Phylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong: An observational study
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 C. Y. Wong, Garnet Kwan-Yue Choi, David Christopher Lung, Vincent Chi‐Chung Cheng, Ivan Fan‐Ngai Hung, Kwok‐Yung Yuen, Kelvin Kai‐Wang To
Abstract
BACKGROUND: Viral 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. METHODS: We 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. FINDINGS: 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. INTERPRETATION: Although 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.