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A Territory-Wide Study of COVID-19 Cases and Clusters with Unknown Source in Hong Kong Community: A Clinical, Epidemiological and Phylogenomic Investigation

55 Pages Posted: 14 Apr 2020

See all articles by Kenneth Siu-Sing Leung

Kenneth Siu-Sing Leung

The University of Hong Kong - Department of Microbiology; Hong Kong Special Administrative Region (HKSAR)

Timothy Ting-Leung Ng

Hong Kong Polytechnic University - Department of Health Technology and Informatics; Hong Kong Special Administrative Region (HKSAR)

Alan Ka-Lun Wu

Pamela Youde Nethersole Eastern Hospital - Department of Clinical Pathology; Government of the Hong Kong Special Administrative Region

Miranda Chong-Yee Yau

Pamela Youde Nethersole Eastern Hospital - Department of Clinical Pathology; Government of the Hong Kong Special Administrative Region

Hiu-Yin Lao

Hong Kong Polytechnic University - Department of Health Technology and Informatics; Hong Kong Special Administrative Region (HKSAR)

Ming-Pan Choi

Hong Kong Polytechnic University - Department of Health Technology and Informatics; Hong Kong Special Administrative Region (HKSAR)

Kingsley King-Gee Tam

The University of Hong Kong - Department of Microbiology; Hong Kong Special Administrative Region (HKSAR)

Lam Kwong Lee

Hong Kong Polytechnic University - Department of Health Technology and Informatics; Hong Kong Special Administrative Region (HKSAR)

Barry Kin-Chung Wong

United Christian Hospital - Department of Pathology; Hong Kong Special Administrative Region (HKSAR)

Alex Yat-Man Ho

Princess Margaret Hospital - Department of Pathology; Hong Kong Special Administrative Region (HKSAR)

Kam-Tong Yip

Tuen Mun Hospital - Department of Clinical Pathology; Hong Kong Special Administrative Region (HKSAR)

Kwok Cheung Lung

Pamela Youde Nethersole Eastern Hospital - Department of Medicine; Hong Kong Special Administrative Region (HKSAR)

Raymond Wai-To Liu

Ruttonjee Hospital - Department of Medicine & Geriatrics; Hong Kong Special Administrative Region (HKSAR)

Eugene Yuk-Keung Tso

United Christian Hospital - Department of Medicine & Geriatrics; Hong Kong Special Administrative Region (HKSAR)

Wai-Shing Leung

Princess Margaret Hospital - Department of Medicine; Hong Kong Special Administrative Region (HKSAR)

Man-Chun Chan

Princess Margaret Hospital - Department of Medicine; Hong Kong Special Administrative Region (HKSAR)

Yuk-Yung Ng

Tuen Mun Hospital - Department of Medicine and Geriatric; Hong Kong Special Administrative Region (HKSAR)

Kit-Man Sin

Tuen Mun Hospital - Department of Medicine and Geriatric; Hong Kong Special Administrative Region (HKSAR)

Kitty Sau-Chun Fung

United Christian Hospital - Department of Pathology; Hong Kong Special Administrative Region (HKSAR)

Sandy Ka-Yee Chau

United Christian Hospital - Department of Pathology; Hong Kong Special Administrative Region (HKSAR)

Wing-Kin To

Princess Margaret Hospital - Department of Pathology; Hong Kong Special Administrative Region (HKSAR)

Tak-Lun Que

Tuen Mun Hospital - Department of Clinical Pathology; Hong Kong Special Administrative Region (HKSAR)

David Ho-Keung Shum

Hong Kong Polytechnic University - Faculty of Health and Social Sciences; Hong Kong Special Administrative Region (HKSAR)

Shea Ping Yip

Hong Kong Polytechnic University - Department of Health Technology and Informatics; Hong Kong Special Administrative Region (HKSAR)

Wing Cheong Yam

The University of Hong Kong - Department of Microbiology; Hong Kong Special Administrative Region (HKSAR)

Gilman Kit-Hang Siu

Hong Kong Polytechnic University - Department of Health Technology and Informatics

More...

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 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).

