Vincent Chi Chung Cheng1,2,3, Jonathan Daniel Ip1, Allen Wing Ho Chu1, Anthony Raymond Tam4, Wan Mui Chan1, Syed Muhammad Umer Abdullah1, Brian Pui Chun Chan1, Shuk Ching Wong3, Mike Yat Wah Kwan5,6, Gilbert T Chua5,7, Patrick Ip5,7, Jacky Man Chun Chan8, Bosco Hoi Shiu Lam9, Wing Kin To9, Vivien Wai Man Chuang10, Kwok Yung Yuen1,2,3,11,12, Ivan Fan Ngai Hung4,13, Kelvin Kai Wang To1,2,3,11,12. 1. 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. 2. Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China. 3. Infection Control Team, Queen Mary Hospital, Hong Kong West Cluster, Hong Kong Special Administrative Region, China. 4. Department of Medicine, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China. 5. Department of Pediatrics and Adolescent Medicine, The Hong Kong Children's Hospital, Hong Kong Special Administrative Region, China. 6. Department of Pediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong Special Administrative Region, China. 7. Department of Pediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China. 8. Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong Special Administrative Region, China. 9. Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China. 10. Quality and Safety Division, Hospital Authority, Hong Kong Special Administrative Region, China. 11. Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China. 12. Centre for Virology, Vaccinology, and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, Chinaand. 13. Department of Medicine, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong, Hong Kong Special Administrative Region, China.
Abstract
BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (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 on 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 February 2022, including 432 residents, visitors, or staff (56.3%) from a single housing estate (KC Estate). The outbreak at the KC Estate had a short doubling time of 1.28 days (95% confidence interval: .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 sublineages.
BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (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 on 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 February 2022, including 432 residents, visitors, or staff (56.3%) from a single housing estate (KC Estate). The outbreak at the KC Estate had a short doubling time of 1.28 days (95% confidence interval: .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 sublineages.
Authors: Chirayu Goswami; Michael Sheldon; Christian Bixby; Mehdi Keddache; Alexander Bogdanowicz; Yihe Wang; Jonathan Schultz; Jessica McDevitt; James LaPorta; Elaine Kwon; Steven Buyske; Dana Garbolino; Glenys Biloholowski; Alex Pastuszak; Mary Storella; Amit Bhalla; Florence Charlier-Rodriguez; Russ Hager; Robin Grimwood; Shareef A Nahas Journal: BMC Infect Dis Date: 2022-04-25 Impact factor: 3.667
Authors: Prerna Arora; Lu Zhang; Nadine Krüger; Cheila Rocha; Anzhalika Sidarovich; Sebastian Schulz; Amy Kempf; Luise Graichen; Anna-Sophie Moldenhauer; Anne Cossmann; Alexandra Dopfer-Jablonka; Georg M N Behrens; Hans-Martin Jäck; Stefan Pöhlmann; Markus Hoffmann Journal: Cell Host Microbe Date: 2022-05-06 Impact factor: 31.316