Abstract
Rabies is a fatal zoonotic disease that causes encephalitis in almost all mammals. Vietnam remains endemic for rabies and shares borders with China, Laos, and Cambodia, where the disease also persists. Nucleoprotein and full-genome sequencing are valuable tools for investigating the genetic diversity and transmission dynamics of circulating rabies virus (RABV) strains. This study aimed to assess the current rabies situation in Vietnam and genetically characterize RABV strains using both sequencing approaches. Human and canine rabies cases are reported annually in Vietnam, where approximately half a million people receiving post-exposure prophylaxis each year, though this number has recently increased. Epidemiological data and RABVs from humans and rabid dogs were analyzed. Vietnamese RABVs were classified into four distinct genetic groups, all phylogenetically related to viruses circulating in neighboring countries. Full-genome analysis revealed regional differences in virus classification, suggesting that local factors may influence viral circulation between Vietnam and neighboring countries. The high genetic similarity between human- and dog-derived RABVs underscores the continued zoonotic threat and highlights the critical need for a One Health approach to rabies prevention and control in Vietnam and its neighboring regions.
Data availability
Sequence data that support the findings of this study have been deposited in the DNA Data Bank of Japan with Accession Numbers LC867577 to LC867593 (LC867577, LC867578, LC867579, LC867580, LC867581, LC867582, LC867583, LC867584, LC867585, LC867586, LC867587, LC867588, LC867589, LC867590, LC867591, LC867592, and LC867593). All data generated or analyzed during this study are included in this published article and its Supplementary Information.
References
Kuhn, J. H. et al. 2021 Taxonomic update of phylum Negarnaviricota (riboviria: orthornavirae), including the large orders bunyavirales and mononegavirales. Arch. Virol. 166, 3513–3566 (2021).
World Health Organization. WHO Expert Consultation on Rabies: Third Report (World Health Organization, 2018).
Fooks, A. R. et al. Rabies. Nat. Rev. Dis. Primer 3, 17091 (2017).
Hampson, K. et al. Estimating the global burden of endemic canine rabies. PLoS Negl. Trop. Dis. 9, e0003709 (2015).
Ling, M. Y. J. et al. Rabies in Southeast asia: a systematic review of its incidence, risk factors and mortality. BMJ Open. 13, e066587 (2023).
Phung, D. et al. The effects of socioecological factors on variation of communicable diseases: A multiple-disease study at the National scale of Vietnam. PLOS ONE. 13, e0193246 (2018).
Rabies deaths in humans. reported, number. https://www.who.int/data/gho/data/indicators/indicator-details/GHO/reported-number-of-human-rabies-deaths
Ross YB, Vo CD, Bonaparte S, Phan MQ, Nguyen DT, Nguyen TX, Nguyen TT, Orciari L, Nguyen TD, Nguyen OKT, Do TT, Dao ATP, REACT Development Team, Wallace R and Nguyen LV. Measuring the impact of an integrated bite case management program on the detection of canine rabies cases in Vietnam. Front. Public Health. 11, 1150228 (2023).
Le, T. P. M. et al. Community knowledge, attitudes, and practices toward rabies prevention in North Vietnam. Int. Q. Community Health Educ. 31, 21–31 (2011).
Nguyen, A. K. T. et al. Risk factors and protective immunity against rabies in unvaccinated butchers working at dog slaughterhouses in Northern Vietnam. Am. J. Trop. Med. Hyg. 105, 788–793 (2021).
Nguyen K. Q. & Taylor-Robinson, A. W. Combatting rabies outbreaks in vietnam: high time to enforce restrictions on dog meat farming, a key source of transmission. IJID Reg. 13, 100490 (2024).
Nguyen, H. T. T. et al. Progress towards rabies control and elimination in Vietnam. Rev. Sci. Tech. OIE. 38, 199–212 (2019).
Banyard, A. C., McElhinney, L. M., Johnson, N. & Fooks, A. R. Introduction history of rabies control by vaccination. Rev. Sci. Tech. 37, 305–322 (2018).
World Health Organization. Rabies: Rationale for Investing in the Global Elimination of Dog-Mediated Human Rabies (World Health Organization, 2015).
World Health Organization, Food and Agriculture Organization of the United Nations, &. World organization for animal health. Zero by 30: the Global Strategic Plan To End Human Deaths from Dog-Mediated Rabies by 2030: United against Rabies Collaboration: First Annual Progress Report: Global Strategic Plan To End Human Deaths from Dog-Mediated Rabies by 2030. (World Health Organization, (2019).
Kadowaki, H. et al. Socio-economic factors associated with voluntary rabies control measures in Vietnam. Prev. Vet. Med. 157, 105–114 (2018).
Nguyen, D. C., Le, B. V., Tan, T. T., Nguyen, T. B. Cooperation in border areas among some Southeast Asian mainland countries: a case study of the Cambodia-Laos-Vietnam Development Triangle. Cogent. Arts. Humanit. 12, 2463203 (2025).
Luo, T. et al. Trends and associated factors of HIV, HCV and syphilis infection among different drug users in the China–Vietnam border area: an 11-year cross-sectional study (2010–2020). BMC Infect. Dis. 23, 575 (2023).
Deng, S. Z. et al. Epidemiological and cluster characteristics of dengue fever in Yunnan Province, Southwestern China, 2013–2023. BMC Infect. Dis. 25, 95 (2025).
Zhang, C. et al. Human immunodeficiency virus, syphilis and hepatitis C virus prevalence trends among cross-border migrant Vietnamese female sex workers in Guangxi, China. BMC Public. Health. 15, 1223 (2015).
Hammett, T. M. et al. Correlates of HIV status among injection drug users in a border region of Southern China and Northern Vietnam. J. Acquir. Immune Defic. Syndr. 38, 228 (2005).
