| Autor: |
Wing-Cheong Yam, Alex Yat-Man Ho, Kenneth Siu Sing Leung, Sandy Ka Yee Chau, Man-Chun Chan, Kam-Tong Yip, Eugene Yuk-Keung Tso, Miranda Chong-Yee Yau, Alan K.L. Wu, Kwok Cheung Lung, Wing-Kin To, Barry Kin-Chung Wong, Gilman Kit Hang Siu, Kingsley King Gee Tam, Yuk-Yung Ng, Timothy Ting-Leung Ng, Kitty S. C. Fung, Hiu-Yin Lao, Shea Ping Yip, Ming-Pan Choi, David Shum, Tak-Lun Que, Raymond W. Liu, Kit-Man Sin, Lam Kwong Lee, Wai-Shing Leung |
| Rok vydání: |
2020 |
| Předmět: |
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| Zdroj: |
SSRN Electronic Journal. |
| ISSN: |
1556-5068 |
| Popis: |
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 Orf3aG251V. 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 3.04×10-3 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. Rapid isolation of suspected or confirmed cases and their close contacts coupled with robust laboratory surveillance is crucial to the containment of COVID-19 transmission. Funding Statement: The project was supported by internal funds from the Faculty of Health and Social Science, and Department of Health Technology and Informatics of The Hong Kong Polytechnic University. Declaration of Interests: The authors declare no competing interests. Ethics Approval Statement: This study was approved by the Institutional Review Boards of The Hong Kong Polytechnic University (RSA20021) and the public hospitals involved (HKECREC-20200014; KCC/KEC2020-0070). |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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