Characterization of nonprimate hepacivirus and construction of a functional molecular clone

First report of Equine Parvovirus-Hepatitis (EqPV-H) in Argentina

The novel Equine Parvovirus-Hepatitis (EqPV-H) was first identified in the serum and liver of a horse that died of equine serum hepatitis, also known as Theiler's disease. Several reports in recent years strongly suggest that EqPV-H is the etiologic agent of Theiler's disease. Brazil is the only South American country where infection with this virus has been reported. This study investigated the presence of EqPV-H DNA in horse serum pools (n=51), commercial horse serum batches (n=5) and individual serum samples from donor horses (n=175) from Argentina. All serum samples were analyzed by quantitative polymerase chain reaction (qPCR) and samples with positive or indeterminate results were further analyzed by NS1 nested-PCR for phylogenetic studies. None of the serum pools was positive by qPCR but 9/51 pools were indeterminate (one or both test sample's Ct values were higher than the limit of detection). The NS1 nested-PCR detected the EqPV-H DNA in 8 of these indeterminate samples (15.7 % of serum pools). Three of the commercial horse serum batches (60 %) contained EqPV-H DNA, detected either by qPCR and/or nested-PCR. From the 175 individual horse serum samples, three (1.71 %) were positive for EqPV-H by both techniques. The genetic analysis of the 12 partial NS1 sequences obtained showed that the local isolates were similar to EqPV-H sequences from Germany and China. This study provides the first evidence of the presence of EqPV-H in horses and in horse sera commercially available in Argentina and emphasizes the importance of controlling the biosecurity of commercial equine sera as well as any other blood-derived biological products of equine origin. DATA AVAILABILITY: Viral sequences generated in this study were uploaded to the NCBI nucleotide database and are available with the accession numbers PP408676-PP408687.

Detection of Equine Parvovirus-Hepatitis Virus and Equine Hepacivirus in Archived Sera from Horses in France and Australia

Reports of newly discovered equine hepatotropic flavi- and parvoviruses have emerged throughout the last decade in many countries, the discovery of which has stimulated a great deal of interest and clinical research. Although commonly detected in horses without signs of disease, equine parvovirus hepatitis (EqPV-H) and equine hepacivirus (EqHV) have been associated with liver disease, including following the administration of contaminated anti-toxin. Our aim was to determine whether EqPV-H and EqHV are present in Australian horses and whether EqPV-H was present in French horses and to examine sequence diversity between strains of both viruses amongst infected horses on either side of the globe. Sera from 188 Australian horses and 256 French horses from horses with and without clinical signs of disease were collected. Twelve out of 256 (4.7%) and 6 out of 188 (3.2%) French and Australian horses, respectively, were positive for the molecular detection of EqPV-H. Five out of 256 (1.9%) and 21 out of 188 (11.2%) French and Australian horses, respectively, were positive for the molecular detection of EqHV. Australian strains for both viruses were genomically clustered, in contrast to strains from French horses, which were more broadly distributed. The findings of this preliminary survey, with the molecular detection of EqHV and EqPV-H in Australia and the latter in France, adds to the growing body of awareness regarding these recently discovered hepatotropic viruses. It has provided valuable information not just in terms of geographic endemicity but will guide equine clinicians, carers, and authorities regarding infectious agents and potential impacts of allogenic tissue contamination. Although we have filled many gaps in the world map regarding equine hepatotropic viruses, further prospective studies in this emerging field may be useful in terms of elucidating risk factors and pathogenesis of these pathogens and management of cases in terms of prevention and diagnosis.

Naturally acquired equine parvovirus-hepatitis is associated with a wide range of hepatic lesions in horses

Equine parvovirus-hepatitis (EqPV-H) is the causative agent of Theiler's disease, or severe acute hepatic necrosis, in horses. However, it is poorly understood whether EqPV-H is associated with other histologic findings in horses with clinical liver disease. The objective of this study was to examine the prevalence and severity of EqPV-H infections in diagnostic liver samples. Archived formalin-fixed, paraffin-embedded (FFPE) liver samples (n = 98) from Cornell University and University of California, Davis, collected between 2007 and 2022 were evaluated for 15 individual histologic features and by EqPV-H in situ hybridization. EqPV-H was detected in 48% (n = 47) of samples. The most common histologic features of EqPV-H-positive samples included individual hepatocyte death (n = 40, 85%), lobular infiltrates (n = 38, 80%), portal infiltrates (n = 35, 74%), and ductular reaction (n = 33, 70%). Centrilobular necrosis, portal infiltrate, and individual hepatocyte death were positively associated with high viral load. Neutrophil infiltrates, bridging fibrosis, and portal edema were negatively associated with a high viral load. Only 4 of 49 tested samples were positive for equine hepacivirus by polymerase chain reaction (PCR), but the PCR assay was unreliable for FFPE tissues. In summary, this study demonstrates that EqPV-H is common in a variety of liver pathologies and should be considered as a differential diagnosis in cases of hepatitis other than Theiler's disease.

First National Prevalence in Italian Horse Population and Phylogenesis Highlight a Fourth Sub-Type Candidate of Equine Hepacivirus

Equine hepacivirus (EqHV, Flaviviridae, hepacivirus) is a small, enveloped RNA virus generally causing sub-clinical hepatitis with occasional fatalities. EqHV is reported in equids worldwide, but for Italy data are limited. To address this, a survey study was set up to estimate prevalence at a national level and among different production categories (equestrian; competition; work and meat; reproduction) and national macro-regions (North, Central, South, and Islands). Data obtained testing 1801 horse serum samples by Real-Time RT PCR were compared within the categories and regions. The NS3 fragment of the PCR-positive samples was sequenced by Sanger protocol for phylogenetic and mutational analysis. The tertiary structure of the NS3 protein was also assessed. The estimated national prevalence was 4.27% [1.97-6.59, 95% CI] and no statistical differences were detected among production categories and macro-regions. The phylogenesis confirmed the distribution in Italy of the three known EqHV subtypes, also suggesting a possible fourth sub-type that, however, requires further confirmation. Mutational profiles that could also affect the NS3 binding affinity to the viral RNA were detected. The present paper demonstrates that EqHV should be included in diagnostic protocols when investigating causes of hepatitis, and in quality control protocols for blood derived products due to its parental transmission.

The emerging role of miRNA-122 in infectious diseases: Mechanisms and potential biomarkers

microRNAs (miRNAs) are small, non-coding RNA molecules that play crucial regulatory roles in numerous cellular processes. Recent investigations have highlighted the significant involvement of miRNA-122 (miR-122) in the pathogenesis of infectious diseases caused by diverse pathogens, encompassing viral, bacterial, and parasitic infections. In the context of viral infections, miR-122 exerts regulatory control over viral replication by binding to the viral genome and modulating the host's antiviral response. For instance, in hepatitis B virus (HBV) infection, miR-122 restricts viral replication, while HBV, in turn, suppresses miR-122 expression. Conversely, miR-122 interacts with the hepatitis C virus (HCV) genome, facilitating viral replication. Regarding bacterial infections, miR-122 has been found to regulate host immune responses by influencing inflammatory cytokine production and phagocytosis. In Vibrio anguillarum infections, there is a significant reduction in miR-122 expression, contributing to the pathophysiology of bacterial infections. Toll-like receptor 14 (TLR14) has been identified as a novel target gene of miR-122, affecting inflammatory and immune responses. In the context of parasitic infections, miR-122 plays a crucial role in regulating host lipid metabolism and immune responses. For example, during Leishmania infection, miR-122-containing extracellular vesicles from liver cells are unable to enter infected macrophages, leading to a suppression of the inflammatory response. Furthermore, miR-122 exhibits promise as a potential biomarker for various infectious diseases. Its expression level in body fluids, particularly in serum and plasma, correlates with disease severity and treatment response in patients affected by HCV, HBV, and tuberculosis. This paper also discusses the potential of miR-122 as a biomarker in infectious diseases. In summary, this review provides a comprehensive and insightful overview of the emerging role of miR-122 in infectious diseases, detailing its mechanism of action and potential implications for the development of novel therapeutic strategies.

