A novel NADC30‐like porcine reproductive and respiratory syndrome virus (PRRSV) plays a limited role in the pathogenicity of porcine circoviruses (PCV2 and PCV3) and PRRSV co‐infection

Co‐infection of porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circoviruses (PCVs) is commonly observed under field conditions and elicits more severe diseases than any singular infection. In this study, the co‐infection of PRRSV, PCV2 and PCV3 was analyzed in tissue samples collected from 150 pigs from April 2016 to April 2018. PRRSV, PCV2 and PCV3 was detected in 55 (36.67%), 43 (28.67%) and 3 (2%) of 150 pigs respectively. Remarkably, one lung sample (SD17‐36) collected from a diseased pig was co‐infected with PRRSV, PCV2 and PCV3. The complete genomes of SD17‐36 viruses of PRRSV, PCV2 and PCV3 were determined, which belong to the subgroups of NADC30‐like PRRSV, PCV2d and PCV3a respectively. Sequence comparison showed that PRRSV SD17‐36 isolate contains a N33 deletion in GP5. Animal challenge study showed that the novel NADC30‐like PRRSV SD17‐36 isolate is low pathogenic. Our results indicate that the co‐infection of PRRSV and PCVs might cause diseases even when PRRSV plays a limited role in the pathogenicity of the co‐infection.     

A potential endemic strain in China: NADC34‑like porcine reproductive and respiratory syndrome virus

Porcine respiratory and reproductive syndrome virus (PRRSV) causes an economically important disease affecting commercial pork production worldwide. NADC34‐like PRRSV has had a strong impact on the U.S. and Peruvian pig industries in recent years and also emerged in northeastern China in 2017. However, the endemic status of NADC34‐like PRRSV in China is unclear. In this study, we examined 650 tissue samples collected from 16 Provinces in China from 2018 to 2019. Six NADC34‐like PRRSV strains were detected in samples from three Provinces, and the complete genomes of four of these strains were sequenced. Phylogenetic analysis showed that these novel PRRSV strains belong to sublineage 1.5 (or NADC34‐like PRRSV), forming two groups in China. Sequence alignment suggested that these novel strains share the same 100‐aa deletion in the Nsp2 protein that was identified in IA/2014/NADC34 isolated from the United States in 2014. Recombination analysis revealed that five of eight complete genome sequences are derived from recombination between IA/2014/NADC34 and ISU30 or NADC30. The number and distribution of NADC34‐like PRRSVs is increasing in China. Importantly, compared with the currently endemic strain NADC30‐like PRRSV, NADC34‐like PRRSV has the potential to be an endemic strain in China. This study will help us understand the epidemic status of NADC34‐like PRRSV in China and provide data for further monitoring this type of PRRSV in China.     

Genetic characterization of a novel recombinant PRRSV2 from lineage 8, 1 and 3 in China with significant variation in replication efficiency and cytopathic effects

There are four major porcine reproductive and respiratory syndrome virus 2 (PRRSV2) lineages circulating in China based on classification system, including lineages 1 (NADC30‐like), 3 (QYYZ‐like), 5.1 (VR2332‐like) and 8 (JXA1‐like/CH‐1a‐Like), which leads to the potential recombination. In the present study, a novel variant of PRRSV2 strain named JS18‐3 was isolated from piglets suffering severe breathing difficulties in Jiangsu Province of China in 2018. Full‐length genome analysis indicated that JS18‐3 shared 86.5%, 87.9%, 84.2%, 82.2% and 86.4% nucleotide similarity with PRRSVs CH‐1a, JXA1, VR2332, QYYZ and NADC30, respectively. 4871–6635 of JS18‐3 shared the highest identity of 99.3% in nucleotide sequence with HP‐PRRSV representative strain JXA1 indicating ongoing evolution to HP‐PRRSV. JS18‐3 was classified into classical lineage 8 of PRRSV2 based on phylogenetic analysis of complete genome and ORF5. Genomic break points in structural (ORF3) and non‐structural (NSP2, NSP3) regions of genomes were detected in recombination analysis. JS18‐3 is a recombinant isolate from lineages 8, 1 and 3. Replication enhancement and severe cytopathic effects caused by JS18‐3 were observed in Marc‐145 cells and porcine alveolar macrophages (PAMs) as compared to JX07, a typical strain of lineage 8. Pathogenicity results indicated that piglets inoculated with JS18‐3 presented persistent fever, dyspnoea, serious microscopic lung lesions and lymph node congestion. The study suggests that lineage 8 of PRRSV2 is involved in continuing evolution by genetic recombination and mutation leading to outbreaks in vaccinated pigs in China.     

