Territorywide study of early coronavirus disease outbreak, Hong Kong, China

Kenneth Siu Sing Leung, Timothy Ting Leung Ng, Alan Ka Lun Wu, Miranda Chong Yee Yau, Hiu Yin Lao, Ming Pan Choi, Kingsley King Gee Tam, Lam Kwong Lee, Barry Kin Chung Wong, Alex Yat Man Ho, Kam Tong Yip, Kwok Cheung Lung, Raymond Wai To Liu, Eugene Yuk Keung Tso, Wai Shing Leung, Man Chun Chan, Yuk Yung Ng, Kit Man Sin, Kitty Sau Chun Fung, Sandy Ka Yee ChauWing Kin To, Tak Lun Que, David Ho Keung Shum, Shea Ping Yip, Wing Cheong Yam, Gilman Kit Hang Siu

Research output: Journal article publicationJournal articleAcademic researchpeer-review

10 Citations (Scopus)


Initial cases of coronavirus disease in Hong Kong were imported from mainland China. A dramatic increase in case numbers was seen in February 2020. Most case-patients had no recent travel history, suggesting the presence of transmission chains in the local community. We collected demographic, clinical, and epidemiologic data from 50 patients, who accounted for 53.8% of total reported case-patients as of February 28, 2020. We performed whole-genome sequencing to determine phylogenetic relationship and transmission dynamics of severe acute respiratory syndrome coronavirus 2 infections. By using phylogenetic analysis, we attributed the community outbreak to 2 lineages; 1 harbored a common mutation, Orf3a-G251V, and accounted for 88.0% of the cases in our study. The estimated time to the most recent common ancestor of local coronavirus disease outbreak was December 24, 2019, with an evolutionary rate of 3.04 × 10−3 substitutions/site/year. The reproduction number was 1.84, indicating ongoing community spread.

Original languageEnglish
Pages (from-to)196-204
Number of pages9
JournalEmerging Infectious Diseases
Issue number1
Publication statusPublished - Jan 2021

ASJC Scopus subject areas

  • Epidemiology
  • Microbiology (medical)
  • Infectious Diseases


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