Detection and genetic characterisation of Hepatitis E virus in Czech pig production herds

Hepatitis E Virus in Livestock-Update on Its Epidemiology and Risk of Infection to Humans

Hepatitis E virus (HEV) is a public health problem worldwide and an important food pathogen known for its zoonotic potential. Increasing numbers of infection cases with human HEV are caused by the zoonotic transmission of genotypes 3 and 4, mainly by consuming contaminated, undercooked or raw porcine meat. Pigs are the main reservoir of HEV. However, it should be noted that other animal species, such as cattle, sheep, goats, and rabbits, may also be a source of infection for humans. Due to the detection of HEV RNA in the milk and tissues of cattle, the consumption of infected uncooked milk and meat or offal from these species also poses a potential risk of zoonotic HEV infections. Poultry infected by avian HEV may also develop symptomatic disease, although avian HEV is not considered a zoonotic pathogen. HEV infection has a worldwide distribution with different prevalence rates depending on the affected animal species, sampling region, or breeding system.

Identification and genetic diversity of hepatitis E virus in domestic swine from Slovakia

Background

Hepatitis E virus (HEV) is agent causing hepatitis worldwide. Originally considered to be limited to developing countries, this virus was also detected in developed countries. In recent years an increasing number of reports indicate that farmed domestic pigs are widely infected with HEV in several European countries. The HEV status in Slovakia is still missing.

Results

In this study, the circulation of HEV among domestic swine in Slovakia and genetic diversity of the virus was studied. Overall HEV RNA was detected in 53/388 (13.7, 95% CI: 10.40–17.48%) pig rectal swabs in five production stages (age categories) with statistically significant differences among all the stages. The highest HEV prevalence was observed in weaners 24/81 (29.6, 95% CI: 19.99–40.81%) and then significantly declined in growers and fatteners. No HEV was detected in suckling piglets and sows. Twenty-eight partial sequences of ORF1 (242 bp) and seventeen of ORF2 (304 bp) were analysed. Phylogenetic analysis and p-distance comparisons confirmed in both ORFs that all Slovak HEV sequences belong to the genotype HEV-3, major clade 3abchij with higher identity to 3a and 3i subtypes. Three sequences were outside of all lastly updated HEV-3 subtypes.

Conclusion

This is the first report to fill the information gap about HEV infection in pigs in Slovakia. The results suggested a lower prevalence of HEV in Slovak pig farms than observed in other European countries. While most HEV isolates were typed as HEV-3 clade 3abchij, three sequences were unclassified.

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.

Co-infection of pigs with Hepatitis E and porcine circovirus 2, Saxony 2016

Hepatitis E virus (HEV) is a recognized zoonotic disease; autochthonous infections in Europe are caused to a great extent by HEV genotype 3. Pigs and wild boar are the main reservoirs for this genotype and normally they develop no or only subclinical symptoms with mild histopathological lesions. However, co-infections with other pig pathogens can lead to severe cases in pigs, including liver hemorrhage and necrosis. During a monitoring program 2016 in Saxony, Germany, farmed pigs with various clinical outcomes including fatalities were analysed for HEV and concurrent infections. We could detect eight HEV infected pigs from which six were co-infected with porcine circovirus 2 (PCV2). Phylogenetic analysis revealed HEV sub-genotypes 3e and 3f as well as PCV2 genotypes 2b and 2d. A direct correlation of the co-infection to the course of disease could not be determined, but the results provide hints that the immune modulatory effects of PCV2 combined with HEV influence the disease pattern in pigs.

Prevalence and phylogenetic analysis of hepatitis E virus in pigs, wild boars, roe deer, red deer and moose in Lithuania

Background

Hepatitis E virus (HEV) is one of the major causes of acute viral hepatitis worldwide. In Europe, food-borne zoonotic transmission of HEV genotype 3 has been associated with domestic pigs and wild boar. Controversial data are available on the circulation of the virus in animals that are used for human consumption, and to date, no gold standard has yet been defined for the diagnosis of HEV-associated hepatitis. To investigate the current HEV infection status in Lithuanian pigs and wild ungulates, the presence of viral RNA was analyzed by nested reverse transcription polymerase chain reaction (RT-nPCR) in randomly selected samples, and the viral RNA was subsequently genotyped.

