Phylogenetic analysis of hepatitis E virus in domestic swine and wild boar in Germany

[Hepatitis E virus-a zoonotic virus: distribution, transmission pathways, and relevance for food safety]

Das Hepatitis-E-Virus (HEV) ist ein Erreger einer akuten Hepatitis beim Menschen. Darüber hinaus treten zunehmend auch chronische Infektionen mit fataler Leberzirrhose bei immunsupprimierten Transplantationspatienten auf. Die Zahl der gemeldeten Hepatitis-E-Fälle in Deutschland hat in den vergangenen Jahren stark zugenommen. Hier kommt vor allem der Genotyp 3 vor, der zoonotisch von Tieren auf den Menschen übertragen werden kann. Haus- und Wildschweine, die ohne die Ausbildung klinischer Symptome infiziert werden, stellen das Hauptreservoir dar. In diesem Artikel werden die Verbreitung von HEV in Tieren in Deutschland, mögliche Übertragungswege des Virus und insbesondere die Bedeutung von Lebensmitteln bei der Übertragung anhand der aktuellen wissenschaftlichen Literatur dargestellt.

HEV ist in Haus- und Wildschweinen in Deutschland stark verbreitet und wird hauptsächlich über direkten Kontakt oder den Verzehr von Lebensmitteln, die aus diesen Tieren hergestellt wurden, auf den Menschen übertragen. Beim HEV-RNA-Nachweis in spezifischen Lebensmitteln bleibt allerdings oft unklar, ob das enthaltene Virus noch infektiös ist oder durch die Herstellungsbedingungen inaktiviert wurde. Neuere Studien weisen auf eine hohe Stabilität des HEV unter verschiedenen physikochemischen Bedingungen hin, wohingegen eine Inaktivierung unter anderem durch Erhitzung erreicht wird. Generell wird deshalb ein ausreichendes Erhitzen von Schweinefleisch und -leber vor dem Verzehr empfohlen und für Risikogruppen zusätzlich der Verzicht auf den Verzehr kurzgereifter Rohwürste.

Weitere Forschungen sind nötig, um relevante Risikolebensmittel zu identifizieren, alternative Übertragungswege zu untersuchen und effiziente Maßnahmen zu entwickeln, die eine zoonotische Virusübertragung zukünftig verringern oder vermeiden.

Development and Optimization of an Enzyme Immunoassay to Detect Serum Antibodies against the Hepatitis E Virus in Pigs, Using Plant-Derived ORF2 Recombinant Protein

Hepatitis E is an emerging global disease, mainly transmitted via the fecal-oral route in developing countries, and in a zoonotic manner in the developed world. Pigs and wild boar constitute the primary Hepatitis E virus (HEV) zoonotic reservoir. Consumption of undercooked animal meat or direct contact with infected animals is the most common source of HEV infection in European countries. The purpose of this study is to develop an enzyme immunoassay (EIA) for the detection of anti-hepatitis E virus IgG in pig serum, using plant-produced recombinant HEV-3 ORF2 as an antigenic coating protein, and also to evaluate the sensitivity and specificity of this assay. A recombinant HEV-3 ORF2 110-610_6his capsid protein, transiently expressed by pEff vector in Nicotiana benthamiana plants was used to develop an in-house HEV EIA. The plant-derived HEV-3 ORF2 110-610_6his protein proved to be antigenically similar to the HEV ORF2 capsid protein and it can self-assemble into heterogeneous particulate structures. The optimal conditions for the in-house EIA (iEIA) were determined as follows: HEV-3 ORF2 110-610_6his antigen concentration (4 µg/mL), serum dilution (1:50), 3% BSA as a blocking agent, and secondary antibody dilution (1:20 000). The iEIA developed for this study showed a sensitivity of 97.1% (95% Cl: 89.9-99.65) and a specificity of 98.6% (95% Cl: 92.5-99.96) with a Youden index of 0.9571. A comparison between our iEIA and a commercial assay (PrioCHECK™ Porcine HEV Ab ELISA Kit, ThermoFisher Scientific, MA, USA) showed 97.8% agreement with a kappa index of 0.9399. The plant-based HEV-3 ORF2 iEIA assay was able to detect anti-HEV IgG in pig serum with a very good agreement compared to the commercially available kit.