Studying T Cell Responses to Hepatotropic Viruses in the Liver Microenvironment

T cells play an important role in the clearance of hepatotropic viruses but may also cause liver injury and contribute to disease progression in chronic hepatitis B and C virus infections which affect millions of people worldwide. The liver provides a unique microenvironment of immunological tolerance and hepatic immune regulation can modulate the functional properties of T cell subsets and influence the outcome of a virus infection. Extensive research over the last years has advanced our understanding of hepatic conventional CD4+ and CD8+ T cells and unconventional T cell subsets and their functions in the liver environment during acute and chronic viral infections. The recent development of new small animal models and technological advances should further increase our knowledge of hepatic immunological mechanisms. Here we provide an overview of the existing models to study hepatic T cells and review the current knowledge about the distinct roles of heterogeneous T cell populations during acute and chronic viral hepatitis.

Dose-Dependent Hepacivirus Infection Reveals Linkage between Infectious Dose and Immune Response

More than 70 million people worldwide are still infected with the hepatitis C virus 30 years after its discovery, underscoring the need for a vaccine. To develop an effective prophylactic vaccine, detailed knowledge of the correlates of protection and an immunocompetent surrogate model are needed. In this study, we describe the minimum dose required for robust equine hepacivirus (EqHV) infection in equids and examined how this relates to duration of infection, seroconversion, and transcriptomic responses. To investigate mechanisms of hepaciviral persistence, immune response, and immune-mediated pathology, we inoculated eight EqHV naive horses with doses ranging from 1-2 copies to 1.3 × 106 RNA copies per inoculation. We characterized infection kinetics, pathology, and transcriptomic responses via next generation sequencing. The minimal infectious dose of EqHV in horses was estimated at 13 RNA copies, whereas 6 to 7 copies were insufficient to cause infection. Peak viremia did not correlate with infectious dose, while seroconversion and duration of infection appeared to be affected. Notably, seroconversion was undetectable in the low-dose infections within the surveillance period (40 to 50 days). In addition, transcriptomic analysis revealed a nearly dose-dependent effect, with greater immune activation and inflammatory response observed in high-dose infections than in low-dose infections. Interestingly, inoculation with 6-7 copies of RNA that did not result in productive infection, but was associated with a strong immune response, similar to that observed in the high-dose infections. IMPORTANCE We demonstrate that the EqHV dose of infection plays an important role for inducing immune responses, possibly linked to early clearance in high-dose and prolonged viremia in low-dose infections. In particular, pathways associated with innate and adaptive immune responses, as well as inflammatory responses, were more strongly upregulated in high-dose infections than in lower doses. Hence, inoculation with low doses may enable EqHV to evade strong immune responses in the early phase and therefore promote robust, long-lasting infection.

Equine Hepacivirus: A Systematic Review and a Meta-Analysis of Serological and Biomolecular Prevalence and a Phylogenetic Update

Simple Summary

This is a comprehensive review containing the most up-to-date information on Equine Hepacivirus, one of the recently discovered hepatic equine viruses, together with an analysis of serological and biomolecular presence presented in apreviously published papers, and an update on its genetic relationship within the species and with similar species. Extensive description of the EqHV features is included, and results are presented with several tables and figures, providing a valuable reference guide for further studies.

Abstract

Viral hepatitis has recently assumed relevance for equine veterinary medicine since a variety of new viruses have been discovered. Equine Hepacivirus (EqHV) is an RNA virus belonging to the Flaviviridae family that can cause subclinical hepatitis in horses, occasionally evolving into a chronic disease. EqHV, to date, is considered the closest known relative of human HCV. EqHV has been reported worldwide therefore assessing its features is relevant, considering both the wide use of blood products and transfusions in veterinary therapies and its similitude to HCV. The present review resumes the actual knowledge on EqHV epidemiology, risk factors and immunology, together with potential diagnostics and good practices for prevention. Moreover, adhering to PRISMA guidelines for systematic reviews a meta-analysis of serological and biomolecular prevalence and an updated phylogenetic description is presented as a benchmark for further studies.

Infection of young foals with Equine Parvovirus-Hepatitis following a fatal non-biologic case of Theiler's disease

Theiler's disease (TD) is a (sub-)acute hepatitis in adult horses and one of the most common causes of acute hepatic failure. Recent findings indicate that equine parvovirus hepatitis (EqPV-H) likely causes TD and that its transmission occurs via iatrogenic and/or natural routes. Following the death of an EqPV-H positive mare with TD, close-contact mares and foals in the same paddock were monitored to evaluate if there was any evidence of EqPV-H. For this purpose, the serum of close contact horses was examined 6 and 42 days after the mare's death for the presence of EqPV-H DNA and changes in liver-associated serum biochemical parameters. The foals had higher EqPV-H viral loads than the mares. Apart from the mare that was euthanized, none of the horses included in this study showed signs of severe disease and nor did they have particularly elevated liver enzymes. Nucleotide sequence analysis revealed no major differences between the viral DNA detected in the serum of the dead mare and any of the in-contact horses. In conclusion, our data confirmed previous findings that horizontal transmission of EqPV-H may occur through close contact between horses.

MicroRNA-122 Regulation of HCV Infections: Insights from Studies of miR-122-Independent Replication

Despite the advancement in antiviral therapy, Hepatitis C remains a global health challenge and one of the leading causes of hepatitis related deaths worldwide. Hepatitis C virus, the causative agent, is a positive strand RNA virus that requires a liver specific microRNA called miR-122 for its replication. Unconventional to the canonical role of miRNAs in translation suppression by binding to 3′Untranslated Region (UTR) of messenger RNAs, miR-122 binds to two sites on the 5′UTR of viral genome and promotes viral propagation. In this review, we describe the unique relationship between the liver specific microRNA and HCV, the current knowledge on the mechanisms by which the virus uses miR-122 to promote the virus life cycle, and how miR-122 impacts viral tropism and pathogenesis. We will also discuss the use of anti-miR-122 therapy and its impact on viral evolution of miR-122-independent replication. This review further provides insight into how viruses manipulate host factors at the initial stage of infection to establish a successful infection.

An Equine Model for Vaccination against a Hepacivirus: Insights into Host Responses to E2 Recombinant Protein Vaccination and Subsequent Equine Hepacivirus Inoculation

Equine hepacivirus (EqHV) is the closest known genetic homologue of hepatitis C virus. An effective prophylactic vaccine is currently not available for either of these hepaciviruses. The equine as potential surrogate model for hepacivirus vaccine studies was investigated, while equine host responses following vaccination with EqHV E2 recombinant protein and subsequent EqHV inoculation were elucidated. Four ponies received prime and booster vaccinations (recombinant protein, adjuvant) four weeks apart (day −55 and −27). Two control ponies received adjuvant only. Ponies were inoculated with EqHV RNA-positive plasma on day 0. Blood samples and liver biopsies were collected over 26 weeks (day −70 to +112). Serum analyses included detection of EqHV RNA, isotypes of E2-specific immunoglobulin G (IgG), nonstructural protein 3-specific IgG, haematology, serum biochemistry, and metabolomics. Liver tissue analyses included EqHV RNA detection, RNA sequencing, histopathology, immunohistochemistry, and fluorescent in situ hybridization. Al-though vaccination did not result in complete protective immunity against experimental EqHV inoculation, the majority of vaccinated ponies cleared the serum EqHV RNA earlier than the control ponies. The majority of vaccinated ponies appeared to recover from the EqHV-associated liver insult earlier than the control ponies. The equine model shows promise as a surrogate model for future hepacivirus vaccine research.

OUP accepted manuscript

Even 30 years after the discovery of the hepatitis C virus (HCV) in humans there is still no vaccine available. Reasons for this include the high mutation rate of HCV, which allows the virus to escape immune recognition and the absence of an immunocompetent animal model for vaccine development. Phylogenetically distinct hepaciviruses (genus Hepacivirus, family Flaviviridae) have been isolated from diverse species, each with a narrow host range: the equine hepacivirus (EqHV) is the closest known relative of HCV. In this study, we used amplicon-based deep-sequencing to investigate the viral intra-host population composition of the genomic regions encoding the surface glycoproteins E1 and E2. Patterns of E1E2 substitutional evolution were compared in longitudinally sampled EqHV-positive sera of naturally and experimentally infected horses and HCV-positive patients. Intra-host virus diversity was higher in chronically than in acutely infected horses, a pattern which was similar in the HCV-infected patients. However, overall glycoprotein variability was higher in HCV compared to EqHV. Additionally, selection pressure in HCV populations was higher, especially within the N-terminal region of E2, corresponding to the hypervariable region 1 (HVR1) in HCV. An alignment of glycoprotein sequences from diverse hepaciviruses identified the HVR1 as a unique characteristic of HCV: hepaciviruses from non-human species lack this region. Together, these data indicate that EqHV infection of horses could represent a powerful surrogate animal model to gain insights into hepaciviral evolution and HCVs HVR1-mediated immune evasion strategy.