Results

In total, 32.98 and 22.55% of the domestic pig samples were HEV-positive using RT-nPCR targeting the ORF1 and ORF2 fragments, respectively. Among ungulates, 25.94% of the wild boar samples, 22.58% of the roe deer samples, 6.67% of the red deer samples and 7.69% of the moose samples were positive for HEV RNA using primers targeting the ORF1 fragment. Using primers targeting the ORF2 fragment of the HEV genome, viral RNA was only detected in 17.03% of the wild boar samples and 12.90% of the roe deer samples. Phylogenetic analysis based on a 348-nucleotide-long region of the HEV ORF2 showed that all obtained sequences detected in Lithuanian domestic pigs and wildlife belonged to genotype 3. In this study, the sequences identified from pigs, wild boars and roe deer clustered within the 3i subtype reference sequences from the GenBank database. The sequences obtained from pig farms located in two different counties of Lithuania were of the HEV 3f subtype. The wild boar sequences clustered within subtypes 3i and 3h, clearly indicating that wild boars can harbor additional subtypes of HEV. For the first time, the ORF2 nucleotide sequences obtained from roe deer proved that HEV subtype 3i can be found in a novel host.

Conclusion

The results of the viral prevalence and phylogenetic analyses clearly demonstrated viral infection in Lithuanian pigs and wild ungulates, thus highlighting a significant concern for zoonotic virus transmission through both the food chain and direct contact with animals. Unexpected HEV genotype 3 subtype diversity in Lithuania and neighboring countries revealed that further studies are necessary to understand the mode of HEV transmission between animals and humans in the Baltic States region.

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.

Detection and Molecular Characterisation of Swine Hepatitis E Virus in Brescia Province, Italy

Hepatitis E virus (HEV) is an important public health concern in many developing countries and it occurs in sporadic forms in industrialized areas. With the discovery of swine HEV in pigs, which is genetically closely related to human HEV, hepatitis E is considered to be a zoonotic disease. To investigate the circulation of HEV within a distinct area of Lombardy region (Northern Italy), 17 pig farms were subjected to monitoring study by collection of fresh stool samples each represented by ground-pooled specimens. In particular, three distinct types of breeding farms were focused, represented by farrow to weaning, farrow to finish and fattening farms, respectively. Epidemiological data confirm that in Europe the seroprevalence in pigs, more than 9 month of age, ranges from 51.4 to 75%, while in 3-9 months fatteners is about 38%. In France and Italy, the positivity among farms is respectively 30 and 97.4% and the seroprevalence in Italy is 50.2%. Since HEV viremia was typically observed in the early period of life in swine, faeces were collected in boxes containing weaning pigs. For the study, 183 stool samples were collected and amplifications were performed with universal primers specific for the ORF2 region of genome. Twentyeight samples resulted positive to HEV RNA and genotyping demonstrated that they were closely related to HEV strains belonging to genotype 3 and circulating in Europe. Comparison with reference strains from GenBank excluded their similarity to genotype 1, 2 or 4 confirming that genotype 3 strains are circulating in Europe. Since it was demonstrated that swine act as a reservoir for HEV, and since many strains into HEV genotype 3 share a strong molecular similarity to human HEV, it was important to detect the presence of HEV in a restricted area with a very high density of pigs.

Hepatitis E virus genotype 3 diversity: phylogenetic analysis and presence of subtype 3b in wild boar in Europe

An increasing number of indigenous cases of hepatitis E caused by genotype 3 viruses (HEV-3) have been diagnosed all around the word, particularly in industrialized countries. Hepatitis E is a zoonotic disease and accumulating evidence indicates that domestic pigs and wild boars are the main reservoirs of HEV-3. A detailed analysis of HEV-3 subtypes could help to determine the interplay of human activity, the role of animals as reservoirs and cross species transmission. Although complete genome sequences are most appropriate for HEV subtype determination, in most cases only partial genomic sequences are available. We therefore carried out a subtype classification analysis, which uses regions from all three open reading frames of the genome. Using this approach, more than 1000 published HEV-3 isolates were subtyped. Newly recovered HEV partial sequences from hunted German wild boars were also included in this study. These sequences were assigned to genotype 3 and clustered within subtype 3a, 3i and, unexpectedly, one of them within the subtype 3b, a first non-human report of this subtype in Europe.

