The first detection of Senecavirus A in pigs in Thailand, 2016

We report the first detection of Senecavirus A (SVA ) in nine of 12 (75%) pigs in Thailand in 2016. The full‐length genome demonstrated that Thai SVA isolates were closely related to the first Canada strain (11‐55910‐3) than the recent strains causing outbreaks in Brazil, the United States and China in 2015–2016.     

The First Identification and Complete Genome of Senecavirus A Affecting Pig with Idiopathic Vesicular Disease in China

Senecavirus A (SVA) infection was recently confirmed in pigs in Brazil. In March, 2015, an outbreak of vesicular disease occurred in Guangdong, China, characterized by vesicular lesions in sows and acute death of neonatal piglets. Cumulative incidence of porcine idiopathic vesicular disease in farm A was 258, which had a total number of 5500 sows. Sows in farm B displayed typical vesicular symptoms by May, 2015, which also had 5500 sows. A total of 278 and 142 of 5500 sows in farm B demonstrated lame and presented vesicles, respectively, associated with a total of 186 mortality in piglets. Routine differential diagnoses for swine vesicular disease were carried out to exclude infection with foot‐and‐mouth disease virus, swine vesicular disease virus, vesicular exanthema of swine virus and vesicular stomatitis virus. In this study, seven pairs of primer were designed to amplify the complete genome of SVA in RT‐PCR assays. Sequence alignment showed that this Chinese strain shares 94.4–97.1% sequence identity to other eight strains of SVA. This is the first report of SVA in China and provides information about the association between SVA infection and vesicular disease.     

Systematic Epidemiological Investigations of Cases of Senecavirus A in US Swine Breeding Herds

Epidemiological investigations were conducted on a case series of six Senecavirus A (SVA)‐affected breeding herds in the United States to determine potential routes of introduction and enhance the swine industry's knowledge of SVA's clinical presentation and spread. Each SVA‐affected herd was evaluated using a standard form to ensure that all relevant data were collected. The form was used to guide a detailed discussion about the clinical presentation of SVA and risk events that occurred in the 4 weeks prior to the first observation of clinical signs with the herd veterinarian and farm personnel. Each event was then subjectively assigned a risk level of low, medium or high likelihood for SVA introduction by the investigation team. The clinical presentation of SVA varied by case. All SVA‐affected herds (six of six) reported increases in pre‐weaning mortality and sow anorexia. Vesicular lesions were observed in four of six herds, and mild‐to‐moderate neonatal diarrhoea was observed in three of six herds. No gross anatomic or histologic lesions were observed in neonatal pigs that tested positive for SVA via PCR. Multiple potential routes of introduction were identified. Events subjectively rated as high risk for SVA introduction were on‐farm employee entry (six of six), carcass disposal (four of six), cull sow removal (three of six) and breeding replacement entry (two of six). Non‐swine domestic animals, rodents, other visitors, repairs outside swine barns, feed delivery, weaned pig removal and semen entry were assigned a high risk level in one of six herds. Cases occurred in breeding herds of all sizes with variable biosecurity in both swine dense and swine sparse areas.     

Identification and genomic characterization of the emerging Senecavirus A in southeast China, 2017

Senecavirus A (SVA ) is an emerging non‐enveloped virus with a single‐stranded, positive‐sense RNA genome that belongs to the Senecavirus genus in the Picornaviridae family. Senecavirus A‐associated swine idiopathic vesicular disease and epidemic transient neonatal losses have caused substantial economic losses for the swine industry. Here, we describe a case of re‐emerging vesicular disease among sows and finishing pigs on a swine farm in Fujian Province of southeast China. Other causative pathogens, including FMDV , SVDV and VSV , were excluded, and a novel SVA strain, CH ‐FJZZ ‐2017, was isolated. Sequencing and phylogenetic analysis of the complete genome and individual viral proteins revealed that CH ‐FJZZ ‐2017 is closely related to the US strains in 2015. The results further showed that Chinese SVA s have formed two distinct subclades with 2016 as the turning point. Viruses causing outbreaks after late 2016 shared higher nucleotide identities with the US strains in 2015. There is still some evolutionary distance between CH ‐FJZZ ‐2017 and other strains isolated in late 2016, suggesting that Chinese SVA isolates have been evolving in different directions. This study provides a basis for the development of effective prevention and control strategies.     

Phylogenetic and genome analysis of seven senecavirus A isolates in China

Senecavirus A (SVA) is the only member of genus Senecavirus that causes vesicular lesions in pigs. We have characterized seven SVA isolates from different swine farms in Guangdong, China. The most variable isolate, CH‐DL‐01‐2016, contained a single amino acid insertion at position 219–220 and a 16 amino acid insertion at position 250–251. The VP1 protein also had four nucleotide changes when compared to 31 other SVA VP1 sequences obtained from GenBank. These mutations have not been identified before. Phylogenetic trees demonstrated that the new SVA isolates were clustered into two different clades and shared 96.3%–97.1% similarity with US strains and 97.9%–98.3% similarity with Brazilian stains on nucleotide level, respectively. Prediction of antigenic epitope indicated that SVA VP1 protein contained both potential B‐cell and potential T‐cell epitopes. This report provides information about variation analysis in SVA in southern China.     

