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

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 Xu, Huifang Lin, Jing Sun, Jinju Peng, Huiming Jiang, Pingping Zhou, Ting Hu, Min Luo, Yingtao Zhang, Huanying Zheng, Jianpeng Xiao, Tao Liu, Mingkai Tan, Rongfei Che, Hanri Zeng, Zhonghua Zheng, Yushi Huang, Jianxiang Yu, Lina Yi, Jie Wu, Jingdiao Chen, Haojie Zhong, Xiaoling Deng, Min Kang, Oliver G. Pybus, Matthew Hall, Katrina A. Lythgoe, Yan Li (), Jun Yuan (), Jianfeng He () and Jing Lu ()
Additional contact information
Baisheng Li: Guangdong Provincial Center for Disease Control and Prevention
Aiping Deng: Guangdong Provincial Center for Disease Control and Prevention
Kuibiao Li: Guangzhou Center for Disease Control and Prevention
Yao Hu: Guangdong Provincial Center for Disease Control and Prevention
Zhencui Li: Guangdong Provincial Center for Disease Control and Prevention
Yaling Shi: Guangzhou 8th People’s Hospital
Qianling Xiong: Guangdong Provincial Center for Disease Control and Prevention
Zhe Liu: Guangdong Provincial Center for Disease Control and Prevention
Qianfang Guo: Guangdong Provincial Center for Disease Control and Prevention
Lirong Zou: Guangdong Provincial Center for Disease Control and Prevention
Huan Zhang: Guangdong Provincial Center for Disease Control and Prevention
Meng Zhang: Guangdong Provincial Center for Disease Control and Prevention
Fangzhu Ouyang: Guangdong Provincial Center for Disease Control and Prevention
Juan Su: Guangdong Provincial Center for Disease Control and Prevention
Wenzhe Su: Guangzhou Center for Disease Control and Prevention
Jing Xu: Guangdong Provincial Center for Disease Control and Prevention
Huifang Lin: Guangdong Provincial Center for Disease Control and Prevention
Jing Sun: Guangdong Provincial Center for Disease Control and Prevention
Jinju Peng: Guangdong Provincial Center for Disease Control and Prevention
Huiming Jiang: Guangdong Provincial Center for Disease Control and Prevention
Pingping Zhou: Guangdong Provincial Center for Disease Control and Prevention
Ting Hu: Guangdong Provincial Center for Disease Control and Prevention
Min Luo: Guangdong Provincial Center for Disease Control and Prevention
Yingtao Zhang: Guangdong Provincial Center for Disease Control and Prevention
Huanying Zheng: Guangdong Provincial Center for Disease Control and Prevention
Jianpeng Xiao: Guangdong Provincial Center for Disease Control and Prevention
Tao Liu: Guangdong Provincial Center for Disease Control and Prevention
Mingkai Tan: Guangzhou 8th People’s Hospital
Rongfei Che: Guangdong Provincial Center for Disease Control and Prevention
Hanri Zeng: Guangdong Provincial Center for Disease Control and Prevention
Zhonghua Zheng: Guangdong Provincial Center for Disease Control and Prevention
Yushi Huang: Guangdong Provincial Center for Disease Control and Prevention
Jianxiang Yu: Guangdong Provincial Center for Disease Control and Prevention
Lina Yi: Guangdong Provincial Center for Disease Control and Prevention
Jie Wu: Guangdong Provincial Center for Disease Control and Prevention
Jingdiao Chen: Guangdong Provincial Center for Disease Control and Prevention
Haojie Zhong: Guangdong Provincial Center for Disease Control and Prevention
Xiaoling Deng: Guangdong Provincial Center for Disease Control and Prevention
Min Kang: Guangdong Provincial Center for Disease Control and Prevention
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
Jun Yuan: Guangzhou Center for Disease Control and Prevention
Jianfeng He: Guangdong Provincial Center for Disease Control and Prevention
Jing Lu: Guangdong Provincial Center for Disease Control and Prevention

Nature Communications, 2022, vol. 13, issue 1, 1-9

Abstract: 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.

Date: 2022
References: View complete reference list from CitEc
Citations: View citations in EconPapers (8)

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DOI: 10.1038/s41467-022-28089-y

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