Li

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Yaling Shi

    (Guangzhou 8th People’s Hospital)

  • Qianling Xiong

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences
    Guangdong Provincial Institution of Public Health)

  • Zhe Liu

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences
    Guangdong Provincial Institution of Public Health)

  • Qianfang Guo

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Lirong Zou

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Huan Zhang

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Meng Zhang

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Fangzhu Ouyang

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Juan Su

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Wenzhe Su

    (Guangzhou Center for Disease Control and Prevention)

  • Jing Xu

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Huifang Lin

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences
    Guangdong Provincial Institution of Public Health)

  • Jing Sun

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences
    Guangdong Provincial Institution of Public Health)

  • Jinju Peng

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences
    Guangdong Provincial Institution of Public Health)

  • Huiming Jiang

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences
    Guangdong Provincial Institution of Public Health)

  • Pingping Zhou

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences
    Guangdong Provincial Institution of Public Health)

  • Ting Hu

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Min Luo

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Yingtao Zhang

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Huanying Zheng

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Jianpeng Xiao

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences
    Guangdong Provincial Institution of Public Health)

  • Tao Liu

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences
    Guangdong Provincial Institution of Public Health)

  • Mingkai Tan

    (Guangzhou 8th People’s Hospital)

  • Rongfei Che

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Hanri Zeng

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Zhonghua Zheng

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Yushi Huang

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Jianxiang Yu

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Lina Yi

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences
    Guangdong Provincial Institution of Public Health)

  • Jie Wu

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Jingdiao Chen

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Haojie Zhong

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Xiaoling Deng

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Min Kang

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Oliver G. Pybus

    (University of Oxford)

  • Matthew Hall

    (University of Oxford)

  • Katrina A. Lythgoe

    (University of Oxford)

  • Yan Li

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Jun Yuan

    (Guangzhou Center for Disease Control and Prevention)

  • Jianfeng He

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences)

  • Jing Lu

    (Guangdong Provincial Center for Disease Control and Prevention
    Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences
    Guangdong Provincial Institution of Public Health)

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.

Suggested Citation

  • Baisheng Li & Aiping Deng & Kuibiao Li & Yao Hu & Zhencui Li & Yaling Shi & Qianling Xiong & Zhe Liu & Qianfang Guo & Lirong Zou & Huan Zhang & Meng Zhang & Fangzhu Ouyang & Juan Su & Wenzhe Su & Jing, 2022. "Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28089-y
    DOI: 10.1038/s41467-022-28089-y
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    Citations

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    Cited by:

    1. Emily E. Bendall & Amy P. Callear & Amy Getz & Kendra Goforth & Drew Edwards & Arnold S. Monto & Emily T. Martin & Adam S. Lauring, 2023. "Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants," Nature Communications, Nature, vol. 14(1), pages 1-7, December.
    2. Cathrine Scheepers & Josie Everatt & Daniel G. Amoako & Houriiyah Tegally & Constantinos Kurt Wibmer & Anele Mnguni & Arshad Ismail & Boitshoko Mahlangu & Bronwen E. Lambson & Darren P. Martin & Eduan, 2022. "Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    3. Diana Rose E. Ranoa & Robin L. Holland & Fadi G. Alnaji & Kelsie J. Green & Leyi Wang & Richard L. Fredrickson & Tong Wang & George N. Wong & Johnny Uelmen & Sergei Maslov & Zachary J. Weiner & Alexei, 2022. "Mitigation of SARS-CoV-2 transmission at a large public university," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    4. Nicolò Gozzi & Matteo Chinazzi & Natalie E. Dean & Ira M. Longini Jr & M. Elizabeth Halloran & Nicola Perra & Alessandro Vespignani, 2023. "Estimating the impact of COVID-19 vaccine inequities: a modeling study," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    5. Biao Zhou & Runhong Zhou & Bingjie Tang & Jasper Fuk-Woo Chan & Mengxiao Luo & Qiaoli Peng & Shuofeng Yuan & Hang Liu & Bobo Wing-Yee Mok & Bohao Chen & Pui Wang & Vincent Kwok-Man Poon & Hin Chu & Ch, 2022. "A broadly neutralizing antibody protects Syrian hamsters against SARS-CoV-2 Omicron challenge," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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