Genetic Diversity and Epidemiological Significance of Wild Boar HEV-3 Strains Circulating in Poland

The wild boar is the most important reservoir of zoonotic HEV-3 strains among different wildlife species. The aim of the study was subtype identification of wild boar HEV-3 strains circulating in Poland. Wild boar liver was used in the study in the form of homogenates prepared from 57 samples positive for HEV in a real-time RT-PCR. These samples were collected from juvenile and adult wild boars hunted in the jurisdictions of different Regional Directorates of State Forests (RDSF) across Poland. Subtype identification of detected HEV strains was based on a phylogenetic analysis of the most conserved HEV ORF2 genome fragment. Out of 57 tested samples, consensus HEV ORF2 sequences of 348 bp were obtained for 45 strains. Nineteen strains were identified and belonged to the HEV gt 3a and 3i subtypes, whereas 26 were not assigned to any virus subtype. HEV gt 3i strains prevailed in the Polish wild boar population, 16 of such were identified, and they were significantly more often observed in the RDSF Katowice area (χ² = 28.6, p = 0.027 (<0.05)) compared to other regions of the country. Circulation of 3a strains was limited only to the RDSF Gdańsk territory (χ² = 48, p = 0.000 (<0.05)). The virus strains detected in the Polish population of wild boars representing previously identified HEV subtypes in wild boars, pigs, or humans in Europe are of epidemiological importance for public health.

Proline-Rich Hypervariable Region of Hepatitis E Virus: Arranging the Disorder

The hepatitis E virus (HEV) hypervariable region (HVR) presents the highest divergence of the entire HEV genome. It is characteristically rich in proline, and so is also known as the “polyproline region” (PPR). HEV genotype 3 (HEV-3) exhibits different PPR lengths due to insertions, PPR and/or RNA-dependent RNA polymerase (RdRp) duplications and deletions. A total of 723 PPR-HEV sequences were analyzed, of which 137 HEV-3 sequences were obtained from clinical specimens (from acute and chronic infection) by Sanger sequencing. Eight swine stool/liver samples were also analyzed. N- and C-terminal fragments were confirmed as being conserved, but they harbored differences between genotypes and were not proline-plentiful regions. The genuine PPR is the intermediate region between them. HEV-3 PPR contains a higher percentage (30.4%) of prolines than other genotypes. We describe for the first time: (1) the specific placement of HEV-3 PPR rearrangements in sites 1 to 14 of the PPR, noting that duplications are more frequently attached to sites 11 and 12 (AAs 74–79 and 113–118, respectively); (2) the cadence of repetitions follows a circular-like pattern of blocks A to J, with F, G, H, and I being the most frequent; (3) a previously unreported insertion homologous to apolipoprotein C1; and (4) the increase in frequency of potential N-glycosylation sites and differences in AAs composition related to duplications.

Swine hepatitis E virus: Cross-species infection, pork safety and chronic infection

Swine hepatitis E virus (swine HEV) belongs to the species Orthohepevirus A within the genus Orthohepevirus in the family Hepeviridae. Four different genotypes of swine HEV within the species Orthohepevirus A have been identified so far from domesticated and wild swine population: genotypes 3 (HEV-3) and 4 (HEV-4) swine HEVs are zoonotic and infect humans, whereas HEV-5 and HEV-6 are only identified from swine. As a zoonotic agent, swine HEV is an emerging public health concern in many industrialized countries. Pigs are natural reservoir for HEV, consumption of raw or undercooked pork is an important route of foodborne HEV transmission. Occupational risks such as direct contact with infected pigs also increase the risk of HEV transmission in humans. Cross-species infection of HEV-3 and HEV-4 have been documented under experimental and natural conditions. Both swine HEV-3 and swine HEV-4 infect non-human primates, the surrogates of man. Swine HEV, predominantly HEV-3, can establish chronic infection in immunocompromised patients especially in solid organ transplant recipients. The zoonotic HEV-3, and to lesser extent HEV-4, have also been shown to cause neurological diseases and kidney injury. In this review, we focus on the epidemiology of swine HEV, host and viral determinants influencing cross-species HEV infection, zoonotic infection and its associated pork safety concern, as well as swine HEV-associated chronic infection and neurological diseases.