Prevalence of Hepatitis E Virus in Populations of Wild Animals in Comparison with Animals Bred in Game Enclosures

Hepatitis E virus (HEV) is now accepted as a zoonotic virus, and domestic pigs, wild boars and deer are recognised as natural reservoirs of the pathogen. In this study, 762 animals (wild boars, fallow deer, red deer, sika deer, roe deer and mouflons) originating from the wild and from game enclosures were tested for the presence of HEV RNA by qRT-PCR. HEV RNA was detected in wild boars (96/450), red deer (2/169), roe deer (1/30) and mouflons (5/39). The sequence relationship between HEV isolates from wild boars and domestic pigs or humans indicate a circulation of HEV in the Czech Republic.

Comparison of three in-house ELISAs for the detection of hepatitis E virus infection in pigs under field conditions

Hepatitis E virus (HEV) is a RNA non-enveloped virus that comprises four genotypes. The genome of HEV is organized into three Open Reading Frames (ORFs), and the ORF2 is responsible for encoding capsid proteins. HEV can infect a wide range of hosts, and pigs are considered the main reservoir. HEV infection is considered a zoonosis and it is responsible for acute hepatitis in humans, especially in developing countries. The development of a blocking ELISA would be of high value for screening purpose, because there is no need of species specific reagents. The present study was conducted to assess three in-house ELISAs for the detection of HEV infection in 779 sera collected from breeding and fattening farms under field conditions. Two assays were indirect ELISAs, while the third was a blocking ELISA. Two different recombinant antigens were generated from specific sequences of the HEV-ORF2, and a Latent Class approach in a Bayesian framework was used to evaluate the diagnostic accuracy of each ELISA. Because the three ELISAs cannot be thought of as independent, all possible dependence structures were modelled starting from the general case of conditional independence to the most complex situation of three mutually dependent assays. Results showed that none of the three ELISAs was significantly superior to the others in terms of sensitivity (posterior median value ranging from 89% to 94%, all 95% posterior credible intervals (95%PCI) overlapped). In terms of specificity, one of the indirect ELISAs was superior to blocking ELISA (posterior median indirect ELISA: 99%, 95%PCI: 98-100%; blocking ELISA: 90%; 95%PCI: 86-94%). However, this difference could be due to the potential wider spectrum of antibodies that blocking ELISA can actually detect.

Endemic hepatitis E in the Czech Republic

BACKGROUND

An increasing incidence of endemic hepatitis E (HE) has been reported in developed countries. Thus, an evaluation of the clinical characteristics of the disease and the utility of the current diagnostic methods is warranted.

METHODS

Fifty-one adult acute patients with HE hospitalized in a single center between the years 2009 and 2012 were evaluated. Serological and molecular techniques (detection of hepatitis E virus [HEV] RNA from stool and serum samples by quantitative reverse transcription polymerase chain reaction) with sequencing and phylogenetic analysis were used for diagnosis, and the clinical, laboratory, and epidemiological parameters of the patients were evaluated.

RESULTS

Forty-nine (96.1%) patients had acute endemic HE and 2 (3.9%) had an imported infection. In the cohort of patients with acute symptomatic HE (n = 47), men outnumbered women (40:7), the patients were in older middle age (mean, 60.57 years), and they had elevated median values of total bilirubin (6.67 mg/dL), alanine aminotransferase (2288.82 U/L), aspartate aminotransferase (1251.76 U/L), gamma-glutamyl transferase (360.53 U/L), and alkaline phosphatase (197.06 U/L). Serology was positive in 50 (98%) of the patients, and 1 case was diagnosed by polymerase chain reaction only. HEV RNA was detected in at least 1 specimen from 84.3% of the patients, and 28 of 29 tested isolates belonged to genotype 3. The eating of meat, innards, other home-prepared pork products, or the tasting of raw meat before cooking were the most frequently reported data (reported by 25 patients [49.0%]).

CONCLUSIONS

Large numbers of the endemic cases of HE were caused by HEV genotype 3, and the clinical characteristics of endemic HE were demonstrated.

