ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Virology
Genomic characterization and recombination analysis of hepatitis E virus in humans and swine across Asia: Implications for food safety
Dingyu Liu 1
Zhenwen He 2
Qin Luo 2
Baoling Liu 2
Zhang Pian 2
Jing Chen 2
Xiaohu Wang 2
Gang Wang 2
Yuan Huang 2
Hua Xiang 2
Rujian Cai 2
1. Huazhong Agricultural University, Wuhan, China
2. Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Abstract
Introduction: Hepatitis E virus (HEV) is a globally prevalent zoonotic pathogen posing major public health risks. Swine, a major meat source, carry HEV strains genetically similar to those in humans, highlighting the risk of zoonotic foodborne transmission. This study aimed to investigate the evolutionary history of HEV through phylogenetic and recombination analyses, further provide key reference bases for public health management, improve food safety standards, and offer support for developing effective strategies to prevent foodborne hepatitis E infections. Methods: We analyzed 348 full-length genomes of HEV isolated from humans and pigs in Asia over the past three decades. Phylogenetic analysis was conducted using the neighbor-joining method in MEGA11. Recombination analysis was performed with seven methods in RDP4, and sequence similarity was visualized using Simplot. Results: HEV-4 predominated in Asia, especially China, whereas HEV-3 was regionally endemic. Through genomic analysis, we identified 34 potential natural recombination events, predominantly occurring in the RNA-dependent RNA polymerase (RdRp) region; 14 events occurred between swine and human strains, supporting the hypothesis of cross-species transmission. Moreover, 20 recombination events occurred in China and mainly involved HEV-4 strains, suggesting that HEV has distinct evolutionary dynamics. The detection of five inter-genotypic recombination events may highlight ongoing genetic exchange within HEV populations in Asia, and the biological significance of these events remains to be determined. Discussion: These findings highlight the importance of tracking the evolutionary dynamics of HEV through genomic surveillance, and further underscore the necessity of conducting ongoing HEV surveillance and research to inform prevention strategies.
Summary
Keywords
Asia, Genetic recombination, Genetic Variation, Hepatitis E virus, phylogenetic analysis, Zoonoses
Received
12 November 2025
Accepted
17 February 2026
Copyright
© 2026 Liu, He, Luo, Liu, Pian, Chen, Wang, Wang, Huang, Xiang and Cai. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Dingyu Liu
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