Evolutionary study of potentially zoonotic hepatitis E virus genotype 3 from swine in Northeast Brazil

Hepatitis E virus (HEV), an emerging virus associated with acute hepatic disease, leads to thousands of deaths worldwide. HEV has already been reported in Brazil; however, there is a lack of epidemiological and molecular information on the genetic variability, taxonomy, and evolution of HEV. It is thus unclear whether hepatitis E is a neglected disease in Brazil or it has low relevance for public health in this country. Here, for the first time, we report the presence of HEV in Northeast Brazil. A total of 119 swine faecal samples were screened for the presence of HEV RNA using real-time polymerase chain reaction (RT-PCR) and further confirmed by conventional RT-PCR; among these, two samples were identified as positive. Molecular evolution analyses based on capsid sequences revealed that the samples had close proximities to HEV sequences belonging to genotype 3 and were genetically related to subtype 3f isolated in humans. Parsimony ancestral states analysis indicated gene flow events from HEV cross-species infection, suggesting an important role of pig hosts in viral spillover. HEV’s ability for zoonotic transmission by inter-species host switching as well as its possible adaptation to new animal species remain important issues for human health.

Hepatitis E virus strains infecting Swedish domestic pigs are unique for each pig farm and remain in the farm for at least 2 years

Hepatitis E virus (HEV) genotype 3 (HEV3) is distributed globally and infects both humans and animals, mainly domestic pigs and wild boars, which are the major reservoirs. In this study, the prevalence of HEV among Swedish pigs was investigated by HEV RNA analysis in 363 faecal samples from 3-month-old piglets sampled twice (2013 and 2014) in 30 Swedish pig farms. Four different types of farms were investigated; organic, conventional closed (keeping the sow), satellites in a sow pool (conventional farms sharing sows) and conventional non-closed farms (purchasing gilts). More than two-thirds (77%) of the farms had HEV-infected pigs. HEV RNA was found in faeces from 79 pigs (22%). Partial ORF1 could be sequenced in 46 strains. Phylogenetic analysis revealed a unique HEV3 strain for each farm. Strains sampled more than a year apart from the same farm were closely related, indicating that the same HEV strain is present for several years on the farm. Despite that only 4% of the Swedish pig farms were investigated, two farms had strains similar to those from humans, another had strains similar to wild boar HEV. The uniqueness of strains from each farm indicates a possibility to identify a source of infection down to farm level. This knowledge may be used by the farms to investigate the effectiveness of good hygiene routines to reduce the amount of HEV and thus the infection risk in the farm, and for Swedish public health authorities to identify cases of HEV transmissions from consumption of uncooked pork.

Phylogenetic analysis of two genotype 3 Hepatitis E viruses from wild boar, Italy

The complete and near-complete genome sequences (7206 nt and 7229 nt) of two wild boar HEV strains detected in Southern Italy were obtained by the next generation sequencing. Phylogenetic analysis and p distance comparisons of one of the strains with HEV-3 reference subtype strains confirmed the detection of a subtype 3i (p distance = 0.110) strain in wild boar, never detected in Italy either in wild boar or pigs. The sequence of the second strain was not classifiable in any of the subtypes defined to date, showing a p distance > 0.138 and a low nucleotide identity with all HEV reference strains. The virus may represent a novel subtype, with a low relationship to other strains of genotype 3 detected in wild boar, pigs, or humans in Europe. This result suggests the circulation in Italy of an emerging or uncommon HEV strain. Sequencing followed by phylogenetic analyses of the complete HEV coding regions are important tools for understanding the evolutionary and epidemiological dynamics underlying the wide genetic diversity of HEV strains.

