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Transmission of SARS-CoV-2 Omicron Variant under a Dynamic Clearance Strategy in Shandong, China.
Xu, Yifei; Liu, Ti; Li, Yan; Wei, Xuemin; Wang, Zhaoguo; Fang, Ming; Zhang, Yuwei; Zhang, Huaning; Zhang, Lifang; Zhang, Jinbo; Xu, Jin; Tian, Yunlong; He, Nianzheng; Zhang, Yuhan; Wang, Yao; Yao, Mingxiao; Pang, Bo; Wang, Shuang; Wen, Hongling; Kou, Zengqiang.
  • Xu Y; Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
  • Liu T; Suzhou Research Institute of Shandong University, Suzhou, Jiangsu, China.
  • Li Y; Shandong Center for Disease Control and Prevention, Jinan, Shandong, China.
  • Wei X; Shandong Center for Disease Control and Prevention, Jinan, Shandong, China.
  • Wang Z; Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
  • Fang M; Qingdao Center for Disease Control and Prevention, Qingdao, Shandong, China.
  • Zhang Y; Shandong Center for Disease Control and Prevention, Jinan, Shandong, China.
  • Zhang H; Shandong Center for Disease Control and Prevention, Jinan, Shandong, China.
  • Zhang L; Shandong Center for Disease Control and Prevention, Jinan, Shandong, China.
  • Zhang J; Binzhou Center for Disease Control and Prevention, Binzhou, Shandong, China.
  • Xu J; Weihai Center for Disease Control and Prevention, Weihai, Shandong, China.
  • Tian Y; Zibo Center for Disease Control and Prevention, Zibo, Shandong, China.
  • He N; Yantai Center for Disease Control and Prevention, Yantai, Shandong, China.
  • Zhang Y; Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
  • Wang Y; Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
  • Yao M; Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
  • Pang B; Shandong Center for Disease Control and Prevention, Jinan, Shandong, China.
  • Wang S; Shandong Center for Disease Control and Prevention, Jinan, Shandong, China.
  • Wen H; Shandong Center for Disease Control and Prevention, Jinan, Shandong, China.
  • Kou Z; Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
Microbiol Spectr ; : e0463222, 2023 Mar 14.
Article in English | MEDLINE | ID: covidwho-2287303
ABSTRACT
SARS-CoV-2 Omicron caused a large wave of COVID-19 cases in China in spring 2022. Shandong was one of the most affected regions during this epidemic yet was also among those areas that were able to quickly contain the transmission. We aimed to investigate the origin, genetic diversity, and transmission patterns of the Omicron epidemic in Shandong under a dynamic clearance strategy. We generated 1,149 Omicron sequences, performed phylogenetic analysis, and interpreted results in the context of available epidemiological information. We observed that there were multiple introductions of distinct Omicron sublineages into Shandong from foreign countries and other regions in China, while a small number of introductions led to majority of local cases. We found evidence suggesting that some local clusters were potentially associated with foreign imported cases. Superspreading events and cryptic transmissions contributed to the rapid spread of this epidemic. We identified a BA.1.1 genome with the R493Q reversion mutation in the spike receptor binding domain, potentially associated with an escape from vaccine and Omicron infection elicited neutralizing immunity. Our findings illustrated how the dynamic clearance strategy constrained this epidemic's size, duration, and geographical distribution. IMPORTANCE Starting in March 2022, the Omicron epidemic caused a large wave of COVID-19 cases in China. Shandong was one of the most affected regions during this epidemic but was also among those areas that were able to quickly contain the transmission. We investigated the origin, genetic diversity, and transmission patterns of Omicron epidemic in Shandong under a dynamic clearance strategy. We found that there were multiple introductions of distinct Omicron sublineages into Shandong from foreign countries and other regions in China, while a small number of introductions led to most local cases. We found evidence suggesting that some local clusters were associated with foreign imported cases. Superspreading events and cryptic transmissions contributed to the rapid spread of this epidemic. Our study illustrated the transmission patterns of Omicron epidemic in Shandong and provided a looking glass onto this epidemic in China.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study Topics: Vaccines / Variants Language: English Journal: Microbiol Spectr Year: 2023 Document Type: Article Affiliation country: Spectrum.04632-22

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study Topics: Vaccines / Variants Language: English Journal: Microbiol Spectr Year: 2023 Document Type: Article Affiliation country: Spectrum.04632-22