First report of equine parvovirus-hepatitis and equine hepacivirus coinfection in horses in Korea

Equine parvovirus-hepatitis (EqPV-H) and equine hepacivirus (EqHV) are etiologically associated with Theiler's disease (TD), causing fulminant equine hepatitis, but the transmission route and co-infection effect remain unclear. We determined EqPV-H and EqHV prevalence and coinfection rate in 160 serum and 114 faecal samples using nested polymerase chain reaction. Amino acid and nucleotide analyses were performed and phylogenetic trees were constructed. By measuring liver-specific parameters (AST, GGT, TBIL and A/G ratio), hepatopathological changes in viremia status were compared. We found a high prevalence (EqPV-H: 10.6% in serum, 5.3% in faeces; EqHV: 8.1% in serum) and coinfection rate (35.3% in EqPV-H) of TD-causing agents. The newly identified EqPV-H genomes showed high nucleotide and amino acid similarities with previously reported strains in the USA, China and Austria. In phylogenetic tree and recombination analysis, a natural recombination event was confirmed between Chinese and Korean strains. In the EqPV-H or EqHV viremic horses, AST was significantly elevated and at least two liver-specific parameters were outside the reference intervals in 43.5% (10/23) of horses. To our knowledge, this is the first prevalence field study of EqPV-H and EqHV using both serum and faeces, providing further evidence of faecal-oral transmission of TD. These epidemiologic and clinicopathologic analyses specify the risk factors of TD infection and promote disease prevention strategy.

Pathogenesis, MicroRNA-122 Gene-Regulation, and Protective Immune Responses After Acute Equine Hepacivirus Infection

BACKGROUND AND AIMS

Equine hepacivirus (EqHV) is phylogenetically the closest relative of HCV and shares genome organization, hepatotropism, transient or persistent infection outcome, and the ability to cause hepatitis. Thus, EqHV studies are important to understand equine liver disease and further as an outbred surrogate animal model for HCV pathogenesis and protective immune responses. Here, we aimed to characterize the course of EqHV infection and associated protective immune responses.

APPROACH AND RESULTS

Seven horses were experimentally inoculated with EqHV, monitored for 6 months, and rechallenged with the same and, subsequently, a heterologous EqHV. Clearance was the primary outcome (6 of 7) and was associated with subclinical hepatitis characterized by lymphocytic infiltrate and individual hepatocyte necrosis. Seroconversion was delayed and antibody titers waned slowly. Clearance of primary infection conferred nonsterilizing immunity, resulting in shortened duration of viremia after rechallenge. Peripheral blood mononuclear cell responses in horses were minimal, although EqHV-specific T cells were identified. Additionally, an interferon-stimulated gene signature was detected in the liver during EqHV infection, similar to acute HCV in humans. EqHV, as HCV, is stimulated by direct binding of the liver-specific microRNA (miR), miR-122. Interestingly, we found that EqHV infection sequesters enough miR-122 to functionally affect gene regulation in the liver. This RNA-based mechanism thus could have consequences for pathology.

CONCLUSIONS

EqHV infection in horses typically has an acute resolving course, and the protective immune response lasts for at least a year and broadly attenuates subsequent infections. This could have important implications to achieve the primary goal of an HCV vaccine; to prevent chronicity while accepting acute resolving infection after virus exposure.

Hepatitis C Virus Vaccine Research: Time to Put Up or Shut Up

Unless urgently needed to prevent a pandemic, the development of a viral vaccine should follow a rigorous scientific approach. Each vaccine candidate should be designed considering the in-depth knowledge of protective immunity, followed by preclinical studies to assess immunogenicity and safety, and lastly, the evaluation of selected vaccines in human clinical trials. The recently concluded first phase II clinical trial of a human hepatitis C virus (HCV) vaccine followed this approach. Still, despite promising preclinical results, it failed to protect against chronic infection, raising grave concerns about our understanding of protective immunity. This setback, combined with the lack of HCV animal models and availability of new highly effective antivirals, has fueled ongoing discussions of using a controlled human infection model (CHIM) to test new HCV vaccine candidates. Before taking on such an approach, however, we must carefully weigh all the ethical and health consequences of human infection in the absence of a complete understanding of HCV immunity and pathogenesis. We know that there are significant gaps in our knowledge of adaptive immunity necessary to prevent chronic HCV infection. This review discusses our current understanding of HCV immunity and the critical gaps that should be filled before embarking upon new HCV vaccine trials. We discuss the importance of T cells, neutralizing antibodies, and HCV genetic diversity. We address if and how the animal HCV-like viruses can be used for conceptualizing effective HCV vaccines and what we have learned so far from these HCV surrogates. Finally, we propose a logical but narrow path forward for HCV vaccine development.

Non-primate hepacivirus transmission and prevalence: Novel findings of virus circulation in horses and dogs in Morocco

Non-primate hepacivirus (NPHV) is a homolog of hepatitis C virus and has been isolated from dogs and horses. Data on NPHV prevalence and distribution are not complete, and there is a particular lack of reports from the African continent. The present study represents the first investigation of NPHV prevalence in horses and dogs in North Africa. Blood was collected from 172 horses and 36 dogs at different locations in Morocco, and screened for NPHV RNA using nested PCR targeting 5'UTR and NS3 regions and analyzed for anti-NPHV NS3 antibody using a Gaussia luciferase immunoprecipitation system-to determine seroprevalence. Eight sequences of the NS3 region isolated from positive serum samples were targeted for phylogenetic analysis. Horses and dogs showed respective NPHV RNA positivity rates of 10.5% and 5.5%, and seroprevalences of 65.7% and 8.33%. Juvenile horses appeared more susceptible to infection, with a 23.5% NHPV RNA positivity rate. Seropositivity was more extensive in mares than stallions (77.14% vs. 46.27%, p < 0.0001). Phylogenetically, that NPHV NS3 genes isolated from horses and dog are clustered together. The NPHV strains we detected showed no correlation with geographic location within Morocco. In conclusion, Moroccan horses showed much evidence of previous and/or current NPHV infection, with young age and female sex as noted potential risk factors. Interestingly, NPHV is circulating in dogs as well as horses, suggesting that it has crossed species barriers and that horses and dogs are potential vectors by which an ancestor to hepatitis C virus was transmitted into human populations.

Investigating the pathogenesis of high-serum gamma-glutamyl transferase activity in Thoroughbred racehorses: A series of case-control studies

BACKGROUND

High-serum γ-Glutamyl Transferase (GGT) activity has been associated with and thought to be a marker of maladaptation to training and possibly poor performance in racehorses, but the cause is unknown.

OBJECTIVES

To investigate possible metabolic and infectious causes for the high GGT syndrome.

STUDY DESIGN

Pilot case-control study and nested case-control study.

METHODS

The case-control study in 2017 included 16 horses (8 cases and 8 controls with median [range] serum GGT 82 [74-148] and 22 [19-28] IU/L, respectively) from the same stable. In 2018, similar testing was performed in a nested case-control study that identified 27 case (serum GGT 50 ≥ IU/L)-control pairs from three stables for further testing. Serum liver chemistries, selenium measurements, viral PCR and metabolomics were performed.

RESULTS

No differences were found in frequency of detection of viral RNA/DNA or copy numbers for equine hepacivirus (EqHV) and parvovirus-hepatitis (EqPV-H) between cases and controls. Mild increases in hepatocellular injury and cholestatic markers in case vs control horses suggested a degree of liver disease in a subset of cases. Metabolomic and individual bile acid testing showed differences in cases compared with controls, including increased abundance of pyroglutamic acid and taurine-conjugated bile acids, and reduced abundance of Vitamin B6. Selenium concentrations, although within or above the reference intervals, were also lower in case horses in both studies.

MAIN LIMITATIONS

Observational study design did not allow us to make causal inferences.

CONCLUSIONS

We conclude that high GGT syndrome is likely a complex metabolic disorder and that viral hepatitis was not identified as a cause for this syndrome in this cohort of racehorses. Our results support a contribution of oxidative stress and cholestasis in its pathophysiology.

