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

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 casepatients 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 x 10(-3) substitutions/site/year. The reproduction number was 1.84, indicating ongoing community spread.

Automated summary

Initial cases of coronavirus disease in Hong Kong were imported from mainland China, but a dramatic increase in case numbers in February 2020 suggested local community transmission. Whole-genome sequencing revealed two lineages in the community outbreak, with one lineage containing a common mutation, Orf3a-G251V, and accounting for 88.0% of cases. The estimated time to the most recent common ancestor of the local outbreak was December 24, 2019, with a reproduction number of 1.84, indicating ongoing community spread.