Origin and epidemic status of porcine epidemic diarrhea virus variants in China

From 2010, porcine epidemic diarrhea virus (PEDV) variants caused sequential outbreaks of disease in Asia and the United States. In this retrospective study, 49 complete spike (S) gene sequences were obtained from PEDV strains collected in China from 2014 to 2016. We observed that variant PEDV strains with novel insertions, deletions, and multiple S gene recombination types were present in China. In addition, mixed infections involving different variant strains were observed in some areas. Based on phylogenetic and recombination analyses, we determined that the newly emerged PEDV variants potentially originated via recombination between the earliest Chinese G1 genogroup strain, JS‐2004‐2 and earlier Korean pandemic strains. These findings provide important information for understanding ongoing PEDV outbreaks and suggest that novel variants make it more difficult to prevent PEDV infection.     

Detection and genome sequencing of porcine circovirus 3 in neonatal pigs with congenital tremors in South China

Porcine circovirus 3 (PCV3) is a novel circovirus first discovered in the United States in piglets and sows with porcine dermatitis and nephropathy syndrome, reproductive failure, cardiac and multisystemic inflammation. Here, seven PCV3 strains were identified for the first time from neonatal pigs with clinical signs of congenital tremors (CT) in South China. The tissue tropism of PCV3 in CT‐affected piglets was analysed by the real‐time quantitative PCR, and the result showed that high loads of viral genomes were detected in the brains and hearts. The complete genomes of seven new PCV3 revealed 96.8%–99.6% nucleotide identities with eleven other PCV3 strains previously reported from the United States and China. Phylogenetic analysis based on the complete genome sequences showed that all PCV3 strains clustered together and were clearly separated from other circovirus species. This study reports on the first identification of PCV3 in CT‐affected newborn piglets and provides the epidemiological information of neonatal piglets with CT in Guangdong and Guangxi Provinces of China.     

Isolation and Characterization of Madariaga Virus from a Horse in Paraíba State,Brazil

Madariaga virus (MADV), the new species designation for the South American isolates of eastern equine encephalitis virus (EEEV), is genetically divergent and substantially different in ecology and pathogenesis from North American EEEV strains. We isolated and characterized a MADV isolate obtained from a horse in Brazil. Our results support previous phylogenetic studies showing there are three genetically distinct MADV lineages. The MADV isolate from Paraíba State belongs to the South American lineage III and is closely related to Peruvian, Colombian and Venezuelan isolates.     

Evidence of viral survival in representative volumes of feed and feed ingredients during long-distance commercial transport across the continental United States

The hypothesis that feed ingredients could serve as vehicles for the transport and transmission of viral pathogens was first validated under laboratory conditions. To bridge the gap from the laboratory to the field, this current project tested whether three significant viruses of swine could survive in feed ingredients during long-distance commercial transport across the continental US. One-metric tonne totes of soybean meal (organic and conventional) and complete feed were spiked with a 10 ml mixture of PRRSV 174, PEDV and SVA and transported for 23 days in a commercial semi-trailer truck, crossing 29 states, and 10,183 km. Samples were tested for the presence of viral RNA by PCR, and for viable virus in soy-based samples by swine bioassay and in complete feed samples by natural feeding. Viable PRRSV, PEDV and SVA were detected in both soy products and viable PEDV and SVA in complete feed. These results provide the first evidence that viral pathogens of pigs can survive in representative volumes of feed and feed ingredients during long-distance commercial transport across the continental United States.     

Genetically divergent porcine sapovirus identified in pigs,United States

Porcine sapoviruses (SaVs) are genetically diverse and widely distributed in pig‐producing countries. Eight genogroups of porcine SaV have been identified, and genogroup III is the predominant type. Most of the eight genogroups of porcine SaV are circulating in the United States. In the present study, we report detection of porcine SaVs in pigs at different ages with clinical diarrhoea using next‐generation sequencing and genetic characterization. All seven cases have porcine SaV GIII strains detected and one pooled case was found to have a porcine SaV GVI strain IA27912‐B‐2018. Sequence analysis showed that seven GIII isolates were genetically divergent and formed four different lineages on the trees of complete genome, RdRP, VP1 and VP2. In addition, these seven GIII isolates had three different deletion/insertion patterns in an identified variable region close to the 3′ end of VP2. The GVI strain IA27912‐B‐2018 was closely related to strains previously detected in the United States and Japan. A 3‐nt deletion in VP1 region of GVI IA27912‐B‐2018 was identified. Our study showed that genetically divergent SaVs of different genogroups are co‐circulating in pigs in the United States. Future studies comparing the virulence of these different genogroups in pigs are needed to better understand this virus and to determine if surveillance and vaccine development are needed to monitor and control porcine SaVs.     

