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Su YCF, Ma JZJ, Ou TP, Pum L, Krang S, Raftery P, Kinzer MH, Bohl J, Ieng V, Kab V, Patel S, Sar B, Ying WF, Jayakumar J, Horm VS, Boukli N, Yann S, Troupin C, Heang V, Garcia-Rivera JA, Sengdoeurn Y, Heng S, Lay S, Chea S, Darapheak C, Savuth C, Khalakdina A, Ly S, Baril L, Manning JE, Simone-Loriere E, Duong V, Dussart P, Sovann L, Smith GJD, Karlsson EA. Genomic epidemiology of SARS-CoV-2 in Cambodia, January 2020 to February 2021. Virus Evol 2022; 9:veac121. [PMID: 36654682 PMCID: PMC9838690 DOI: 10.1093/ve/veac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/05/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
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.
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Affiliation(s)
- Yvonne C F Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd 169857, Singapore
| | - Jordan Z J Ma
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd 169857, Singapore
| | - Tey Putita Ou
- Virology Unit, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, 5 Preah Monivong Blvd (93), Phnom Penh 12201, Cambodia
- Ecole Doctorale GAIA, University of Montpelier, 641 Av. du Doyen Gaston Giraud, Montpellier 34000, France
| | - Leakhena Pum
- Virology Unit, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, 5 Preah Monivong Blvd (93), Phnom Penh 12201, Cambodia
| | - Sidonn Krang
- Communicable Disease Control Department, Ministry of Health, 80, 289 Samdach Penn Nouth St. (289), Phnom Penh 120407, Cambodia
| | - Philomena Raftery
- World Health Organization Country Office, 5 - St 205, Phnom Penh 12355, Cambodia
| | - Michael H Kinzer
- United States Centers for Disease Control and Prevention, 80, 289 Samdach Penn Nouth St. (289), Phnom Penh 120407, Cambodia
| | - Jennifer Bohl
- Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Phnom Penh, Cambodia
| | - Vanra Ieng
- World Health Organization Country Office, 5 - St 205, Phnom Penh 12355, Cambodia
| | - Vannda Kab
- World Health Organization Country Office, 5 - St 205, Phnom Penh 12355, Cambodia
| | - Sarika Patel
- World Health Organization Country Office, 5 - St 205, Phnom Penh 12355, Cambodia
| | - Borann Sar
- United States Centers for Disease Control and Prevention, 80, 289 Samdach Penn Nouth St. (289), Phnom Penh 120407, Cambodia
| | - Wong Foong Ying
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd 169857, Singapore
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd 169857, Singapore
| | - Viseth Srey Horm
- Virology Unit, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, 5 Preah Monivong Blvd (93), Phnom Penh 12201, Cambodia
| | - Narjis Boukli
- Virology Unit, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, 5 Preah Monivong Blvd (93), Phnom Penh 12201, Cambodia
| | - Sokhoun Yann
- Virology Unit, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, 5 Preah Monivong Blvd (93), Phnom Penh 12201, Cambodia
| | - Cecile Troupin
- Virology Unit, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, 5 Preah Monivong Blvd (93), Phnom Penh 12201, Cambodia
| | - Vireak Heang
- Sequencing Mini-Platform, Institut Pasteur du Cambodge, 5 Preah Monivong Blvd (93), Phnom Penh 12201, Cambodia
- Naval Medical Research Unit TWO, Lot#: 80, 289 Samdach Penn Nout, Phnom Penh 120407, Cambodia
| | - Jose A Garcia-Rivera
- Naval Medical Research Unit TWO, Lot#: 80, 289 Samdach Penn Nout, Phnom Penh 120407, Cambodia
| | - Yi Sengdoeurn
- Communicable Disease Control Department, Ministry of Health, 80, 289 Samdach Penn Nouth St. (289), Phnom Penh 120407, Cambodia
| | - Seng Heng
- Communicable Disease Control Department, Ministry of Health, 80, 289 Samdach Penn Nouth St. (289), Phnom Penh 120407, Cambodia
| | - Sreyngim Lay
- Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Sophana Chea
- Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Chau Darapheak
- National Institute for Public Health, Lot#: 80, 289 Samdach Penn Nouth St (289), Phnom Penh 120407, Cambodia
| | - Chin Savuth
- National Institute for Public Health, Lot#: 80, 289 Samdach Penn Nouth St (289), Phnom Penh 120407, Cambodia
| | - Asheena Khalakdina
- World Health Organization Country Office, 5 - St 205, Phnom Penh 12355, Cambodia
| | - Sowath Ly
- Epidemiology and Public Health Unit, Institute Pasteur du Cambodge, 5 Preah Monivong Blvd (93), Phnom Penh 12201, Cambodia
| | - Laurence Baril
- Direction, Institute Pasteur du Cambodge, 5 Preah Monivong Blvd (93), Phnom Penh 12201, Cambodia
| | - Jessica E Manning
- Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | | | - Veasna Duong
- Virology Unit, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, 5 Preah Monivong Blvd (93), Phnom Penh 12201, Cambodia
| | - Philippe Dussart
- Virology Unit, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, 5 Preah Monivong Blvd (93), Phnom Penh 12201, Cambodia
| | - Ly Sovann
- Communicable Disease Control Department, Ministry of Health, 80, 289 Samdach Penn Nouth St. (289), Phnom Penh 120407, Cambodia
| | - Gavin J D Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd 169857, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, 8 College Rd 169857, Singapore
- Duke Global Health Institute, Duke University, 310 Trent Dr, Durham, NC 27710, USA
| | - Erik A Karlsson
- Virology Unit, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, 5 Preah Monivong Blvd (93), Phnom Penh 12201, Cambodia
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