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Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong

Author

Listed:
  • Haogao Gu

    (The University of Hong Kong)

  • Ruopeng Xie

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

  • Dillon C. Adam

    (The University of Hong Kong)

  • Joseph L.-H. Tsui

    (The University of Hong Kong)

  • Daniel K. Chu

    (The University of Hong Kong)

  • Lydia D. J. Chang

    (The University of Hong Kong)

  • Sammi S. Y. Cheuk

    (The University of Hong Kong)

  • Shreya Gurung

    (The University of Hong Kong)

  • Pavithra Krishnan

    (The University of Hong Kong)

  • Daisy Y. M. Ng

    (The University of Hong Kong)

  • Gigi Y. Z. Liu

    (The University of Hong Kong)

  • Carrie K. C. Wan

    (The University of Hong Kong)

  • Samuel S. M. Cheng

    (The University of Hong Kong)

  • Kimberly M. Edwards

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

  • Kathy S. M. Leung

    (The University of Hong Kong
    Hong Kong Science and Technology Park)

  • Joseph T. Wu

    (The University of Hong Kong
    Hong Kong Science and Technology Park)

  • Dominic N. C. Tsang

    (The Government of Hong Kong Special Administrative Region)

  • Gabriel M. Leung

    (The University of Hong Kong
    Hong Kong Science and Technology Park)

  • Benjamin J. Cowling

    (The University of Hong Kong
    Hong Kong Science and Technology Park)

  • Malik Peiris

    (The University of Hong Kong
    The University of Hong Kong
    Hong Kong Science and Technology Park)

  • Tommy T. Y. Lam

    (The University of Hong Kong
    Hong Kong Science and Technology Park
    Hong Kong Science and Technology Park)

  • Vijaykrishna Dhanasekaran

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

  • Leo L. M. Poon

    (The University of Hong Kong
    The University of Hong Kong
    Hong Kong Science and Technology Park)

Abstract

Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission. By analyzing 1899 genome sequences (>18% of confirmed cases) from 23-January-2020 to 26-January-2021, we reveal the effects of fluctuating control measures on the evolution and epidemiology of SARS-CoV-2 lineages in Hong Kong. Despite numerous importations, only three introductions were responsible for 90% of locally-acquired cases. Community outbreaks were caused by novel introductions rather than a resurgence of circulating strains. Thus, local outbreak prevention requires strong border control and community surveillance, especially during periods of less stringent social restriction. Non-adherence to prolonged preventative measures may explain sustained local transmission observed during wave four in late 2020 and early 2021. We also found that, due to a tight transmission bottleneck, transmission of low-frequency single nucleotide variants between hosts is rare.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28420-7
    DOI: 10.1038/s41467-022-28420-7
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    Cited by:

    1. Haogao Gu & Ahmed Abdul Quadeer & Pavithra Krishnan & Daisy Y. M. Ng & Lydia D. J. Chang & Gigi Y. Z. Liu & Samuel M. S. Cheng & Tommy T. Y. Lam & Malik Peiris & Matthew R. McKay & Leo L. M. Poon, 2023. "Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. 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.

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