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

Abstract

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.

Keywords: COVID-19; China; Hong Kong; SARS-CoV-2; clinical demographic; community outbreak; molecular evolutionary analysis; molecular phylogeny; novel coronavirus; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; whole genome sequencing.

Figure 1

Demographics of coronavirus disease patients, Hong Kong, February 2020. Rectangular boxes indicate men or boys and stadium-shaped boxes indicate women or girls. Travel history within the 14-day incubation period before symptom onset is highlighted in cyan for local case without travel history, pink for travel history to Wuhan <14 days from symptom onset, orange for travel history to other regions in mainland China, and green for travel history to regions outside mainland China. Contact histories are highlighted by red lines for family contacts and green lines for nonfamily contacts. Case numbers are those used by the Centre of Health Protection, Department of Health, Hong Kong (6). Within each cluster, cases of primary infection (leftmost column) are arranged from top to bottom in order of the date (DD/MM) of symptom onset. SSE, superspreading event.

Figure 2

Maximum-likelihood phylogenetic tree of 50 coronavirus disease cases, Hong Kong, February 2020. The tree was rooted on the earliest published genome of severe acute respiratory syndrome coronavirus 2 (GenBank accession no. NC_045512.2). Bootstrap value was set at 1,000× and nodes with bootstrap value >50% were shown. Branch lengths were measured in number of substitutions per site. Samples are color-coded by epidemiologic link. Cases 84 and 102 were asymptomatic at the time of sample collection and are marked with asterisks. Each case is identified by case number used by the Centre of Health Protection, Department of Health, Hong Kong, and date of symptom onset. SSE, superspreading event.

Figure 3

Geographic distribution of 50 coronavirus disease cases, Hong Kong, February 2020. Geographic information is marked according to the residence of the index case-patient in each cluster. Clusters known to be caused by superspreading events are marked by asterisks; other clusters are marked by dots.