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Gladkikh AS, Cao TM, Klyuchnikova EO, Dao MH, Sharova AA, Melnichenko VD, Popova MR, Arbuzova TV, Sbarzaglia VA, Tsyganova NA, Ramsay E, Dedkov VG. Correction: Near complete genome sequences from Southern Vietnam revealed local features of genetic diversity and intergenerational changes in SARS- CoV-2 variants in 2020-2021. BMC Infect Dis 2023; 23:898. [PMID: 38129796 PMCID: PMC10734165 DOI: 10.1186/s12879-023-08853-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Affiliation(s)
- Anna S Gladkikh
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint, Petersburg, 197101, Russia
| | - Thang M Cao
- Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | - Manh H Dao
- Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Alena A Sharova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint, Petersburg, 197101, Russia
| | | | - Margarita R Popova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint, Petersburg, 197101, Russia
| | - Tatiana V Arbuzova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint, Petersburg, 197101, Russia
| | - Valeriya A Sbarzaglia
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint, Petersburg, 197101, Russia
| | - Nadezhda A Tsyganova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint, Petersburg, 197101, Russia
| | - Edward Ramsay
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint, Petersburg, 197101, Russia
| | - Vladimir G Dedkov
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint, Petersburg, 197101, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne, Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
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Gladkikh AS, Cao TM, Klyuchnikova EO, Dao MH, Sharova AA, Melnichenko VD, Popova MR, Arbuzova TV, Sbarzaglia VA, Tsyganova NA, Ramsay E, Dedkov VG. Near complete genome sequences from Southern Vietnam revealed local features of genetic diversity and intergenerational changes in SARS- CoV-2 variants in 2020-2021. BMC Infect Dis 2023; 23:806. [PMID: 37974125 PMCID: PMC10655423 DOI: 10.1186/s12879-023-08814-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Since its beginnings in 2019, the COVID-19 pandemic is still a problem of global medical concern. Southern Vietnam is one of the country's vast regions, including 20 provinces and the densely populated metropolis Ho Chi Minh City. A randomized retrospective study was performed to investigate the epidemiology and genetic diversity of COVID-19. Whole-genome sequencing of 126 SARS-CoV-2 samples collected from Southern Vietnam between January 2020 and December 2021 revealed the main circulating variants and their distribution. METHODS Epidemiological data were obtained from the Department of Preventive Medicine of the Vietnamese Ministry of Health. To identify circulating variants, RNA, extracted from 126 nasopharyngeal swabs of patients with suspected COVID-19 were sequenced on Illunina MiSeq to obtain near complete genomes SARS-CoV-2. RESULTS Due to the effectiveness of restrictive measures in Vietnam, it was possible to keep incidence at a low level. The partial relaxation of restrictive measures, and the spread of Delta lineages, contributed to the beginning of a logarithmic increase in incidence. Lineages 20A-H circulated in Southern Vietnam during 2020. Spread of the Delta lineage in Southern Vietnam began in March 2021, causing a logarithmic rise in the number of COVID-19 cases. CONCLUSIONS Pandemic dynamics in Southern Vietnam feature specific variations in incidence, and these reflect the success of the restrictive measures put in place during the early stages of the pandemic.
