Diagnostic performance of a reverse transcription-polymerase chain reaction test for porcine reproductive and respiratory syndrome virus

Genetic diversity of porcine reproductive and respiratory syndrome virus and evaluation of three one-step real-time RT-PCR assays in Korea

Background

Porcine reproductive and respiratory syndrome virus (PRRSV) has caused huge economic losses in the global swine industry. Frequent genetic variations in this virus cause difficulties in controlling and accurately diagnosing PRRSV.

Methods

In this study, we investigated the genetic characteristics of PRRSV-1 and PRRSV-2 circulating in Korea from January 2018 to September 2021 and evaluated three one-step real-time reverse transcription polymerase chain reaction (RT-PCR) assays.

Results

A total of 129 lung samples were collected, consisting of 47 samples for PRRSV-1, 62 samples for PRRSV-2, and 20 PRRSV-negative samples. Nucleotide sequence analysis of open reading frames (ORFs) 5, ORF6, and ORF7 genes from PRRSV samples showed that PRRSV-1 belonged to subgroup A (43/47, 91.49%) and subgroup C (4/47, 8.51%), whereas PRRSV-2 was classified as lineage 1 (25/62, 40.32%), Korean lineage (Kor) C (13/62, 20.97%), Kor B (10/62, 16.13%), lineage 5 (9/62, 14.52%), and Kor A (5/62, 8.06%). Amino acid sequence analysis showed that the neutralizing epitope and T cell epitope of PRRSV-1, and the decoy epitope region and hypervariable regions of PRRSV-2 had evolved under positive selection pressure. In particular, the key amino acid substitutions were found at positions 102 and 104 of glycoprotein 5 (GP5) in some PRRSV-2, and at positions 10 and 70 of membrane protein (M) in most PRRSV-2. In addition, one-step real-time RT-PCR assays, comprising two commercial tests and one test recommended by the World Organization for Animal Health (OIE), were evaluated.

Conclusion

The results revealed that two of the real-time RT-PCR assays had high sensitivities and specificities, whereas the real-time RT-PCR assay of the OIE had low sensitivity due to mismatches between nucleotides of Korean PRRSVs and forward primers. In this study, we genetically characterized recent PRRSV occurrences and evaluated three one-step real-time RT-PCR assays used in Korea.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03407-0.

Development of indirect ELISAs for differential serodiagnosis of classical and highly pathogenic porcine reproductive and respiratory syndrome virus

The objective of this study was to develop two indirect enzyme-linked immunosorbent assays (iELISAs) for detection of serum antibodies against classical vaccine strain of porcine reproductive and respiratory syndrome virus (PRRSV) and highly pathogenic PRRSV (HP-PRRSV). To detect the common antibodies against classical and HP-PRRSV, the coating antigen used in the iELISA (designated iELISA-180) was the antigen of Nsp2-180, the 180aa at amino terminal of Nsp2. To detect the different antibodies against classical and HP-PRRSV, the coating antigen in the second iELISA (designated iELISA-D29) was Nsp2-D29, the deleted 29aa in Nsp2 of HP-PRRSV. The antigen concentration and serum dilutions were optimized using a draughtboard titration. The cut-off values of 0.361 at OD(450nm) for the iELISA-180 and 0.27 at OD(450nm) for the iELISA-D29 were determined by testing a panel of 120 classical PRRSV positive and 198 PRRSV negative pig serum samples, which generated the specificity of 97.1% and 96.7%, the sensitivity of 96.9% and 96.3% for iELISA-180 and iELISA-D29, respectively. The agreements between the Western blot and iELISA-180 and iELISA-D29 were 98%, 96.7%, respectively. The developed iELISAs can be used to differentiate serologically HP-PRRSV from the vaccinated or classical PRRSV in clinical serum samples.

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV): A Ring Test Performed in Germany to Assess RT-PCR Detection Methods

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major pathogen of swine. Due to genetic variation between the European and the US genotype as well as within both genotypes detection of PRRSV is a diagnostic challenge. This paper reports on a ring test to compare different established reverse transcriptase polymerase chain reaction methods applied routinely in 16 different laboratories in Germany. Three different sets of samples were sent to the laboratories which were to be analysed as follows: (i) basis package: detection of PRRS (yes/no); (ii) differentiation package I: differentiation of EU and US genotypes; and (iii) differentiation package II: differentiation of EU field isolates and EU vaccine strain. A total of 80% of the samples of the basic package were analysed correctly, the analysis of the differentiation package I revealed 61.82% correctly tested samples and the two laboratories that analysed the differentiation package II showed only one correct result. The ring test showed that the majority of incorrect diagnoses were false-negative results.

Characterization of the carrier state in porcine reproductive and respiratory syndrome virus infection

Porcine reproductive and respiratory syndrome (PRRS) virus infection results in clinically normal, but persistently infected animals. An understanding of the carrier state is necessary for prevention, control and/or elimination of PRRS virus. The objective of this experiment was to estimate the proportion of PRRS virus carriers over time and determine which combination of sample and diagnostic assay could most effectively identify persistently infected animals. Sixty 3-week-old pigs were inoculated with PRRS virus ATCC VR-2332 and followed for up to 105 days post-inoculation (PI). Sixty age-matched animals served as uninoculated controls. Samples (serum, peripheral blood leukocytes, oropharyngeal scrapings, tonsil, bronchoalveolar lavage, lung tissue and tracheobronchial lymph nodes) were collected periodically and tested for evidence of PRRS virus infection by virus isolation (VI), swine bioassay and reverse transcriptase-nested polymerase chain reaction (RT-nPCR). The PRRS virus-specific antibody response was monitored with a commercial enzyme-linked immunosorbent assay (ELISA). Overall, PRRS virus was found in 51 of the 59 (84%) necropsied animals by VI or swine bioassay between 63 and 105 days PI, including 10 of the 11 (91%) of animals at day 105 PI. RT-nPCR on oropharyngeal scrapings was the most effective combination of assay and sample for detecting carriers. There was no significant difference in the antibody response of carrier vs. non-carrier animals. Infectious PRRS virus is present in most pigs the first 105 days following infection. Antibody response, as measured by a commercial ELISA, cannot be used to determine carrier status. RT-nPCR is a useful tool for detection of carriers, but diagnostic sample selection is critical if false negative results are to be avoided.

Quantitative TaqMan RT-PCR for the detection and differentiation of European and North American strains of porcine reproductive and respiratory syndrome virus

Since two different types of porcine reproductive and respiratory syndrome virus (PRRSV), the European (EU) and the North American (US) strain, occur or coexist in European swine herds, their rapid and reliable detection and differentiation is essential for disease surveillance. A quantitative TaqMan reverse transcription-polymerase chain reaction (RT-PCR) is described for PRRSV detection and strain differentiation. Sensitivity and specificity were compared with a conventional PRRSV RT-PCR and to the detection of both PRRSV types in cell cultures and both were found to be equal or superior to the reference methods. Reproducibility was tested and proved that the assay was very reliable. Standard dilutions included in each test allowed absolute quantitation of the amount of viral RNA. The TaqMan assay described below is time-saving, easy to handle, exhibits a decreased risk of cross-contamination and is highly sensitive and specific. It is, therefore, considered to be a powerful tool for the rapid detection and differentiation of PRRSV.