Outbreak Investigation of NADC30‐Like PRRSV in South‐East China

Epidemiological outbreak investigations were conducted on NADC30‐like porcine reproductive and respiratory syndrome virus (PRRSV) to investigate the prevalence of the disease in south‐east China in 2015. Two more provinces were found to have NADC30‐like PRRSV circulating besides previously reported six provinces. Phylogenetic analysis showed that these virus isolates were clustered in an independent branch and shared high nucleotide similarity to NADC30, a type 2 PRRSV that has been isolated in Unite States in 2008. One NADC30‐like PRRSV strain from Henan province was successfully isolated on porcine alveolar macrophages and was tested on 6‐week‐old specific pathogen‐free pigs for pathogenic study. The virus‐inoculated pigs showed typical PRRSV clinical symptoms, but all pigs survived throughout the study with a period of 14 days. At necropsy, the lungs of infected pigs developed PRRSV‐specific interstitial pneumonia, and virus antigen was detected in lung samples. Therefore, our results indicated NADC30‐like PRRSV has widely spread in China and could cause clinical disease on pigs.     

Porcine reproductive and respiratory syndrome virus NADC30‐like strain accelerates Streptococcus suis serotype 2 infection in vivo and in vitro

Porcine reproductive and respiratory syndrome (PRRS), an economically significant pandemic disease, commonly results in increased impact of bacterial infections, including those by Streptococcus suis (S. suis). In recent years, PRRS virus (PRRSV) NADC30‐like strain has emerged in different regions of China, and coinfected with S. suis and PRRSV has also gradually increased in clinical performance. However, the mechanisms involved in host innate responses towards S. suis and their implications of coinfection with NADC30‐like strain remain unknown. Therefore, the pathogenicity of NADC30‐like strain and S. suis serotype 2 (SS2) coinfection in vivo and in vitro was investigated in this study. The results showed that NADC30‐like increased the invasion and proliferation of SS2 in blood and tissues, resulting in more severe pneumonia, myocarditis, and peritonitisas well as higher mortality rate in pigs. In vitro, NADC30‐like strain increased the invasion and survival of SS2 in porcine alveolar macrophages (PAM) cells, causing more drastic expression of inflammatory cytokines and activation of NF‐ĸB signalling. These results pave the way for understanding the interaction of S. suis with the swine immune system and their modulation in a viral coinfection.     

A modified‐live porcine reproductive and respiratory syndrome virus (PRRSV)‐1 vaccine protects late‐term pregnancy gilts against heterologous PRRSV‐1 but not PRRSV‐2 challenge