Jiang, L. & Huang, T. Comparison of the epidemiological aspects of acute infectious diseases between foreign and native imported cases in the border counties of Southwest China, 2008–2017. Epidemiol. Infect. 147, e230 (2019).
Gigante, C. M. et al. Portable rabies virus sequencing in canine rabies endemic countries using the Oxford nanopore minion. Viruses. 12, 1255 (2020).
Nguyen, A. K. T. et al. Molecular epidemiology of rabies virus in Vietnam (2006–2009). Jpn J. Infect. Dis. 64, 391–396 (2011).
Yamagata, J. et al. Molecular epidemiology of rabies in Vietnam. Microbiol. Immunol. 51, 833–840 (2007).
Jaswant, G. et al. Molecular characterisation of human rabies in Tanzania and kenya: a case series report and phylogenetic investigation. Infect. Dis. Poverty. 13, 79 (2024).
Trewby, H., Nadin-Davis, S. A., Real, L. A. & Biek, R. Processes underlying rabies virus incursions across US–Canada border as revealed by Whole-Genome Phylogeography. Emerg. Infect. Dis. 23, 1454-1461 (2017).
Lushasi, K. et al. Integrating contact tracing and whole-genome sequencing to track the elimination of dog-mediated rabies: An observational and genomic study. eLife 12, e85262 (2023).
Zhang, J. et al. The full-length genome analysis of a street rabies virus strain isolated in Yunnan Province of China. Virol. Sin. 27, 204–213 (2012).
Ahmed, K. et al. Molecular epidemiology of rabies viruses Circulating in two rabies endemic provinces of laos, 2011–2012: regional diversity in Southeast Asia. PLoS Negl. Trop. Dis. 9, e0003645 (2015).
Tang, H. B. et al. Complete genome sequence of a rabies virus isolate from cattle in Guangxi, Southern China. Genome. Announc. 1, e00137-12 (2013).
Chu, T. V. & Duong, V. H. From the border of ‘barrier’ to the border of ‘connectivity’: the current development and connectivity of Vietnam-China cross-border infrastructure. J. Infrastruct. Policy Dev. 8, 8119 (2024).
Pham QD, Phan LT, Nguyen TPT, Doan QMN, Nguyen HD, Luong QC and Nguyen TV (2021) An Evaluation of the Rabies Surveillance in Southern Vietnam. Front. Public Health 9, 610905 (2021).
Guo, Z. et al. National borders effectively halt the spread of rabies: the current rabies epidemic in China is dislocated from cases in neighboring countries. PLoS Negl. Trop. Dis. 7, e2039 (2013).
Djuicy, D. D. et al. Molecular epidemiology of recurrent zoonotic transmission of mpox virus in West Africa. medRxiv. 24309115 (2024).
Veytsel, G. et al. Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut. Virus Evol. 11, veae114 (2024).
số, T. tin D. Population of Vietnam’s provinces - Data from General Statistics Office. Thông tin Dân số (2024). https://danso.info/en/population-of-vietnam-provinces/
Nosaki, Y. et al. Fourth imported rabies case since the eradication of rabies in Japan in 1957. J. Travel Med. 28, taab151 (2021).
World Health Organization, Rupprecht, C. E., Fooks, A. R. & Abela-Ridder, B. Laboratory Techniques in Rabies, Volume 1 (World Health Organization, 2018).
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Andrew Rambaut & FigTree FigTree download page http://tree.bio.ed.ac.uk/software/figtree/
Acknowledgements
We would like to sincerely thank Drs. Tran Thi Nguyen Hoa, Vu Manh Hung, Dao Thi Hai Anh from the Department of Virology, NIHE, and other members of the National Institute of Hygiene and Epidemiology, as well as the National Center for Veterinary Diseases, for taking the time to participate and support us in conducting this research. We also express our gratitude to the provincial Centers for Disease Control, the provincial Animal Health Departments, and the hospitals that participated in the collection and transportation of the samples used in this study. Special thanks go to Drs. Tran Nhu Duong and Kim Oanh for their leadership in guiling national rabies surveillance activities.
Funding
This research was funded by the Japan Agency for Medical Research and Development (Grant Nos. JP21fk0108141, JP21fk0108615, and 24fk0108696 to K.M., and 24fk0108683 and 25fk0108683 to A.O.).
Author information
Authors and Affiliations
Contributions
Conceptualization, Michiko Harada; resources, Thu Tuyet Nguyen, Dong Vinh Nguyen, Giang Chau Ngo, Huong TT. Nguyen, Phuong TM. Nguyen, and Tho Dang Nguyen; methodology, Michiko Harada, Thu Tuyet Nguyen, Dong Vinh Nguyen, Giang Chau Ngo, and Keita Ishijima; investigation, Thu Tuyet Nguyen; data analysis, Michiko Harada and Keita Ishijima; writing—original draft preparation, Michiko Harada; writing—review and editing, Michiko Harada, Thu Tuyet Nguyen, Akiko Okutani, Satoshi Inoue, and Ken Maeda; supervision, Ken Maeda; project administration, Akiko Okutani; funding acquisition, Akiko Okutani and Ken Maeda. All authors have read and agreed to the published version of the manuscript.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Consent to participate
Informed consent was obtained from all individual participants included in the study, including for the providing of saliva and CSF samples used in this study.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
About this article
Cite this article
Harada, M., Nguyen, T.T., Nguyen, D.V. et al. Four genetically distinct types of rabies virus exist in Vietnam, including the SEA1 and SEA3 subclades within the Asian clade. Sci Rep (2026). https://doi.org/10.1038/s41598-026-38638-w
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41598-026-38638-w
