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

Author

Listed:
  • Ruopeng Xie

    (The University of Hong Kong
    The University of Hong Kong)

  • Kimberly M. Edwards

    (The University of Hong Kong
    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
    The University of Hong Kong)

  • Weijia Xiong

    (The University of Hong Kong)

  • Xiaoman Wei

    (The University of Hong Kong
    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
    Hong Kong Science and Technology Park, New Territories)

  • Gabriel M. Leung

    (The University of Hong Kong
    Hong Kong Science and Technology Park, New Territories)

  • Malik Peiris

    (The University of Hong Kong
    Hong Kong Science and Technology Park, New Territories)

  • Benjamin J. Cowling

    (The University of Hong Kong
    Hong Kong Science and Technology Park, New Territories)

  • Leo L. M. Poon

    (The University of Hong Kong
    The University of Hong Kong
    Hong Kong Science and Technology Park, New Territories)

  • Vijaykrishna Dhanasekaran

    (The University of Hong Kong
    The University of Hong Kong)

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.

Suggested Citation

  • 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. C, 2023. "Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38201-5
    DOI: 10.1038/s41467-023-38201-5
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    References listed on IDEAS

    as
    1. Haogao Gu & Ruopeng Xie & Dillon C. Adam & Joseph L.-H. Tsui & Daniel K. Chu & Lydia D. J. Chang & Sammi S. Y. Cheuk & Shreya Gurung & Pavithra Krishnan & Daisy Y. M. Ng & Gigi Y. Z. Liu & Carrie K. C, 2022. "Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
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