Hepatitis E Seroprevalence and Genotyping in a Cohort of Wild Boars in Southern Germany and Eastern Alsace

In the last few years it has been realized that the hepatitis E virus (HEV) is endemic in most industrialized countries and that it is a zoonotic disease. Potential reservoirs for HEV have been identified to be wild boars and deers, but HEV has also been found in domestic pigs and other animals. Due to the probable spread of the virus via contaminated food or contact to infected animals, HEV antibodies are present in more than 16% of the German adult population and rates are increasing with age. We collected blood from 104 wild boars in southern Germany and the border region of Alsace. We found an anti-HEV seroprevalence of 11.5% in our cohort, using ELISA. Furthermore, we observed active infection in 3.85% of the animals by positive HEV PCR in the sera of the boars. In our cohort, no regional differences of seroprevalence or active infection were seen. Sequencing revealed rather close homology of some detected HEV sequences to genotypes isolated from patients in Germany. Hence wild boars are a potential source of HEV infection in Middle Europe and the rate of infectious animals is quite high.

Challenges in research and management of hepatitis E virus infection in Cuba, Mexico, and Uruguay

The symposium "Epidemiology of Hepatitis E virus (HEV) Infection and Associated Immune Response" was held at the Universidad de Guadalajara, Mexico, on 14 June 2017, to define the status of research on HEV infection in three countries in Latin America and the Caribbean (LAC)-Cuba, Mexico, and Uruguay-compared to the situation in Germany. Scientists identified specific research gaps in understanding HEV transmission and the resulting impact on development of disease in the three abovementioned LAC countries. Specific recommendations for implementing standardized serologic and molecular diagnostic methods and epidemiologic, basic, and applied research aimed to develop prevention and handling strategies for this infection, along with the associated comorbidities in the three LAC countries, were also discussed. Given similar demographic, sanitary, and economic conditions in other LAC countries that could predispose them to be at high risk for HEV transmission and infection, these research gaps and recommendations might apply to the entire LAC region. This report was -prepared by meeting participants based on 1) symposium presentations, 2) literature reviews, and 3) group discussions.

Comprehensive Molecular Approach for Characterization of Hepatitis E Virus Genotype 3 Variants

Autochthonous hepatitis E virus genotype 3 (HEV-3) infections in industrialized countries are more frequent than previously assumed. HEV-3 is zoonotic and the causal pathogen of chronic hepatitis E. According to the latest classification of the family Hepeviridae, 10 designated HEV-3 subtypes (HEV-3a to HEV-3j) and 7 unassigned HEV-3 subtypes are proposed. In order to identify and characterize the HEV-3 variants in circulation, we developed a molecular approach combining a sensitive HEV-specific real-time reverse transcription-PCR (RT-PCR) targeting the overlapping region of HEV ORF2 and ORF3 (the ORF2/3 region) and two newly designed consensus nested RT-PCRs targeting the HEV ORF1 and ORF2 genes, respectively. Since complete genome sequences are required for new HEV-3 subtype assignment, we implemented a straightforward approach for full-length HEV-3 genome amplification. Twenty-nine human serum samples and six human feces samples from chronic hepatitis E patients were selected for evaluation of the system. Viral loads ranged from 1 × 10⁴ to 1.9 × 10¹⁰ copies/ml of serum and from 1.8 × 10⁴ to 1 × 10¹² copies/g of feces. Sequence and phylogenetic analyses of partial ORF1 and ORF2 sequences showed that HEV strains had considerable genetic diversity and clustered into the HEV-3c (29/35), HEV-3e (2/35), HEV-3f (2/35), and unassigned HEV-3 (2/35) subtypes. Moreover, from these strains, three full-length HEV-3 genome sequences were generated and characterized. DE/15-0030 represents a typical HEV-3c strain (95.7% nucleotide identity to wbGER27), while DE/15-0031 and SW/16-0282 have <89.2% homology to known HEV-3 strains and are phylogenetically divergent, indicating novel HEV-3 subtypes. In summary, our approach will significantly facilitate the detection, quantification, and determination of HEV-3 strains and will thus help to improve molecular diagnostics and our knowledge of HEV diversity and evolution.