A longitudinal study revealing hepatitis E virus infection and transmission at a swine test station

Hepatitis E virus (HEV) is a zoonotic agent that causes acute hepatitis in humans, and infects several animal species, most importantly swine. In the current study, that presents the first evidence of HEV infections in pigs in Finland, genetic divergence and transmission of HEV was investigated among pigs at a swine test station at two occasions. In 2007, HEV RNA was found in 25% of pens, and 35% of 2-3 month-old pigs at the station. Three different isolates, comprising 13 sequences of HEV genotype 3 e that were imported from different farms were detected. In 2010, 39% of pigs were HEV RNA positive on weeks 1, 3, or 5 of a 3-month follow-up, and 11 sequences, all representing one of the isolates that was also present in 2007, were detected. The isolate was considered to be either re-introduced to, or to persist at the station, and it was transmitted between the pigs. The study sheds light on the rate and time of HEV transmission in swine, and describes the epidemiologic variability of HEV isolates over time.

Hepatitis E virus in pork production chain in Czech Republic, Italy, and Spain, 2010

Processing does not substantially abate endogenous virus.

We evaluated the prevalence of hepatitis E virus (HEV) in the pork production chain in Czech Republic, Italy, and Spain during 2010. A total of 337 fecal, liver, and meat samples from animals at slaughterhouses were tested for HEV by real-time quantitative PCR. Overall, HEV was higher in Italy (53%) and Spain (39%) than in Czech Republic (7.5%). HEV was detected most frequently in feces in Italy (41%) and Spain (39%) and in liver (5%) and meat (2.5%) in Czech Republic. Of 313 sausages sampled at processing and point of sale, HEV was detected only in Spain (6%). HEV sequencing confirmed only g3 HEV strains. Indicator virus (porcine adenovirus) was ubiquitous in fecal samples and absent in liver samples and was detected in 1 slaughterhouse meat sample. At point of sale, we found porcine adenovirus in sausages (1%–2%). The possible dissemination of HEV and other fecal viruses through pork production demands containment measures.

Optimisation of a triplex real time RT-PCR for detection of hepatitis E virus RNA and validation on biological samples

The aim of this study was to optimise a two-tube reverse transcription triplex quantitative real time PCR (qRT-PCR) combining amplification of two loci with an internal amplification control (IAC) for detection and quantitation of hepatitis E virus (HEV) RNA and to validate its performance on a pool of biological samples. Optimisation was performed on serially diluted "home-made" RNA standards. The limit of detection was determined experimentally as 10 copies/μl of the RNA standard for both amplification targets. The qRT-PCR was validated on a cohort of samples originating from 48 wild boars (Sus scrofa), 17 fallow deer (Dama dama) and 28 mouflons (Ovis musimon), with nested RT-PCR used as a reference method. qRT-PCR was found to be more specific for the detection of HEV RNA in examined samples. HEV RNA was detected in samples of five more animals (one wild boar and four mouflons) in comparison with nested RT-PCR.

Detection and phylogenetic characterization of human hepatitis E virus strains, Czech Republic

To determine the origin of hepatitis E virus in the Czech Republic, we analyzed patient clinical samples. Five isolates of genotypes 3e, 3f, and 3g were obtained. Their genetic relatedness with Czech strains from domestic pigs and wild boars and patient recollections suggest an autochthonous source likely linked to consumption of contaminated pork.

Hepatitis E virus in domestic pigs and surface waters in Slovenia: prevalence and molecular characterization of a novel genotype 3 lineage

A novel hepatitis E virus (HEV) genotype 3 lineage was identified in Slovenian pig herds. Stool samples from six Slovenian pig farms were collected and tested for the presence of HEV RNA. Of 85 individual samples 15 (20.3%) were positive for HEV RNA of which 2/38 (5.3%), 6/21 (28.6%) and 7/26 (26.9%) were from suckling, weanling and fattening pigs, respectively. Additionally, 51 pooled porcine stool samples were tested in one of the biggest pig farm and the estimated infection rate of individual pig was calculated, resulting in 7.8%, 10.6% and 24.2% for suckling, weanling and fattening pigs, respectively. The majority of HEV positive porcine samples were from the same pig farm. Out of 17 Slovenian patients with confirmed recent hepatitis E in the period 1999-2011, the serum samples of 10 patients were tested and 3 samples turned out to be HEV RNA positive. Furthermore, 60 surface water samples were tested throughout the country, of which 2 (3.3%) were positive for HEV RNA, one of them in the near vicinity of a pig farm. All HEV strains were analysed at 5' ORF1 and 5' ORF2 regions and both genome regions confirmed that Slovenian HEV strains represent a distinct genotype 3 lineage, diverse from all other genotype 3 lineages available in GenBank and described in the literature to date. All but one HEV strains detected in pigs in Slovenia represent a monophyletic branch in phylogenetic trees, with a high degree of sequence identity. One human HEV strain belonged to genotype 1 and two to genotype 3 but did not match the new genotype 3 lineage detected in Slovenian pig herds.

