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

SARS-CoV-2 wastewater surveillance in the Czech Republic: Spatial and temporal differences in SARS-CoV-2 RNA concentrations and relationship to clinical data and wastewater parameters

This study presents the results of systematic wastewater monitoring of SARS-CoV-2 RNA and basic wastewater parameters from four different wastewater treatment plants (WWTPs) in the Czech Republic over the 2020-2022 epidemic. Two-step reverse-transcription quantitative PCR targeting genes encoding the N and Nsp12 proteins was employed to detect SARS-CoV-2 RNA loading in 420 wastewater samples. The results obtained were used to evaluate the potential of wastewater analysis for describing the epidemiological situation in cities of different sizes and determining temporal differences based on the prevailing SARS-CoV-2 variant. Strong correlations between the number of active and hospitalised COVID-19 cases in each WWTP catchment area and the concentration of SARS-CoV-2 RNA detected in the wastewater clearly demonstrated the suitability of this wastewater-based epidemiological approach for WWTPs of different sizes and characteristics, despite differences in SARS-CoV-2 variant waves, with some WWTPs showing high predictive potential. This study demonstrated on the data from the Czech Republic that targeted systematic monitoring of wastewater provides sufficiently robust data for surveillance of viral loads in sample populations, and thus contributes to preventing the spread of infection and subsequent introduction of appropriate measures.

MOL-PCR and xMAP technology – a novel approach to the detection of African swine fever virus DNA

African swine fever (ASF) is highly contagious haemorrhagic viral disease of domestic pigs and wild boars. The causative agent can be transmitted by direct contact with infected animals or via a contaminated environment, fomites, feed, meat and products thereof. Soft ticks (genus Ornithodoros) are known reservoirs and transmission vectors of the virus. As the disease causes serious problems in many countries, rapid detection of the agent and early diagnosis could help in prevention of its spread. Therefore, a multiple-analyte profile (xMAP) technology based on multiple oligonucleotide ligation followed by polymerase chain reaction (MOL-PCR) was introduced and verified. A system targeting two independent loci of the virus genome was designed to increase the likelihood of different strains detection and an internal control was employed to verify the correct course of the analysis. The sensitivity was experimentally determined as 10 genomic copies of the virus in one µl of isolated DNA. The system was verified on samples originating from a recent ASF outbreak in the Czech Republic (six spleen) and the Czech market (eight liver and heart tissues) with real-time polymerase chain reaction used as a reference method. The results of both methods were in agreement, even in samples with a low concentration of the virus genome (9.45 × 101 genomic copies/µl of DNA). The system introduced represents an open method allowing the detection and semi-quantification of up to 50 targets/agents in one reaction. It can, therefore, be used for rapid one-step screening and as an effective tool for risk management.

Real-Time PCR-Based Methods for Detection of Hepatitis E Virus in Pork Products: A Critical Review

Standard methods for detection of hepatitis A virus and norovirus in at-risk foodstuffs are available, but currently there is no standard method for detection of hepatitis E virus (HEV) in pork products or other foods that can be contaminated with the virus. Detection assays for HEV are mainly based on nucleic acid amplification, particularly the reverse transcription polymerase chain reaction (RTPCR) in real-time format. RTPCR-based methods can be sensitive and specific, but they require a suite of controls to verify that they have performed correctly. There have been several RTPCR methods developed to detect HEV in pork products, varying in details of sample preparation and RTPCR target sequences. This review critically discusses published HEV detection methods, with emphasis on those that have been successfully used in subsequent studies and surveys. RTPCR assays have been used both qualitatively and quantitatively, although in the latter case the data acquired are only reliable if appropriate assay calibration has been performed. One particular RTPCR assay appears to be ideal for incorporation in a standard method, as it has been demonstrated to be highly specific and sensitive, and an appropriate control and calibration standard is available. The review focuses on the detection of HEV in pork products and similar foodstuffs (e.g., boar). The information may be useful to inform standardisation activities.

MOL-PCR and xMAP Technology: A Multiplex System for Fast Detection of Food- and Waterborne Viruses

Viruses are common causes of food- and waterborne diseases worldwide. Conventional identification of these agents is based on cultivation, antigen detection, electron microscopy, or real-time PCR. Because recent technological advancements in detection methods are focused on fast and robust analysis, a rapid multiplexing technology, which can detect a broad spectrum of pathogenic viruses connected to food or water contamination, was utilized. A new semiquantitative magnetic bead-based multiplex system has been designed for simultaneous detection of several targets in one reaction. The system includes adenoviruses 40/41 (AdV), rotavirus A (RVA), norovirus (NoV), hepatitis E virus (HEV), hepatitis A virus (HAV), and a target for external control of the system. To evaluate the detection system, interlaboratory ring tests were performed in four independent laboratories. Analytical specificity of the tool was tested on a cohort of pathogenic agents and biological samples with quantitative PCR as a reference method. Limit of detection (analytical sensitivity) of 5 × 10⁰ (AdV, HEV, and RVA) and 5 × 10¹ (HAV and NoV) genome equivalents per reaction was reached. This robust, senstivie, and rapid multiplexing technology may be used to routinely monitor and manage viruses in food and water to prevent food and waterborne diseases.

