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

Gu H, Xie R, Adam DC, Tsui JL, Chu DK, Chang LDJ, Cheuk SSY, Gurung S, Krishnan P, Ng DYM, Liu GYZ, Wan CKC, Cheng SSM, Edwards KM, Leung KSM, Wu JT, Tsang DNC, Leung GM, Cowling BJ, Peiris M, Lam TTY, Dhanasekaran V, Poon LLM. 2022. Nat Commun


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.