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- Title
Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong.
- Authors
Gu, Haogao; Xie, Ruopeng; Adam, Dillon C.; Tsui, Joseph L.-H.; Chu, Daniel K.; Chang, Lydia D. J.; Cheuk, Sammi S. Y.; Gurung, Shreya; Krishnan, Pavithra; Ng, Daisy Y. M.; Liu, Gigi Y. Z.; Wan, Carrie K. C.; Cheng, Samuel S. M.; Edwards, Kimberly M.; Leung, Kathy S. M.; Wu, Joseph T.; Tsang, Dominic N. C.; Leung, Gabriel M.; Cowling, Benjamin J.; Peiris, Malik
- 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. Hong Kong has used an elimination strategy to control SARS-CoV-2 with stringent measures including traveller quarantine. Here, the authors show that the majority of community-acquired cases until January 2021 resulted from three importations, and that increased transmission followed prolonged periods of restrictions, likely due to adherence fatigue.
- Subjects
HONG Kong (China); SINGLE nucleotide polymorphisms; SARS-CoV-2; TRAVEL regulations; EPIDEMIOLOGY; BORDER security
- Publication
Nature Communications, 2022, Vol 13, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-022-28420-7