A territory wide study of early COVID 19 outbreak in Hong Kong community: A clinical, epidemiological and phylogenomic investigation
Background: Initial cases of coronavirus disease 2019 (COVID 19) reported in Hong Kong were mostly imported cases from Mainland China. However, most cases reported in February 2020 were local infections with unknown source, indicating local community transmissions. This study aimed to report the clinical, epidemiological and phylogenomic characteristics of the local cases of COVID 19 in our community. Methods: We extracted the demographic, clinical and epidemiological data from 50 COVID 19 patients, who accounted for 53.8% of the cases in Hong Kong by the end of February 2020. We used both Nanopore and Illumina platforms to perform whole genome sequencing (WGS) of the severe acute respiratory syndrome coronavirus 2 (SARS CoV 2) from these patients. Phylogenetic relatedness among these local cases and their placement in the global phylogeny were examined. The evolutionary rate and divergence time of transmission were also determined. Findings: Of these 50 patients, only three (6.0% had visited Wuhan while 43 (86.0% did not have recent travel records. The average interval from symptom onset to hospital admission was 8.5 days. The most common signs and symptoms on admission were cough (74.0% and fever (58.0% Radiographic abnormality was found in 46 (92.0% patients. Three (6.0% patients required ICU admission. Phylogenetic analysis concurred with epidemiological investigation that 42 (84.0% cases could be grouped into six transmission clusters. Forty four (88.0% cases harboured a common mutation Orf3a G251V. Global phylogeny of SARS CoV 2 revealed that most (88.0% cases in Hong Kong were clustered in two subclades with the strains from other countries. The estimated time to the most recent common ancestor (tMRCA) of COVID 2019 outbreak in Hong Kong was December 24, 2019 with an evolutionary rate of 3.04x10 3 substitutions per site per year. The reproduction number value was 1.84 as of February 28, 2020 in Hong Kong. Interpretation: We provided a territory wide overview of COVID 19 in Hong Kong, which has borders connecting to Mainland China. Transmission in closed settings especially during family and religious gatherings is a hallmark of the recently reported cases. The reproduction number value indicated an ongoing outbreak in the community. Social distancing and vigilant epidemiological control are crucial to the containment of COVID 19 transmission
medRxiv