Evolutionary selection of pestivirus variants with altered or no microRNA dependency

Host microRNA (miRNA) dependency is a hallmark of the human pathogen hepatitis C virus (HCV) and was also described for the related pestiviruses, which are important livestock pathogens. The liver-specific miR-122 binds within the HCV 5′ untranslated region (UTR), whereas the broadly expressed let-7 and miR-17 families bind two sites (S1 and S2, respectively) in the pestiviral 3′ UTR. Here, we dissected the mechanism of miRNA dependency of the pestivirus bovine viral diarrhea virus (BVDV). Argonaute 2 (AGO2) and miR-17 binding were essential for viral replication, whereas let-7 binding was mainly required for full translational efficiency. Furthermore, using seed site randomized genomes and evolutionary selection experiments, we found that tropism could be redirected to different miRNAs. AGO cross-linking and immunoprecipitation (CLIP) experiments and miRNA antagonism demonstrated that these alternative variants bound and depended on the corresponding miRNAs. Interestingly, we also identified miRNA-independent variants that were obtained through acquisition of compensatory mutations near the genomic 3′ terminus. Rescue experiments demonstrated that miRNA binding and 3′ mutagenesis contribute to replication through mutually exclusive mechanisms. Altogether, our findings suggest that pestiviruses, although capable of miRNA-independent replication, took advantage of miRNAs as essential host factors, suggesting a favorable path during evolutionary adaptation.

The Role of the Liver-Specific microRNA, miRNA-122 in the HCV Replication Cycle

Hepatitis C virus (HCV) replication requires annealing of a liver specific microRNA, miR-122 to 2 sites on 5' untranslated region (UTR). While, microRNAs downregulate gene expression by binding to the 3' untranslated region of the target mRNA, in this case, the microRNA anneals to the 5'UTR of the viral genomes and upregulates the viral lifecycle. In this review, we explore the current understandings of the mechanisms by which miR-122 promotes the HCV lifecycle, and its contributions to pathogenesis. Annealing of miR-122 has been reported to (a) stimulate virus translation by promoting the formation of translationally active internal ribosome entry site (IRES) RNA structure, (b) stabilize the genome, and (c) induce viral genomic RNA replication. MiR-122 modulates lipid metabolism and suppresses tumor formation, and sequestration by HCV may influence virus pathogenesis. We also discuss the possible use of miR-122 as a biomarker for chronic hepatitis and as a therapeutic target. Finally, we discuss roles for miR-122 and other microRNAs in promoting other viruses.

Equine pegiviruses cause persistent infection of bone marrow and are not associated with hepatitis

Pegiviruses frequently cause persistent infection (as defined by >6 months), but unlike most other Flaviviridae members, no apparent clinical disease. Human pegivirus (HPgV, previously GBV-C) is detectable in 1–4% of healthy individuals and another 5–13% are seropositive. Some evidence for infection of bone marrow and spleen exists. Equine pegivirus 1 (EPgV-1) is not linked to disease, whereas another pegivirus, Theiler’s disease-associated virus (TDAV), was identified in an outbreak of acute serum hepatitis (Theiler’s disease) in horses. Although no subsequent reports link TDAV to disease, any association with hepatitis has not been formally examined. Here, we characterized EPgV-1 and TDAV tropism, sequence diversity, persistence and association with liver disease in horses. Among more than 20 tissue types, we consistently detected high viral loads only in serum, bone marrow and spleen, and viral RNA replication was consistently identified in bone marrow. PBMCs and lymph nodes, but not liver, were sporadically positive. To exclude potential effects of co-infecting agents in experimental infections, we constructed full-length consensus cDNA clones; this was enabled by determination of the complete viral genomes, including a novel TDAV 3’ terminus. Clone derived RNA transcripts were used for direct intrasplenic inoculation of healthy horses. This led to productive infection detectable from week 2–3 and persisting beyond the 28 weeks of study. We did not observe any clinical signs of illness or elevation of circulating liver enzymes. The polyprotein consensus sequences did not change, suggesting that both clones were fully functional. To our knowledge, this is the first successful extrahepatic viral RNA launch and the first robust reverse genetics system for a pegivirus. In conclusion, equine pegiviruses are bone marrow tropic, cause persistent infection in horses, and are not associated with hepatitis. Based on these findings, it may be appropriate to rename the group of TDAV and related viruses as EPgV-2.

Transmissible hepatitis in horses (Theiler’s disease) has been known for 100 years without knowledge of causative infectious agents. Recently, two novel equine pegiviruses (EPgV) were discovered. Whereas EPgV-1 was not associated to disease, the other was identified in an outbreak of acute serum hepatitis and therefore named Theiler’s disease-associated virus (TDAV). This finding was surprising since human and monkey pegiviruses typically cause long-term infection without associated clinical disease. Whereas no subsequent reports link TDAV to disease, the original association to hepatitis has not been formally examined. Here, we studied EPgV-1 and TDAV and found that their natural history of infection in horses were remarkably similar. Examination of various tissues identified the bone marrow as the primary site of replication for both viruses with no evidence of replication in the liver. To exclude potential effects of other infectious agents, we developed molecular full-length clones for EPgV-1 and TDAV and were able to initiate infection in horses using derived synthetic viral genetic material. This demonstrated long-term infection, but no association with hepatitis. These findings call into question the connection between TDAV, liver infection, and hepatitis in horses.

Priming of Antiviral CD8 T Cells without Effector Function by a Persistently Replicating Hepatitis C-Like Virus

Immune-competent animal models for the hepatitis C virus (HCV) are nonexistent, impeding studies of host-virus interactions and vaccine development. Experimental infection of laboratory rats with a rodent hepacivirus isolated from Rattus norvegicus (RHV) is a promising surrogate model due to its recapitulation of HCV-like chronicity. However, several aspects of rat RHV infection remain unclear, for instance, how RHV evades host adaptive immunity to establish persistent infection. Here, we analyzed the induction, differentiation, and functionality of RHV-specific CD8 T cell responses that are essential for protection against viral persistence. Virus-specific CD8 T cells targeting dominant and subdominant major histocompatibility complex class I epitopes proliferated considerably in liver after RHV infection. These populations endured long term yet never acquired antiviral effector functions or selected for viral escape mutations. This was accompanied by the persistent upregulation of programmed cell death-1 and absent memory cell formation, consistent with a dysfunctional phenotype. Remarkably, transient suppression of RHV viremia with a direct-acting antiviral led to the priming of CD8 T cells with partial effector function, driving the selection of a viral escape variant. These data demonstrate an intrinsic abnormality within CD8 T cells primed by rat RHV infection, an effect that is governed at least partially by the magnitude of early virus replication. Thus, this model could be useful in investigating mechanisms of CD8 T cell subversion, leading to the persistence of hepatotropic pathogens such as HCV.IMPORTANCE Development of vaccines against hepatitis C virus (HCV), a major cause of cirrhosis and cancer, has been stymied by a lack of animal models. The recent discovery of an HCV-like rodent hepacivirus (RHV) enabled the development of such a model in rats. This platform recapitulates HCV hepatotropism and viral chronicity necessary for vaccine testing. Currently, there are few descriptions of RHV-specific responses and why they fail to prevent persistent infection in this model. Here, we show that RHV-specific CD8 T cells, while induced early at high magnitude, do not develop into functional effectors capable of controlling virus. This defect was partially alleviated by short-term treatment with an HCV antiviral. Thus, like HCV, RHV triggers dysfunction of virus-specific CD8 T cells that are vital for infection resolution. Additional study of this evasion strategy and how to mitigate it could enhance our understanding of hepatotropic viral infections and lead to improved vaccines and therapeutics.

Animal Models of Hepatitis C Virus Infection

Hepatitis C virus (HCV) is an important and underreported infectious disease, causing chronic infection in ∼71 million people worldwide. The limited host range of HCV, which robustly infects only humans and chimpanzees, has made studying this virus in vivo challenging and hampered the development of a desperately needed vaccine. The restrictions and ethical concerns surrounding biomedical research in chimpanzees has made the search for an animal model all the more important. In this review, we discuss different approaches that are being pursued toward creating small animal models for HCV infection. Although efforts to use a nonhuman primate species besides chimpanzees have proven challenging, important advances have been achieved in a variety of humanized mouse models. However, such models still fall short of the overarching goal to have an immunocompetent, inheritably susceptible in vivo platform in which the immunopathology of HCV could be studied and putative vaccines development. Alternatives to overcome this include virus adaptation, such as murine-tropic HCV strains, or the use of related hepaciviruses, of which many have been recently identified. Of the latter, the rodent/rat hepacivirus from Rattus norvegicus species-1 (RHV-rn1) holds promise as a surrogate virus in fully immunocompetent rats that can inform our understanding of the interaction between the immune response and viral outcomes (i.e., clearance vs. persistence). However, further characterization of these animal models is necessary before their use for gaining new insights into the immunopathogenesis of HCV and for conceptualizing HCV vaccines.

