Rocahepevirus ratti: molecular evolution, zoonotic potential and public health impact

Introduction

Hepatitis E is a well-recognised cause of acute viral hepatitis worldwide¹, accounting for an estimated 19.5 million cases annually, and contributing to 5.4% of the global disability-adjusted life years (DALYs) due to acute hepatitis². The clinical entity of hepatitis E was considered synonymous with infection by the hepatitis E virus (HEV)³, now classified as Paslahepevirus balayani within the Hepeviridae family⁴. HEV exhibits a dichotomous epidemiology⁵: large waterborne outbreaks occur in low- and middle-income countries⁶, caused exclusively by human-restricted genotypes 1 and 2⁷, whereas sporadic zoonotic infections, linked to the consumption of undercooked pork or game meat carrying genotypes 3 or 4⁸, are globally distributed, and infections by camelid-associated genotype 7 have been reported in specific settings in Middle Eastern countries⁹. Until recently, other members of Hepeviridae were long regarded as strictly host-restricted: Avihepevirus in poultry, Chirohepevirus in bats, and Rocahepevirus in rodents, shrews and mustelids, with no recognised role in human disease⁴. This long-standing assumption was fundamentally challenged in 2018, when a member of the Rocahepevirus genus was confirmed to infect humans.

Rocahepevirus ratti (rat hepatitis E virus, ratHEV) was first identified in wild Rattus norvegicus in Germany in 2010¹⁰, revealing a genetically distinct lineage within the Hepeviridae family¹¹. Initially regarded as a rodent-restricted virus with no relevance to human health¹², it remained largely overlooked until the first confirmed human infection was reported in Hong Kong in a liver transplant recipient with chronic hepatitis of unknown origin¹³. Subsequent case report in Canada revealed that ratHEV infection is not confined to immunocompromised hosts, indicating that zoonotic spillover can also occur in immunocompetent individuals¹⁴. Since then, retrospective analyses and active surveillance have identified dozens of additional cases across Asia and Europe^15–19, confirming that ratHEV is not a sporadic spillover but a zoonotic virus with established human transmission. This evidence reveals a new zoonotic threat, forcing a rethinking of the hepatitis E landscape and raising urgent questions about its true distribution, sources and public health impact.

This review synthesises current knowledge on ratHEV, highlighting the diagnostic blind spots, hidden epidemiology and unresolved transmission ecology that make it an underrecognized zoonotic threat. By integrating advances in molecular virology, animal ecology, clinical medicine and environmental surveillance, it provides a framework to guide clinicians, researchers and public health authorities in recognising, diagnosing and mitigating the public health impact of ratHEV. Addressing the knowledge gaps surrounding ratHEV is essential for accurate diagnosis and prevention, and a crucial step toward a comprehensive One Health framework for hepatitis E that explicitly integrates both classical HEV and the emerging ratHEV.

Taxonomy and virological features

Within the family Hepeviridae, subfamily Orthohepevirinae, the genus Rocahepevirus currently includes two recognised species⁴: Rocahepevirus ratti (ratHEV) and Rocahepevirus eothenomi, detected into voles. In addition, putative or unassigned Rocahepevirus-like viruses have been reported in Asian and South-American rodents, broadening the ecological niche of the genus^20,21. RatHEV is organised in five genotypes (C1–C5): genotype C1 circulates in rats and shrews²², whereas C2 is restricted to mustelids (ferrets and minks)^23,24, and three additional rodent-associated lineages (C3–C5) have been identified through environmental and wildlife surveillance^25,26. RatHEV is a positive-sense, single-stranded RNA virus of approximately 6.6–7.0 kb, structurally similar to other Hepeviridae yet highly divergent from HEV⁴ (Fig. 1). In analogy with HEV, the ratHEV particle can occur in two forms: as a non-enveloped particle or as a quasi-enveloped particle containing a lipid membrane derived from the host cell²⁷. Its genome contains three canonical open reading frames (ORFs): ORF1 encoding the non-structural polyprotein with methyltransferase, helicase and RNA-dependent RNA polymerase domains; ORF2 encoding the capsid protein; and ORF3 encoding a small multifunctional phosphoprotein involved in virion egress. Additionally, a putative fourth open reading frame (ORF4), overlapping ORF1, has been reported in some ratHEV strains¹¹, but seems not consistently found across all rodent-associated hepeviruses²⁰, suggesting lineage-specific retention or loss. Experimental mutagenesis of infectious cDNA clones indicates that ORF4 encodes a protein dispensable for viral replication in vitro but potentially modulating replication efficiency under certain conditions, hinting at a role in fine-tuning the viral life cycle²⁸. Its distribution across ratHEV lineages remains poorly mapped.