The objective of this study was to determine the efficacy of a commercially available porcine reproductive and respiratory syndrome virus (PRRSV )‐1 modified‐live virus (MLV ) vaccine against PRRSV ‐1 and PRRSV ‐2 challenge in late‐term pregnancy gilts. Gilts were vaccinated with the PRRSV ‐1 MLV vaccine at 4 weeks prior to breeding and then challenged intranasally with PRRSV ‐1 or PRRSV ‐2 at 93 days of gestation. After PRRSV ‐1 challenge, vaccinated pregnant gilts had a significantly longer gestation period, significantly higher numbers of live‐born and weaned piglets and a significantly lower number of stillborn piglets at birth compared to unvaccinated pregnant gilts. No significant improvement in reproductive performance was observed between vaccinated and unvaccinated pregnant gilts following PRRSV ‐2 challenge. Vaccinated pregnant gilts also exhibited a significantly improved reproductive performance after challenge with PRRSV ‐1 compared to vaccinated pregnant gilts following PRRSV ‐2 challenge. The PRRSV ‐1 MLV vaccine was able to reduce PRRSV ‐1 but not PRRSV ‐2 viremia in pregnant gilts. Vaccinated gilts also showed a significantly higher number of PRRSV ‐1‐specific IFN ‐γ‐secreting cells (IFN ‐γ‐SC ) compared to PRRSV ‐2‐specific IFN ‐γ‐SC . The data presented here suggest that the vaccination of pregnant gilts with a PRRSV ‐1 MLV vaccine provides good protection against PRRSV ‐1 but only limited protection against PRRSV ‐2 challenge in late‐term pregnancy gilts based on improvement of reproductive performance, reduction in viremia and induction of IFN ‐γ‐SC .     

Emergence of a novel highly pathogenic porcine reproductive and respiratory syndrome virus in China

From 2014 to 2015, four novel highly pathogenic PRRS virus (HP‐PRRSV) strains named 14LY01‐FJ, 14LY02‐FJ 15LY01‐FJ, and 15LY02‐FJ were isolated from high morbidity (100%) and mortality (40%–80%) in piglets and sows in Fujian Province. To further our knowledge about these novel virus strains, we characterized their complete genomes and determined their pathogenicity in piglets. Full‐length genome sequencing analysis showed that these four isolates were closely related to type 2 (North American type, NA‐type) isolates, with 88.1%–96.3% nucleotide similarity, but only 60.6%–60.8% homology to the Lelystad virus (LV) (European type, EU‐type). The full length of the four isolates was determined to be 15017 or 15018 nucleotides (nt), excluding the poly(A) tail. Furthermore, the four isolates had three discontinuous deletions (aa 322–432, aa 483, and aa 504–522) within hypervariable region II (HV‐II) of Nsp2, as compared to the reference strain VR‐2332. This deletion pattern in the four isolates is consistent with strain MN184 and strain NADC30 isolated from America. Phylogenetic and molecular evolutionary analyses indicated that these virulent strains originated from a natural recombination event between the JXA1‐like HP‐PRRSV (JXA‐1 is one of the earliest Chinese HP‐PRRSV strains; sublineage 8.7) and the NADC30‐like (lineage 1) PRRSV. Animal experiments demonstrated that these four strains caused significant weight loss and severe histopathological lung lesions as compared to the negative control group. High mortality rate (40% or 80%) was found in piglets infected with any one of the four strains, similar to that found with other Chinese HP‐PRRSV strains. This study showed that the novel variant PRRSV was HP‐PRRSV, and it is therefore critical to monitor PRRSV evolution in China and develop a method for controlling PRRS.     

Pathogenicity of porcine reproductive and respiratory syndrome virus (ORF5 RFLP 1‐7‐4 viruses) in China