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Affiliation(s)
- Anna S Gladkikh
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Thang M Cao
- Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | - Manh H Dao
- Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Alena A Sharova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | | | - Margarita R Popova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Tatiana V Arbuzova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Valeriya A Sbarzaglia
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Nadezhda A Tsyganova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Edward Ramsay
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Vladimir G Dedkov
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
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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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4
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Dao MH, Nguyen HT, Nguyen TV, Nguyen AH, Luong QC, Vu NHP, Pham HTT, Nguyen TNT, Thach DH, Nguyen LV, Bui LV, Nguyen HM, Huynh LKT, Nguyen LT, Cao TM, Pham QD, Nguyen TV, Phan LT. New SARS-CoV-2 variant of concern imported from the United Kingdom to Vietnam, December 2020. J Med Virol 2021; 93:2628-2630. [PMID: 33638484 PMCID: PMC8013811 DOI: 10.1002/jmv.26908] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 12/24/2022]
Affiliation(s)
- Manh H Dao
- 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
| | - Thinh V Nguyen
- Department for Disease Control and Prevention, 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
| | - Quang C Luong
- Department for Disease Control and Prevention, 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
| | - Hang T T Pham
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thao N T Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Dung H Thach
- Tra Vinh Provincial Center for Disease Control, Tra Vinh City, Vietnam
| | - Lo V Nguyen
- Tra Vinh Provincial Center for Disease Control, Tra Vinh City, Vietnam
| | - Luan V Bui
- Tra Vinh Hospital for Tuberculosis and Respiratory Diseases, Tra Vinh City, Vietnam
| | - Hang M Nguyen
- General Department of Preventive Medicine, Hanoi, Vietnam
| | - Loan K T Huynh
- Microbiology and Immunology Department, 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
| | - Thang M Cao
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, 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
- Directorial Board, 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
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5
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Phan LT, Nguyen TV, Huynh LKT, Dao MH, Vo TAN, Vu NHP, Pham HTT, Nguyen HT, Nguyen TT, Le HQ, Nguyen TV, Nguyen QH, Huynh TP, Nguyen SN, Nguyen AH, Nguyen NT, Nguyen TNT, Nguyen LT, Luong QC, Cao TM, Pham QD. Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam. J Med Virol 2020; 92:2209-2215. [PMID: 32462705 PMCID: PMC7283826 DOI: 10.1002/jmv.26075] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 04/30/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 01/08/2023]
Abstract
In January 2020, we identified two severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2)‐infected patients in a familial cluster with one person coming from Wuhan, China. The complete genome sequences of two SARS‐CoV‐2 strains isolated from these patients were identical and 99.98% similar to strains isolated in Wuhan. This is genetically suggestive of human‐to‐human transmission of SARS‐CoV‐2 and indicates Wuhan as the most plausible origin of the early outbreak in Vietnam. The younger patient had a mild upper respiratory illness and a brief viral shedding, whereas the elderly with multi‐morbidity had pneumonia, prolonged viral shedding, and residual lung damage. The evidence of nonsynonymous substitutions in the ORF1ab region of the viral sequence warrants further studies. Transmission of SARS‐CoV‐2 is a global public health and clinical concern. This report describes clinical features, virus isolation, and complete genome sequences from the first two SARS‐CoV‐2 infections in Vietnam. Epidemiological and phylogenetic analysis suggested evidence of human‐to‐human transmission of SARS‐CoV‐2. Comparison of SARS‐CoV‐2 strains isolated from these two patients with those from Wuhan showed high similarities. Nonsynonymous substitutions existed in the ORF1ab region of the viral sequence. Compared with mild clinical and virological manifestations in the younger patient, the elderly suffered from pneumonia, prolonged viral shedding, and residual lung damage.
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Affiliation(s)
- Lan T Phan
- Directorial Board, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thuong V Nguyen
- Directorial Board, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Loan K T Huynh
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Manh H Dao
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Tho A N Vo
- Department of Tropical Diseases, Cho Ray Hospital, 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
| | - Hang T T Pham
- 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
| | - Thuc T Nguyen
- Directorial Board, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Hung Q Le
- Department of Tropical Diseases, Cho Ray Hospital, 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
| | - Quan H Nguyen
- 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
| | - Sang N Nguyen
- Department of Tropical Diseases, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Anh H Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Ngoc T Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thao N T Nguyen
- Microbiology and Immunology Department, 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
| | - Quang C Luong
- Department for Disease Control and Prevention, 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 D Pham
- Planning Division and Training Center, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
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6
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Pescia G, Dao MH, Weihs D, Gaide AC, Loertscher A, Hohlfeld P, Marguerat P, Nguyen The H, Paccaud F, Maillard C. [Triple screening for trisomy 21: prospective results of 7039 assessments]. Rev Med Suisse Romande 1993; 113:277-80. [PMID: 7684852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- G Pescia
- Division autonome de génétique médicale, CHUV, Lausanne
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