SARS-CoV-2 genomic surveillance in southern Vietnam (2020-2023): Tracking variant evolution and public health impact in a limited-resource setting.
| Title: | SARS-CoV-2 genomic surveillance in southern Vietnam (2020-2023): Tracking variant evolution and public health impact in a limited-resource setting. |
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| Authors: | Cao MT; Pasteur Institute in Ho Chi Minh City, Vietnam.; Dao HM; Pasteur Institute in Ho Chi Minh City, Vietnam.; Duong MH; Pasteur Institute in Ho Chi Minh City, Vietnam. Electronic address: hangdm@pasteurhcm.edu.vn.; Vu PHN; Pasteur Institute in Ho Chi Minh City, Vietnam.; Pham TTH; Pasteur Institute in Ho Chi Minh City, Vietnam.; Hoang TND; Pasteur Institute in Ho Chi Minh City, Vietnam.; Le MH; Pasteur Institute in Ho Chi Minh City, Vietnam.; Nguyen VT; Pasteur Institute in Ho Chi Minh City, Vietnam.; Luong CQ; Pasteur Institute in Ho Chi Minh City, Vietnam.; Pham QD; Pasteur Institute in Ho Chi Minh City, Vietnam.; Nguyen VT; Pasteur Institute in Ho Chi Minh City, Vietnam.; Nguyen VT; Pasteur Institute in Ho Chi Minh City, Vietnam. |
| Source: | Acta tropica [Acta Trop] 2025 Sep; Vol. 269, pp. 107754. Date of Electronic Publication: 2025 Jul 22. |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: Elsevier Country of Publication: Netherlands NLM ID: 0370374 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-6254 (Electronic) Linking ISSN: 0001706X NLM ISO Abbreviation: Acta Trop Subsets: MEDLINE |
| Imprint Name(s): | Publication: Amsterdam : Elsevier; Original Publication: Basel. |
| MeSH Terms: | SARS-CoV-2*/genetics ; SARS-CoV-2*/classification ; SARS-CoV-2*/isolation & purification ; COVID-19*/epidemiology ; COVID-19*/virology ; Genome, Viral*; Vietnam/epidemiology ; Humans ; Phylogeny ; Public Health ; Evolution, Molecular ; Genomics ; High-Throughput Nucleotide Sequencing |
| Abstract: | The COVID-19 pandemic highlighted the urgent need for genomic surveillance to monitor viral evolution and guide public health responses, especially in limited-resource settings. This study describes the establishment and implementation of a SARS-CoV-2 genomic surveillance system by Pasteur Institute in Ho Chi Minh City (PIHCM), covering 20 provinces in southern Vietnam from January 2020 to June 2023. Nasopharyngeal swabs were systematically collected, screened by RT-PCR (Ct < 28), and sequenced using adaptable Next-Generation Sequencing technologies, including Illumina MiSeq and later Oxford Nanopore MinION, supported by international training and resources. Phylogenetic analyses tracked viral lineage dynamics across five pandemic phases. A total of 2207 genomes were sequenced, revealing temporal shifts in variant dominance, particularly Delta and Omicron variants and an average mutation count of 52,5 per sample. The data were instrumental in managing local outbreaks, informing national responses, and contributing to global databases like GISAID. This study demonstrates that adaptive genomic surveillance is both feasible and effective in resource-constrained settings. It underscores the critical role of real-time genomic data in pandemic response and advocates for sustained investment in capacity building, infrastructure and global collaboration, offering a scalable model for future preparedness in low - and middle - income countries.; (Copyright © 2025 Elsevier B.V. All rights reserved.) |
| Competing Interests: | Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. |
| Contributed Indexing: | Keywords: Genomic surveillance; Next-generation sequencing; SARS-CoV-2; Vietnam; Whole genome sequencing; limited-resource settings |
| Entry Date(s): | Date Created: 20250724 Date Completed: 20250825 Latest Revision: 20250825 |
| Update Code: | 20260130 |
| DOI: | 10.1016/j.actatropica.2025.107754 |
| PMID: | 40706826 |
| Database: | MEDLINE |
Journal Article