Porcine reproductive and respiratory syndrome virus (PRRSV) is an RNA virus that causes reproductive failure in sows and respiratory problems in piglets. PRRSV infection leads to substantial pig mortality and causing huge economic losses so that disease outbreaks caused by the new PRRSV strain from other regions have caused great concern in China. In this study, we analysed the pathogenicity of the novel ORF5 RFLP 1‐7‐4‐like PRRSV strain, named PRRSV‐ZDXYL‐China‐2018‐1 in pigs. The viral challenge test showed that PRRSV‐ZDXYL‐China‐2018‐1 infection can cause persistent fever, moderate dyspnoea, serum viraemia and interstitial pneumonia in piglets. The levels of viral loads in serum and PRRSV‐specific antigen were also detected in lung tissues were used one‐step Taq‐Man RT‐qPCR and Immunohistochemistry, respectively. At 28dpi, the level of specific antibodies was increased among infected piglets. Importantly, the new virus appeared be a moderately virulent isolate with pathogenicity compared to HP‐PRRSV strain LQ (JXA1‐like strain). Histological examination revealed severe monocyte haemorrhage and interstitial pneumonia associated with monocyte infiltration in the lung tissue of pigs infected with PRRSV‐ZDXYL‐China‐2018‐1 and LQ‐JXA1 strains. Immunohistochemistry (IHC) results showed positive brown‐red epithelial cells and macrophages in pig lungs. Therefore, it is critical to establish an effective strategy to control the spread of PRRSV in China.     

Pathogenicity and Distribution of Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus in Pigs

The pathogenesis of highly pathogenic porcine reproductive and respiratory syndrome virus (PRRSV) strain (HuN4) is poorly understood. Therefore, highly pathogenic PRRSV strain (HuN4) and its derivative strain (HuN4‐F112) (obtained by propagation in MARC145 cells for 112 passages) were inoculated into a total of 48 PRRSV‐sero‐negative pigs (age: 4–5 weeks) by the intranasal route. Virological, pathological and in situ hybridization analyses were performed. The results exhibited that pigs infected with HuN4 showed a loss of appetite, decrease in body weight, raised body temperature and respiratory symptoms, along with interstitial pneumonia lesions. In the HuN4 group, multifocal interstitial pneumonia with macrophage infiltration was found in the lung. The lesions in the lymph node were characterized by collapsed follicles, depletion of germinal centres and reduction in lymphocytes. Perivascular cuffing and glial nodules were observed in the brains of some pigs. By comparison, the HuN4‐F112 group had milder lesions. PRRSV was detected in macrophages, alveolar epithelial cells and vascular endothelial cells in the tonsil and lymph nodes. The PRRSV amounts in the pigs infected with HuN4 were 10⁵–10⁹ copies/ml in the blood and 10¹⁰–10¹¹ copies/g in the lung tissues, whereas the virus amounts with HuN4‐F112 were 10^2.15–10^3.13 copies/ml in the blood and 10^3.0–10^3.6 copies/g in the lung. Our results demonstrate that the PRRS HuN4 virus infects alveolar epithelial cells, macrophages and vascular endothelial cells causing diffuse alveolar damage and lymph node necrosis. Its higher pathogenicity compared with HuN4‐F112 virus may be explained in part by higher replication rate in the previously mentioned organs.     

First detection of novel enterovirus G recombining a torovirus papain‐like protease gene associated with diarrhoea in swine in South Korea

Enterovirus species G (EV‐G) comprises a highly diversity of 20 genotypes that is prevalent in pig populations, with or without diarrhoea. In the present study, a novel EV‐G strain (KOR/KNU‐1811/2018) that resulted from cross‐order recombination was discovered in diagnostic faecal samples from neonatal pigs with diarrhoea that were negative for swine enteric coronaviruses and rotavirus. The recombinant EV‐G genome possessed an exogenous 594‐nucleotide (198‐amino acid) sequence, flanked by two viral 3C^pro cleavage sites at the 5′ and 3′ ends in its 2C/3A junction region. This insertion encoded a predicted protease similar to the porcine torovirus papain‐like cysteine protease (PLCP), which was recently found in the EV‐G1, ‐G2, and ‐G17 genomes. The complete KNU‐1811 genome shared 73.7% nucleotide identity with a prototype EV‐G1 strain, but had 83.9%–86.7% sequence homology with the global EV‐G1‐PLCP strains. Genetic and phylogenetic analyses demonstrated that the Korean recombinant EV‐G's own VP1 and inserted foreign PLCP genes are most closely related independently to contemporary chimeric G1‐PLCP and G17‐PLCP strains respectively. These results implied that the torovirus‐derived PLCP gene might have undergone continuous nucleotide mutations in the respective EV‐G genome following its independent acquisition through naturally occurring recombination. Our results advance the understanding of the genetic evolution of EV‐G driven by infrequent viral recombination events, by which EV‐G populations laterally gain an exotic gene encoding a virulence factor from heterogeneous virus families, thereby causing clinical disease in swine.     

Comparative Analysis of Immune Responses in Pigs to High and Low Pathogenic Porcine Reproductive and Respiratory Syndrome Viruses Isolated in China

The CH‐1a and HuN4 strains of porcine reproductive and respiratory syndrome virus (PRRSV) show different pathogenicities in pigs. To understand host immune responses against these viruses, we investigated the dynamic changes in cytokine levels produced in peripheral blood of piglets infected with the highly pathogenic PRRSV HuN4 strain or the CH‐1a strain. Clinical signs, virus loads and serum cytokine levels [interferon(IFN)‐α, Interleukin (IL)‐1, TNF‐α, IL‐6, IL‐12, IFN‐γ, IL‐10 and TGF‐β] were tested. The results showed that while piglets developed effective cellular immune responses against CH‐1a infection, those infected with HuN4 displayed ineffective cellular immunity, organ lesions and persistent elevated levels of immunoregulatory cytokines (IL‐10 and TGF‐β), which delayed the development of PRRSV‐specific immune responses. These results demonstrated that HuN4 infection induced higher cytokine levels than that of CH‐1a infection induced. The changes in inflammatory cytokines intensified the inflammatory reaction and damaged the tissues and organs.     

Detection of porcine reproductive and respiratory syndrome virus (PRRSV) 1‐7‐4‐type strains in Peru

Porcine reproductive and respiratory syndrome virus (PRRSV) causes significant economic losses to the swine industry worldwide. While PRRSV has been endemic in North America since 1989, it was not until 1999 that the virus was first described in South America. Notably, recently an increased number of PRRSV outbreaks have been reported in South American countries. However, epidemiological information related to these outbreaks is limited and the genetic characteristics of the PRRSV strains circulating in the region are poorly understood. In this study, we describe the genetic analyses of PRRSV strains associated with severe PRRS outbreaks in Peru. Samples originating from 14 farms located in two Departments in Peru (Lima and Arequipa), were subjected to RT‐PCR amplification of the PRRSV ORF5 gene and sequencing followed by restriction fragment length polymorphism (RFLP) analysis. Results demonstrated the circulation of PRRSV‐2 in Peru. Notably ORF5 RFLP typing revealed that 15 (75%) of the PRRSV strains detected in this study belong to the RFLP 1‐7‐4 type. Phylogenetic analysis showed that the Peruvian strains are closely related to the highly virulent PRRSV 1‐7‐4 strains that emerged in the US in 2013–2014. Results here indicate the presence of highly virulent PRRSV 1‐7‐4 strains in Peru and provide important information on the geographical distribution of PRRSV, confirming the recent geographical expansion of this important swine pathogen towards South America.     

A recombination between two Type 1 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV‐1) vaccine strains has caused severe outbreaks in Danish pigs

Porcine reproductive and respiratory syndrome virus (PRRSV) is prevalent in Danish swine herds. In July 2019, PRRSV‐1 was detected in a PRRSV‐negative boar station and subsequently spread to more than 38 herds that had received semen from the boar station. Full genome sequencing revealed a sequence of 15.098 nucleotides. Phylogenetic analyses showed that the strain was a recombination between the Amervac strain (Unistrain PRRS vaccine; Hipra) and the 96V198 strain (Suvaxyn PRRS; Zoetis AH). The major parent was the 96V198 strain that spanned ORFs 1–2 and part of ORF 3 and the minor parent was the Amervac strain, which constituted the remaining part of the genome. The virus seems to be highly transmissible and has caused severe disease in infected herds despite a high level of genetic identity to the attenuated parent strains. The source of infection was presumable a neighbouring farm situated 5.8 km from the boar station.     

