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: During 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 . 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.
Index: COVID19, Next generation sequencing, Outbreak, Phylodynamic, Phylogenetic, SARS-CoV-2, Viral genome