Virus causes 20 million infections annually as study uncovers hidden drivers of its evolution

Researchers examine the evolution of hepatitis E virus, which infects 20 million people annually and causes 44,000 deaths worldwide

Study: Ancient evolutionary origins of hepatitis E virus in rodents. Image Credit: Shutterstock AI / Shutterstock.com

A recent study published in PNAS describes the evolutionary origins of hepatitis E virus in rodents. These findings emphasize the crucial need to increase monitoring and risk assessments for rodent-associated hepeviruses.

The epidemiology of hepatitis E

Hepatitis E virus is a small single-stranded ribonucleic acid (RNA) virus belonging to the family Hepeviridae. Current estimates indicate that over 20 million hepatitis E infections occur each year throughout the world, 44,000 of which result in death. The primary mode of viral transmission is through the fecal-oral route, mainly through contaminated water. 

Hepatitis E virus has eight genotypes, of which genotypes one and two have only been detected in humans. Other genotypes have been reported in animals, including swine, rabbit, and camelid.

Most hepatitis E infections in industrialized countries arise due to zoonotic genotypes three and four. These infections predominantly originate from ungulates and occasionally from rats, thus highlighting the zoonotic potential of rodent-associated hepeviruses.

Study findings

In the current study, scientists perform host genomic data mining to characterize divergent hepeviruses in rodents. A total of 7.67 million sequencing runs from nonhuman mammals were analyzed, from which two genetically divergent rodent-associated hepeviruses were identified. Two bat-associated hepeviruses genetically related to known bat-associated strains were also reported.

Based on this observation, 2,565 liver samples from 108 rodents and shrew species were analyzed to detect hepeviruses using the reverse transcription-polymerase chain reaction (RT-PCR) assay. These samples were obtained between 2011 and 2018 from largely understudied regions and hosts for hepatitis E-related viruses in Africa, Asia, and Latin America.

A total of 63 positive samples were identified, 61 of which were from 12 rodent species and two were from shrew species. Rodent livers exhibited a high viral load. 

Twenty-four near complete hepevirus genomes were isolated from rodents, shrews, and bats. These genomes exhibited a typical hepevirus organization containing open reading frame 1 (ORF1), ORF2, and ORF3, as well as common functional domains and motifs.

All rodent- and shrew-associated hepeviruses were associated with high sequence divergence from paslahepeviruses and rocaviruses, as demonstrated by high percentages of amino acid sequence distance. The highest sequence distance was observed near ORF1 and ORF3, which could be due to host adaptation or recombination events.

Two coinfections with genetically divergent hepeviruses were identified in two dwarf fat-tailed jerboas, which indicates predominant circulation of genetically divergent hepeviruses in these rodents. The phylogenetic analysis of these samples revealed that rodent-associated hepeviruses are not monophyletic, which is defined as being closely related organisms with a common ancestor. Rodent-associated hepeviruses formed five clades clustering in basal sister relationship to human- and rat-associated hepatitis E virus.

As compared to rodents that hosted a large diversity of hepeviruses, bat- and bird-associated hepeviruses formed monophyletic clades that grouped distantly to human-associated hepeviruses. Thus, bats and birds appear to have a limited role in the evolutionary origins of human-associated hepatitis E virus.

By conducting ancestral state reconstruction in a Bayesian framework, a direct origin of human-associated hepatitis E virus was identified in ungulates like swine and camelids. Furthermore, a nonrecent origin of ungulate- and human-associated hepatitis E virus was observed in rodents.

Parsimony-based ancestral state reconstruction and cophylogenetic reconciliations revealed that rodents are primary sources of hepeviral cross-order host shifts. Moreover, certain shrew hepeviruses were grouped in rodent-associated hepevirus clades, thus suggesting viral cross-order host shifts between geographically overlapping animals.

Distance-based cophylogenetic reconstructions were also performed, which validated an overall long-term evolutionary association between hepeviruses and their rodent and ungulate hosts.  

Conclusions

The study findings provide novel insights into the ancient evolutionary origins of human hepatitis E virus and highlight the need for increased surveillance and risk factor assessments in rodent-associated hepeviruses.

Notable limitations of the current study include nonsystematic sampling and RT-PCR-based testing, which may prevent the ability to identify divergent hepeviruses. Another limitation is the potential for disproportionate representation of host genomic data in public databases. However, the large sample size, detection of highly divergent hepeviruses, and intense data mining ensure the robustness of evolutionary reconstructions.

Establishing a controllable animal model for human-associated hepatitis E virus poses several challenges. One potential model animal could be immunocompetent gerbils, which are susceptible to both zoonotic and nonzoonotic hepatitis E virus genotypes. Furthermore, this animal model only requires a few genetic changes to induce hepatitis E infection.

Thus, divergent rodent-associated hepeviruses and rodent hosts may support future studies aiming to optimize animal models for hepatitis E virus infection.