Two Commercial Type 1 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV)‐Modified Live Vaccines Reduce Seminal Shedding of Type 1 PRRSV but not Type 2 PRRSV in Infected Boars

The objective of this study was to compare the effects of two commercial type 1 porcine reproductive and respiratory syndrome virus (PRRSV)‐modified live vaccines on type 1 and type 2 PRRSV shedding in the semen of experimentally infected boars. Upon challenge with PRRSV, unvaccinated boars exhibited an increase in daily rectal temperature (39.4–39.7°C). Vaccination of boars with type 1 PRRSV significantly reduced the amount of type 1 PRRSV load in blood and semen after challenge with type 1 PRRSV, but barely reduced the amount of type 2 PRRSV load in blood and semen after the type 2 PRRSV challenge. There were no significant differences in the reduction of viremia and seminal shedding of type 1 and type 2 PRRSV between the two commercial vaccines. The seminal shedding of PRRSV is independent of viremia. The reduction of type 1 PRRSV seminal shedding coincided with the appearance of type 1 PRRSV‐specific interferon‐γ secreting cells (IFN‐γ‐SC) in vaccinated type 1 PRRSV‐challenged boars. The frequencies of type 1 PRRSV‐specific IFN‐γ‐SC induced by type 1 PRRSV vaccine are relatively high compared to type 2 PRRSV‐specific IFN‐γ‐SC induced by the same vaccine which may explain why type 1 PRRSV vaccine is more effective in reducing seminal shedding of type 1 PRRSV when compared to type 2 PRRSV in vaccinated challenged boars. These results provide clinical information on how to reduce seminal shedding of type 1 PRRSV in boars using type 1 PRRSV‐modified live vaccine.     

Novel goose parvovirus in domestic Linwu sheldrakes with short beak and dwarfism syndrome,China

Recently, short beak and dwarfism syndrome (SBDS) had a sudden outbreak in Cherry Valley duck flocks, followed by Pekin ducks and mule ducks in various regions of mainland China. This widely spreading infectious disease was characterized by growth retardation, smaller beak and tarsus with high morbidity and low mortality rate. In this study, we identified and characterized virus from domestic Linwu sheldrakes (namely as HuN18) with SBDS. HuN18 isolates shared high nucleotide identity with novel goose parvovirus (N‐GPV). A 5110‐nucleotide full‐length genome sequence of HuN18 was found with no deletion in ITR region. Alignment studies of HuN18 showed 96.8%–99.0% identity with other N‐GPVs and 92.9%–96.3% identity with classic GPV. According to the recombination analysis, HuN18 showed the potential major parent was the N‐GPV sdlc01 strain, the potential minor parent was the classical GPV Y strain, and the secondary potential minor parent was the SYG61v strain. To the best of our knowledge, this is the first report of N‐GPV in domestic Linwu sheldrakes with SBDS; these data provide evidence that attenuated live viruses are involved in genetic recombination with prevailing wild parvoviruses, which contributes to the novel emerging variants of waterfowl parvoviruses.     

Development of universal and quadruplex real‐time RT‐PCR assays for simultaneous detection and differentiation of porcine reproductive and respiratory syndrome viruses