Prevalence of equine hepacivirus infection in Mongolia

Equine hepacivirus (EHV) belongs to the hepacivirus A and is related to hepatitis C virus (HCV). This virus shows hepatic tropism and is known to chronically infect horses. EHV has been reported from various countries, but the prevalence in Mongolia, where large horse populations are pastured, remains unknown. This study collected serum samples from horses in six areas across Mongolia, in order to investigate the status of infection. The possibility of human infection was also examined. The results showed an infection rate among horses of about 40 % in all regions. However, no evidence of EHV viremia was found in human serum. A mutation characteristic of Mongolian EHV was found in the 5'-untranslated region of the viral sequence. Molecular phylogenetic trees for core, NS3, and NS5B sequences showed the formation of two clusters depending on the area from which samples were taken. The same results were obtained from molecular phylogenetic analyses using the full genome. From detailed calculations of genetic diversity calculated using the full genome, EHV appears divisible into two subgenotypes. Blood samples were collected again after a 7-month interval to examine infection persistence. Seventeen of 19 horses retested showed positive results for EHV after 7 months, suggesting a high rate of persistent infection. These results indicate a relatively higher frequency of EHV infection in Mongolia than in Europe or North America, with virus strains divided into at least two subgenotypes.

First report of equine parvovirus-hepatitis-associated Theiler's disease in Europe

BACKGROUND

Equine parvovirus-hepatitis (EqPV-H) has been proposed as the aetiological cause of Theiler's disease, also known as serum hepatitis. EqPV-H-associated Theiler's disease has not been previously reported in Europe.

OBJECTIVES

To determine whether EqPV-H infection was associated with a 2018-2019 outbreak of Theiler's disease in four horses on a studfarm.

STUDY DESIGN

Descriptive case series.

METHODS

The medical records of four horses from the same farm diagnosed with fatal Theiler's disease were examined retrospectively. Information collected included a clinical history, physical examination findings, tetanus antitoxin exposure, serum biochemistry and necropsy reports. Liver tissue from all four horses was tested for EqPV-H using PCR and in situ hybridisation (ISH) assays.

RESULTS

Three of the horses had a history of recent (7-11 weeks) tetanus antitoxin administration. Liver tissue from all four horses tested positive for EqPV-H with PCR. In situ hybridisation revealed a widespread distribution of viral nucleic acid in hepatocytes in one case, and a more sporadic distribution in the remaining three cases.

MAIN LIMITATIONS

Case controls were not available from the farm in question given the retrospective nature of analysis.

CONCLUSIONS

This case series documents the first reported EqPV-H-associated Theiler's disease in Europe and the first use of ISH to visualise the viral nucleic acid in liver tissues of horses with Theiler's disease.

Horses as a Crucial Part of One Health

One Health (OH) is a crucial concept, where the interference between humans, animals and the environment matters. This review article focusses on the role of horses in maintaining the health of humans and the environment. Horses' impact on environmental health includes their influence on soil and the biodiversity of animal and plant species. Nevertheless, the effect of horses is not usually linear and several factors like plant-animal coevolutionary history, climate and animal density play significant roles. The long history of the relationship between horses and humans is shaped by the service of horses in wars or even in mines. Moreover, horses were essential in developing the first antidote to cure diphtheria. Nowadays, horses do have an influential role in animal assisted therapy, in supporting livelihoods in low income countries and as a leisure partner. Horses are of relevance in the spillover of zoonotic and emerging diseases from wildlife to human (e.g., Hendra Virus), and in non-communicable diseases (e.g., post-traumatic osteoarthritis in horses and back pain in horse riders). Furthermore, many risk factors-such as climate change and antimicrobial resistance-threaten the health of both horses and humans. Finally, the horse is a valuable factor in sustaining the health of humans and the environment, and must be incorporated in any roadmap to achieve OH.

The association of Equine Parvovirus-Hepatitis (EqPV-H) with cases of non-biologic-associated Theiler's disease on a farm in Ontario, Canada

Theiler's disease was confirmed within a group horses located on a farm in southwestern Ontario during the summer and autumn of 2005. Five sudden deaths occurred between 3 July and 21 August, 2005, none of which were necropsied, however two of the horses showed clinical signs compatible with hepatic encephalopathy prior to death. No horse on the farm had received a biologic product of equine blood origin in the preceding six months. The only biologics used on the property were the administration of killed vaccines for rabies, tetanus and West Nile Virus to all horses 30 days prior to the onset of the first sudden death. Between 22 August, 2005 and 21 October, 2005, a further four horses died suddenly or were euthanized with all having a confirmed histopathologic diagnosis of acute hepatic necrosis. Serum was collected from all horses on the farm on 30 September, 2005 and this was repeated on 29 October, 2005. Equine parvovirus-hepatitis (EqPV-H) DNA was detected by quantitative-PCR in the serum of 61.8% (34/55) of the horses on the farm on either one or both sampling dates with viral loads ranging from <3.75 × 10³ copies/mL to 3.64 × 10⁷ copies/mL. EqPV-H DNA was present in serum samples of three horses with a confirmed diagnosis of Theiler's disease, five horses with subclinical liver disease, and in clinically normal in-contact horses. Subsequent phylogenetic analysis based on partial NS1 of EqPV-H revealed not only high similarity on nucleotide level within the sequenced samples but also within other previously published sequences.

Further Evidence for in Utero Transmission of Equine Hepacivirus to Foals

(1) Background: Equine hepacivirus (EqHV), also referred to as non-primate hepacivirus (NPHV), infects horses—and dogs in some instances—and is closely related to hepatitis C virus (HCV) that has infected up to 3% of the world’s human population, causing an epidemic of liver cirrhosis and cancer. EqHV also chronically infects the liver of horses, but does not appear to cause serious liver damages. Previous studies have been looking to identify route(s) of EqHV transmission to and between horses. (2) Methods: In this retrospective study, we sought to evaluate the prevalence of vertical transmission taking place in utero with measuring by quantitative RT-PCR the amounts of EqHV genome in samples from 394 dead foals or fetuses, paired with the allantochorion whenever available. (3) Results: Detection of EqHV in three foals most likely resulted from a vertical transmission from the mares to the fetuses, consistent with the in utero transmission hypothesis. In support of this observation, the presence of EqHV genome was found for the first time in two of the allantochorions. (4) Conclusions: As seemingly benign viruses could turn deadly (e.g., Zika flavivirus) and EqHV happens to have infected a significant proportion of the world’s horse herds, EqHV infectious cycle should be further clarified.

Structure-function analysis of the equine hepacivirus 5' untranslated region highlights the conservation of translational mechanisms across the hepaciviruses

Equine hepacivirus (EHcV) (now also classified as hepacivirus A) is the closest genetic relative to hepatitis C virus (HCV) and is proposed to have diverged from HCV within the last 1000 years. The 5' untranslated regions (UTRs) of both HCV and EHcV exhibit internal ribosome entry site (IRES) activity, allowing cap-independent translational initiation, yet only the HCV 5'UTR has been systematically analysed. Here, we report a detailed structural and functional analysis of the EHcV 5'UTR. The secondary structure was determined using selective 2' hydroxyl acylation analysed by primer extension (SHAPE), revealing four stem-loops, termed SLI, SLIA, SLII and SLIII, by analogy to HCV. This guided a mutational analysis of the EHcV 5'UTR, allowing us to investigate the roles of the stem-loops in IRES function. This approach revealed that SLI was not required for EHcV IRES-mediated translation. Conversely, SLIII was essential, specifically SLIIIb, SLIIId and a GGG motif that is conserved across the Hepaciviridae. Further SHAPE analysis provided evidence that this GGG motif mediated interaction with the 40S ribosomal subunit, whilst a CUU sequence in the apical loop of SLIIIb mediated an interaction with eIF3. In addition, we showed that a microRNA122 target sequence located between SLIA and SLII mediated an enhancement of translation in the context of a subgenomic replicon. Taken together, these results highlight the conservation of hepaciviral translation mechanisms, despite divergent primary sequences.

