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Dao MH, Phan LT, Cao TM, Luong QC, Pham HTT, Vu NHP, Khuu NV, Nguyen TV, Nguyen LT, Nguyen HT, Nguyen AH, Huynh LKT, Huynh TP, Nguyen QH, Truong HC, Nguyen HM, Trinh TX, Nguyen DT, Nguyen TB, Do HT, Pham QD, Nguyen TV. Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. J Med Virol 2021; 93:5660-5665. [PMID: 34042186 PMCID: PMC8242548 DOI: 10.1002/jmv.27103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 11/18/2022]
Abstract
Genome‐wide analysis of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) strains is essential to better understand infectivity and virulence and to track coronavirus disease 2019 (COVID‐19) cases and outbreaks. We performed whole‐genome sequencing of 27 SARS‐CoV‐2 strains isolated between January 2020 and April 2020. A total of 54 mutations in different genomic regions was found. The D614G mutation, first detected in March 2020, was identified in 18 strains and was more likely associated with a lower cycle threshold (<25) in real‐time reverse‐transcription polymerase chain reaction diagnostic tests than the original D614 (prevalence ratio = 2.75; 95% confidence interval, 1.19–6.38). The integration of sequencing and epidemiological data suggests that SARS‐CoV‐2 transmission in both quarantine areas and in the community in Vietnam occur at the beginning of the epidemic although the country implemented strict quarantine quite early, with strict contact tracing, and testing. These findings provide insights into the nature of the epidemic, as well as shape strategies for COVID‐19 prevention and control in Vietnam.
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Affiliation(s)
- Manh H Dao
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Lan T Phan
- Directorial Board, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thang M Cao
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Quang C Luong
- Department for Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hang T T Pham
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Nhung H P Vu
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Nghia V Khuu
- Department for Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thinh V Nguyen
- Department for Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Long T Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hieu T Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Anh H Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Loan Kim Thi Huynh
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thao P Huynh
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Quan H Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hieu C Truong
- Department for Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | - Dung T Nguyen
- Ho Chi Minh City Center for Diseases Control, Ho Chi Minh City, Vietnam
| | | | - Hung T Do
- Pasteur Institute of Nha Trang, Nha Trang, Vietnam
| | - Quang D Pham
- Planning Division, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam.,Training Center, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thuong V Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
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