Phylogeny and evolutionary genetics of porcine parvovirus in wild boars

Isolation, characterization, and phylogenetic analysis of two new porcine parvovirus 1 isolates from Northern China

Porcine parvovirus (PPV) is a pathogen of infectious reproductive disease, which can cause stillbirth, mummification, embryo death, and infertility (SMEDI) syndrome in pigs. The objective of this study was to gain new insights into the evolution and phylogeny of the PPV1 genome. In this study, we isolated two new PPV1 (HLJ202108-Y and SDLC202109) from northern China and sequenced their whole genomes. The new isolates were found to have three amino acid substitutions (K195R, K562R, and S578P) in nonstructural protein 1. The VP2 amino acid site contained nine nonsynonymous substitutions, including six substitutions of the Kresse strain corresponding to the NADL-2 strain and three substitutions of A414S, S436T, and N555K. Genetic evolution analysis was conducted on 107 reference sequences available in the GenBank database, and 4-5 PPV1 taxa were defined. The new isolates were in the same phylogenetic cluster as strain 27a. The changes in the cluster, specifically marker amino acids, and their potential role in enhancing pathogenicity are discussed in this study. Furthermore, the evolutionary tree map results showed that the strains in China were evolving in two directions: one was becoming increasingly similar to early NADL-2 strains, while the other was evolving toward 27a-like strains. We also compared the proliferation ability of the isolated strains in susceptible cells by analyzing the multistep growth curves. The results showed that the virulence titer of the mutant strain was high. In summary, this study introduced the latest changes in PPV and discussed the virus characteristics that were considered to affect virulence.

The Novel Porcine Parvoviruses: Current State of Knowledge and Their Possible Implications in Clinical Syndromes in Pigs

Parvoviruses (PVs) affect various animal species causing different diseases. To date, eight different porcine parvoviruses (PPV1 through PPV8) are recognized in the swine population, all of which are distributed among subfamilies and genera of the Parvoviridae family. PPV1 is the oldest and is recognized as the primary agent of SMEDI, while the rest of the PPVs (PPV2 through PPV8) are called novel PPVs (nPPVs). The pathogenesis of nPPVs is still undefined, and whether these viruses are putative disease agents is unknown. Structurally, the PPVs are very similar; the differences occur mainly at the level of their genomes (ssDNA), where there is variation in the number and location of the coding genes. Additionally, it is considered that the genome of PVs has mutation rates similar to those of ssRNA viruses, that is, in the order of 10-5-10-4 nucleotide/substitution/year. These mutations manifest mainly in the VP protein, constituting the viral capsid, affecting virulence, tropism, and viral antigenicity. For nPPVs, mutation rates have already been established that are similar to those already described; however, within this group of viruses, the highest mutation rate has been reported for PPV7. In addition to the mutations, recombinations are also reported, mainly in PPV2, PPV3, and PPV7; these have been found between strains of domestic pigs and wild boars and in a more significant proportion in VP sequences. Regarding affinity for cell types, nPPVs have been detected with variable prevalence in different types of organs and tissues; this has led to the suggestion that they have a broad tropism, although proportionally more have been found in lung and lymphoid tissue such as spleen, tonsils, and lymph nodes. Regarding their epidemiology, nPPVs are present on all continents (except PPV8, only in Asia), and within pig farms, the highest prevalences detecting viral genomes have been seen in the fattener and finishing groups. The relationship between nPPVs and clinical manifestations has been complicated to establish. However, there is already some evidence that establishes associations. One of them is PPV2 with porcine respiratory disease complex (PRDC), where causality tests (PCR, ISH, and histopathology) lead to proposing the PPV2 virus as a possible agent involved in this syndrome. With the other nPPVs, there is still no clear association with any pathology. These have been detected in different systems (respiratory, reproductive, gastrointestinal, urinary, and nervous), and there is still insufficient evidence to classify them as disease-causing agents. In this regard, nPPVs (except PPV8) have been found to cause porcine reproductive failure (PRF), with the most prevalent being PPV4, PPV6, and PPV7. In the case of PRDC, nPPVs have also been detected, with PPV2 having the highest viral loads in the lungs of affected pigs. Regarding coinfections, nPPVs have been detected in concurrence in healthy and sick pigs, with primary PRDC and PRF viruses such as PCV2, PCV3, and PRRSV. The effect of these coinfections is not apparent; it is unknown whether they favor the replication of the primary agents, the severity of the clinical manifestations, or have no effect. The most significant limitation in the study of nPPVs is that their isolation has been impossible; therefore, there are no studies on their pathogenesis both in vitro and in vivo. For all of the above, it is necessary to propose basic and applied research on nPPVs to establish if they are putative disease agents, establish their effect on coinfections, and measure their impact on swine production.

Detection of porcine circovirus 2, porcine parvovirus 1, and torque teno sus virus k2a in wild boars from northeastern Patagonia, Argentina

Wild boars can act as a reservoir of pathogenic viruses that affect the pig industry. Here, we assessed the presence of porcine circovirus 2, porcine parvovirus 1, and torque teno sus virus k2a in wild boars in northeastern Patagonia (Argentina). Total DNA was extracted from the tonsils of 27 animals (collected between early 2016 and mid-2019) and used to prepare sample pools, which were subjected to viral detection through two-round PCR assays. Sequencing of the amplification products and phylogenetic analysis confirmed the occurrence of all of the aforementioned infectious agents.

A Phylogeographic Analysis of Porcine Parvovirus 1 in Africa

Porcine parvovirus 1 (PPV1) is recognized as a major cause of reproductive failure in pigs, leading to several clinical outcomes globally known as SMEDI. Despite being known since the late 1960s its circulation is still of relevance to swine producers. Additionally, the emergence of variants such as the virulent 27a strain, for which lower protection induced by vaccines has been demonstrated, is of increasing concern. Even though constant monitoring of PPV1 using molecular epidemiological approaches is of pivotal importance, viral sequence data are scarce especially in low-income countries. To fill this gap, a collection of 71 partial VP2 sequences originating from eight African countries (Burkina Faso, Côte d'Ivoire, Kenya, Mozambique, Namibia, Nigeria, Senegal, and Tanzania) during the period 2011-2021 were analyzed within the context of global PPV1 variability. The observed pattern largely reflected what has been observed in high-income regions, i.e., 27a-like strains were more frequently detected than less virulent NADL-8-like strains. A phylogeographic analysis supported this observation, highlighting that the African scenario has been largely shaped by multiple PPV1 importation events from other continents, especially Europe and Asia. The existence of such an international movement coupled with the circulation of potential vaccine-escape variants requires the careful evaluation of the control strategies to prevent new strain introduction and persistence.

A Plant-Produced Porcine Parvovirus 1-82 VP2 Subunit Vaccine Protects Pregnant Sows against Challenge with a Genetically Heterologous PPV1 Strain

Porcine parvovirus (PPV) causes reproductive failure in sows, and vaccination remains the most effective means of preventing infection. The NADL-2 strain has been used as a vaccine for ~50 years; however, it does not protect animals against genetically heterologous PPV strains. Thus, new effective and safe vaccines are needed. In this study, we aimed to identify novel PPV1 strains, and to develop PPV1 subunit vaccines. We isolated and sequenced PPV1 VP2 genes from 926 pigs and identified ten PPV1 strains (belonging to Groups C, D and E). We selected the Group D PPV1-82 strain as a vaccine candidate because it was close to the highly pathogenic 27a strain. The PPV1-82 VP2 protein was produced in Nicotiana benthamiana. It formed virus-like particles and exhibited a 2¹¹ agglutination value. The PPV1-190313 strain (Group E), isolated from an aborted fetus, was used as the challenging strain because it was pathogenic. The unvaccinated sow miscarried at 8 days postchallenge, and mummified fetuses were all PPV1-positive. By contrast, pregnant sows vaccinated with PPV1-82 VP2 had 9-11 Log₂ antibody titers and produced normal fetuses after PPV1-190313 challenge. These results suggest the PPV1-82 VP2 subunit vaccine protects pregnant sows against a genetically heterologous PPV1 strain by inducing neutralizing antibodies.

Polymerase chain reaction-based detection of coinfecting DNA viruses in Vietnamese pigs in 2017 and 2021

Background and Aim: Many studies have reported on the phenomenon of co-infections involving two or more pathogens (bacteria or viruses) over the past few years. However, very few studies on this issue were conducted in Vietnam. Therefore, this study aimed to determine the circulation of single and multiple porcine parvovirus (PPV) (e.g., PPV1, PPV2, PPV3, and PPV4), porcine bocavirus (PBoV), and torque teno virus (TTV) (TTV1 and TTV2) infections in Vietnamese pigs. Materials and Methods: A total of 174 porcine circovirus 2-positive samples from pigs (n = 86 for 2017 and n = 88 for 2021), including from the sera and internal organs, across 11 provinces were examined by polymerase chain reaction. Results: This study demonstrated the wide distribution of DNA viruses among pig farms in Vietnam in 2021, with the detection rate for PPV ranging from 3.4% to 27.3% among PPV1-PPV4. Moreover, the detection rates of TTV genotypes were confirmed to be 14.8% (TTV1) and 63.6% (TTV2), respectively, and the positive rate of PBoV was 65.9%. The most frequent combinations were double and triple infections. Double infection was found in 16/86 (18.6%) in 2017 and 26/88 (29.5%) in 2021, while triple infection was found at 19/86 (22.1%) in 2017 and 26/88 (29.5%) in 2021. The incidence of simultaneous detection of more than three viruses was low. Conclusion: These results provide at least partial information about the occurrence of three viruses, including PPV (including PPV1 to 4), PBoV, and TTV (TTV1 and TTV2), in pigs. Determination of particular viruses in pigs will help to prevent the porcine respiratory disease complex caused by DNA viruses in Vietnamese pigs in the future.

Seroprevalence and Risk Factors Investigations of Parvovirus Disease in Tibetan Pigs: First Report from Tibet

Porcine parvovirus (PPV) disease is a worldwide spread animal disease with high infection rate and serious impact on meat economy causing significant losses in livestock production. The purpose of this paper is to investigate and analyze the regional seroprevalence of PPV in Tibetan pigs in Tibet and evaluate risk factors related to the disease. A total of 356 serum samples of Tibetan pigs were collected from four counties and districts in Tibet, and anti-PPV antibodies were detected by using a commercial competitive ELISA. Our results show a seroprevalence of 91.01% (324 serum samples were found to be positive for anti-PPV antibodies). The positive rate among different district was 100%, 96.55%, 93.68% and 72.83%, respectively in the Mainling County, in Bayi district, Nang County and Bomê County. We found significant differences between different age and gender groups; particularly female animals show a seroprevalence of 96.03% while the males only 83.46%. From the perspective of the growth stage, our results indicate that subadults show a seroprevalence significative higher than other age groups (100%). This study describes for the first time the PPV seroprevalence among Tibetan pigs characterizing risk factors involved in its transmission and providing information to be taken into account for eventual surveillance or eradication plans.

Allele-Specific Dual PCRs to Identify Members of the 27a Cluster of PPV

Porcine Parvovirus (PPV) is one of the most important infectious agents causing severe reproductive failure in pigs. In the last two decades a particular, a novel genotype emerged in Europe and PPV-27a was named as the prototype of this genetic cluster. It was suggested that members of the PPV-27a cluster may adversely influence effective vaccination against PPV. For a reliable updated 27a definition, we aligned 93 databank-deposited partial or full nucleotide and protein sequences of the VP2 of different PPV isolates. We confirmed that the 27a cluster could indeed be distinguished from other members of the species, however, some divergences were identified compared to earlier defined genetic markers. Based on genetic differences, we developed a dual allele-specific polymerase chain reaction for the easy and quick discrimination of members of the 27a cluster from other PPV strains. The detection limit of dual PCR was found <1.66 × 104 copies/reaction. To sensitize and make it more user friendly, the method was further developed for qPCR application with fluorescent probes. Regarding the detection limit of the two PCRs (<1.66 × 104 copies/reaction of the dual PCR versus <2.40 × 102 copy/reaction of the dual qPCR), approximately two log improvement was achieved in the sensitivity of the method.

Viral Co-Infections of Warthogs in Namibia with African Swine Fever Virus and Porcine Parvovirus 1

Simple Summary

Wild animals can transmit diseases to domestic animals. In Africa, warthogs are known to be carriers of pathogens that can infect pigs; consequently, it is important to identify these pathogens in order to protect pigs from infection. In this study, two important swine pathogens i.e., African swine fever virus (ASFV) and porcine parvovirus 1 (PPV1) were identified in warthogs in Namibia and characterized genetically. The results will be of interest to those working in swine disease management and control in Namibia.

Abstract

Understanding virus circulation in wild animals, particularly those that have contact with domestic animals, is crucial for disease management and control. In Africa, warthogs are known to be asymptomatic carriers of porcine pathogens; a recent study in Namibia has shown them to be positive for Porcine circovirus-2 (PCV-2). In this study, the same samples used for the PCV-2 investigation in Namibia were further screened for the presence of African swine fever virus (ASFV) and porcine parvovirus 1 (PPV1) by PCR. Of the 42 animals tested, 2 (4.8%) and 13 (31%) were positive for AFSV and PPV1, respectively. The two AFSV were also co-infected with PPV1. Combing the results of this study with the results of the previous PCV-2 investigation, four warthogs were shown to be co-infected with both PPV1 and PCV-2. Sequence and phylogenetic analysis revealed that the AFSV belonged to genotype (Ib) but were from different serogroups. Unexpectedly, the ASFVs from the warthogs were genetically distinct to those observed in an outbreak in the same region of Namibia that occurred less than fifteen months prior to the sampling of the warthogs. In fact, a stronger genetic relationship was observed between the warthog viruses and historical Namibian and South African ASFVs identified in 1980, 2004 and 2008. For the PPV1s, the closest relative to the Namibian PPV1 were viruses identified in wild boar in Romania in 2011. This study confirms that warthogs are carriers of porcine pathogens and the data should encourage further studies on larger populations of wild and domestic swine to more fully understand the epidemiology and transmission of viral pathogens from these species.

Molecular Epidemiology of Porcine Parvovirus Type 1 (PPV1) and the Reactivity of Vaccine-Induced Antisera Against Historical and Current PPV1 Strains

Porcine Parvovirus Type 1 (PPV1) contributes to important losses in the swine industry worldwide. During a PPV1 infection, embryos and fetuses are targeted, resulting in stillbirth, mummification, embryonic death, and infertility (SMEDI syndrome). Even though vaccination is common in gilts and sows, strains mainly belonging to the 27a-like group have been spreading in Europe since early 2000s, resulting in SMEDI problems and requiring in-depth studies into the molecular epidemiology and vaccination efficacy of commercial vaccines. Here, we show that PPV1 has evolved since 1855 [1737, 1933] at a rate of 4.71 × 10⁻⁵ nucleotide substitutions per site per year. Extensive sequencing allowed evaluating and reassessing the current PPV1 VP1-based classifications, providing evidence for the existence of four relevant phylogenetic groups. While most European strains belong to the PPV1a (G1) or PPV1b (G2 or 27a-like) group, most Asian and American G2 strains and some European strains were divided into virulent PPV1c (e.g. NADL-8) and attenuated PPV1d (e.g. NADL-2) groups. The increase in the swine population, vaccination degree, and health management (vaccination and biosafety) influenced the spread of PPV1. The reactivity of anti-PPV1 antibodies from sows vaccinated with Porcilis^© Parvo, Eryseng^© Parvo, or ReproCyc^© ParvoFLEX against different PPV1 field strains was the highest upon vaccination with ReproCyc^© ParvoFLEX, followed by Eryseng^© Parvo, and Porcilis^© Parvo. Our findings contribute to the evaluation of the immunogenicity of existing vaccines and support the development of new vaccine candidates. Finally, the potential roles of cluster-specific hallmark amino acids in elevated pathogenicity and viral entry are discussed.

Molecular detection of porcine parvovirus 1-associated reproductive failure in southern India

This study used 56 aborted and stillborn fetuses from organized swine farms in Tamil Nadu and Kerala, southern states of India. All samples were screened by using a PCR assay that targets the NS1 gene for PPV. Furthermore, the PCR positive samples were subjected to amplification of the VP2 gene of PPV1 with designed primers and sequenced for further study. The PCR screening of 56 samples found that 14.3% (n = 8) were positive for PPV genome. According to VP2 gene–based PCR for PPV1, 897 bp specific amplicons were detected in all eight of the samples. Two of the eight positive samples (L17 and T5) were sequenced and annotated randomly. The BLAST analysis of contig sequence INDTNCHN-T5 revealed 100% sequence homology with Chinese PPV1genome, whereas sequence from INDTNCHN-L17 revealed 99.43% sequence homology with Spain, Chinese, and German. PPV1 sequences and both the sequences INDTNCHN-T5 and INDTNCHN-L17 were submitted to the GenBank under the accession numbers MW822566 and MW822567 respectively. A phylogenetic analysis of the sequences in this study revealed specific grouping along with PPV1 strains in cluster E. Amino acid analysis of both isolated sequences in addition to the reference sequence from PPV1 showed variations in position 215 (I to T) in both the isolates, variation at position 228 (Q to E) in T5 isolate and variations at position 59 (L to M) and 314 (K to E) in L17 isolate. This study represents the first report of PPV1 cluster E in Tamil Nadu, southern India.

A Systematic Investigation Unveils High Coinfection Status of Porcine Parvovirus Types 1 through 7 in China from 2016 to 2020

Porcine parvovirus genotype 1 (PPV1) causes reproductive disorder in swine and is prevalent in China. Recently, six new genotypes of PPVs (PPV2 through PPV7) have also been detected in Chinese swine herds. However, the coinfection status of all these seven genotypes of PPVs (PPV1-7) in China was not clarified yet. In this study, we developed a panel of PPV1–7 PCR assays with satisfied specificity, sensitivity and reproducibility and then applied to the detection of PPV1–7 in 435 clinical samples collected from eight provinces of China in 2016–2020. A total of 55.40% samples (241 out of 435) were PPV positive, while PPV2 and PPV3 (both 22.53%) belonging to the genus of Tetraparvovirus were the most prevalent genotypes. Noticeably, PPV1–7 strains were more prevalent in nursery and finishing pigs than in suckling pigs. In addition, coinfection could be detected in all eight provinces and 27.36% (119/435) samples were coinfected with two to five genotypes of PPVs. Meanwhile, the coinfection of PPVs with PCV2 was 22.30% (97/435). Twenty complete genomes of representative PPV1–7 were determined, and phylogenetic analysis confirmed the genotyping results by sequence comparisons and PCR assays. Remarkably, the PPV7 HBTZ20180519-152 strain from domestic pig was recombined from parental JX15-like and JX38-like isolates from wild boars. Selective pressure analysis based on VP2 sequences of PPV1–7 showed that they were predominantly under negative selection, while few positive selection sites could be detected in VP2 of PPV7. Overall, this systematic investigation unveils high prevalence and coinfection of PPV1–7 in China from 2016 to 2020.

IMPORTANCE Porcine parvoviruses (PPVs) are prevalent in China associating with reproductive failure in swine. The coinfection of seven genotypes of PPVs (PPV1-7) might have synergistic effects on PPV1 associated SMEDI syndrome. However, the coinfection status of PPV1–7 in China is not clear yet. This study showed that PPV1–7 strains are highly prevalent (55.40%) in China and mainly in nursery and finishing pigs in recent years. In addition, the coinfections of different genotypes of PPVs (27.36%) and PPVs with PCV2 (22.30%) are common. Geographic analysis indicated that different genotypes of PPVs are widely cocirculating in China. Intriguingly, a PPV7 strain from the domestic pig was detected as a recombinant from two wild boar isolates. Selective pressure analyses showed that PPV1–7 are mainly under purifying selection. Our findings provide the first systematic investigation on the prevalence, coinfection, and evolution of PPV1 through PPV7 in Chinese swineherds from 2016 to 2020.

Viral fitness and antigenic determinants of porcine parvovirus at the amino acid level of the capsid protein

Since 2001, strains of porcine parvovirus (PPV), designated 27a-like strains, were observed in Europe, suggesting a predominance of these viruses over older strains. The reasons for the obvious evolutionary advantage are unknown. Here, a series of mutants containing amino acid replacements found in the predominant field strains were generated in a PPV-NADL2 background and their impact on replication efficiency and antibody binding activity was determined. Some amino acid substitutions observed in the 27a-like strains significantly increased viral fitness and decreased neutralization activity of sera raised against commercial vaccines and old virus strains (e.g. NADL2). These mutant viruses and a monoclonal antibody raised against a classical PPV strain defined an 27a-specific neutralizing epitope around amino acid 228 of the capsid protein VP2. Based on the analysis of the mutant viruses, it is hypothesized that the predominant factor for the global spread of the PPV-27a strain substitutions is an increased viral fitness of the 27a-like viruses, possibly supported by a partial immune selection. This is reminiscent to the evolution of canine parvovirus and worldwide replacement of the original virus by the so-called new antigenic types. Importance Porcine parvovirus is one of the most important causes of reproductive failure in swine. Recently, despite the continuous use of vaccines, "new" strains emerged, leading to the hypothesis that the emergence of new amino acid substitutions could be a viral adaptation to the immune response against the commercial vaccines. Our results indicate the amino acid substitutions observed in the 27a-like strains can modify viral fitness and antigenicity. However, an absolute immune escape was not evident.

Genetic analysis of porcine parvoviruses detected in South Korean wild boars

Porcine parvovirus 1 (PPV1) is a major cause of reproductive failure in pigs. To date, six additional porcine parvoviruses (PPV2-PPV7) have been identified. In this study, we detected 11 PPV1 strains, five PPV3 strains, three PPV4 strains, six PPV5 strains, five PPV6 strains, and one PPV7 strain in Korean wild boars. PPV1, -3, and -5, and PPV6 from Korean wild boars harbor conserved motifs within the Ca²⁺ binding loop and the catalytic center of the PLA1 motif. Intra-species recombination among PPV7 strains was also identified. Genetic characterization revealed that PPV1 from Korean wild boars may be similar to virulent PPV strains.

Genetic Analysis and Distribution of Porcine Parvoviruses Detected in the Organs of Wild Boars in Serbia

Porcine parvoviruses (PPVs) are diverse and persistently evolving viruses found in domestic pigs and wild boars. Porcine parvovirus 1 (PPV1) causes reproductive problems in adult animals, although the veterinary relevance of PPV2, PPV3, and PPV4 has not been clarified. The detection and sequence analysis of PPVs circulating in wild boar populations in Serbia was performed to determine their phylogenetic relationships and prevalence in 122 organ samples collected during 2018. The DNA of PPV1, PPV2, and PPV3 was detected in 56.6% of the examined samples, whilst PPV4 was not identified. Overall, PPV3 was the most prevalent in 69.6% of the positive samples, followed by PPV1 in 63.8%, and PPV2 in 21.7% samples. Single infections were more common, although concurrent infections were confirmed in 34.8% samples for two, and 10.1% samples for three viruses. Sequence analysis of wild boar PPV1 showed no significant nucleotide differences from domestic pig PPV1 strains detected in Europe and the USA, however separate clustering from strains from China and the NADL-2 strain was demonstrated. Examination of the selected PPV2 sequences might suggest a certain geographical distribution of genetically diverse PPV2 strains considering high similarities to the strains from neighboring countries, and variability in comparison with other reported PPV2 sequences from different parts of the world. Wild boar PPV3 sequences clustered separately from most of the strains detected in wild boars, as well as the original porcine hokovirus strain. It is further noted that genetically different PPV3 strains circulate amongst Serbian domestic pigs and wild boars.

First investigation of the prevalence of parvoviruses in slaughterhouse pigs and genomic characterization of ungulate copiparvovirus 2 in Vietnam

Ungulate protoparvovirus 1, also known as porcine parvovirus 1 (PPV1), is considered to be one of the major causes of reproductive failure in pig breeding herds. Other parvoviruses have also been identified in pigs, including ungulate tetraparvovirus 3, or PPV2, ungulate tetraparvovirus 2, or PPV3, and ungulate copiparvovirus 2, or PPV4, but their significance for pigs is unknown. In the present study, the prevalence of PPV1-4 was investigated using a total of 231 lung and serum samples collected from slaughterhouses in 13 provinces throughout Vietnam. The overall prevalence was 54.5% (126/231) for PPV1, 28.0% (65/231) for PPV2, 17.7% (41/231) for PPV3, and 7.8% (18/231) for PPV4. While PPV1 and PPV2 were found in 11 provinces, PPV4 was detected in only three provinces. Co-circulation of PPV1, PPV2 and PPV3 was frequently observed, with PPV1/PPV2 coinfection predominating, with 20.8% (48/231). All four PPVs were detected together in only one sample from Thua Thien Hue. Three nearly complete PPV4 genome sequences of 5,453 nt were determined and deposited in the GenBank database. Alignment and comparison of the three genome sequences showed 99.5-99.6% nucleotide sequence identity, and the deduced amino acid sequences of open reading frames 1-3 were 99.6-99.9% identical to each other, 98.9-99.3% identical to those of other Vietnamese strains and 99.4-99.7% identical to those of Chinese strains). Phylogenetic analysis further confirmed a close relationship between Vietnamese and Chinese PPV4 strains. These results are the first to report the prevalence of PPV1, PPV2, PPV3, and PPV4 and nearly complete genomic sequences of PPV4 in pigs from slaughterhouses in Vietnam.

Detection and Characterization of Viral Pathogens Associated with Reproductive Failure in Wild Boars in Central Italy

Simple Summary

Suid herpesvirus 1, porcine circovirus 2 and porcine parvovirus are causative agents of reproductive failures in swine and are widely diffused in the wild boar population. No data describing the impact of those viruses on the reproductive performance of wild boar are so far available. We aimed to investigate the ability of the above viruses to infect foetuses of free-ranging pregnant wild boar sows living in a highly-populated area. Molecular investigation revealed that although all investigated viruses were detected in pregnant sows, only herpesvirus and circovirus were detected in the foetuses. Phylogenetic analysis revealed a close relationship between the strains circulating in wild boar and those already described in domestic swine. This study highlights the importance of monitoring the circulation of pathogens that are shared between domestic and wild pigs. This information is essential for the pig industry to avoid possible economic losses.

Abstract

Wild boar and domestic swine share several pathogens, including viruses responsible for reproductive failures, representing an important sanitary and economic risk for the swine industry. Among them, suid herpesvirus 1 (SuHV-1), porcine circovirus 2 (PCV2) and porcine parvovirus 1 (PPV1) are widely diffused in the wild boar population. Unfortunately, little is known about their pathogenetic mechanisms and impact on the reproductive parameters of wild animals. This study aims to investigate the presence of viruses responsible for reproductive failure in pregnant wild boar sows and their foetuses. The investigation was conducted on 46 pregnant wild boar and their foetuses by molecular analysis; a phylogenetic study was performed on the positive samples. All of the investigated pathogens were identified in sows, while only herpesvirus and circovirus were detected in the tissues of their foetuses. Phylogenetic analysis revealed that the viral sequences obtained from the positive wild boars were closely related to those previously identified in domestic swine belonging to the same study areas. The results suggest that SuHV-1 and PCV2 can infect wild boar foetuses, with a possible impact on wild boar reproductive performance. Moreover, our data highlight the importance of continuous monitoring of swine pathogens circulating in wild environments, so as to carry out adequate sanitary actions.

PCR-based detection and genetic characterization of porcine parvoviruses in South Korea in 2018

Background

with the advantage of sequencing technology, many novel porcine parvoviruses (PPV) rather than PPV1 has been reported. This study ultilized specific PCR- based method and gene- based analysis to study the presence and genetic diversity of porcine parvoviruses in South Korea in 2018.

Results

The present study was conducted in 2018 and found PPV1 and PPV7 in nine out of 151 field samples (organs and semen) by the PCR method. Among these, the complete genome sequences of five strains (N2, N91, N108, N133, and N141) were recovered. Phylogenic analysis revealed that the strains N2, N91, and N108 belong to the PPV1 genotype, while N133 and N141 belong to PPV7 genotype. The PPV7 strains collected in this study had deletion mutations in the VP2 gene but differed from that of PPV7 strains collected in 2017. Among the PPV1 strains, the amino acid variations in the B cell epitopes of the VP2 protein were observed between three Korean PPV1 field strains (N2, N91, and N108) and the reference PPV1 strains. Those substitutions resulted in six out of 12 predicted epitopes having significant differences in antigenic index compared to the other PPV1 strains.

Conclusions

This study confirmed the presence of different genotypes of porcine parvoviruses in South Korea. The PPVs circulating in South Korea were phylogenetically classified as PPV1 and PPV7 genotypes. Three Korean PPV1 strains collected in 2018 were predicted to have antigenic alteration in VP2 compared to several reference strains of PPV1.

Vaccine Protection Against Experimental Challenge Infection with a PPV-27a Genotype Virus in Pregnant Gilts

Background/Introduction

Porcine parvovirus (PPV), the causative agent of severe reproductive failures in pigs, is present worldwide. The witnessed spread of the virulent 27a type PPV strains since its recognition raised concerns about the efficacy of the available commercial vaccines.

Methods

To address this question, vaccinated pregnant gilts were challenged with a PPV-27a-like virus strain and parameters related to vaccine efficacy were compared.

Results

The K22 vaccine strain of Parvoruvax^® (PVX) was characterized as “Kresse-like” based on the epitope mapping data. Vaccination of the gilts induced a low level of antibody responses. Based on foetal mortality, the number of sows which had challenge virus-affected foetuses, the percent of PPV positive piglets/litters plus their PPV genome and viral load PVX outscored the other vaccinated groups.

Conclusion

Stronger protection was provided by the “Kresse-like” K22 PPV strain-based vaccine than by the NADL-2 and NADL-like strain-based commercial vaccines against a PPV-27a cluster strain challenge. Vaccine-induced antibody levels as measured pre-challenge were not found to be an accurate indicator of protection.

Detection and molecular characterization of porcine parvovirus in fetal tissues from sows without reproductive failure in Argentina

Porcine parvovirus (PPV) is one of many pathogens responsible for reproductive failure in pregnant sows. Several studies have reported the appearance of new PPV strains that differ from previous isolates both genetically and antigenically. Thus, the protective effects of commercially inactivated vaccines could not be complete. In South America, the information about PPV is limited. Thus, the aim of the present study was to detect and characterize the PPV strains present in 131 mummies or stillbirths from normal deliveries in sows from a commercial swine farm of Argentina that uses the commercial vaccine. PCR results showed that 17/131 were positive to PPV. Ten of these viruses were isolated and sequenced. All viruses were related to the PPV1 sequence (NADL-2), maintaining the amino acid differences in positions 436 (S–P) and 565 (R–K). This study is the first to report the isolation of PPV in Argentina and the results suggest that PPV can cross the placenta even in vaccinated sows, thus affecting some of the fetuses and being able to cause fetal death in sows without reproductive failure. The results also suggest that vaccination only reduces clinical signs and reproductive disorders and may thus not be a perfect tool to manage PPV infection. This study provides information that needs to be studied in depth to improve strategies to prevent and control PPV infection in swine farms.

Isolation and phylogenetic analysis of a new Porcine parvovirus strain GD2013 in China

Porcine parvovirus (PPV), a causative agent of an infectious reproductive disorder causing stillbirth, mummification, embryonic death and infertility (SMEDI) syndrome in swine, is a threat to both domestic pigs and wild boars regardless of age and gender. Recent studies found that the observed average substitution rate in the PPV genome was close to those of the RNA viruses and new strains showing serological neutralization activities different from that of the vaccine strain NADL-2 have been reported. These observations have increased the need for the development of new commercial vaccine strains. In this study, a new PPV strain, GD2013, was isolated from Guangdong, China, and its entire genome sequenced. A phylogenetic tree based on the complete coding region of the genomes of 32 PPV strains was constructed using the Bayesian Markov Chain Monte Carlo (MCMC) method. The results showed that strain GD2013 fell into the same phylogenetic cluster as the classical vaccine strains NADL-2 and POVCAP, suggesting a close relationship to the vaccine strains. Multiple sequence alignments and amino acid mutation analyses of the PPV VP2 gene revealed a new amino acid polymorphism site at Thr45 on VP2 that could be used to identify low virulence strains as vaccine candidates. Selective pressure analysis of the NS1 and VP2 genes by calculating the mean rates of non-synonymous substitutions (dN) over synonymous substitutions (dS) implied that both of these genes were under negative selection. Therefore, by using phylogenetic and amino acid mutation analyses, a likely candidate strain suitable for evaluation as an attenuated vaccine strain was identified.

Increasing diversity of swine parvoviruses and their epidemiology in African pigs

Detection of infectious viral agents has been on the increase globally with the advent and usage of more sensitive and selective novel molecular techniques in the epidemiological study of viral diseases of economic importance to the swine industry. The observation is not different for the pig-infecting member of the subfamily Parvovirinae in the family Parvoviridae as the application of novel molecular methods like metagenomics has brought about the detection of many other novel members of the group. Surprisingly, the list keeps increasing day by day with some of them possessing zoonotic potentials. In the last one decade, not less than ten novel swine-infecting viruses have been added to the subfamily, and ceaseless efforts have been in top gear to determine the occurrence and prevalence of the old and new swine parvoviruses in herds of pig-producing countries worldwide. The story, however, is on the contrary on the African continent as there is presently a dearth of information on surveillance initiatives of the viruses among swine herds of pig-producing countries in the region. Timely detection and characterization of the viral pathogens is highly imperative for the implementation of effective control and prevention of its spread. This review therefore presents a concise overview on the epidemiology of novel porcine parvoviruses globally and also provides up-to-date highlights on the reported cases of the viral agents in the African sub-region.

Biology of Porcine Parvovirus (Ungulate parvovirus 1)

Porcine parvovirus (PPV) is among the most important infectious agents causing infertility in pigs. Until recently, it was thought that the virus had low genetic variance, and that prevention of its harmful effect on pig fertility could be well-controlled by vaccination. However, at the beginning of the third millennium, field observations raised concerns about the effectiveness of the available vaccines against newly emerging strains. Subsequent investigations radically changed our view on the evolution and immunology of PPV, revealing that the virus is much more diverse than it was earlier anticipated, and that some of the “new” highly virulent isolates cannot be neutralized effectively by antisera raised against “old” PPV vaccine strains. These findings revitalized PPV research that led to significant advancements in the understanding of early and late viral processes during PPV infection. Our review summarizes the recent results of PPV research and aims to give a comprehensive update on the present understanding of PPV biology.

Perspectives on the Evolution of Porcine Parvovirus

Porcine parvovirus (PPV) is one of the main causes of porcine reproductive failure. It is important for swine industries to understand the recent trends in PPV evolution. Previous data show that PPV has two genetic lineages originating in Germany. In this study, two more genetic lineages were defined, one of which was distinctly Asian. Additionally, amino acid substitutions in European strains and Asian strains showed distinct differences in several regions of the VP2 gene. The VP1 gene of the recent PPV isolate (T142_South Korea) was identical to that of Kresse strain isolated in the USA in 1985, indicating that modern PPV strains now resemble the original strains (Kresse and NADL-2). In this study, we compared strains isolated in the 20th century to recent isolates and confirmed the trend that modern strains are becoming more similar to previous strains.

Molecular Detection of Pseudorabies Virus (PrV), Porcine Parvovirus (PPV) and Porcine Circovirus 2 (PCV2) in Swine in Republic of Montenegro

The presence of pseudorabies virus (PrV), porcine parvovirus (PPV) and porcine circovirus 2 (PCV2) was examined in sixty samples (spleen and lymph nodes) and thirty samples of sacral ganglia collected from non-vaccinated swine by virus isolation and polymerase chain reaction (PCR). Using PCR method PrV was detected in three samples, PPV in seven samples and six samples were found positive for PCV2. The phylogenetic analysis of the nucleotide sequences of three PrV isolates identified in this study showed high similarity and significant clustering within the PrV genotype I strains such as Kaplan and Bartha isolated from pigs in Hungary, strain Becker isolated in USA and strain Kolchis isolated in Greece. The nucleotide sequences of two PPV isolates showed high level of similarity with the strain Challenge isolated from pigs in UK, strain Kresse isolated in USA and strains 77 and LZ isolated in China. The phylogenetic analysis of the nucleotide sequences of two PCV2 isolates showed high level of similarity and significant clustering within genotype PCV2b strains such as NIVS-3, NIVS-5 and NIVS-6 isolated in Serbia, strain 3959 isolated in Austria, strain PM165 isolated from pigs in Brasil, and strain XT2008 isolated in China. The results of our study present the molecular characterization of PrV, PPV and PCV2 identified in swine in Republic of Montenegro. Besides that, these results confirmed that PCR is a very useful method for rapid detection of these viruses in subclinically infected swine.

A TaqMan qPCR for quantitation of Ungulate protoparvovirus 1 validated in several matrices

Ungulate protoparvovirus 1 (UPV1) is one of the major causes of reproductive disorders in swine. Recently, the rapid viral evolution of UPV1 and its viral persistence in several tissues has been described. Based upon this, a real-time qPCR method using upgraded primers targeting VP1 and applying the TaqMan technology was developed in this study for UPV1, and it was validated in feces, serum and tissue. Within the results, the limit of detection of the qPCR was 100copies of the viral genome per reaction of serum and feces and 1000copies of the viral genome per reaction of the grinded tissue (pre-inoculated matrices with diluted serially viruses). No cross reactivity was observed with other viruses associated with reproductive disorders. The assay was specific and reproducible, presenting low intra- and inter-assay variation (0.93% and 1.06%, respectively). In 50 clinical samples, the method was found to be more sensitive than immunofluorescence and a SYBR Green PCR. In conclusion, this qPCR represents an upgraded and useful tool to quantify UPV1 in different sample matrices for diagnostic and research purposes.

Production and immunogenicity of VP2 protein of porcine parvovirus expressed in Pichia pastoris

Viral protein 2 (VP2) of porcine parvovirus (PPV) is the major viral structural protein and is responsible for eliciting neutralizing antibodies in immunized animals. In this study, we constructed and characterized a recombinant yeast vector encoding the VP2 protein, designated as pGAPZαA-VP2. The construct was confirmed by restriction enzyme digestion, PCR, and sequencing and then introduced into P. pastoris strain SMD1168 by electroporation. The expressed VP2 protein was analyzed by SDS-PAGE and western blot. Immunization of mice with the VP2 protein elicited a PPV-specific humoral immune response. Notably, a preparation of VP2 protein containing adjuvant induced a much better antibody response than VP2 alone. Clearly, the adjuvant strongly enhanced the immunogenicity of VP2. This study provides a foundation for the application of the VP2 protein in the clinical diagnosis of PPV and in vaccination against PPV in the future.

Population dynamics and in vitro antibody pressure of porcine parvovirus indicate a decrease in variability

To estimate the impact of porcine parvovirus (PPV) vaccines on the emergence of new phenotypes, the population dynamic history of the virus was calculated using the Bayesian Markov chain Monte Carlo method with a Bayesian skyline coalescent model. Additionally, an in vitro model was performed with consecutive passages of the ‘Challenge’ strain (a virulent field strain) and NADL2 strain (a vaccine strain) in a PK-15 cell line supplemented with polyclonal antibodies raised against the vaccine strain. A decrease in genetic diversity was observed in the presence of antibodies in vitro or after vaccination (as estimated by the in silico model). We hypothesized that the antibodies induced a selective pressure that may reduce the incidence of neutral selection, which should play a major role in the emergence of new mutations. In this scenario, vaccine failures and non-vaccinated populations (e.g. wild boars) may have an important impact in the emergence of new phenotypes.

Emerging novel porcine parvoviruses in Europe: origin, evolution, phylodynamics and phylogeography

To elucidate the spatiotemporal phylodynamics, dispersion and evolutionary processes underlying the emergence of novel porcine parvovirus 2 (PPV2), PPV3 and PPV4 species, we analysed all available complete capsid genes, together with ours, obtained in Europe. Bayesian phylogeography indicates that Romania (PPV2 and PPV4) and Croatia (PPV3) are the most likely ancestral areas from which PPVs have subsequently spread to other European countries and regions. The timescale of our reconstruction supported a relatively recent history of the currently circulating novel PPV species (1920s to 1980s) in the domestic or sylvatic host. While PPV2 strains exhibited a large genetic exchange characterized by significant recombination and gene flow between distinct regions and hosts, PPV3 and PPV4 showed a diversification reflected by the accumulation of geographically structured polymorphisms. The RNA-like evolutionary rates detected inter- and intrahost recombination and the positive selection sites provided evidence that the PPV2-4 capsid gene plays a prominent role in host adaptation.

Development of a loop-mediated isothermal amplification assay for the detection of porcine hokovirus

Hokoviruses have recently been detected as pathogens belonging to the family Parvoviridae, which comprises porcine hokovirus (PHoV) and bovine hokovirus (BHoV). In this study, we developed a loop-mediated isothermal amplification (LAMP) assay for the rapid, specific and sensitive detection of PHoV. A set of four primers specific for six regions within the PHoV VP1/2 genes was designed using online software. The reaction temperature and time were optimized at 65°C and 60 min, respectively. LAMP products were detected by agarose gel electrophoresis or by visual inspection of a color change caused by a fluorescent dye. The method was highly specific for PHoV, and no cross-reaction was observed with porcine circovirus type 2 (PCV2), porcine parvovirus (PPV), porcine bocavirus (PBoV), pseudorabies virus (PRV), porcine reproductive and respiratory syndrome virus (PRRSV), classic swine fever virus (CSFV), or Japanese encephalitis virus (JEV). The detection limit was approximately 10 copies per reaction, which was 10 times more sensitive than conventional PCR. Furthermore, the efficiency of detection of PHoV in clinical samples was comparable to that of PCR and sequencing. These results show that the LAMP assay is a simple, rapid, sensitive and specific method for detecting PHoV. It does not require specialized equipment and can be used to detect PHoV both in the laboratory and in the field.