Keywords: Novel Coronavirus; COVID-19, SARS-CoV-2,whole genome sequencing, molecular phylogeny, molecular evolutionary analysis, community transmission, Hong Kong

Suggested Citation

Leung, Kenneth Siu-Sing and Ng, Timothy Ting-Leung and Wu, Alan Ka-Lun and Yau, Miranda Chong-Yee and Lao, Hiu-Yin and Choi, Ming-Pan and Tam, Kingsley King-Gee and Lee, Lam Kwong and Wong, Barry Kin-Chung and Ho, Alex Yat-Man and Yip, Kam-Tong and Lung, Kwok Cheung and Liu, Raymond Wai-To and Tso, Eugene Yuk-Keung and Leung, Wai-Shing and Chan, Man-Chun and Ng, Yuk-Yung and Sin, Kit-Man and Fung, Kitty Sau-Chun and Chau, Sandy Ka-Yee and To, Wing-Kin and Que, Tak-Lun and Shum, David Ho-Keung and Yip, Shea Ping and Yam, Wing Cheong and Siu, Gilman Kit-Hang, A Territory-Wide Study of COVID-19 Cases and Clusters with Unknown Source in Hong Kong Community: A Clinical, Epidemiological and Phylogenomic Investigation (3/23/2020). Available at SSRN: https://ssrn.com/abstract=3559611 or http://dx.doi.org/10.2139/ssrn.3559611

Kenneth Siu-Sing Leung

The University of Hong Kong - Department of Microbiology

Hong Kong

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Timothy Ting-Leung Ng

Hong Kong Polytechnic University - Department of Health Technology and Informatics

Hong Kong

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Alan Ka-Lun Wu

Pamela Youde Nethersole Eastern Hospital - Department of Clinical Pathology

Hong Kong

Government of the Hong Kong Special Administrative Region

Hong Kong

Miranda Chong-Yee Yau

Pamela Youde Nethersole Eastern Hospital - Department of Clinical Pathology

Hong Kong

Government of the Hong Kong Special Administrative Region

Hong Kong

Hiu-Yin Lao

Hong Kong Polytechnic University - Department of Health Technology and Informatics

Hong Kong

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Ming-Pan Choi

Hong Kong Polytechnic University - Department of Health Technology and Informatics

Hong Kong

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Kingsley King-Gee Tam

The University of Hong Kong - Department of Microbiology

Hong Kong

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Lam Kwong Lee

Hong Kong Polytechnic University - Department of Health Technology and Informatics

Hong Kong

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Barry Kin-Chung Wong

United Christian Hospital - Department of Pathology

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Alex Yat-Man Ho

Princess Margaret Hospital - Department of Pathology

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Kam-Tong Yip

Tuen Mun Hospital - Department of Clinical Pathology

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Kwok Cheung Lung

Pamela Youde Nethersole Eastern Hospital - Department of Medicine

Hong Kong

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Raymond Wai-To Liu

Ruttonjee Hospital - Department of Medicine & Geriatrics

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Eugene Yuk-Keung Tso

United Christian Hospital - Department of Medicine & Geriatrics

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Wai-Shing Leung

Princess Margaret Hospital - Department of Medicine

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Man-Chun Chan

Princess Margaret Hospital - Department of Medicine

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Yuk-Yung Ng

Tuen Mun Hospital - Department of Medicine and Geriatric

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Kit-Man Sin

Tuen Mun Hospital - Department of Medicine and Geriatric

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Kitty Sau-Chun Fung

United Christian Hospital - Department of Pathology

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Sandy Ka-Yee Chau

United Christian Hospital - Department of Pathology

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Wing-Kin To

Princess Margaret Hospital - Department of Pathology

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Tak-Lun Que

Tuen Mun Hospital - Department of Clinical Pathology

China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

David Ho-Keung Shum

Hong Kong Polytechnic University - Faculty of Health and Social Sciences

Room GH122
The Hong Kong Polytechnic University
Hong Kong, Hung Hom, Kowloon
China

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Shea Ping Yip

Hong Kong Polytechnic University - Department of Health Technology and Informatics

Hong Kong

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Wing Cheong Yam

The University of Hong Kong - Department of Microbiology

Hong Kong

Hong Kong Special Administrative Region (HKSAR)

Hong Kong

Gilman Kit-Hang Siu (Contact Author)

Hong Kong Polytechnic University - Department of Health Technology and Informatics ( email )

China

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