Rapid detection of encephalomyocarditis virus by one-step reverse transcription loop-mediated isothermal amplification method

Prevalence of viral agents causing swine reproductive failure in Korea and the development of multiplex real-time PCR and RT-PCR assays

This study aimed to investigate the prevalence of viral agents causing reproductive failure in pigs in Korea. In addition, two types of multiplex real-time PCR (mqPCR) were developed for the simultaneous detection of Aujeszky's disease virus (ADV) and porcine parvovirus (PPV) in mqPCR and encephalomyocarditis virus (EMCV) and Japanese encephalitis virus (JEV) in reverse transcription mqPCR (mRT-qPCR). A total of 150 aborted fetus samples collected from 2020 to 2022 were analyzed. Porcine reproductive and respiratory syndrome virus was the most prevalent (49/150 32.7%), followed by porcine circovirus type 2 (31/150, 20.7%), and PPV1 (7/150, 4.7%), whereas ADV, EMCV, and JEV were not detected. The newly developed mqPCR and mRT-qPCR could simultaneously detect and differentiate with high sensitivities and specificities. When applied to aborted fetuses, the newly developed mqPCR for PPV was 33.3% more sensitivities than the previously established diagnostic method. Amino acid analysis of the VP2 sequences of PPV isolates revealed considerable similarity to the highly pathogenic Kresse strain. This study successfully evaluated the prevalence of viral agents causing reproductive failure among swine in Korea, the developed mqPCR and mRT-qPCR methods could be utilized as effective and accurate diagnostic methods for the epidemiological surveillance of ADV, PPV, EMCV, and JEV.

Abortion and fetal death in sows

Abortion in sows or the expulsion of foetuses between days 35 and 109 of gestation results in major financial losses. Abortion is the result of maternal failure due to factors interfering with either the endocrine control of pregnancy or causing endometrial damage. In addition, causes of fetal origin, due to infections with a special affinity for the fetus, can also lead to abortion. Many different non-infectious and infectious factors may be involved. Non-infectious risk factors include inappropriate ambient temperature, seasonal effects, different stress factors, and toxic substances. Microorganisms that may cause abortion can be classified as facultative pathogenic and specific pathogenic microorganisms. The first category includes mostly bacteria that are endemic in many pig farms and that are normally harmless commensals. They can cause abortion only in case of decreased immunity or other predisposing factors. Different specific pathogenic microorganisms, especially viruses and bacteria, can cause fetal death and abortion. Some may have a special affinity for the reproductive tract and the foetuses (e.g. Aujeszky's disease virus, parvovirus, Leptospira sp.), while others may cause clinical disease or fever in sows (e.g. swine influenza viruses, Erysipelothrix rhusiopathiae), subsequently leading to abortion. Diagnosis of fetal death and abortion is challenging due to the broad array of processes that may be involved, and the fact that the inciting cause may happen well in advance of the abortion. The diagnostic process should start with a thorough evaluation of the clinical problem and the farm. In case an infectious cause is suspected, proper samples should be collected, preferably from different sows and foetuses, for the detection of specific pathogens. Prevention of abortion mainly relies on the implementation of good management practices, hygiene and biosecurity measures, and for some pathogens also on vaccination.

Visual and Rapid Detection of Porcine Epidemic Diarrhea Virus (PEDV) Using Reverse Transcription Loop-Mediated Isothermal Amplification Method

Porcine epidemic diarrhea virus (PEDV) can cause severe infectious porcine epidemic diarrhea (PED) and infect different ages of pigs, resulting in sickness and death among suckling pigs. For PEDV detection, finding an effective and rapid method is a priority. In this study, we established an effective reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for PEDV detection. Three sets of primers, specific for eight different sequences of the PEDV N gene, were designed in this study. The optimized RT-LAMP amplification program was as follows: 59 min at 61.9 °C and 3 min at 80 °C. The RT-LAMP results were confirmed with the addition of SYBR Green I fluorescence dye and with the detection of a ladder-like band by conventional gel electrophoresis analysis, which demonstrated a significant agreement between the two methods. The LOD of PEDV by RT-LAMP was 0.0001 ng/μL. Compared with RT-LAMP, the traditional RT-PCR method is 100-fold less sensitive. The RT-LAMP results had no cross-reaction with porcine parvovirus (PPV), porcine circovirus type 1 (PCV1), porcine pseudorabies virus (PRV), porcine circovirus type 2 (PCV2), rotavirus (RV), transmissible gastroenteritis virus (TGEV) and porcine reproductive and respiratory syndrome virus (PRRSV). Consequently, the newly developed RT-LAMP method could provide an accurate and reliable tool for PEDV diagnosis.

