A territory-wide study of early COVID-19 outbreak in Hong Kong community: A clinical, epidemiological and phylogenomic investigation

Abstract

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

Clustering and superspreading potential of SARS-CoV-2 infections in Hong Kong

“…The most recent case confirmed in this cluster was a monk who worked at the temple and reported no symptoms before confirmation. It is probable, but not definitive, that given the other 11 primary cases reported attending the temple over multiple days, the monk was the source of some or all of the other 11 temple cases 10 . All remaining local and imported SARS-CoV-2 clusters in Hong Kong, including three additional SSEs (SSE #5-7), are shown in Fig.…”

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic

“…Genomic sequencing can be used to rapidly and accurately identify the transmission routes of the pathogen [4,5]. This can then be used to trace the path of transmission within a population and to possibly identify the probable source, potentially leading to an improved public health response [6][7][8][9][10][11][12].…”

Effect of COVID-19 on Dental Education and Endodontic Practice in Hong Kong

“…The comprehensive measures undertaken by the local government coupled with the collective effort of its citizens likely helped initially mitigate the more dire effects of the outbreak (5,6). However, the recent spike in COVID-19 infections and clustered community outbreaks have been attributed to relaxed social distancing policies, an increase in social gatherings, asymptomatic spread, and transmission from imported cases (7). Furthermore, the mental and physical burn out from heightened stress levels, social isolation, and changes in routine have left many Hong Kong citizens fatigued and frustrated.…”