Hepatitis E Virus in Wild Boars and Spillover Infection in Red and Roe Deer, Germany, 2013-2015

To determine animal hepatitis E virus (HEV) reservoirs, we analyzed serologic and molecular markers of HEV infection among wild animals in Germany. We detected HEV genotype 3 strains in inner organs and muscle tissues of a high percentage of wild boars and a lower percentage of deer, indicating a risk for foodborne infection of humans.

Risk Analysis and Occurrence of Hepatitis E Virus (HEV) in Domestic Swine in Northeast Brazil

Anti-HEV antibodies were detected in animals from abattoir and in farms from northeast Brazil. Our results suggest that HEV is highly disseminated in the swine population and might present a great risk to animal handlers and for consumption of raw or undercooked meat and meat products in northeast Brazil.

A cross-sectional study among Polish hunters: seroprevalence of hepatitis E and the analysis of factors contributing to HEV infections

Hepatitis E virus (HEV) is known as zoonotic agent. The main reservoirs of HEV in Europe are pigs, wild boars, and deer. Hunting activity is considered to be a risk factor for HEV infection. We conducted a cross-sectional study among 1021 Polish hunters. To understand socio-demographic characteristics of this population and to gather information on potential exposures, all participants completed a questionnaire. Commercial immunoassays were employed to estimate seroprevalence anti-HEV. Samples with confirmed positive result of anti-HEV IgM were examined for HEV RNA. Anti-HEV IgG were identified in 227 people, 22.2% of the studied group. Seroprevalence among the studied hunters was associated with age ≥65 [adjusted prevalence ratio (aPR) 1.6, p = 0.037), living in a house (aPR 1.54, p = 0.013), professional contact with farm animals (aPR 1.09, p = 0.01), and consumption of stewed offal (aPR 1.61, p = 0.00). Washing hands after disembowelment was linked to lower seroprevalence (aPR 0.53; p = 0.00). Lower prevalence of anti-HEV IgG among hunters living in cities was associated with age: 35–49 (aPR 0.52, p = 0.011) and 50–64 (aPR 0.93, p = 0.58), living in a house (aPR 1.58, p = 0.002) and owning a cat (aPR 0.58, p = 0.042). Among hunters living in rural areas, seropositivity was associated with contact with farm animals (aPR 1.66, p = 0.013) and consumption of stewed offal (aPR 1.81; p = 0.001). Contrary to initial assumptions, it was concluded that hunting was of significantly lesser importance than other factors. Due to the high level of HEV seroprevalence identified, we recommend conducting a large-scale study in the general population of Poland.

Hepatitis E Virus in Domestic Pigs, Wild Boars, Pig Farm Workers, and Hunters in Estonia

While hepatitis E is a growing health concern in Europe, epidemiological data on hepatitis E virus (HEV) in Estonia are scarce. Along with imported HEV infections, autochthonous cases are reported from European countries. Both domestic and wild animals can be a source of human cases of this zoonosis. Here, we investigated the presence of anti-HEV antibodies and HEV RNA in domestic pigs and wild boars, as well as in pig farm workers and hunters in Estonia. Anti-HEV antibodies were detected in 234/380 (61.6%) of sera from domestic pigs and in all investigated herds, and in 81/471 (17.2%) of meat juice samples from wild boars. HEV RNA was detected by real-time PCR in 103/449 (22.9%) of fecal samples from younger domestic pigs and 13/81 (16.0%) of anti-HEV-positive wild boar samples. Analysis of sera from 67 pig farm workers and 144 hunters revealed the presence of HEV-specific IgG in 13.4 and 4.2% of the samples, respectively. No HEV RNA was detected in the human serum samples. Phylogenetic analyses of HEV sequences from domestic pigs and wild boars, based on a 245 bp fragment from the open reading frame 2 showed that all of them belonged to genotype 3. The present study demonstrates the presence of HEV in Estonian domestic pig and wild boar populations, as well as in humans who have direct regular contact with these animals. Our results suggest that HEV infections are present in Estonia and require attention.