Replicons of a Rodent Hepatitis C Model Virus Permit Selection of Highly Permissive Cells

Animal hepaciviruses represent promising surrogate models for hepatitis C virus (HCV), for which there are no efficient immunocompetent animal models. Experimental infection of laboratory rats with rodent hepacivirus isolated from feral Rattus norvegicus (RHV-rn1) mirrors key aspects of HCV infection in humans, including chronicity, hepatitis, and steatosis. Moreover, RHV has been adapted to infect immunocompetent laboratory mice. RHV in vitro systems have not been developed but would enable detailed studies of the virus life cycle crucial for designing animal experiments to model HCV infection. Here, we established efficient RHV-rn1 selectable subgenomic replicons with and without reporter genes. Rat and mouse liver-derived cells did not readily support the complete RHV life cycle, but replicon-containing cell clones could be selected with and without acquired mutations. Replication was significantly enhanced by mutations in NS4B and NS5A and in cell clones cured of replicon RNA. These mutations increased RHV replication of both mono- and bicistronic constructs, and CpG/UpA-dinucleotide optimization of reporter genes allowed replication. Using the replicon system, we show that the RHV-rn1 NS3-4A protease cleaves a human mitochondrial antiviral signaling protein reporter, providing a sensitive readout for virus replication. RHV-rn1 replication was inhibited by the HCV polymerase inhibitor sofosbuvir and high concentrations of HCV NS5A antivirals but not by NS3 protease inhibitors. The microRNA-122 antagonist miravirsen inhibited RHV-rn1 replication, demonstrating the importance of this HCV host factor for RHV. These novel RHV in vitro systems will be useful for studies of tropism, molecular virology, and characterization of virus-host interactions, thereby providing important complements to in vivo systems.IMPORTANCE A vaccine against hepatitis C virus (HCV) is crucial for global control of this important pathogen, which induces fatal human liver diseases. Vaccine development has been hampered by the lack of immunocompetent animal models. Discovery of rodent hepacivirus (RHV) enabled establishment of novel surrogate animal models. These allow robust infection and reverse genetic and immunization studies of laboratory animals, which develop HCV-like chronicity. Currently, there are no RHV in vitro systems available to study tropism and molecular virology. Here, we established the first culture systems for RHV, recapitulating the intracellular phase of the virus life cycle in vitro These replicon systems enabled identification of replication-enhancing mutations and selection of cells highly permissive to RHV replication, which allow study of virus-host interactions. HCV antivirals targeting NS5A, NS5B, and microRNA-122 efficiently inhibited RHV replication. Hence, several important aspects of HCV replication are shared by the rodent virus system, reinforcing its utility as an HCV model.

Characterization of the viral genomes present in commercial batches of horse serum obtained by high-throughput sequencing

Horses are often used as blood donors for commercial horse serum (HS) production and to manufacture biologicals. HS is an alternative for fetal bovine serum (FBS) used as a supplement for cell culture and vaccine production. Furthermore, HS is also frequently obtained in order to produce antisera toxins and pathogens. The advent of high-throughput sequencing (HTS) has promoted changes in virus detection, since previous knowledge of targets is not required. Thus, the present study aimed to describe the virome of five different batches of commercial HS from New Zealand (three batches) and Brazil and the United States (one batch each) using HTS. Each HS pool were processed and sequenced using an Illumina MiSeq platform. Sequences-related to viruses belonging to the Flaviviridae, Herpesviridae, and Parvoviridae families were detected. Particularly, equine hepacivirus (EqHV), equine pegivirus (EPgV), and Theiler's disease-associated virus (TDAV) were more frequent found in the batches analyzed. The presence of viral genomes in cell culture sera illustrates that these commercial sera can contain a mixture of different viruses and, therefore, can be regarded as potentially infectious for susceptible hosts. Moreover, the innocuity of commercial HS is important for the efficiency and security of diagnostics and the production of biological products.

Chronic equine hepacivirus infection in an adult gelding with severe hepatopathy

Background: Equine hepacivirus (EqHV) in equids represents the closest homologue to hepatitis C virus (HCV) infecting humans. A majority of HCV infected patients develop a chronic course of infection leading to liver fibrosis, cirrhosis and liver failure. However, in horses mostly transient mild subclinical infections are reported for EqHV to date. Objectives: EqHV can be involved in chronic liver diseases of horses. Methods: Biochemical parameters in serum samples were measured. Viral load was determined using qPCR. Next generation sequencing (NGS) of serum was performed. Liver tissue was stained with haematoxylin and eosin and analysed for viral RNA with fluorescent in situ‐hybridization. Results: The horse showed symptoms of severe hepatopathy and was chronically infected with EqHV. Viral RNA was detectable in the liver during disease. To rule out other infectious agents NGS was performed and showed the highest abundance for EqHV. The identified virus sequence was similar to other circulating equine hepaciviruses. Conclusions: EqHV can be associated with liver disease in horses. Whether it causes the disease or contributes in a multifactorial manner needs further investigation.

What Do We Know About Hepatitis Viruses in Horses?

Theiler disease (serum hepatitis or idiopathic acute hepatic necrosis) has long been suspected to have a viral etiology. Four viruses have been described in association with hepatitis in horses. Further investigation suggests equine pegivirus and Theiler disease-associated virus (a second pegivirus) are neither hepatotropic nor pathogenic. Nonprimate hepacivirus (NPHV) causes subclinical disease in experimental models and has been associated with hepatitis in some clinical cases. Equine parvovirus-hepatitis (EqPV-H) experimentally causes subclinical-to-clinical liver disease and is found in the vast majority of Theiler disease cases. EqPV-H is likely of clinical significance, whereas the significance of NPHV is unknown.

The prevalence of elevated gamma-glutamyltransferase and sorbitol dehydrogenase activity in racing Thoroughbreds and their associations with viral infection

BACKGROUND

In racehorses, serum gamma-glutamyltransferase (GGT) activity is positively correlated with cumulative days in training and, when ≥100 IU/L, has been associated with poor performance. The prevalence of increased GGT activity in North American Thoroughbreds and its aetiopathogenesis are unknown. Four emerging viruses, pegivirus E (PgV E; equine pegivirus), hepacivirus A (HcV A; equine hepacivirus), pegivirus D (PgV D; Theiler's disease virus), and equine parvovirus-hepatitis (EqPV-H) have been identified in horses with clinical and subclinical hepatopathy. Available prevalence data indicate these viruses may commonly infect racehorses and contribute to increased liver enzyme activity in this population.

OBJECTIVES

To investigate the association between viral infection and increased liver enzyme activity in racing Thoroughbreds.

STUDY DESIGN

Cross-sectional study.

METHODS

Prerace blood samples were collected from 802 Thoroughbreds and tested for GGT and sorbitol dehydrogenase (SDH) activity, and the presence of PgV E, HcV A, PgV D and EqPV-H nucleic acid.

RESULTS

Increased SDH and/or GGT were detected in 56.2% of the 802 serum samples. The infection prevalence and relative risk (RR) of having concurrently increased liver enzyme activity were: PgV E = 18.2% (RR = 0.820, 95% CI = 0.662-0.978, P = 0.03), HcV A = 2.5% (RR = 1.132, 95% CI = 0.719-1.466, P = 0.6), PgV D = 0.5% (RR = 0.875, 95% CI = 0.165-1.598, P>0.9), EqPV-H = 2.9% (RR = 0.916, 95% CI = 0.564-1.266, P = 0.7).

MAIN LIMITATIONS

Longitudinal samples were not tested.

CONCLUSIONS

While viral infection was common among Thoroughbreds in this study, infection did not explain the high prevalence of increased liver enzyme activity. In fact, PgV E infection was associated with a reduced risk of having increased liver enzyme activity, indicating PgV E is unlikely to be a cause of hepatitis in horses. Importantly, like GGT, increased SDH activity was highly prevalent in this study, and provides additional evidence that hepatocellular injury was occurring in these horses.

Evolutionary biology of human hepatitis viruses

Hepatitis viruses are major threats to human health. During the last decade, highly diverse viruses related to human hepatitis viruses were found in animals other than primates. Herein, we describe both surprising conservation and striking differences of the unique biological properties and infection patterns of human hepatitis viruses and their animal homologues, including transmission routes, liver tropism, oncogenesis, chronicity, pathogenesis and envelopment. We discuss the potential for translation of newly discovered hepatitis viruses into preclinical animal models for drug testing, studies on pathogenesis and vaccine development. Finally, we re-evaluate the evolutionary origins of human hepatitis viruses and discuss the past and present zoonotic potential of their animal homologues.

