Abstract
Background
The SARS-CoV-2 Omicron variant BA.2 sublineage has increased rapidly in Europe and Asia since January 2022. Here, we report the epidemiological and genomic analysis of a large single source BA.2 outbreak in a housing estate.
Methods
We analyzed the epidemiological information of a community outbreak of BA.2 (STY outbreak). We performed whole viral genome sequencing using the Oxford Nanopore MinION device. We calculated the doubling time of the outbreak within a housing estate.
Results
The STY outbreak involved a total of 768 individuals as of 5 th February 2022, including 432 residents, visitors or staff (56.3%) from a single housing estate (KC Estate). The outbreak at the KC Estate has a short doubling time of 1.28 days (95% confidence interval: 0.560-1.935). The outbreak was promptly controlled with the lockdown of 3 buildings within the housing estate. Whole genome sequencing was performed for 133 patients in the STY outbreak, including 106 residents of the KC Estate. All 133 sequences from the STY outbreak belonged to the BA.2 sublineage, and phylogenetic analysis showed that these sequences cluster together. All individuals in the STY cluster had the unique mutation C12525T.
Conclusions
Our study highlights the exceptionally high transmissibility of the Omicron variant BA.2 sublineage in Hong Kong where stringent measures are implemented as part of the elimination strategy. Continual genomic surveillance is crucial in monitoring the emergence of epidemiologically important Omicron sub-variants.
Keywords: COVID-19, SARS-CoV-2 Omicron variant, BA.2, community outbreak, housing estate
Contributor Information
Vincent Chi-Chung Cheng, State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Infection Control Team, Queen Mary Hospital, Hong Kong West Cluster, Hong Kong Special Administrative Region, China.
Jonathan Daniel Ip, State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong Special Administrative Region, China.
Allen Wing-Ho Chu, State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong Special Administrative Region, China.
Anthony Raymond Tam, Department of Medicine, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.
Wan-Mui Chan, State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong Special Administrative Region, China.
Syed Muhammad Umer Abdullah, State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong Special Administrative Region, China.
Brian Pui-Chun Chan, State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong Special Administrative Region, China.
Shuk-Ching Wong, Infection Control Team, Queen Mary Hospital, Hong Kong West Cluster, Hong Kong Special Administrative Region, China.
Mike Yat-Wah Kwan, Department of Paediatrics and Adolescent Medicine, The Hong Kong Children’s Hospital, Hong Kong Special Administrative Region, China; Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong Special Administrative Region, China.
Gilbert T Chua, Department of Paediatrics and Adolescent Medicine, The Hong Kong Children’s Hospital, Hong Kong Special Administrative Region, China; Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
Patrick Ip, Department of Paediatrics and Adolescent Medicine, The Hong Kong Children’s Hospital, Hong Kong Special Administrative Region, China; Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
Jacky Man-Chun Chan, Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong Special Administrative Region, People’s Republic of China.
Bosco Hoi-Shiu Lam, Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China.
Wing-Kin To, Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China.
Vivien Wai-Man Chuang, Quality & Safety Division, Hospital Authority, Hong Kong Special Administrative Region, China.
Kwok-Yung Yuen, State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Infection Control Team, Queen Mary Hospital, Hong Kong West Cluster, Hong Kong Special Administrative Region, China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
Ivan Fan-Ngai Hung, Department of Medicine, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Department of Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong Special Administrative Region, China.
Kelvin Kai-Wang To, State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Infection Control Team, Queen Mary Hospital, Hong Kong West Cluster, Hong Kong Special Administrative Region, China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
Supplementary Material
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.