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Published: 10 March 2022
Vincent Chi-Chung Cheng, Jonathan Daniel Ip, Allen Wing-Ho Chu, Anthony Raymond Tam, Wan-Mui Chan, Syed Muhammad Umer Abdullah, Brian Pui-Chun Chan, Shuk-Ching Wong, Mike Yat-Wah Kwan, Gilbert T Chua,
Patrick Ip, Jacky Man-Chun Chan, Bosco Hoi-Shiu Lam, Wing-Kin To, Vivien Wai-Man Chuang, Kwok-Yung Yuen, Ivan Fan-Ngai ****, Kelvin Kai-Wang To
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.
Published: 10 March 2022
Vincent Chi-Chung Cheng, Jonathan Daniel Ip, Allen Wing-Ho Chu, Anthony Raymond Tam, Wan-Mui Chan, Syed Muhammad Umer Abdullah, Brian Pui-Chun Chan, Shuk-Ching Wong, Mike Yat-Wah Kwan, Gilbert T Chua,
Patrick Ip, Jacky Man-Chun Chan, Bosco Hoi-Shiu Lam, Wing-Kin To, Vivien Wai-Man Chuang, Kwok-Yung Yuen, Ivan Fan-Ngai ****, Kelvin Kai-Wang To
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.
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