Porcine reproductive and respiratory syndrome virus 1 (PRRSV1) and 2 (PRRSV2) (including 3 major subtypes: classical (CA‐PRRSV2), highly pathogenic (HP‐PRRSV2) and NADC30‐like (NL‐PRRSV2)) are currently coexisting in Chinese swine herds but with distinct virulence. Reliable detection and differentiation assays are crucial to monitor the prevalence of PRRSV and to adopt effective control strategies. However, current diagnostic methods cannot simultaneously differentiate the four major groups of PRRSV in China. In this study, universal and quadruplex real‐time RT‐PCR assays using TaqMan‐MGB probes were developed for simultaneous detection and differentiation of Chinese PRRSV isolates. The newly developed real‐time RT‐PCR assays exhibited good specificity, sensitivity, repeatability and reproducibility. In addition, the newly developed real‐time RT‐PCR assays were further validated by comparing with a universal PRRSV conventional RT‐PCR assay on the detection of 664 clinical samples collected from 2016 to 2019 in China. Based on the clinical performance, the agreements between the universal and quadruplex real‐time RT‐PCR assays and the conventional RT‐PCR assay were 99.55% and 99.40%, respectively. Totally 90 samples were detected as PRRSV‐positive, including 2 samples that were determined to be co‐infected with NL‐PRRSV2 and HP‐PRRSV2 isolates by the quadruplex real‐time RT‐PCR assay. ORF5 sequencing confirmed the real‐time RT‐PCR results that 2, 6, 27 and 57 of the 92 sequences were PRRSV1, CA‐PRRSV2, NL‐PRRSV2 and HP‐PRRSV2, respectively. This study provides promising alternative tools for simultaneous detection and differentiation of PRRSV circulating in Chinese swine herds.     

Natural viral co‐infections in pig herds affect hepatitis E virus (HEV) infection dynamics and increase the risk of contaminated livers at slaughter

Hepatitis E virus (HEV) is a zoonotic pathogen, in particular genotype 3 HEV is mainly transmitted to humans through the consumption of contaminated pork products. This study aimed at describing HEV infection patterns in pig farms and at assessing the impact of immunomodulating co‐infections namely Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Porcine Circovirus Type 2 (PCV2), as well as other individual factors such as piglets’ immunity and litters’ characteristics on HEV dynamics. A longitudinal follow‐up was conducted in three farrow‐to‐finish farms known to be HEV infected. Overall, 360 piglets were individually monitored from birth to slaughter with regular blood and faecal sampling as well as blood and liver samples collected at slaughterhouse. Virological and serological analyses were performed to detect HEV, PCV2 and PRRSV genome and antibodies. The links between 12 explanatory variables and four outcomes describing HEV dynamics were assessed using cox‐proportional hazard models and logistic regression. HEV infection dynamics was found highly variable between farms and in a lower magnitude between batches. HEV positive livers were more likely related to short time‐intervals between HEV infection and slaughter time (<40 days, OR = 4.1 [3.7–4.5]). In addition to an influence of piglets' sex and sows' parity, the sequence of co‐infections was strongly associated with different HEV dynamics: a PRRSV or PCV2/PRRSV pre‐ or co‐infection was associated with a higher age at HEV shedding (Hazard Ratio = 0.3 [0.2–0.5]), as well as a higher age at HEV seroconversion (HR = 0.5 [0.3–0.9] and HR = 0.4 [0.2–0.7] respectively). A PCV2/PRRSV pre‐ or co‐infection was associated with a longer duration of shedding (HR = 0.5 [0.3–0.8]). Consequently, a PRRSV or PCV2/PRRSV pre‐ or co‐infection was strongly associated with a higher risk of having positive livers at slaughter (OR = 4.1 [1.9–8.9] and OR = 6.5 [3.2–13.2] respectively). In conclusion, co‐infections with immunomodulating viruses were found to affect HEV dynamics in the farrow‐to‐finish pig farms that were followed in this study.     