Genomes and seroprevalence of severe fever with thrombocytopenia syndrome virus and Nairobi sheep disease virus in Haemaphysalis longicornis ticks and goats in Hubei, China

Ticks are medically-important arthropods that maintain and transmit numerous emerging viruses. China suffers severely from tick-borne viral diseases such as tick-borne encephalitis and severe fever with thrombocytopenia syndrome (SFTS), but the background of tick-borne viruses is very limited. Here we report the virome profiling of ticks and goat sera from SFTS-epidemic areas, and serological investigation of SFTS virus (SFTSV) and Nairobi sheep disease virus (NSDV). Results revealed divergent viruses in ticks and goat sera, including SFTSV and NSDV. Sequence and phylogenetic analyses showed that the SFTSV identified here was most closely related to human SFTSV in sampling and surrounding areas, and the NSDV to the previously identified NSDV from northeast China. Serological investigation of SFTSV infection in goats revealed intensive activity in those areas. Surprisingly, two different methods of NSDV serological investigation showed no sera positive for this virus.

Functional Interplay between RNA Viruses and Non-Coding RNA in Mammals

Exploring virus–host interactions is key to understand mechanisms regulating the viral replicative cycle and any pathological outcomes associated with infection. Whereas interactions at the protein level are well explored, RNA interactions are less so. Novel sequencing methodologies have helped uncover the importance of RNA–protein and RNA–RNA interactions during infection. In addition to messenger RNAs (mRNAs), mammalian cells express a great number of regulatory non-coding RNAs, some of which are crucial for regulation of the immune system whereas others are utilized by viruses. It is thus becoming increasingly clear that RNA interactions play important roles for both sides in the arms race between virus and host. With the emerging field of RNA therapeutics, such interactions are promising antiviral targets. In this review, we discuss direct and indirect RNA interactions occurring between RNA viruses or retroviruses and host non-coding transcripts upon infection. In addition, we review RNA virus derived non-coding RNAs affecting immunological and metabolic pathways of the host cell typically to provide an advantage to the virus. The relatively few known examples of virus–host RNA interactions suggest that many more await discovery.

New Parvovirus Associated with Serum Hepatitis in Horses after Inoculation of Common Biological Product

Equine serum hepatitis (i.e., Theiler's disease) is a serious and often life-threatening disease of unknown etiology that affects horses. A horse in Nebraska, USA, with serum hepatitis died 65 days after treatment with equine-origin tetanus antitoxin. We identified an unknown parvovirus in serum and liver of the dead horse and in the administered antitoxin. The equine parvovirus-hepatitis (EqPV-H) shares <50% protein identity with its phylogenetic relatives of the genus Copiparvovirus. Next, we experimentally infected 2 horses using a tetanus antitoxin contaminated with EqPV-H. Viremia developed, the horses seroconverted, and acute hepatitis developed that was confirmed by clinical, biochemical, and histopathologic testing. We also determined that EqPV-H is an endemic infection because, in a cohort of 100 clinically normal adult horses, 13 were viremic and 15 were seropositive. We identified a new virus associated with equine serum hepatitis and confirmed its pathogenicity and transmissibility through contaminated biological products.

Viral testing of 10 cases of Theiler's disease and 37 in-contact horses in the absence of equine biologic product administration: A prospective study (2014-2018)

Background

A novel equine parvovirus (EqPV‐H) was recently discovered in the equine liver with Theiler's disease.

Objectives

To determine the prevalence of EqPV‐H infection in naturally occurring Theiler's disease cases and in‐contact horses in the absence of historical equine biologic product administration.

Animals

Ten cases of Theiler's disease from 6 separate properties were included in the study, based on the criteria of acute onset of clinical signs of liver failure with laboratory or histopathologic findings characteristic of Theiler's disease and no history of receiving an equine biologic product within the preceding 4 months. In addition, 37 in‐contact horses from 4 of the 6 properties were screened for EqPV‐H infection and hepatitis.

Methods

In prospective case series, cases were diagnosed with Theiler's disease by the attending veterinarian and were tested for EqPV‐H by PCR of liver or serum. In‐contact horses were assessed via serum chemistry and PCR at the attending veterinarian's discretion. Hepatitis was defined as serum gamma‐glutamyltransferase activity above reference interval. The association of EqPV‐H with hepatitis was determined by Fisher's exact test.

Results

Nine of 10 (90%) Theiler's disease cases and 54% of tested in‐contact horses were EqPV‐H positive. Hepatitis was significantly associated with EqPV‐H infection (P = .036).

Conclusions and Clinical Importance

Although further study is required to identify EqPV‐H as the causative agent of Theiler's disease, EqPV‐H appears strongly associated with cases of fatal Theiler's disease and subclinical hepatitis in horses in contact with those cases. The prevalence of EqPV‐H infection on affected properties can be high.

Viral testing of 18 consecutive cases of equine serum hepatitis: A prospective study (2014-2018)

Background

Three flaviviruses (equine pegivirus [EPgV]; Theiler's disease–associated virus [TDAV]; non‐primate hepacivirus [NPHV]) and equine parvovirus (EqPV‐H) are present in equine blood products; the TDAV, NPHV, and EqPV‐H have been suggested as potential causes of serum hepatitis.

Objective

To determine the prevalence of these viruses in horses with equine serum hepatitis.

Animals

Eighteen horses diagnosed with serum hepatitis, enrolled from US referral hospitals.

Methods

In the prospective case study, liver, serum, or both samples were tested for EPgV, TDAV, NPHV, and EqPV‐H by PCR.

Results

Both liver tissue and serum were tested for 6 cases, serum only for 8 cases, and liver only for 4 cases. Twelve horses received tetanus antitoxin (TAT) 4‐12.7 weeks (median = 8 weeks), 3 horses received commercial equine plasma 6‐8.6 weeks, and 3 horses received allogenic stem cells 6.4‐7.6 weeks before the onset of hepatic failure. All samples were TDAV negative. Two of 14 serum samples were NPHV‐positive. Six of 14 serum samples were EPgV‐positive. All liver samples were NPHV‐negative and EPgV‐negative. EqPV‐H was detected in the serum (N = 8), liver (N = 4), or both samples (N = 6) of all 18 cases. The TAT of the same lot number was available for virologic testing in 10 of 12 TAT‐associated cases, and all 10 samples were EqPV‐H positive.

Conclusions and Clinical Importance

We demonstrated EqPV‐H in 18 consecutive cases of serum hepatitis. EPgV, TDAV, and NPHV were not consistently present. This information should encourage blood product manufacturers to test for EqPV‐H and eliminate EqPV‐H–infected horses from their donor herds.

Virus discovery reveals frequent infection by diverse novel members of the Flaviviridae in wild lemurs

Lemurs are highly endangered mammals inhabiting the forests of Madagascar. In this study, we performed virus discovery on serum samples collected from 84 wild lemurs and identified viral sequence fragments from 4 novel viruses within the family Flaviviridae, including members of the genera Hepacivirus and Pegivirus. The sifaka hepacivirus (SifHV, two genotypes) and pegivirus (SifPgV, two genotypes) were discovered in the diademed sifaka (Propithecus diadema), while other pegiviral fragments were detected in samples from the indri (Indri indri, IndPgV) and the weasel sportive lemur (Lepilemur mustelinus, LepPgV). Although data are preliminary, each viral species appeared host species-specific and frequent infection was detected (18 of 84 individuals were positive for at least one virus). The complete coding sequence and partial 5' and 3' untranslated regions (UTRs) were obtained for SifHV and its genomic organization was consistent with that of other hepaciviruses, with one unique polyprotein and highly structured UTRs. Phylogenetic analyses showed the SifHV belonged to a clade that includes several viral species identified in rodents from Asia and North America, while SifPgV and IndPgV were more closely related to pegiviral species A and C, that include viruses found in humans as well as New- and Old-World monkeys. Our results support the current proposed model of virus-host co-divergence with frequent occurrence of cross-species transmission for these genera and highlight how the discovery of more members of the Flaviviridae can help clarify the ecology and evolutionary history of these viruses. Furthermore, this knowledge is important for conservation and captive management of lemurs.