Evidence of Hepatitis E Virus in Goat and Sheep Milk

Hepatitis E virus (HEV) is the etiological agent behind hepatitis E infection. Domestic pigs and wild boars are the main animal reservoirs of HEV. Very few papers describe HEV infection in goats and sheep. As the data pertaining to the presence of HEV virus in the milk of small ruminants in Europe are lacking, the aim of this paper was to examine a representative number of milk samples from these animals. The detection of HEV genome (HEV RNA) was performed using reverse transcriptase real-time polymerase chain reaction (RT-qPCR). HEV RNA was found in 2.8% of the examined samples. Positivity ranged from 10¹ to 10³ genome equivalents/mL (GE/mL) with a median of 9.99 × 10² GE/mL. On the basis of these results, the milk of small ruminants could represent a source of HEV infection to consumers.

Preliminary Study of Sars-Cov-2 Occurrence in Wastewater in the Czech Republic

The virus SARS-CoV-2, which has caused the recent COVID-19 pandemic, may be present in the stools of COVID-19 patients. Therefore, we aimed to detect SARS-CoV-2 in wastewater for surveillance of SARS-CoV-2 in the population. Samples of untreated wastewater were collected from 33 wastewater treatment plants (WWTPs) of different sizes within the Czech Republic. SARS-CoV-2 RNA was concentrated from wastewater and viral RNA was determined using real-time reverse transcription polymerase chain reaction (RT-qPCR). SARS-CoV-2 RNA was detected in 11.6% of samples and more than 27.3% of WWTPs; in some of them, SARS-CoV-2 was detected repeatedly. Our preliminary results indicate that an epidemiology approach that focuses on the determination of SARS-CoV-2 in wastewater could be suitable for SARS-CoV-2 surveillance in the population.

Foodborne Bacterial, Viral, and Protozoan Pathogens in Field and Market Strawberries and Environment of Strawberry Farms

Field-grown strawberries, the environment of strawberry farms and fresh strawberries from marketplaces were examined for bacterial, viral, and protozoan pathogens. The presence of bacteria was determined using culture and real-time PCR (qPCR), presence of protozoa and viruses using qPCR and reverse transcription qPCR, respectively. The highest proportion of positivity was observed for Escherichia coli both in field and purchased strawberries (up to 48.6%). Finding of Cronobacter ranged from 0.6% to 9% both for field and market strawberries. The prevalence of other pathogens (Listeria monocytogenes, Giardia intestinalis, Cryptosporidium sp., and Norovirus) in strawberries was below 4.5%; HAV was not detected at all. Positivity of the environment was determined to be lower than 2.1% for all microorganisms, except for E. coli. The concentration of pathogens in most samples did not exceed 100 CFU/g using culture and 1.8 × 10² GE/g of strawberries or swabbing area 6.1 × 10² GE/mL or swabbing area of environmental samples using qPCR. All studied farms applied preventive measures such as drip irrigation, avoidance of organic fertilizers, and use of mulch foils or gloves for workers to decrease contamination of strawberries. Despite this, certain pathogens were found in fresh strawberries. Even at low concentrations, these pathogens can be a source of infection for consumers. Thus, their presence in strawberries is of particular significance as these are mostly consumed fresh and without any thermal processing. PRACTICAL APPLICATION: Nonlegislatively monitored pathogens of bacterial, viral and parasitic origin were found in strawberries. Monitoring the presence of these pathogens in ready-to-eat food is therefore meaningful and important in terms of food safety, especially in relation to pathogens with low infectious dose (for example, viruses, parasites).

