Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China

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

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.