Molecular identification and characterization of nonprimate hepaciviruses in equines

Hepatitis C virus (HCV) is a positive-sense RNA virus belonging to the genus Hepacivirus, family Flaviviridae. Its genome has a length of 9.6 kb and encodes a single polyprotein flanked by two untranslated regions. HCV can cause liver cirrhosis and hepatocellular carcinoma, and approximately 2% of the world's population is chronically infected. The investigation of pathogenesis is complicated due to the lack of an animal model. The origin of this virus remains unclear, but in the last few years, relatives of HCV were initially identified in dogs and later in horses, rodents, bats and Old World monkeys. Non-primate hepacivirus (NPHV), which infects dogs and horses, is the closest relative to HCV. We established a pan-reactive "panHepaci"-RT-qPCR assay, which is able to detect human HCV as well as equine NPHV, and additionally, an equine-specific "equHepaci"-RT-qPCR for confirmation of positive results. Serum samples from 1158 clinically inconspicuous horses from Germany and several samples from other mammalian species were screened. We found 2.4% of the horses positive for hepacivirus RNA, and furthermore, the "panHepaci"-RT-qPCR assay also detected a hepacivirus in a donkey from Egypt. This virus had only 78% sequence identity in the E2 gene when compared to other known NPHVs. The established method could be useful for screening purposes, since it is likely that related hepaciviruses also occur in other species.

Identification and genetic characterization of a novel parvovirus associated with serum hepatitis in horses in China

A novel equine parvovirus, equine parvovirus-hepatitis (EqPV-H), was first discovered in a horse that died of equine serum hepatitis in the USA in 2018. EqPV-H was shown to be a novel etiological agent associated with equine serum hepatitis. Following this initial report, no additional studies on EqPV-H have been published. In this study, a total of 143 serum samples were collected from racehorses at 5 separate farms in China and were analyzed to detect EqPV-H DNA via nested PCR. The results indicated a high prevalence of EqPV-H (11.9%, 17/143) in the studied animals. In addition, a remarkably high coinfection rate (58.8%, 10/17) with 2 equine flaviviruses (equine hepacivirus and equine pegivirus) was observed in the EqPV-H positive equines. However, all equines tested negative for Theiler’s disease-associated virus, an etiological agent associated with equine serum hepatitis. The genomes of six field EqPV-H strains were sequenced and analyzed, with the results indicating that the Chinese EqPV-H strains have low genetic diversity and high genetic similarity with the USA EqPV-H strain BCT-01. A phylogenetic analysis demonstrated that the Chinese EqPV-H strains clustered with BCT-01 in the genus Copiparvovirus but were distantly related to another equine parvovirus identified in horse cerebrospinal fluid. In addition, liver enzyme levels were detected in the EqPV-H positive serum samples, and all the values were in the normal range, indicating that infection can occur without concurrent liver disease. This study will promote an understanding of the geographical distribution, genetic diversity, and pathogenicity of EqPV-H.

Further characterization of bovine hepacivirus: Antibody response, course of infection, and host tropism

Bovine hepacivirus (BovHepV) is a recently added member to the growing genus Hepacivirus within the family Flaviviridae. Animal hepaciviruses are rarely characterized so far. Apart from norway rat hepacivirus which represents a promising HCV surrogate model, only equine hepaciviruses have been studied to some extent. BovHepV has been initially identified in bovine samples and was shown to establish persistent infections in cattle. However, consequences of those chronic infections, humoral immune response and the possibility of an extended host spectrum have not been explored so far. Therefore, we here investigated (a) the presence of anti-NS3-antibodies and viral RNA in cattle herds in Germany, (b) the course of infection in cattle, and (c) the host tropism including zoonotic potential of bovine hepaciviruses. Our results show that 19.9% of investigated bovine serum samples had antibodies against BovHepV. In 8.2% of investigated samples, viral RNA was detected. Subsequent genetic analysis revealed a novel genetic cluster of BovHepV variants. For 25 selected cattle in a BovHepV positive herd the presence of viral genomic RNA was monitored over one year in two to three months intervals by RT-PCR in order to discriminate acute versus persistent infection. In persistently infected animals, no serum antibodies were detected. Biochemical analyses could not establish a link between BovHepV infection and liver injury. Apart from a single sample of a pig providing a positive reaction in the antibody test, neither BovHepV-specific antibodies nor viral RNA were detected in porcine, equine or human samples implying a strict host specificity of BovHepV.

Hepacivirus A Infection in Horses Defines Distinct Envelope Hypervariable Regions and Elucidates Potential Roles of Viral Strain and Adaptive Immune Status in Determining Envelope Diversity and Infection Outcome

Hepacivirus A (also known as nonprimate hepacivirus and equine hepacivirus) is a hepatotropic virus that can cause both transient and persistent infections in horses. The evolution of intrahost viral populations (quasispecies) has not been studied in detail for hepacivirus A, and its roles in immune evasion and persistence are unknown. To address these knowledge gaps, we first evaluated the envelope gene (E1 and E2) diversity of two different hepacivirus A strains (WSU and CU) in longitudinal blood samples from experimentally infected adult horses, juvenile horses (foals), and foals with severe combined immunodeficiency (SCID). Persistent infection with the WSU strain was associated with significantly greater quasispecies diversity than that observed in horses who spontaneously cleared infection (P = 0.0002) or in SCID foals (P < 0.0001). In contrast, the CU strain was able to persist despite significantly lower (P < 0.0001) and relatively static envelope diversity. These findings indicate that envelope diversity is a poor predictor of hepacivirus A infection outcomes and could be dependent on strain-specific factors. Next, entropy analysis was performed on all E1/E2 genes entered into GenBank. This analysis defined three novel hypervariable regions (HVRs) in E2, at residues 391 to 402 (HVR1), 450 to 461 (HVR2), and 550 to 562 (HVR3). For the experimentally infected horses, entropy analysis focusing on the HVRs demonstrated that these regions were under increased selective pressure during persistent infection. Increased diversity in the HVRs was also temporally associated with seroconversion in some horses, suggesting that these regions may be targets of neutralizing antibody and may play a role in immune evasion.IMPORTANCE Hepacivirus C (hepatitis C virus) is estimated to infect 150 million people worldwide and is a leading cause of cirrhosis and hepatocellular carcinoma. In contrast, its closest relative, hepacivirus A, causes relatively mild disease in horses and is frequently cleared. The relationship between quasispecies evolution and infection outcome has not been explored for hepacivirus A. To address this knowledge gap, we examined envelope gene diversity in horses with resolving and persistent infections. Interestingly, two strain-specific patterns of quasispecies diversity emerged. Persistence of the WSU strain was associated with increased quasispecies diversity and the accumulation of amino acid changes within three novel hypervariable regions following seroconversion. These findings provided evidence that envelope gene mutation is influenced by adaptive immune pressure and may contribute to hepacivirus persistence. However, the CU strain persisted despite relative evolutionary stasis, suggesting that some hepacivirus strains may use alternative mechanisms to persist in the host.

Viral persistence, liver disease, and host response in a hepatitis C-like virus rat model

The lack of a relevant, tractable, and immunocompetent animal model for hepatitis C virus (HCV) has severely impeded investigations of viral persistence, immunity, and pathogenesis. In the absence of immunocompetent models with robust HCV infection, homolog hepaciviruses in their natural host could potentially provide useful surrogate models. We isolated a rodent hepacivirus from wild rats (Rattus norvegicus), RHV-rn1; acquired the complete viral genome sequence; and developed an infectious reverse genetics system. RHV-rn1 resembles HCV in genomic features including the pattern of polyprotein cleavage sites and secondary structures in the viral 5' and 3' untranslated regions. We used site-directed and random mutagenesis to determine that only the first of the two microRNA-122 seed sites in the viral 5' untranslated region is required for viral replication and persistence in rats. Next, we used the clone-derived virus progeny to infect several inbred and outbred rat strains. Our results determined that RHV-rn1 possesses several HCV-defining hallmarks: hepatotropism, propensity to persist, and the ability to induce gradual liver damage. Histological examination of liver samples revealed the presence of lymphoid aggregates, parenchymal inflammation, and macrovesicular and microvesicular steatosis in chronically infected rats. Gene expression analysis demonstrated that the intrahepatic response during RHV-rn1 infection in rats mirrors that of HCV infection, including persistent activation of interferon signaling pathways. Finally, we determined that the backbone drug of HCV direct-acting antiviral therapy, sofosbuvir, effectively suppresses chronic RHV-rn1 infection in rats.

CONCLUSION

We developed RHV-rn1-infected rats as a fully immunocompetent and informative surrogate model to delineate the mechanisms of HCV-related viral persistence, immunity, and pathogenesis. (Hepatology 2018).