Tracing of Selected Viral, Bacterial, and Parasitic Agents on Vegetables and Herbs Originating from Farms and Markets

Fresh vegetables and herbs are usually prepared and eaten raw without cooking or heating, which leads to a high risk of foodborne infection. The aim of the present study was to assess the contamination of raw vegetables, herbs, and the environment of food chains. Vegetable and herb samples originating both from the Czech Republic as well as from other countries were examined. The work was focused on the detection of commonly found, but also less frequently monitored foodborne pathogens, including viruses of the genus Norovirus (NoVs), hepatitis A virus (HAV), Listeria monocytogenes and Cronobacter spp. bacteria, and the parasites Cryptosporidium spp. and Giardia intestinalis. All samples were analyzed using individual RT-qPCR/qPCR assays; bacterial pathogens were also simultaneously detected using culture methods. The prevalence of the studied microorganisms in 623 samples ranged from 0.6% to 44.3% for individual pathogens. None of the samples were positive for the presence of HAV. Analysis of 157 environmental samples from 12 farms revealed the presence of NoVs in the environment of four farms. NoVs were detected in water samples as well as on the hands and gloves of workers. Escherichia coli was detected in all farms in the environmental samples and in eight farms in water samples. However, no sample of water exceeded the level of 100 CFU/mL for E. coli. None of the samples of water were positive for the presence of the studied parasites. Vegetables and herbs available from Czech markets and farms may pose a certain risk of foodborne disease, especially in the case of NoVs and parasites. PRACTICAL APPLICATION: This study provides valuable information on the microbiological quality of raw vegetables and herbs available from Czech markets and farms. Good hygienic practices aimed at reducing the incidence of pathogenic agents on fresh produce should not be neglected. Emphasis should be placed on the control of irrigation water, especially with respect to norovirus contamination. It is appropriate to combine culture methods and qPCR methods for the detection of bacterial agents.

Identification of pathogens for differential diagnosis of fever with jaundice in the Central African Republic: a retrospective assessment, 2008-2010

Background

Febrile jaundice results clinically in generalized yellow coloration of the teguments and mucous membranes due to excess plasma bilirubin, accompanied by fever. Two types are found: conjugated and unconjugated bilirubin jaundice. Jaundice is a sign in several diseases due to viruses (viral hepatitis and arbovirus), parasites (malaria) and bacteria (leptospirosis). In the Central African Republic (CAR), only yellow fever is included on the list of diseases for surveillance. The aim of this study was to identify the other pathogens that can cause febrile jaundice, for better management of patients.

Methods

Between 2008 and 2010, 198 sera negative for yellow fever IgM were randomly selected from 2177 samples collected during yellow fever surveillance. Laboratory analyses targeted four groups of pathogens: hepatitis B, C, delta and E viruses; dengue, chikungunya, Zika, Crimean–Congo haemorrhagic fever, West Nile and Rift Valley arboviruses; malaria parasites; and bacteria (leptospirosis).

Results

Overall, 30.9% sera were positive for hepatitis B, 20.2% for hepatitis E, 12.3% for hepatitis C and 8.2% for malaria. The majority of positive sera (40.4%) were from people aged 16–30 years. Co-infection with at least two of these pathogens was also found.

Conclusion

These findings suggest that a systematic investigation should be undertaken of infectious agents that cause febrile jaundice in the CAR.

High frequency of hepatitis E virus infection in swine from South Brazil and close similarity to human HEV isolates

Hepatitis E virus is responsible for acute and chronic liver infections worldwide. Swine hepatitis E virus has been isolated in Brazil, and a probable zoonotic transmission has been described, although data are still scarce. The aim of this study was to investigate the frequency of hepatitis E virus infection in pigs from a small-scale farm in the rural area of Paraná State, South Brazil. Fecal samples were collected from 170 pigs and screened for hepatitis E virus RNA using a duplex real-time RT-PCR targeting a highly conserved 70nt long sequence within overlapping parts of ORF2 and ORF3 as well as a 113nt sequence of ORF2. Positive samples with high viral loads were subjected to direct sequencing and phylogenetic analysis. hepatitis E virus RNA was detected in 34 (20.0%) of the 170 pigs following positive results in at least one set of screening real-time RT-PCR primers and probes. The swine hepatitis E virus strains clustered with the genotype hepatitis E virus-3b reference sequences in the phylogenetic analysis and showed close similarity to human hepatitis E virus isolates previously reported in Brazil.

Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices

The detection and quantification of enteric RNA viruses is based on isolation of viral RNA from the sample followed by quantitative reverse transcription polymerase chain reaction (RT-qPCR). To control the whole process of analysis and in order to guarantee the validity and reliability of results, process control viruses (PCV) are used. The present article describes the process of preparation and use of such PCV– MS2 phage-like particles (MS2 PLP) – in RT-qPCR detection and quantification of enteric RNA viruses. The MS2 PLP were derived from bacteriophage MS2 carrying a unique and specific de novo-constructed RNA target sequence originating from the DNA of two extinct species. The amount of prepared MS2 particles was quantified using four independent methods – UV spectrophotometry, fluorimetry, transmission electron microscopy and a specifically developed duplex RT-qPCR. To evaluate the usefulness of MS2 PLP in routine diagnostics different matrices known to harbor enteric RNA viruses (swab samples, liver tissue, serum, feces, and vegetables) were artificially contaminated with specific amounts of MS2 PLP. The extraction efficiencies were calculated for each individual matrix. The prepared particles fulfill all requirements for PCV – they are very stable, non-infectious, and are genetically distinct from the target RNA viruses. Due to these properties they represent a good morphological and physiochemical model. The use of MS2 PLP as a PCV in detection and quantification of enteric RNA viruses was evaluated in different types of matrices.

Hepatitis E virus seroprevalence among schistosomiasis patients in Northeastern Brazil

Background

Hepatitis E virus (HEV) can cause chronic infection with rapid progression to liver cirrhosis in immunocompromised patients. HEV seroprevalence in patients with Schistosoma mansoni in Brazil is unknown. We evaluated the prevalence of past or present HEV infection in schistosomiasis patients in Recife, Pernambuco, Brazil. A total of 80 patients with Schistosoma mansoni were consecutively enrolled in a cross-sectional study. Serum samples were tested for the presence of anti-HEV IgG antibodies by enzyme immunoassay (Wantai anti-HEV IgG, Beijing, China) and for the presence of HEV RNA using real time reverse transcriptase-polymerase chain reaction with primers targeting the HEV ORF2 and ORF3. Clinical and laboratory tests as well as abdominal ultrasound were performed at the same day of blood collection.

Results

Anti-HEV IgG was positive in 18.8% (15/80) of patients with SM. None of the samples tested positive for anti-HEV IgM or HEV-RNA. Patients with anti-HEV IgG positive presented higher levels of alanine aminotranferase (p = 0.048) and gama-glutamil transferase (p = 0.022) when compared to patients without anti-HEV IgG antibodies.

Conclusion

This study demonstrates that the seroprevalence of HEV is high in patients with Schistosoma mansoni in Northeastern of Brazil. Past HEV infection is associated with higher frequency of liver enzymes abnormalities. HEV infection and its role on the severity of liver disease should be further investigated among patients with Schistosoma mansoni.

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.

A new cultivation-independent tool for fast and reliable detection of Mycobacterium marinum

The Mycobacterium marinum group (MMG) is a class of mycobacteria that includes M. marinum, the cause of chronic systemic infections in fish. This species occasionally causes granulomatous skin lesions in humans. Other members of MMG are mycolactone-producing mycobacteria (MPM; M. ulcerans, M. shottsii and M. pseudoshottsii). The cultivation-independent approach presented in this study brings a fast and reliable alternative to classically used cultivation methods. The developed triplex erp/IS2404 qPCR assay is based on a primary species-specific erp detection, which allows enumeration of MMG in analysed samples, and secondary IS2404 detection is suitable for the differentiation of M. marinum from MPM. The detection of M. marinum in clinical specimens and in artificially contaminated tissue samples has proven its applicability for diagnostic purposes.

Presence of Mycobacterium avium subspecies and hepatitis E virus in raw meat products

Meat and meat products may be the source of various pathogenic and potentially pathogenic agents for humans. We ascertained the occurrence of Mycobacterium avium subsp. paratuberculosis, subsp. avium, and subsp. hominissuis, and hepatitis E virus in retail raw meat products. The DNA of at least one of the target M. avium subspecies was detected in 26 (29.2%) of 89 analyzed samples of meat products. Fourteen (15.7%), 1 (1.1%), and 17 (19.1%) samples contained the DNA of Mycobacterium avium subsp. paratuberculosis, subsp. avium, and subsp. hominissuis, respectively. The number of mycobacterial cells per gram of meat products determined by real-time quantitative PCR ranged from 1.15 × 10(2) to 6.97 × 10(3). Mycobacterium chitae and Mycobacterium nonchromogenicum were isolated from three (3.4%) samples. Culture examination was not positive for any M. avium subspecies. Hepatitis E virus RNA was not detected in any of the samples.