Comparative genomic analyses show that ratHEV diverges substantially from HEV across all three canonical ORFs. In ORF1, amino acid identity is generally below 50%, with marked divergence in the hypervariable region and the N-terminal portion of the methyltransferase domain, suggesting potential differences in host–protein interactions and replication dynamics²⁰. Unlike HEV, in which insertions and recombination events have been described, no such insertions have yet been identified in ratHEV, indicating a more stable evolutionary pattern^29,30. Other domains of ORF1, such as the helicase and RNA-dependent RNA polymerase, remain comparatively conserved^29,30. ORF2, which encodes the capsid protein, is the most divergent, sharing less than 60 % identity with HEV, a level of divergence that underlies partial serological cross-reactivity and frequent diagnostic escape³¹. ORF3 also shows high sequence divergence (48–55% identity) yet retains conserved late-domain motifs such as PSAP³², indicating preservation of key functional roles despite extensive variation²⁰. Comparative evolutionary analyses indicate that ratHEV represents an ancient lineage that diverged millions of years before the diversification of human and animal HEV²⁰. This deep divergence, supported by recent phylogenomic reconstructions^20–22, underscores the long-standing circulation of ratHEV in rodent reservoirs. The absence of recombination or major insertions to date may reflect ecological stability within commensal rat populations.

Phylogenetic analyses reveal that ratHEV genotype C1 is structured into two major clades (I and II) and six subtypes (a–f) (Fig. 2), reflecting long-standing circulation and local adaptation in rat populations^22,33. Most genetic diversity described to date originates from Asia, where multiple subtypes have been defined, whereas subtype Ia predominates in Europe, the Americas and Africa. Clade I encompasses most European and North American strains, including all documented human cases from these regions, whereas Clade II is dominated by sequences from Hong Kong and southern China, with human infections clustering in the II.b lineage³⁴. These subtype designations, however, are based on a still limited number of genomes from a few geographic regions, and a universally accepted subtyping framework for ratHEV remains to be established. Molecular clock estimates indicate that the II.b subcluster emerged several decades before the first recognised human case, suggesting that human exposure likely predated its formal recognition by years or even decades³³. Codon usage analyses show that C1 strains, regardless of host origin, are highly compatible with the human translational machinery, supporting a genotype-wide zoonotic potential³³. In contrast, the ORF2 capsid of human-derived strains exhibits signs of relaxed purifying selection³¹, a pattern consistent with early adaptive steps toward sustained human-to-human compatibility³³. At the molecular level, this continuum translates into specific host–cell interactions that define its zoonotic potential. RatHEV genotype C1 can attach to and enter human hepatocyte-derived cells, relying on heparan sulfate proteoglycans for initial binding³⁵, similar to HEV, with additional, as-yet undefined cofactors likely required for productive entry. Once internalised, the virus can complete its replication cycle and produce infectious particles, although replication efficiency is mostly lower than that of genotype 3 HEV³⁶. By contrast, ratHEV genotype C2 and the divergent rodent lineages C3–C5 fail to attach to or replicate in human hepatocytes, indicating negligible zoonotic potential³⁴. Experimental infection data further support this restriction, showing no productive infection in relevant in vivo mammalian models³⁷. This molecular and evolutionary pattern helps to explain why only genotype C1 has acquired zoonotic capacity, whereas other lineages remain host-restricted.

Epidemiology

Diagnosis

Clinical management and prevention

The clinical course of ratHEV infection closely mirrors that of HEV (Fig. 4), ranging from subclinical infections to acute hepatitis and, in some cases, fulminant liver failure with a fatal outcome^{15–19,84,86}. A complete list of all confirmed human ratHEV infections (n = 51) reported to date, including demographics, immune status, clinical presentation and outcome, is provided in Supplementary Table 1. In immunosuppressed patients, predominantly transplant recipients and people living with HIV, ratHEV can persist and lead to chronic hepatitis^{13,15,16,89–91}. Such cases have been documented in both Asian and European settings, suggesting that viral lineage does not appear to constrain the risk of progression, although their true frequency remains uncertain due to limited case numbers and diagnostic under-ascertainment. In addition to hepatic disease, individual reports of glomerulonephritis and encephalitis in immunosuppressed patients with confirmed ratHEV infection raise the possibility of extrahepatic involvement^15,16,19, mirroring the systemic complications described for HEV⁹⁹. However, no systematic investigations have evaluated whether ratHEV contributes to neurological, renal or haematological syndromes, given that molecular screening to date has been limited to individuals with liver-related disease. Data on pregnancy are similarly scarce. In vitro experiments indicate that ratHEV replicates inefficiently in placental tissue compared with HEV, with limited cytopathic effect¹⁰⁰. Consistently, only three ratHEV infections have been documented in pregnant women to date, and none developed clinically overt hepatitis¹⁸. These sparse but reassuring observations are insufficient to define obstetric risk, which remains an important gap for future surveillance and clinical studies.

Management is currently guided by clinical experience with HEV, as no ratHEV-specific guidelines exist. The European Association for the Study of the Liver (EASL) recommendations for hepatitis E therefore provide a pragmatic framework for clinical decision-making¹⁰¹. In immunocompetent individuals, infection is usually self-limiting with supportive care¹⁶, although severe hepatitis, including cases without underlying liver disease, has been reported^14,16,19. In immunocompromised patients, particularly transplant recipients, reduction of immunosuppressive therapy may be attempted, but sustained viral clearance with this approach alone has not been documented^13,15,16. Evidence regarding the efficacy, optimal dosing and duration of therapy for chronic ratHEV infection is extremely limited. Nevertheless, ribavirin is generally considered the mainstay of treatment, with several cases descriptions suggesting favourable outcomes^88,90. Alternative antivirals show in vitro activity against ratHEV^102,103, but have not been evaluated in human infection.

