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

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. Wan, Samuel S. M. Cheng, Kimberly M. Edwards, Kathy S. M. Leung, Joseph T. Wu, Dominic N. C. Tsang, Gabriel M. Leung, Benjamin J. Cowling, Malik Peiris, Tommy T. Y. Lam, Vijaykrishna Dhanasekaran () and Leo L. M. Poon ()
Additional contact information
Haogao Gu: The University of Hong Kong
Ruopeng Xie: 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
Kathy S. M. Leung: The University of Hong Kong
Joseph T. Wu: The University of Hong Kong
Dominic N. C. Tsang: The Government of Hong Kong Special Administrative Region
Gabriel M. Leung: The University of Hong Kong
Benjamin J. Cowling: The University of Hong Kong
Malik Peiris: The University of Hong Kong
Tommy T. Y. Lam: The University of Hong Kong
Vijaykrishna Dhanasekaran: The University of Hong Kong
Leo L. M. Poon: The University of Hong Kong

Nature Communications, 2022, vol. 13, issue 1, 1-10

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-28420-7

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