Viral and antibody HEV prevalence in swine at slaughterhouse in Italy

Hepatitis E is an acute disease of humans caused by a small RNA virus, Hepatitis E virus (HEV). In recent years, an increasing number of autochthonous human infections have been reported in industrialized countries. Genotype 3 is the main HEV type circulating in swine, and is also reported in sporadic cases of hepatitis E in humans worldwide. To date one serotype has been described. We have conducted a survey to detect antibodies against HEV in 48 swine at a slaughterhouse in Northern Italy, using ELISA test. Mean seroprevalence in the studied animal group was 87.0%. Bile, liver and feces from the 48 animals were also collected, and HEV RNA was detected by nested reverse transcription-polymerase chain reaction, amplifying a fragment of the ORF2. HEV genome was most frequently detected in bile samples (51.1%), followed by feces (33.3%) and liver (20.8%). Thirty-one out of 48 studied pigs (64.6%) were positive for HEV RNA in at least one sample. Overall, HEV RNA was found at a statistically higher rate in the 3-4-month-old than in 9-10-month-old animals (95.0% vs. 42.9%). Genetic characterization of swine strains identified was performed by sequencing and database alignment. Phylogenetic analysis on the nucleotide sequences from 14 positive PCR products indicated that all strains belonged to genotype 3, clustering in two branches subtypes g3c and g3f.

Hepatitis E virus load in swine organs and tissues at slaughterhouse determined by real-time RT-PCR

Although uncommon in North America, Hepatitis E virus (HEV) has been identified in some industrialized countries in patients without a history of travel to HEV-endemic countries. Its presence is ubiquitous worldwide in swine populations. Zoonotic transmission of swine HEV to non human primates has been achieved experimentally and transmission of HEV after ingestion of contaminated raw or undercooked meat is well documented. In Canada, so far, no HEV outbreak has been documented but HEV genotype 3 strains have been identified in sera and faecal samples of swine origin. The objective of the present study was to determine the viral load of HEV in liver, loin, bladder, hepatic lymph node, bile, tonsil, plasma and faeces samples of 43 pigs at slaughter. Feline calicivirus (FCV) was used as sample process control to validate the RNA extraction process, as a confirmation of the absence of sample inhibitors and as an amplification control. Using FCV/HEV multiplex TaqMan RT-qPCR system, HEV RNA was detected in 14 out of the 43 animals tested. HEV was detected in lymph nodes (11/43), bladder (10/43), liver (9/43), bile (8/43), faeces (6/43), tonsils (3/43), plasma (1/43) samples from infected animals. No HEV-positive loin samples were observed. Viral loads of 10(3) to 10(7) copies/g were estimated in positive liver and bile samples.

Detection of Hepatitis E Virus (HEV) in Italian pigs displaying different pathological lesions

In this study we investigated the HEV prevalence in Italian pigs displaying different pathological lesions, possible risk factors related to the infection, and the possible relations occurring between HEV and other concomitant pig pathogens. Genetic characterization of some of the identified strains was also performed. Detection of HEV RNA was accomplished using a nested reverse-transcription polymerase chain reaction on bile samples from 137 pigs of 2-4months of age submitted for diagnostic purposes. Forty-one of the 137 examined pigs (29.9%) tested positive for HEV RNA. Animals of 80-120days of age showed a higher prevalence of HEV infection (46.9% against 20% of younger animals). No statistically significant correlations between HEV positivity and the presence of other pathological conditions detected at necropsy, or concomitant coinfections with PCV2 and/or PRRSV were detected. All identified strains belonged to genotype 3, and were similar to other HEV subtypes 3e, 3f, 3c circulating in Europe.