Although not developed for ratHEV, growing experimental evidence suggests that the licensed HEV genotype 1 vaccine (Hecolin) confers partial cross-protection. Monoclonal antibodies derived from B-cells of vaccine recipients recognise ratHEV antigens and neutralise ratHEV-like particles in vitro¹⁰⁴, and in a rat challenge model, immunisation significantly reduced viral loads and attenuated hepatic lesions, although sterilising immunity was not achieved³¹. Consistently, experimental data in Mongolian gerbils showed that prior HEV infection does not prevent subsequent ratHEV infection, reinforcing that cross-immunity between HEV and ratHEV is incomplete¹⁰⁵. However, there are no clinical efficacy data in humans. Pending a specific ratHEV vaccine, prevention should focus on reducing contact of humans to rodents and their excretions through hygiene, environmental sanitation and targeted rodent control¹⁵.

Conclusions

The 21st century has brought increasing recognition of HEV as a zoonotic pathogen, primarily associated with swine and related animal reservoirs. The identification of ratHEV marks a new chapter, highlighting zoonotic risk from a genetically divergent variant of HEV with completely differing animal reservoirs and transmission pathways (Box 1). Our understanding of its impact on human health remains nascent. Although current data suggest that ratHEV is an uncommon cause of hepatitis in developed regions, systematic surveillance has thus far been limited to Western Europe and parts of China. Expanding surveillance efforts to underrepresented regions, particularly the Global South, is a priority given the high seroprevalence reported in some settings. The inclusion of ratHEV in HEV international guidelines may facilitate increased diagnostic uptake and targeted research investment.

Rodents are the primary reservoir of ratHEV and are presumed to be the main source of human infection. However, the precise transmission routes remain poorly defined. Direct contact with rodents is rarely reported by infected individuals, suggesting that indirect exposure, via contaminated environments or food, may be more common. The high detection frequency of ratHEV RNA in urban wastewater, treated effluents and bivalve molluscs underscores the potential for environmental persistence to drive exposure. Evidence of infection in other species, including domestic pigs and experimentally infected birds, raises questions about possible secondary transmission pathways that warrant further study. While human-to-human transmission is well documented for other enterically transmitted viruses such as hepatitis A virus, there is currently no evidence that this applies to ratHEV. Nonetheless, the occurrence of infections in people living with HIV, men who have sex with men, and children indicates that the epidemiological spectrum is broader than initially appreciated. Blood-borne and transplant-related transmission cannot be ruled out.

A major obstacle to defining the true burden of disease is the absence of standardised, sensitive diagnostic tools. No commercial molecular assays or ratHEV-specific IgM kits are available, limiting acute-phase diagnosis. Current qPCR protocols vary widely in sensitivity and genomic coverage, necessitating the combined use of multiple assays. Expanding NGS protocols capable of recovering complete genomes, even from low-RNA clinical samples, would strengthen molecular epidemiology, improve cluster detection and enable monitoring of antiviral resistance. As more cases are identified, the clinical spectrum of ratHEV will become clearer. Reports of extrahepatic manifestations, including renal and neurological syndromes, highlight the need for systematic evaluation of outcomes beyond hepatic disease. Animal models are essential to explore pathogenesis and test therapeutics in both immunocompetent and immunocompromised settings. Importantly, ratHEV is more readily adapted to small animal models than HEV¹⁰⁶, offering an accessible platform for preclinical evaluation of antivirals¹⁰⁷. These models, together with improved in vitro systems, should also be leveraged in the development of broad-spectrum, pan-hepevirus vaccines capable of protecting against both HEV and ratHEV.

To address these gaps, international coordination will be essential to develop validated diagnostics, harmonise surveillance protocols and strengthen early detection of emerging zoonotic threats. Centres with experience in clinical diagnosis and molecular confirmation of ratHEV should lead efforts to develop reference materials for public health laboratories and academic institutions seeking to investigate local circulation. However, the challenge posed by ratHEV goes beyond technical preparedness. It exposes deeper structural gaps in our ability to identify and respond to pathogens at the interface of human, rodent and environmental health¹⁰⁸. As highlighted by the Lancet One Health Commission¹⁰⁹, One Health must evolve from a conceptual aspiration to an operational and institutionalised framework, underpinned by sustained investment and governance. RatHEV should serve as a sentinel example for the importance of such transdisciplinary integration, not only to contain this emerging pathogen, but to build resilience against future zoonotic threats.

Supplementary information

Author contributions

A.R.-J., R.J., and S.S. jointly conceived the Review, performed the literature search, evaluated and cross-checked the evidence, wrote and revised the manuscript, and approved the final version.

Peer review

Competing interests

The authors declare no competing interests.

Supplementary information

The online version contains supplementary material available at 10.1038/s41467-026-71382-3.