Rapid detection of porcine encephalomyocarditis virus (EMCV) by isothermal reverse transcription recombinase polymerase amplification assays

In this study, we combined reverse transcription recombinase polymerase amplification assay with the fluorescence detection platform (qRT-RPA) and lateral flow biosensor (LFB RT-RPA) to allow for rapid detection of porcine encephalomyocarditis virus (EMCV). Primers and probes were designed to target the highly conserved region of 3D gene of porcine EMCV. The optimal reaction condition of qRT-RPA and LFB RT-RPA was set as 42 °C for 20 min. The assays were highly specific to EMCV and no cross-reactions were observed with seven other porcine viruses. With a 10-fold serially diluted EMCV genomic RNA as template, the limit of detection was 1.0 × 10² and 1.0 × 10¹ copies for qRT-RPA assay and LFB RT-RPA assay, respectively. A total of 92 samples from different sources were examined using qRT-RPA, LFB RT-RPA and qRT-PCR. We found 100% diagnostic agreement between qRT-RPA (23/92) and qRT-PCR (23/92), and 97.83% diagnostic agreement between LFB RT-RPA (25/92) and qRT-PCR (23/92). There was no significant difference in performance between the RT-RPA assays developed in this study and a previously described qRT-PCR. However, RT-RPA assays were rapid and easy to perform while LFB RT-RPA exhibited higher sensitivity for EMCV than qRT-PCR. Therefore, the developed EMCV RT-RPA assays provide an attractive and promising tool for effective detection of EMCV in low-resource settings.

Molecular Detection and Genetic Characterization of Potential Zoonotic Swine Enteric Viruses in Northern China

Despite significant economic and public health implications, swine enteric viruses that do not manifest clinical symptoms are often overlooked, and data on their epidemiology and pathogenesis are still scarce. Here, an epidemiological study was carried out by using reverse transcription-polymerase chain reaction (RT-PCR) and sequence analysis in order to better understand the distribution and genetic diversity of porcine astrovirus (PAstV), porcine encephalomyocarditis virus (EMCV), porcine kobuvirus (PKV), and porcine sapovirus (PSaV) in healthy pigs reared under specific pathogen-free (SPF) or conventional farms. PKV was the most prevalent virus (51.1%, 247/483), followed by PAstV (35.4%, 171/483), then PSaV (18.4%, 89/483), and EMCV (8.7%, 42/483). Overall, at least one viral agent was detected in 300 out of 483 samples. Out of the 300 samples, 54.0% (162/300), 13.0% (39/300), or 1.0% (3/300) were found coinfected by two, three, or four viruses, respectively. To our knowledge, this is the first report of EMCV detection from porcine fecal samples in China. Phylogenetic analysis revealed genetically diverse strains of PAstV, PKV, and PSaV circulating in conventional and SPF farms. Detection of swine enteric viruses with a high coinfection rate in healthy pigs highlights the importance of continuous viral surveillance to minimize future economic and public health risks.

Development of a real time reverse transcription loop-mediated isothermal amplification method (RT-LAMP) for detection of a novel swine acute diarrhea syndrome coronavirus (SADS-CoV)

A novel swine acute diarrhea syndrome Coronavirus (SADS-CoV) that causes severe diarrhea in suckling piglets was identified in southern China in 2017. A simple and rapid detection test was developed for this virus using real-time RT-LAMP based on the conserved N gene of the virus. The method had a detection limit of 1.0 × 10¹ copies/μL with no cross-reactions with classical swine fever virus, porcine and respiratory syndrome virus NA, porcine and respiratory syndrome virus EU, transmissible gastroenteritis coronavirus, foot and mouth disease virus, porcine epidemic diarrhea virus (S-INDEL and non-S-INDEL), swine influenza virus subtype H1N1, porcine circovirus type 2, seneca valley virus, porcine parvovirus, porcine deltacoronavirus and rotavirus. This method was also reproducible. Twenty of 24 clinical samples were identified as SADS-CoV RNA-positive by the real-time RT-LAMP and the results were consistent with that of the real time RT-PCR method. This new method for detecting SADS-CoV is specific and sensitive for the detection of SADS-CoV.

A real-time loop-mediated isothermal amplification method for rapid detection of Lawsonia intracellularis in porcine fecal samples

Porcine proliferative enteritis is a common diarrheal disease characterized by thickening of the intestinal mucosa in swine due to enterocyte proliferation, which is caused by Lawsonia intracellularis. In this study, a real-time loop-mediated isothermal amplification (LAMP) assay was developed to detect L. intracellularis based on the conserved region of the 16S ribosomal RNA gene. The optimal reaction conditions of the real-time LAMP was 65 °C for 60 min. The LAMP products could be detected by both real-time turbidity and direct visual inspection. The assay was specific for L. intracellularis, as no cross-reaction was observed with other pathogens. The detection limit of the real-time LAMP assay was 1.4 × 10^-1pg of L. intracellularis DNA, which was the same as that of real-time PCR and approximately 100 times more sensitive than that of conventional PCR. Of the 136 clinical samples, L. intracellularis DNA was identified in 60 samples by real-time LAMP, which was the same as real-time PCR and higher than conventional PCR (36.8%, 50/136). The specific, sensitive and rapid real-time LAMP assay developed in this study could be a useful alternative tool in point-of-care (POC) diagnosis of L. intracellularis infection.

