Phylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong : An observational study
© 2021 The Author(s). Published by Elsevier Ltd..
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:10 |
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| Enthalten in: |
The Lancet regional health. Western Pacific - 10(2021) vom: 20. Mai, Seite 100130 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Chan, Wan-Mui [VerfasserIn] |
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| Links: |
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| Themen: |
COVID19 |
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| Anmerkungen: |
Date Revised 07.11.2023 published: Print-Electronic Citation Status PubMed-not-MEDLINE |
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| doi: |
10.1016/j.lanwpc.2021.100130 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM323346383 |
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| 100 | 1 | |a Chan, Wan-Mui |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Phylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong |b An observational study |
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| 500 | |a Citation Status PubMed-not-MEDLINE | ||
| 520 | |a © 2021 The Author(s). Published by Elsevier Ltd. | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
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| 650 | 4 | |a Next generation sequencing | |
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| 650 | 4 | |a Phylodynamic | |
| 650 | 4 | |a Phylogenetic | |
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| 700 | 1 | |a Ip, Jonathan Daniel |e verfasserin |4 aut | |
| 700 | 1 | |a Chu, Allen Wing-Ho |e verfasserin |4 aut | |
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| 700 | 1 | |a Tam, Anthony Raymond |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Xin |e verfasserin |4 aut | |
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| 700 | 1 | |a Yau, Yat-Sun |e verfasserin |4 aut | |
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| 700 | 1 | |a Chik, Thomas Shiu-Hong |e verfasserin |4 aut | |
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| 700 | 1 | |a To, Kelvin Kai-Wang |e verfasserin |4 aut | |
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