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Phylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong: An observational study.
Chan, Wan-Mui; Ip, Jonathan Daniel; Chu, Allen Wing-Ho; Tse, Herman; Tam, Anthony Raymond; Li, Xin; Kwan, Mike Yat-Wah; Yau, Yat-Sun; Leung, Wai-Shing; Chik, Thomas Shiu-Hong; To, Wing-Kin; Ng, Anthony Chin-Ki; Yip, Cyril Chik-Yan; Poon, Rosana Wing-Shan; Chan, Kwok-Hung; Wong, Sally Cheuk-Ying; Choi, Garnet Kwan-Yue; Lung, David Christopher; Cheng, Vincent Chi-Chung; Hung, Ivan Fan-Ngai; Yuen, Kwok-Yung; To, Kelvin Kai-Wang.
  • Chan WM; 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.
  • Ip JD; 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.
  • Chu AW; 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.
  • Tse H; Department of Pathology, Hong Kong Children's Hospital, Kowloon, Hong Kong Special Administrative Region, China.
  • Tam AR; Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China.
  • Li X; 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.
  • Kwan MY; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China.
  • Yau YS; Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong Special Administrative Region, China.
  • Leung WS; Department of Paediatrics, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region, China.
  • Chik TS; Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong Special Administrative Region, China.
  • To WK; Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong Special Administrative Region, China.
  • Ng AC; Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China.
  • Yip CC; 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.
  • Poon RW; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China.
  • Chan KH; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China.
  • Wong SC; 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.
  • Choi GK; Department of Pathology, Hong Kong Children's Hospital, Kowloon, Hong Kong Special Administrative Region, China.
  • Lung DC; Department of Pathology, Hong Kong Children's Hospital, Kowloon, Hong Kong Special Administrative Region, China.
  • Cheng VC; Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region, China.
  • Hung IF; Department of Pathology, Hong Kong Children's Hospital, Kowloon, Hong Kong Special Administrative Region, China.
  • Yuen KY; Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region, China.
  • To KK; 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 ; 10: 100130, 2021 May.
Article in English | MEDLINE | ID: covidwho-2254259
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.
Keywords

Full text: Available Collection: International databases Database: MEDLINE Type of study: Cohort study / Observational study / Prognostic study Language: English Journal: Lancet Reg Health West Pac Year: 2021 Document Type: Article Affiliation country: J.lanwpc.2021.100130

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Cohort study / Observational study / Prognostic study Language: English Journal: Lancet Reg Health West Pac Year: 2021 Document Type: Article Affiliation country: J.lanwpc.2021.100130