File Download
  Links for fulltext
     (May Require Subscription)
Supplementary

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

TitlePhylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong: An observational study
Authors
KeywordsCOVID19
SARS-CoV-2
Phylogenetic
Phylodynamic
Viral genome
Issue Date2021
PublisherElsevier: Creative Commons Licenses. The Journal's web site is located at https://www.thelancet.com/regional-health/western-pacific
Citation
The Lancet Regional Health - Western Pacific, 2021, v. 10, p. article no. 100130 How to Cite?
AbstractBackground: 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. Funding: Richard and Carol Yu, Michael Tong, and the Government Consultancy Service (see acknowledgments for full list).
Persistent Identifierhttp://hdl.handle.net/10722/304979
ISSN
2023 Impact Factor: 7.6
2023 SCImago Journal Rankings: 2.197
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorChan, WM-
dc.contributor.authorIp, JD-
dc.contributor.authorChu, AWH-
dc.contributor.authorTse, H-
dc.contributor.authorTam, AR-
dc.contributor.authorLi, X-
dc.contributor.authorKwan, MYW-
dc.contributor.authorYau, YS-
dc.contributor.authorLeung, WS-
dc.contributor.authorChik, TSH-
dc.contributor.authorTo, WK-
dc.contributor.authorNg, ACK-
dc.contributor.authorYip, CCY-
dc.contributor.authorPoon, RWS-
dc.contributor.authorChan, KH-
dc.contributor.authorWong, SCY-
dc.contributor.authorChoi, GKY-
dc.contributor.authorLung, DC-
dc.contributor.authorCheng, VCC-
dc.contributor.authorHung, IFN-
dc.contributor.authorYuen, KY-
dc.contributor.authorTo, KKW-
dc.date.accessioned2021-10-05T02:37:59Z-
dc.date.available2021-10-05T02:37:59Z-
dc.date.issued2021-
dc.identifier.citationThe Lancet Regional Health - Western Pacific, 2021, v. 10, p. article no. 100130-
dc.identifier.issn2666-6065-
dc.identifier.urihttp://hdl.handle.net/10722/304979-
dc.description.abstractBackground: 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. Funding: Richard and Carol Yu, Michael Tong, and the Government Consultancy Service (see acknowledgments for full list).-
dc.languageeng-
dc.publisherElsevier: Creative Commons Licenses. The Journal's web site is located at https://www.thelancet.com/regional-health/western-pacific-
dc.relation.ispartofThe Lancet Regional Health - Western Pacific-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectCOVID19-
dc.subjectSARS-CoV-2-
dc.subjectPhylogenetic-
dc.subjectPhylodynamic-
dc.subjectViral genome-
dc.titlePhylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong: An observational study-
dc.typeArticle-
dc.identifier.emailChan, WM: mbally@hku.hk-
dc.identifier.emailChu, AWH: awhchu@hku.hk-
dc.identifier.emailLi, X: xinli@hku.hk-
dc.identifier.emailYip, CCY: yipcyril@hku.hk-
dc.identifier.emailPoon, RWS: rosana@hkucc.hku.hk-
dc.identifier.emailChan, KH: chankh2@hkucc.hku.hk-
dc.identifier.emailHung, IFN: ivanhung@hkucc.hku.hk-
dc.identifier.emailYuen, KY: kyyuen@hkucc.hku.hk-
dc.identifier.emailTo, KKW: kelvinto@hku.hk-
dc.identifier.authorityTse, H=rp00519-
dc.identifier.authorityLi, X=rp02808-
dc.identifier.authorityYip, CCY=rp01721-
dc.identifier.authorityChan, KH=rp01921-
dc.identifier.authorityHung, IFN=rp00508-
dc.identifier.authorityYuen, KY=rp00366-
dc.identifier.authorityTo, KKW=rp01384-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1016/j.lanwpc.2021.100130-
dc.identifier.pmid33778795-
dc.identifier.pmcidPMC7985010-
dc.identifier.scopuseid_2-s2.0-85104106226-
dc.identifier.hkuros326081-
dc.identifier.volume10-
dc.identifier.spagearticle no. 100130-
dc.identifier.epagearticle no. 100130-
dc.identifier.isiWOS:000659894600006-
dc.publisher.placeUnited Kingdom-

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats