Genetic dissection of complete genomes of Type 2 PRRS viruses isolated in Denmark over a period of 15 years

Refining PRRSV-2 genetic classification based on global ORF5 sequences and investigation of their geographic distributions and temporal changes

IMPORTANCE

In this study, comprehensive analysis of 82,237 global porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) open reading frame 5 sequences spanning from 1989 to 2021 refined PRRSV-2 genetic classification system, which defines 11 lineages and 21 sublineages and provides flexibility for growth if additional lineages, sublineages, or more granular classifications are needed in the future. Geographic distribution and temporal changes of PRRSV-2 were investigated in detail. This is a thorough study describing the molecular epidemiology of global PRRSV-2. In addition, the reference sequences based on the refined genetic classification system are made available to the public for future epidemiological and diagnostic applications worldwide. The data from this study will facilitate global standardization and application of PRRSV-2 genetic classification.

Deep Sequencing of Porcine Reproductive and Respiratory Syndrome Virus ORF7: A Promising Tool for Diagnostics and Epidemiologic Surveillance

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major concern worldwide. Control of PRRSV is a challenging task due to various factors, including the viral diversity and variability. In this study, we evaluated an amplicon library preparation protocol targeting the ORF7 region of both PRRSV species, Betaarterivirus suid 1 and Betaarterivirus suid 2. We designed tailed primers for a two-step PCR procedure that generates ORF7-specific amplicon libraries suitable for use on Illumina sequencers. We tested the method with serum samples containing common laboratory strains and with pooled serum samples (n = 15) collected from different pig farms during 2019-2021 in Hungary. Testing spiked serum samples showed that the newly designed method is highly sensitive and detects the viral RNA even at low copy numbers (corresponding to approx. Ct 35). The ORF7 sequences were easily assembled even from clinical samples. Two different sequence variants were identified in five samples, and the Porcilis MLV vaccine strain was identified as the minor variant in four samples. An in-depth analysis of the deep sequencing results revealed numerous polymorphic sites along the ORF7 gene in a total of eight samples, and some sites (positions 12, 165, 219, 225, 315, 345, and 351) were found to be common in several clinical specimens. We conclude that amplicon deep sequencing of a highly conserved region of the PRRSV genome could support both laboratory diagnosis and epidemiologic surveillance of the disease.

Transmission Dynamics of Imported Vaccine-Origin PRRSV-2 within and between Commercial Swine Integrations in Hungary

This study reports on the molecular epidemiology of Ingelvac-PRRS-MLV-associated cases in Hungary for the period 2020-2021. Field epidemiology investigations led the experts to conclude that imported pigs, which were shipped through transit stations in Denmark, introduced the vaccine virus. The movement of fatteners and the neglect of disease control measures contributed to the spread of the virus to PRRS-free pig holdings in the vicinity. Deep sequencing was performed to genetically characterize the genes coding for the virion antigens (i.e., ORF2 through ORF7). The study isolates exhibited a range of 0.1 to 1.8% nucleotide sequence divergence from the Ingelvac PRRS MLV and identified numerous polymorphic sites (up to 57 sites) along the amplified 3.2 kilo base pair genomic region. Our findings confirm that some PRRSV-2 vaccine strains can accumulate very high number of point mutations within a short period in immunologically naive pig herds.

Genetic diversity of imported PRRSV-2 strains, 2005-2020, Hungary

Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) remains sporadic in Europe. In this study, we investigated the molecular epidemiology of PRRSV-2 infections encompassing 15 years in Hungary. Partial (423 bp long) ORF5 sequences (n = 44) from 20 Hungarian pig herds were analyzed. The study strains fell into two genetic lineages, L1 and L5, being L5 strains more prevalent (88.6 vs. 11.4%). Pairwise sequence identities within Hungarian representative PRRSV-2 strains ranged between 84.7 to 100% (nucleotide, nt) and 85 to 100% (amino acid, aa). When compared with reference strains, identity values fell between 87 and 100% (L1, nt 87–91%, aa 87–93%, reference strain IAF-exp91; L5, nt 87–100%, aa 88–100%, reference strain Ingelvac MLV). Epidemiologic examination implied that the majority of L5 strains were imported repeatedly from other European countries where Ingelvac MLV was approved for routine use. The emergence of L1 strains was thought to be associated with a single introduction and subsequent dissemination between pig farms of a large integrator. Results presented here contribute to a better understanding of the epizootiology of PRRSV-2 infections and shed light on the genetic diversity of viral strains in non-endemic countries.

Impacts of Quarterly Sow Mass Vaccination with a Porcine Reproductive and Respiratory Syndrome Virus Type 1 (PRRSV-1) Modified Live Vaccine in Two Herds

In recent years, there has been a considerable increase in the use of Modified Live PRRSV Vaccines (MLV) for mass vaccination in Denmark. The potential risks and negative impact of this strategy have been sparsely studied. The aim of this study was to investigate the impact of quarterly sow mass vaccination in two Danish sow herds. The study was performed as an observational prospective cohort of 120 sows in each of two commercial breeding herds in a paired design. Blood samples were taken from sows and oral fluid samples from nursery pigs (four to ten weeks old) before and after vaccination. The presence of PRRSV-1 RNA was measured by real time quantitative reverse transcription-polymerase chain reaction (RT-qPCR), and the level of PRRSV-1 specific antibodies was measured by two different serological assays. PRRS virus was not detected in the sow herds two days before and two weeks after vaccination, but the vaccine strain virus was detected in the nursery pigs. The prevalence of sows without antibodies towards PRRSV-1 went from 6-15% before vaccination to 1-4% after vaccination depending on the serological assay used, despite the fact that they had previously been repeatedly vaccinated. Four sows tested negative for antibodies in both assays after vaccination.

Histopathological Lesions Accompanied with First-Time Isolation of a PRRSV-2 Strain in Greece

Genotype 2 strains of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV-2) have been reported sporadically in Europe. Even if, PRRSV-2 reported to be genetically homogenous in Europe due to the introduction of an MLV vaccine strain, independent introductions of PRRSV-2 field strains have been reported. The aim of the present study was to report the complete genome sequence and evaluate the histopathological lesions of a PRRSV-2 strain, isolated for the first time in Greece. During a routine blood sampling in a commercial pig farm, the results revealed positive samples in weaners of 40-60 days for the PRRSV-2, using real-time polymerase chain reaction. The clinical picture was characterized from respiratory symptoms in weaners, as well as coughing and poor performance at finishing stage and less than 3% mortality rate from weaning stage to finishing stage. The use of ORF5 for PRRSV phylogenetic analysis of the isolated PRRSV strain, named "x1544-1 strain", was successfully determined, belonging to the genotype PRRSV-2. Comparison of the obtained sequence revealed nucleotide sequence identity >98% with PRRSV-2 strain VR2332 and other related strains from Denmark and China. The histopathological evaluation revealed diffuse interstitial pneumonia, multifocal interstitial nephritis, while in the lymphoid organs, follicular and paracortical hyperplasia, coexisting with necrosis and depletion of germ cells were detected. The results of current study undersign the importance for veterinary practitioners to have up-to-date access to phylogenetic data linked to phenotypic information to follow-up the control and prevention strategies against PRRSV.

Genetic analysis of porcine productive and respiratory syndrome virus between 2013 and 2014 in Southern parts of China: identification of several novel strains with amino acid deletions or insertions in nsp2

Background

Porcine respiratory and reproductive syndrome virus (PRRSV) is one of the most economically significant pathogens in the Chinese swine industry. ORF5 and nsp2 are highly variable regions of the PRRSV genome. Therefore, nsp2 and GP5 are often selected for investigation of variations and phylogenetic analyses for their genetic diversities. Knowledge of the molecular evolution of PRRSV field strains may contribute to the control of PRRS in China.

Results

The results of multiple sequence alignments of GP5 showed that there is 84.5–100% aa identity among the 56 strains in this study. These strains shared 84.5–99.0% aa identity with the prototypical type 2 PRRSV VR-2332 and 56.6–59.2% with strain LV, prototypical type 1 PRRSV. Phylogenetic analysis showed there is considerable diversity among PRRSV ORF5 and the existence of two lineages (5 and 8). Most of the strains were classified into lineage 8 with multiple sub-lineages (3, 4 and 6). Moreover, PRRSV strains with 5 novel patterns of deletions or insertions in the nsp2 region were found.

Conclusions

Phylogenetic analysis based on ORF5 sequences indicated the diversity of PRRSV in southern parts of China and the strains with 30 aa deletion in nsp2 are dominant in the porcine population. Also, new PRRSV strains with different patterns of deletions or insertions in nsp2 are emerging. The data presented here constitute a useful basis for further epidemiological studies regarding the heterogeneity of PRRSV strains in China and provide a basis for the prevention of PRRS in southern parts of China.

Electronic supplementary material

The online version of this article (10.1186/s12917-019-1906-9) contains supplementary material, which is available to authorized users.

Efficacy and safety of simultaneous vaccination with two modified live virus vaccines against porcine reproductive and respiratory syndrome virus types 1 and 2 in pigs

The objective of the study was to compare responses of pigs vaccinated with a PRRS MLV vaccine against PRRSV-1 or PRRSV-2 with the responses of pigs vaccinated simultaneously with both vaccines. Furthermore, the efficacy of the two PRRSV MLV vaccination strategies was assessed following challenge. The experimental design included four groups of 4-weeks old SPF-pigs. On day 0 (DPV0), groups 1-3 (N=18 per group) were vaccinated with modified live virus vaccines (MLV) containing PRRSV-1 virus (VAC-T1), PRRSV-2 virus (VAC-T2) or both (VAC-T1T2). One group was left unvaccinated (N=12). On DPV 62, the pigs from groups 1-4 were mingled in new groups and challenged (DPC 0) with PRRSV-1, subtype 1, PRRSV-1, subtype 2 or PRRSV-2. On DPC 13/14 all pigs were necropsied. Samples were collected after vaccination and challenge. PRRSV was detected in all vaccinated pigs and the majority of the pigs were positive until DPV 28, but few of the pigs were still viremic 62 days after vaccination. Virus was detected in nasal swabs until DPV 7-14. No overt clinical signs were observed after challenge. PRRSV-2 vaccination resulted in a clear reduction in viral load in serum after PRRSV-2 challenge, whereas there was limited effect on the viral load in serum following challenge with the PRRSV-1 strains. Vaccination against PRRSV-1 had less impact on viremia following challenge. The protective effects of simultaneous vaccination with PRRSV Type 1 and 2 MLV vaccines and single PRRS MLV vaccination were comparable. None of the vaccines decreased the viral load in the lungs at necropsy. In conclusion, simultaneous vaccination with MLV vaccines containing PRRSV-1 and PRRSV-2 elicited responses comparable to single vaccination and the commercial PRRSV vaccines protected only partially against challenge with heterologous strains. Thus, simultaneous administration of the two vaccines is an option in herds with both PRRSV types.

Genetic and biological characterization of a Porcine Reproductive and Respiratory Syndrome Virus 2 (PRRSV-2) causing significant clinical disease in the field

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the cause of severe reproductive and respiratory disease in swine worldwide. In Denmark, both PRRSV-1 and PRRSV-2 are circulating and approximately 35% of pig herds are seropositive for PRRSV. In November 2010, a pig herd in the Northern part of Denmark experienced an infection with PRRSV-2 with clinical signs that were much more severe than normally reported from current Danish PRRSV-2 affected herds. Due to the clinical observations of reproductive failure in sows and high mortality in piglets, it was speculated that a new, more pathogenic or vaccine evading PRRSV strain had emerged in Denmark. The overall aim of the present study was to perform a genetic and biological characterization of the virus isolated from the diseased herd. Complete genome sequencing of isolates from this herd revealed that although the case strain had some unique genetic features including a deduced 3 amino acid deletion, it was in overall very similar to the other PRRS-2 viruses circulating in Denmark. In an experimental trial in growing pigs, no overt clinical signs or pathology were observed following intranasal inoculation with the new virus isolate. Virus shedding, acute phase protein responses and serological responses were comparable to those seen after experimental challenge with a Danish PRRSV-2 reference strain isolated in 1997. Vaccination with a commercial modified live PRRSV-2 vaccine had a clear reducing effect on virus shedding, magnitude, and duration of viremia and viral load in the lungs. Overall, the results indicate that the severe disease observed in the field was contributed by additional factors in combination with the PRRS virus infection.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): porcine reproductive and respiratory syndrome (PRRS)

Porcine reproductive and respiratory syndrome (PRRS) has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on the eligibility of PRRS to be listed, Article 9 for the categorisation of PRRS according to disease prevention and control rules as in Annex IV and Article 8 on the list of animal species related to PRRS. The assessment has been performed following a methodology composed of information collection and compilation, expert judgement on each criterion at individual and, if no consensus was reached before, also at collective level. The output is composed of the categorical answer, and for the questions where no consensus was reached, the different supporting views are reported. Details on the methodology used for this assessment are explained in a separate opinion. According to the assessment performed, PRRS can be considered eligible to be listed for Union intervention as laid down in Article 5(3) of the AHL. The disease would comply with the criteria as in Sections 4 and 5 of Annex IV of the AHL, for the application of the disease prevention and control rules referred to in points (d) and (e) of Article 9(1). The animal species to be listed for PRRS according to Article 8(3) criteria are domestic pigs and wild boar.

Molecular evolution of type 2 porcine reproductive and respiratory syndrome viruses circulating in Vietnam from 2007 to 2015

Background

Porcine respiratory and reproductive syndrome (PRRS) virus is one of the most economically significant pathogens in the Vietnamese swine industry. ORF5, which participates in many functional processes, including virion assembly, entry of the virus into the host cell, and viral adaptation to the host immune response, has been widely used in molecular evolution and phylogeny studies. Knowing of molecular evolution of PRRSV fields strains might contribute to PRRS control in Vietnam.

Results

The results showed that phylogenetic analysis indicated that all strains belonged to sub-lineages 8.7 and 5.1. The nucleotide and amino acid identities between strains were 84.5–100% and 82–100%, respectively. Furthermore, the results revealed differences in nucleotide and amino acid identities between the 2 sub-lineage groups. N-glycosylation prediction identified 7 potential N-glycosylation sites and 11 glycotypes. Analyses of the GP5 sequences, revealed 7 sites under positive selective pressure and 25 under negative selective pressure.

Conclusions

Phylogenetic analysis based on ORF5 sequence indicated the diversity of PRRSV in Vietnam. Furthermore, the variance of N-glycosylation sites and position under selective pressure were demonstrated. This study expands existing knowledge on the genetic diversity and evolution of PRRSV in Vietnam and assists the effective strategies for PRRS vaccine development in Vietnam.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-016-0885-3) contains supplementary material, which is available to authorized users.

Highly pathogenic porcine reproductive and respiratory syndrome virus infection and induction of apoptosis in bone marrow cells of infected piglets

Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) has been shown to have a wide range of tissue tropism, and can directly and indirectly induce cellular apoptosis. However, the impact of HP-PRRSV infection on the bone marrow (BM) of piglets remains unclear. In this study, we investigated the BM as a novel site of infection by the HP-PRRSV strain in piglets. HP-PRRSV infected SWC3+SWC8- cells in the BM and induced BM cells to undergo apoptosis. The number of apoptotic cells highlights the striking effects of HP-PRRSV on the central immune organs (BM and thymus) that may enhance the susceptibility of pigs to secondary infections and lead to high mortality. This study is, to the best of our knowledge, the first to report the impact of HP-PRRSV on the BM and implicate the depletion of BM cells during HP-PRRSV infection in the development of immunosuppression in this disease.

Spatial analysis and temporal trends of porcine reproductive and respiratory syndrome in Denmark from 2007 to 2010 based on laboratory submission data

BACKGROUND

Porcine reproductive and respiratory syndrome (PRRS) has been a cause for great concern to the Danish pig industry since it was first diagnosed in 1992. The causative agent of PRRS is an RNA virus which is divided into different genotypes. The clinical signs, as well as its morbidity and mortality, is highly variable between herds and regions. Two different genotypes of PRRS virus (PRRSV) are found in Denmark: type 1 and type 2. Approximately 40% of Danish swine herds are seropositive for one or both PRRSV types. The objective of this study was to describe the temporal trend and spatial distribution of PRRSV in Danish swine herds from 2007 to 2010, based on type-specific serological tests from the PRRS surveillance and control program in Denmark using the results stored in the information management system at the National Veterinary Institute, Technical University of Denmark (DTU Vet).

RESULTS

The average monthly seroprevalence of PRRSV type 1 was 9% (minimum of 5%; maximum of 13%) in breeding herds, and 20% (minimum of 14%; maximum of 26%) in production herds; PRRSV type 2 had an average seroprevalence of 3% (minimum of 1%; maximum of 9%) in breeding herds and of 9% (minimum of 5%; maximum of 13%) within production herds. The seroconversion rate followed a similar and consistent pattern, being higher for type 1 than for type 2 for both PRRSV types. Regarding the spatiotemporal results, the relative risk distribution maps changed over time as a consequence of the changes in PRRSV seroprevalence, suggesting a general decline in the extent of areas with higher relative risk for both type 1 and 2. Local spatial analysis results demonstrated the existence of statistically significant clusters in areas where the relative risk was higher for both herds.

CONCLUSIONS

PRRSV type 1 seroprevalence was constantly higher than for PRRSV type 2 in both herd types. Significant spatial clusters were consistently found in Denmark, suggesting that PRRSV is endemic in these areas. Furthermore, relative risk distribution maps revealed different patterns over time as a consequence of the changes in seroprevalence.

Diagnosis of the Lelystad strain of Porcine reproductive and respiratory syndrome virus infection in individually housed pigs: comparison between serum and oral fluid samples for viral nucleic acid and antibody detection

There has been a developing interest in the use of oral fluid for the diagnosis of different pathogens such as Porcine reproductive and respiratory syndrome virus (PRRSV). PRRSV and PRRSV-specific antibodies have been shown to be present in oral fluid samples, but the correlation between diagnostic results in oral fluid and serum samples has been insufficiently addressed. Studies investigating this correlation focused on boars older than 6 months and type 2 strains, but it is known that the outcome of a PRRSV infection is age and strain dependent. To address this gap, the current study reports on the detection of PRRSV and PRRSV-specific antibodies in serum and oral fluid samples collected over a 6-week period after an experimental infection of 8-week-old individually housed pigs with Lelystad virus, the type 1 prototype strain. Quantitative reverse transcription polymerase chain reaction analysis showed that significantly more serum samples were PRRSV RNA-positive than oral fluid until 5 days postinfection (dpi). Between 7 and 21 dpi, PRRSV RNA detection was similar in both samples but higher detection rates in oral fluid were found from 28 dpi. Compared with existing literature, this highlights that detection rates at particular time points postinfection might vary in function of strain virulence and animal age and provides useful information for the interpretation of pen-based oral fluid results. An excellent agreement between the oral fluid and serum enzyme-linked immunosorbent assay results was observed at every time point, further supporting the usefulness of oral fluid as a diagnostic sample for antibody detection.

Full genome sequence analysis of a wild, non-MLV-related type 2 Hungarian PRRSV variant isolated in Europe

Porcine reproductive and respiratory syndrome virus (PRRSV) is a widespread pathogen of pigs causing significant economic losses to the swine industry. The expanding diversity of PRRSV strains makes the diagnosis, control and eradication of the disease more and more difficult. In the present study, the authors report the full genome sequencing of a type 2 PRRSV strain isolated from piglet carcasses in Hungary. Next generation sequencing was used to determine the complete genome sequence of the isolate (PRRSV-2/Hungary/102/2012). Recombination analysis performed with the available full-length genome sequences showed no evidence of such event with other known PRRSV. Unique deletions and an insertion were found in the nsp2 region of PRRSV-2/Hungary/102/2012 when it was compared to the highly virulent VR2332 and JXA-1 prototype strains. The majority of amino acid alterations in GP4 and GP5 of the virus were in the known antigenic regions suggesting an important role for immunological pressure in PRRSV-2/Hungary/102/2012 evolution. Phylogenetic analysis revealed that it belongs to lineage 1 or 2 of type 2 PRRSV. Considering the lack of related PRRSV in Europe, except for a partial sequence from Slovakia, the ancestor of PRRSV-2/Hungary/102/2012 was most probably transported from North-America. It is the first documented type 2 PRRSV isolated in Europe that is not related to the Ingelvac MLV.

