Indels and Host-Derived Sequences in Rat Hepatitis E Virus Genomes

Abstract

Rat hepatitis E virus genotype 1 (rHEV) is an emerging zoonotic pathogen found globally in commensal rodents and is a significant cause of hepatitis, especially in immunocompromised populations. We systematically analyzed 99 rHEV genomes and identified multiple insertions and deletions predominantly within the macro X domain of ORF1, including a recurrent deletion of a 7−39 amino acid region in a large cluster of subtype II.b. Significant homology to human gene fragments was detected in 14% of genomes, including sequences related to transcription factors and phosphatases. This marks the first evidence of host genome-derived gene insertions in rHEV, expanding the understanding of rHEV genome plasticity, and highlights the need for further functional studies to elucidate the role of these variants in viral pathogenesis and zoonotic adaptation.

Keywords

hepatitis E / zoonoses / evolution / recombination

Author Contributions

S.F.S.H. and S.S. conceived the study. S.F.S.H. conducted all bioinformatics analyses. S.F.S.H. and S.S. prepared and reviewed the manuscript. All authors agree to the authorship of this manuscript.

Funding

This research was funded by the Partnership Programme on Enhancing Laboratory Surveillance and Investigation of Emerging Infectious Diseases and Antimicrobial Resistance for Department of Health; Lo Ying Shek Chi Wai Foundation Award for Young Investigator 2022-23; Health@InnoHK, Innovation and Technology Commission, the Government of the Hong Kong Special Administrative Region, and a donation from Respiratory Viral Research Foundation Limited.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The genome sequences used in this study are available from NCBI GenBank and the accession numbers for the individual sequences are provided in Tables 1−3.

Conflicts of Interest

The authors declare no conflict of interest.

Use of AI and AI-Assisted Technologies

No AI tools were utilized for this paper.

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