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

Nat Commun. 2022 Feb 8;13(1):736. doi: 10.1038/s41467-022-28420-7.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • COVID-19 / epidemiology*
  • COVID-19 / transmission
  • COVID-19 / virology
  • Genomics
  • Hong Kong / epidemiology
  • Humans
  • Public Health
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / isolation & purification
  • SARS-CoV-2 / physiology
  • Travel