• Wan-Mui Chan, Jonathan Daniel Ip, Allen Wing-Ho Chu, Herman Tse, Anthony Raymond Tam, Xin Li, Mike Yat-Wah Kwan, Yat-Sun Yau, Wai-Shing Leung, Thomas Shiu-Hong Chik, Wing-Kin To, Anthony Chin-Ki Ng, Cyril Chik-Yan Yip, Rosana Wing-Shan Poon, Kwok-Hung Chan, Sally Cheuk-Ying Wong, Garnet Kwan-Yue Choi, David Christopher Lung, Vincent Chi-Chung Cheng, Ivan Fan-Ngai Hung, Kwok-Yung Yuen, and 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, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
• Lancet Reg Health West Pac. 2021 May 1; 10: 100130.

BackgroundViral genomic surveillance is vital for understanding the transmission of COVID-19. In Hong Kong, breakthrough outbreaks have occurred in July (third wave) and November (fourth wave) 2020. We used whole viral genome analysis to study the characteristics of these waves.MethodsWe analyzed 509 SARS-CoV-2 genomes collected from Hong Kong patients between 22nd January and 29th November, 2020. Phylogenetic and phylodynamic analyses were performed, and were interpreted with epidemiological information.FindingsDuring the third and fourth waves, diverse SARS-CoV-2 genomes were identified among imported infections. Conversely, local infections were dominated by a single lineage during each wave, with 96.6% (259/268) in the third wave and 100% (73/73) in the fourth wave belonging to B.1.1.63 and B.1.36.27 lineages, respectively. While B.1.1.63 lineage was imported 2 weeks before the beginning of the third wave, B.1.36.27 lineage has circulated in Hong Kong for 2 months prior to the fourth wave. During the fourth wave, 50.7% (37/73) of local infections in November was identical to the viral genome from an imported case in September. Within B.1.1.63 or B.1.36.27 lineage in our cohort, the most common non-synonymous mutations occurred at the helicase (nsp13) gene.InterpretationAlthough stringent measures have prevented most imported cases from spreading in Hong Kong, a single lineage with low-level local transmission in October and early November was responsible for the fourth wave. A superspreading event or lower temperature in November may have facilitated the spread of the B.1.36.27 lineage.© 2021 The Author(s). Published by Elsevier Ltd.

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