Dataset Information

Phylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong: An observational study.

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

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.

SUBMITTER: Chan WM

PROVIDER: S-EPMC7985010 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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Publications

Phylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong: An observational study.

Chan Wan-Mui WM Ip Jonathan Daniel JD Chu Allen Wing-Ho AW Tse Herman H Tam Anthony Raymond AR Li Xin X Kwan Mike Yat-Wah MY Yau Yat-Sun YS Leung Wai-Shing WS Chik Thomas Shiu-Hong TS To Wing-Kin WK Ng Anthony Chin-Ki AC Yip Cyril Chik-Yan CC Poon Rosana Wing-Shan RW Chan Kwok-Hung KH Wong Sally Cheuk-Ying SC Choi Garnet Kwan-Yue GK Lung David Christopher DC Cheng Vincent Chi-Chung VC Hung Ivan Fan-Ngai IF Yuen Kwok-Yung KY To Kelvin Kai-Wang KK

The Lancet regional health. Western Pacific 20210323

<h4>Background</h4>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.<h4>Methods</h4>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 ...[more]

PMID: 33778795

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Dataset Information

Phylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong: An observational study.

Background

Methods

Findings

Interpretation

Publications

Phylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong: An observational study.

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