Epidemiologic and Phylogenetic Characteristics of Porcine Reproductive and Respiratory Syndrome Viruses in Conventional Swine Farms of Jeju Island as a Candidate Region for PRRSV Eradication

Jeju island is the biggest island in Korea. The imports of pigs or their relatives from mainland Korea to this island has been banned since 1998. With this unique geographical and epidemiological context, epidemiology of porcine reproductive and respiratory syndrome virus (PRRSV) was investigated on the island. While all investigated farms showed 100% of seropositive rate for PRRSV, pigs on 37.2% (16/43) of the farms had viremia with type II PRRSV. The seropositive and viremia‐positive rates for PRRSV in 30‐ to 60‐day‐old pigs were significantly higher in the western area (‘swine farm complex’ area) than the eastern area (‘Scattered swine farm’ area) of Jeju island. When 21 ORF5 sequences obtained from viremic sera were phylogenetically analysed, lineage 5 and Kor (newly termed in this study) of type II PRRSV were only found in Jeju island without changes from a previous report (2002–2003). Because other lineages of type II PRRSV (lineage 1 and 3) and type I PRRSV have recently emerged in mainland Korea, the banning of pigs’ movement might be effective to protect the island from the introduction of these new PRRSV genotypes. Under this epidemiological condition (no introduction of new strains except for the modified‐live vaccine (MLV) strain), the positive selection sites were analysed based on ORF5 of the virus. The amino acid 58 of GP5 (located on the hypervariable region) was predicted as a strong positive selection site. Although 51.2% (22/43) of the investigated farms had applied MLV, field strains of type II PRRSV were still circulating with strong positive selection. However, the restricted population of type II PRRSV (lineage 5 and Kor) without introduction of type I PRRSV or the other lineages of type II PRRSV indicate that the island has an effective quarantine system, which would allow PRRSV eradication.     

A Bayesian Phylogeographical Analysis of Type 1 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV)

Understanding viral transmission is an important factor for the effective prevention one of the most devastating swine diseases, porcine reproductive and respiratory syndrome. Focusing on molecular epidemiology of type 1 PRRSV, this study analysed a large ORF5 dataset collected worldwide from 1991 to 2012 using a coalescent‐based Bayesian Markov chain Monte Carlo approach. The results suggested that the virus diversified into unique subpopulations in Russia & Belarus and Italy approximately 100 years ago. Previously unreported consecutive diffusions of the virus were identified, which showed that some countries, such as Spain and Germany, acted as distribution sources to some extent. This study also provided statistical evidence for the existence of an ORF5‐based phylogeographical structure of type 1 PRRSV, in which the virus tended to cluster by geographical locations more tightly than expected by chance. In contrast to this tight geographical structure, the evolution of the ORF5 gene, based on mapping of non‐synonymous/synonymous substitutions, was best described by a non‐homogeneous process that could be implicated as a mechanism for viral immune evasion.     

HoBi‐like is the most prevalent ruminant pestivirus in Northeastern Brazil

The ruminant pestiviral species BVDV ‐1, BVDV ‐2 and BDV , along with the putative species HoBi‐like, may cause substantial economic losses in cattle, sheep and goats. Brazil's large size, variable biomes and wide range of ruminant animal production within different geographic regions suggest that the presence and prevalence of ruminant pestivirus may differ by regions within Brazil. This study investigated the genetic diversity of ruminant pestiviruses and determined the frequency of active infections within two states of the Northeast Region of Brazil, Maranhão and Rio Grande do Norte. Serum samples from 16,621 cattle and 2,672 small ruminants from 569 different herds residing in this region were tested by RT ‐PCR followed by DNA sequencing. Seventeen positive cattle were detected (0.1%) from fifteen different herds (2.64%). All isolates were classified as HoBi‐like pestiviruses based on phylogenetic analysis. All small ruminant samples tested negative. The findings presented herein suggest that the Northeast Region of Brazil has a uniquely high prevalence of HoBi‐like viruses. The increasing reports of HoBi‐like viruses detected in cattle in the field suggest that natural infection with these viruses may be more widespread than previously thought. The identification of HoBi‐like viruses as the most prevalent type of ruminant pestivirus circulating in the Northeast Region of Brazil indicates the need for both continued monitoring and determination of the extent of economic losses associated with HoBi‐like virus infections. In addition, it must be taken into account in the choice of diagnostic tests and in vaccine formulations.