The emergence of hepatitis E virus in Europe

ABSTRACT 

Hepatitis E virus (HEV) infections appear to be an emerging problem in Europe. Infections are mainly caused by viruses of genotype 3. Pigs and wild boar are the main reservoirs of HEV in Europe and most autochthonous infections are probably caused by the consumption of uncooked or undercooked infected meat. Nevertheless, transfusion-associated transmission has been described in different European countries but the efficiency of this route of transmission need to be further investigated. Most acute infections are asymptomatic or the induced symptoms are rather nonspecific. Although people that are otherwise completely healthy can spontaneously clear an HEV infection, people with underlying liver disease and/or suffering from immune deficiencies may require treatment to avoid chronicity and exacerbation of liver disease. In this review, we give an epidemiological overview of HEV in Europe and the potential complications.

Yersinia enterocolitica Isolates from Wild Boars Hunted in Lower Saxony, Germany

Yersiniosis is strongly associated with the consumption of pork contaminated with enteropathogenic Yersinia enterocolitica, which is harbored by domestic pigs without showing clinical signs of disease. In contrast to data on Y. enterocolitica isolated from conventionally reared swine, investigations into the occurrence of Y. enterocolitica in wild boars in Germany are rare. The objectives of the study were to get knowledge about these bacteria and their occurrence in wild boars hunted in northern Germany by isolation of the bacteria from the tonsils, identification of the bioserotypes, determination of selected virulence factors, macrorestriction analysis, multilocus sequence typing (MLST), and testing of antimicrobial susceptibility. Altogether, tonsils from 17.1% of 111 tested wild boars were positive for Y. enterocolitica by culture methods. All but two isolates belonged to biotype (BT) 1A, with the majority of isolates bearing a ystB nucleotide sequence which was revealed to have 85% identity to internal regions of Y. enterocolitica heat-stable enterotoxin type B genes. The remaining Y. enterocolitica isolates were identified to be BT 1B and did not carry the virulence plasmid. However, two BT 1A isolates carried the ail gene. Macrorestriction analysis and results from MLST showed a high degree of genetic diversity of the isolates, although the region where the samples were taken was restricted to Lower Saxony, Germany, and wild boars were shot during one hunting season. In conclusion, most Y. enterocolitica isolates from wild boars investigated in this study belonged to biotype 1A. Enteropathogenic Y. enterocolitica bioserotypes 4/O:3 and 2/O:9, usually harbored by commercially raised pigs in Europe, could not be identified.

Hepatitis E Virus and Related Viruses in Animals

Hepatitis E is an acute human liver disease in healthy individuals which may eventually become chronic. It is caused by the hepatitis E virus (HEV) and can have a zoonotic origin. Nearly 57,000 people die yearly from hepatitis E-related conditions. The disease is endemic in both developing and developed countries with distinct epidemiologic profiles. In developing countries, the disease is associated with inadequate water treatment, while in developed countries, transmission is associated with animal contact and the ingestion of raw or uncooked meat, especially liver. All human HEV are grouped into at least four genotypes, while HEV or HEV-related viruses have been identified in an increasing number of domestic and wild animal species. Despite a high genetic diversity, only one single HEV serotype has been described to date for HEV genotypes 1-4. The discovery of new HEV or HEV-related viruses leads to a continuing increase in the number of genotypes. In addition, the genome organization of all these viruses is variable with overlapping open reading frames (ORF) and differences in the location of ORF3. In spite of the role of some domestic and wild animals as reservoir, the origin of HEV and HEV-related viruses in humans and animals is still unclear. This review discusses aspects of the detection, molecular virology, zoonotic transmission and origin of HEV and HEV-related viruses in the context of 'One Health' and establishes a link between the previous and the new taxonomy of this growing virus family.