Beyond the whole genome consensus: unravelling of PRRSV phylogenomics using next generation sequencing technologies

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NGS allows the whole genome sequencing of PRRSV without any prior knowledge.

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Low frequency variants within the co-evolving quasispecies can be detected.

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Both macro- and micro-evolutionary events can be followed using NGS.

The highly heterogeneous porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent responsible for an economically important pig disease with the characteristic symptoms of reproductive losses in breeding sows and respiratory illnesses in young piglets. The virus can be broadly divided into the European and North American-like genotype 1 and 2 respectively. In addition to this intra-strains variability, the impact of coexisting viral quasispecies on disease development has recently gained much attention; owing very much to the advent of the next-generation sequencing (NGS) technologies. Genomic data produced from the massive sequencing capacities of NGS have enabled the study of PRRSV at an unprecedented rate and details. Unlike conventional sequencing methods which require knowledge of conserved regions, NGS allows de novo assembly of the full viral genomes. Evolutionary variations gained from different genotypic strains provide valuable insights into functionally important regions of the virus. Together with the advancement of sophisticated bioinformatics tools, ultra-deep NGS technologies make the detection of low frequency co-evolving quasispecies possible. This short review gives an overview, including a proposed workflow, on the use of NGS to explore the genetic diversity of PRRSV at both macro- and micro-evolutionary levels.

Analysis of ORF5 and full-length genome sequences of porcine reproductive and respiratory syndrome virus isolates of genotypes 1 and 2 retrieved worldwide provides evidence that recombination is a common phenomenon and may produce mosaic isolates

Recombination is currently recognized as a factor for high genetic diversity, but the frequency of such recombination events and the genome segments involved are not well known. In the present study, we initially focused on the detection of recombinant porcine reproductive and respiratory syndrome virus (PRRSV) isolates by examining previously published data sets of ORF5 sequences (genotypes 1 and 2) obtained worldwide. We then examined full-length genome sequences in order to determine potential recombination breakpoints along the viral genome. For ORF5, 11 sets of genotype 1 sequences from different geographical areas, including 2 Asian, 1 American, and 7 European regions, and three sets of genotype 2, including sets from China, Mexico, and the United States, were analyzed separately. Potential recombination breakpoints were detected in 10/11 genotype 1 sets, including 9 cases in which the clustering of at least one isolate was different before and after the breakpoints. In genotype 2, potential breakpoints and different tree clustering of at least one strain before and after the breakpoint were observed in 2 out of 3 sets. The results indicated that most of the ORF5 data sets contained at least one recombinant sequence. When the full-length genome sequences were examined, both genotype 1 and 2 sets presented breakpoints (10 and 9, respectively), resulting in significantly different topologies before and after the breakpoints. Mosaic genomes were detected in genotype 1 sequences. These results may have significant implications for the understanding of the molecular epidemiology of PRRSV.

IMPORTANCE

PRRSV is one of the most important viruses affecting swine production worldwide, causing big economic losses and sanitary problems. One of the key questions on PRRSV arises from its genetic diversity, which is thought to have a direct impact on immunobiology, epidemiology, diagnosis, and vaccine efficacy. One of the causes of this genetic diversity is recombination among strains. This study provides evidence that recombinant PRRSV isolates are common in most of the countries with significant swine production, especially PRRSV genotype 1. This observation has implications in the proper characterization of PRRSV strains, in the future development of phylogenetic studies, and in the development of new PRRSV control strategies. Moreover, the present paper emphasizes the need for a deeper understanding of the mechanisms and circumstances involved in the generation of genetic diversity of PRRSV.