Evaluation of a duplex reverse-transcription real-time PCR assay for the detection of encephalomyocarditis virus

We evaluated a fluorogenic probe-based assay for the detection of encephalomyocarditis virus (EMCV) by comparing a set of published primers and probe to a new set of primers and probe. The published reagents failed to amplify a range of Australian isolates and an Italian reference strain of EMCV. In contrast, an assay based on 2 new sets of primers and probes that were run in a duplex reverse-transcription real-time PCR (RT-rtPCR) worked well, with high amplification efficiency. The analytical sensitivity was ~100-fold higher than virus isolation in cell culture. The intra-assay variation was 0.21-4.90%. No cross-reactivity was observed with a range of other porcine viruses. One hundred and twenty-two clinical specimens were tested simultaneously by RT-rtPCR and virus isolation in cell culture; 72 specimens gave positive results by RT-rtPCR, and 63 of these were also positive by virus isolation. Of 245 archived cell culture isolates of EMCV that were tested in the RT-rtPCR, 242 samples were positive. The new duplex RT-rtPCR assay is a reliable tool for the detection of EMCV in clinical specimens and for use in epidemiologic investigations.

Development and application of an indirect ELISA for the detection of antibodies against encephalomyocarditis virus

Encephalomyocarditis virus (EMCV) can cause acute myocarditis in young pigs or reproductive failure in sows. It has been recognized worldwide as a pathogen infecting many species and causes substantial economic losses. In the present study, an indirect ELISA was developed for the detection of antibodies to EMCV. The VP1 gene of EMCV was amplified by reverse transcription-quantitative polymerase chain reaction and expressed in Escherichia coli with 49.3 kDa under the condition of isopropyl-β-d-thiogalactoside. Following this, the authors obtained the recombinant protein VP1 as a coating antigen. The antigen concentration and serum dilution were optimized using a checkerboard titration. Compared with viral neutralization tests, the sensitivity and specificity of the indirect ELISA was 95.7% and 92.9%, respectively. A total of 265 clinical swine serum samples from different pig farms in China were used to a serological survey. The seropositive rate of the serum samples was 81.9%. In conclusion, the developed indirect ELISA assay is sensitive and specific, which will be useful for large-scale serological survey in EMCV infection and monitoring antibodies titers against EMCV.

Development of a real-time reverse transcription loop-mediated isothermal amplification method for the rapid detection of porcine epidemic diarrhea virus

Background

Porcine epidemic diarrhea (PED) is an acute and highly contagious enteric disease characterized by severe enteritis, vomiting and watery diarrhea in swine. Recently, the outbreak of the epidemic disease has been a serious problem in swine industry. The objective of this study is to develop a rapid, sensitive, and real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for the detection of porcine epidemic diarrhea virus (PEDV) in less equipped laboratories.

Results

The optimal reaction condition of the current real-time RT-LAMP for PEDV was 62 °C for 45 min. It was capable of detecting PEDV from clinical samples and differentiating PEDV from several related porcine viruses, while it did not require additional expensive equipment. The minimum detection limit of the real-time RT-LAMP assay was 0.07PFU per reaction for PEDV RNA, making this assay approximately 100-fold more sensitive than that of one-step RT-PCR. By screening a panel of clinical specimens, the results showed that this method presented a similar sensitivity with real-time RT-PCR and was somewhat sensitive than one-step RT-PCR in detection of clinical samples.

Conclusions

In this study, we have developed a new real-time RT-LAMP method, which is rapid, sensitive and efficient to detect PEDV.This method holds great promises not only in laboratory detection and discrimination of PEDV but also in large scale field and clinical studies.

Development of a TaqMan-based real-time reverse transcription polymerase chain reaction assay for the detection of encephalomyocarditis virus

Encephalomyocarditis virus (EMCV) is one of the major zoonosis pathogens and can cause acute myocarditis in young pigs or reproductive failure in sows. In this study, a TaqMan-based real-time reverse transcription polymerase chain reaction (RT-PCR) assay targeting 3D gene of EMCV was developed and their sensitivities and specificities were investigated. The results indicated that the standard curve had a wide dynamic range (10(1)-10(6) copies/μL) with a linear correlation (R(2)) of 0.996 between the cycle threshold (Ct) value and template concentration. The real-time RT-PCR assay is highly sensitive and able to detect 1.4×10(2) copies/μL of EMCV RNA, as no cross-reaction was observed with other viruses. These data suggested that the real-time RT-PCR assay developed in this study will be suitable for future surveillance and specific diagnosis of EMCV-infection.