Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong

Ruopeng Xie, Kimberly M. Edwards, Dillon C. Adam, Kathy S. M. Leung, Tim K. Tsang, Shreya Gurung, Weijia Xiong, Xiaoman Wei, Daisy Y. M. Ng, Gigi Y. Z. Liu, Pavithra Krishnan, Lydia D. J. Chang, Samuel M. S. Cheng, Haogao Gu, Gilman K. H. Siu, Joseph T. Wu, Gabriel M. Leung, Malik Peiris, Benjamin J. Cowling, Leo L. M. Poon and Vijaykrishna Dhanasekaran ()
Additional contact information
Ruopeng Xie: The University of Hong Kong
Kimberly M. Edwards: The University of Hong Kong
Dillon C. Adam: The University of Hong Kong
Kathy S. M. Leung: The University of Hong Kong
Tim K. Tsang: The University of Hong Kong
Shreya Gurung: The University of Hong Kong
Weijia Xiong: The University of Hong Kong
Xiaoman Wei: The University of Hong Kong
Daisy Y. M. Ng: The University of Hong Kong
Gigi Y. Z. Liu: The University of Hong Kong
Pavithra Krishnan: The University of Hong Kong
Lydia D. J. Chang: The University of Hong Kong
Samuel M. S. Cheng: The University of Hong Kong
Haogao Gu: The University of Hong Kong
Gilman K. H. Siu: The Hong Kong Polytechnic University
Joseph T. Wu: The University of Hong Kong
Gabriel M. Leung: The University of Hong Kong
Malik Peiris: The University of Hong Kong
Benjamin J. Cowling: The University of Hong Kong
Leo L. M. Poon: The University of Hong Kong
Vijaykrishna Dhanasekaran: The University of Hong Kong

Nature Communications, 2023, vol. 14, issue 1, 1-11

Abstract: Abstract Hong Kong experienced a surge of Omicron BA.2 infections in early 2022, resulting in one of the highest per-capita death rates of COVID-19. The outbreak occurred in a dense population with low immunity towards natural SARS-CoV-2 infection, high vaccine hesitancy in vulnerable populations, comprehensive disease surveillance and the capacity for stringent public health and social measures (PHSMs). By analyzing genome sequences and epidemiological data, we reconstructed the epidemic trajectory of BA.2 wave and found that the initial BA.2 community transmission emerged from cross-infection within hotel quarantine. The rapid implementation of PHSMs suppressed early epidemic growth but the effective reproduction number (Re) increased again during the Spring festival in early February and remained around 1 until early April. Independent estimates of point prevalence and incidence using phylodynamics also showed extensive superspreading at this time, which likely contributed to the rapid expansion of the epidemic. Discordant inferences based on genomic and epidemiological data underscore the need for research to improve near real-time epidemic growth estimates by combining multiple disparate data sources to better inform outbreak response policy.

Date: 2023
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DOI: 10.1038/s41467-023-38201-5

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