Comparison of real-time reverse transcriptase PCR assays for detection of swine hepatitis E virus in fecal samples

Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in people in many developing countries and is also endemic in many industrialized countries. Mammalian HEV (mHEV) isolates can be divided into at least four recognized major genotypes. Several nucleic acid amplification techniques have been developed for mHEV detection, with great differences in sensitivity. The aim of this study was to compare the performances of two singleplex real-time reverse transcriptase (RT) PCR assays for broad detection of all four mHEV genotypes (assays A and B) and two duplex real-time RT-PCR assays for detection and differentiation of mHEV genotypes 3 and 4 (assays C and D). RNAs extracted from 28 fecal samples from pigs experimentally inoculated with HEV genotype 3 and 186 fecal samples from commercial pigs with unknown HEV exposure were tested by all four assays. In experimental samples, HEV RNA was detected in 96.4% (assay A), 39.2% (assay B), 14.2% (assay C), and 0% (assay D) of the samples. In field samples with unknown HEV exposure, HEV RNA was detected in 67.2% (assay A), 36.4% (assay B), 1.1% (assay C), and 0.5% (assay D) of the samples. The assays showed overall poor agreement (κ = 0.19 to 0.03), with differences in detection rates between assays (P < 0.01). Assays A and B, which broadly detect HEV genotypes 1 to 4, had significantly higher detection rates for HEV RNA than the duplex assays C and D, which were both designed to detect and differentiate between HEV genotypes 3 and 4.

Novel hepatitis E like virus found in Swedish moose

A novel virus was detected in a sample collected from a Swedish moose (Alces alces). The virus was suggested as a member of the Hepeviridae family, although it was found to be highly divergent from the known four genotypes (gt1–4) of hepatitis E virus (HEV). Moose are regularly hunted for consumption in the whole of Scandinavia. Thus, the finding of this virus may be important from several aspects: (a) as a new diverged HEV in a new animal species, and (b) potential unexplored HEV transmission pathways for human infections. Considering these aspects, we have started the molecular characterization of this virus. A 5.1 kb amplicon was sequenced, and corresponded to the partial ORF1, followed by complete ORF2, ORF3 and poly(A) sequence. In comparison with existing HEVs, the moose HEV genome showed a general nucleotide sequence similarity of 37–63 % and an extensively divergent putative ORF3 sequence. The junction region between the ORFs was also highly divergent; however, two putative secondary stem–loop structures were retained when compared to gt1–4, but with altered structural appearance. In the phylogenetic analysis, the moose HEV deviated and formed its own branch between the gt1–4 and other divergent animal HEVs. The characterization of this highly divergent genome provides important information regarding the diversity of HEV infecting various mammalian species. However, further studies are needed to investigate its prevalence in the moose populations and possibly in other host species, including the risk for human infection.

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.

Hepatitis E virus infection in Latin America: a review

Data reported during recent years reveal the complex picture of the epidemiology of hepatitis E virus (HEV) infection in Latin America. Whereas in countries like Argentina and Brazil is almost identical to the characteristic of most countries from North America and Europe, HEV in the Caribbean and Mexico involves the water-borne, non-zoonotic viral genotypes responsible for epidemics in Asia and Africa. Nevertheless, Latin America has been considered a highly endemic region for hepatitis E in the scientific literature, a generalization that ignores the above complexity. In addition, reports from isolated Amerindian communities, which display well known, important and very specific epidemiological features for hepatitis B and D virus infections are neither taken into account when considering the epidemiology of hepatitis E in the region. This review updates compilation of the available information for the HEV infection, both among humans and other mammals, in Latin America, discusses the strengths and the weaknesses of our current knowledge, and identifies future areas of research.

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.

Validation of an internally controlled multiplex real time RT-PCR for detection and typing of HEV genotype 3 and 4

Hepatitis E virus (HEV) genotypes 1 and 2 are restricted to humans, whereas genotypes 3 (HEV 3) and genotype 4 (HEV 4) infect humans and a variety of animal species. Cross-species infections by animal strains raise potential public health concerns for zoonotic HEV transmission. Therefore, a real-time reverse transcription polymerase chain reaction (RT-qPCR) combining the HEV 3-tpye specific RT-qPCR assay with the HEV 4-tpye specific assay was developed. Furthermore, a heterologous RNA, an in vitro transcript of the enhanced green fluorescent protein (EGFP) gene, was introduced as an internal control. The data showed that EGFP gene provided a very reliable and simple way of monitoring both the sample manipulation and amplification procedures. The final multiplex RT-qPCR assay showed a high analytical sensitivity of less than 50 copies RNA per reaction for both HEV genotypes. The specificity and amplification efficiency of the multiplex assay for the respective HEV were confirmed by co-amplification of the other target. By comparing with the results of mono-specific assay and nested PCR as well as sequencing, HEV infection in a panel of clinical samples was reliably detected and typed, which indicated that the novel multiplex RT-qPCR assay could be used for sensitive detection and rapid differentiation of zoonotic HEV genotype 3 and 4.