1. Genomic epidemiology of SARS-CoV-2 in Cambodia, January 2020 to February 2021
- Author
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Yvonne C F Su, Jordan Z J Ma, Tey Putita Ou, Leakhena Pum, Sidonn Krang, Philomena Raftery, Michael H Kinzer, Jennifer Bohl, Vanra Ieng, Vannda Kab, Sarika Patel, Borann Sar, Wong Foong Ying, Jayanthi Jayakumar, Viseth Srey Horm, Narjis Boukli, Sokhoun Yann, Cecile Troupin, Vireak Heang, Jose A Garcia-Rivera, Yi Sengdoeurn, Seng Heng, Sreyngim Lay, Sophana Chea, Chau Darapheak, Chin Savuth, Asheena Khalakdina, Sowath Ly, Laurence Baril, Jessica E Manning, Etienne Simone-Loriere, Veasna Duong, Philippe Dussart, Ly Sovann, Gavin J D Smith, Erik A Karlsson, Duke-NUS Medical School [Singapore], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Université de Montpellier (UM), Ministry of Health [Phnom Penh], World Health Organization [Phnom Penh] (WHO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Centers for Disease Control and Prevention [Phnom Penh], Embassy of the United States of America, National Institute of Allergy and Infectious Diseases [Phnom Penh, Cambodia] (NIAID), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), US Naval Medical Research Unit n°2, National Institute of Public Health [Phnom Penh, Cambodge], Département de Virologie - Department of Virology, Institut Pasteur [Paris] (IP), Duke University [Durham], The work at Institut Pasteur du Cambodge is supported by the WHO, the European Union, The Pasteur International Center for Research on Emerging Infectious Diseases National Institutes of Health, Department of Health and Human Services funded project No. 1U01AI151758-01, Wellcome Trust grant 222574/Z/21/Z, the British Embassy in Cambodia, and French Development Agency-funded ECOnomic development, ECOsystem MOdifications, and emerging infectious diseases Risk Evaluation (ECOMORE) 2 COVID-19 top up project No. CZZ 2146 01A. E.A.K. was funded, in part, by federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services Contract No. 75N93021C00015. The study was supported by the Duke-NUS Signature Research Programme funded by the Ministry of Health, Singapore, and by contracts HHSN272201400006C and 75N93021C00016 from the National Institute of Allergy and Infectious Disease, National Institutes of Health, Department of Health and Human Services, USA. This work was funded in part by the Division of Intramural Research at National Institute of Allergy and Infectious Diseases at the National Institutes of Health and Bill and Melinda Gates Foundation Grant OPP1211806. E.S.L. acknowledges funding from the INCEPTION programme (Investissements d’Avenir), grant number ANR-16-CONV-0005., and ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016)
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pandemic ,[SDV]Life Sciences [q-bio] ,Virology ,coronavirus ,COVID-19 ,genetic diversity ,phylogeny ,Microbiology - Abstract
The first case of coronavirus disease 2019 (COVID-19) in Cambodia was confirmed on 27 January 2020 in a traveller from Wuhan. Cambodia subsequently implemented strict travel restrictions, and although intermittent cases were reported during the first year of the COVID-19 pandemic, no apparent widespread community transmission was detected. Investigating the routes of severe acute respiratory coronavirus 2 (SARS-CoV-2) introduction into the country was critical for evaluating the implementation of public health interventions and assessing the effectiveness of social control measures. Genomic sequencing technologies have enabled rapid detection and monitoring of emerging variants of SARS-CoV-2. Here, we detected 478 confirmed COVID-19 cases in Cambodia between 27 January 2020 and 14 February 2021, 81.3 per cent in imported cases. Among them, fifty-four SARS-CoV-2 genomes were sequenced and analysed along with representative global lineages. Despite the low number of confirmed cases, we found a high diversity of Cambodian viruses that belonged to at least seventeen distinct PANGO lineages. Phylogenetic inference of SARS-CoV-2 revealed that the genetic diversity of Cambodian viruses resulted from multiple independent introductions from diverse regions, predominantly, Eastern Asia, Europe, and Southeast Asia. Most cases were quickly isolated, limiting community spread, although there was an A.23.1 variant cluster in Phnom Penh in November 2020 that resulted in a small-scale local transmission. The overall low incidence of COVID-19 infections suggests that Cambodia’s early containment strategies, including travel restrictions, aggressive testing and strict quarantine measures, were effective in preventing large community outbreaks of COVID-19.
- Published
- 2022
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