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.     

Emergence of a virulent porcine reproductive and respiratory syndrome virus in Taiwan in 2018

In March 2018, an abortion storm caused by porcine reproductive and respiratory syndrome virus was confirmed in a farrow‐to‐finish pig herd in Taiwan. Open reading frame 5 and non‐structural protein 2 of the virus confirmed that the virus is closely related to the virulent strains circulating in the United States.     

Experimental Infection of Young Pigs with an Early European Strain of Porcine Epidemic Diarrhoea Virus and a Recent US Strain

Outbreaks of porcine epidemic diarrhoea (PED) were reported across Europe during the 1980s and 1990s, but only sporadic outbreaks occurred in recent years. PED virus (PEDV) spread for the first time into the USA in 2013 and has caused severe economic losses. Retrospectively, it was found that two different strains of PEDV have been introduced into the United States, both are closely related to strains circulating in China where a new wave of the disease occurred from 2010 onwards. Since autumn 2014, new outbreaks of PED have occurred in Europe. In this study, weaned piglets were inoculated with an early European isolate (Br1/87) or faecal/intestinal suspensions derived from pigs infected with a recent European strain of PEDV (from Germany) or a US strain of PEDV. No evidence for infection resulted from inoculation of pigs with the German sample that contained high levels of PEDV RNA; there were no clinical signs, excretion of viral RNA or anti‐PEDV antibody production. In contrast, all the pigs in the other two groups showed evidence of infection. Mild clinical signs of disease, mainly diarrhoea, occurred in piglets inoculated with the Br1/87 and US PEDV strains. PEDV RNA was detected throughout the intestine in euthanized animals at 4 days post‐inoculation. In addition, within these animals, low levels of viral RNA were detected in lungs and livers with higher levels in spleens. Seroconversion against PEDV occurred in all surviving infected animals within 10 days. PEDV RNA excretion occurred for at least 2 weeks. The US PEDV RNA was detected at low levels in serum samples on multiple days. It is apparent that current diagnostic systems can detect infection by the different virus strains.     

Diagnostic specificity of the African swine fever virus antibody detection enzyme‐linked immunosorbent assay in feral and domestic pigs in the United States

African swine fever (ASF) is a highly contagious haemorrhagic disease of pigs that has the potential to cause mortality nearing 100% in naïve animals. While an outbreak of ASF in the United States’ pig population (domestic and feral) has never been reported, an introduction of the disease has the potential to cause devastation to the pork industry and food security. During the recovery phase of an outbreak, an antibody detection diagnostic assay would be required to prove freedom of disease within the previously infected zone and eventually nationwide. Animals surviving an ASF infection would be considered carriers and could be identified through the persistence of ASF viral antibodies. These antibodies would demonstrate exposure to the disease and not vaccination, as there is no ASF vaccine available. A well‐established commercial enzyme‐linked immunosorbent assay (ELISA) detects antibodies against ASF virus (ASFV), but the diagnostic specificity of the assay had not been determined using serum samples from the pig population of the United States. This study describes an evaluation of the World Organization for Animal Health (OIE)‐recommended Ingezim PPA COMPAC ELISA using a comprehensive cohort (n = 1791) of samples collected in the United States. The diagnostic specificity of the assay was determined to be 99.4% (95% confidence interval (CI): [98.9, 99.7]). The result of this study fills a gap in understanding the performance of the Ingezim PPA COMPAC ELISA in the ASF naïve pig population of the United States.     

Porcine sapelovirus among diarrhoeic piglets in India

Porcine sapelovirus (PSV ) A belongs to the genus Sapelovirus, family Picornaviridae. PSV infections in pigs have been reported from European countries, United States, Japan, China, Korea and Brazil. The virus has been isolated/detected from faeces of healthy pigs as well as those affected with diarrhoea, respiratory signs, encephalitis, skin lesions and fertility disorders. This study was planned to investigate whether PSV is prevalent among pigs in India and to characterize PSV encountered in the study population. The study revealed that five of 70 (7.14%) faecal samples were found positive for PSV using RT ‐PCR . Three viruses were successfully isolated from faecal samples using IB ‐RS ‐2 cell line. Complete genome sequencing and analysis of one Indian PSV isolate revealed highest homology (88%) with V13 strain from England. Phylogenetic analysis of the complete polyprotein nucleotide sequences of 14 strains of PSV classified the viruses into four distinct clades. This first report from India adds to our knowledge on genetic diversity of PSV detected so far among pigs in different countries. A large‐scale surveillance of the virus is required to understand its genomic diversity and economic impact.     

Semi‐quantitative duplex RT‐PCR reveals the low occurrence of Porcine Pegivirus and Atypical Porcine Pestivirus in diagnostic samples from the United States

Porcine Pegivirus (PPgV) and Atypical Porcine Pestivirus (APPV) are two recently identified porcine viruses. In this study, the identification of two viruses by metagenomic sequencing, and a duplex semi‐quantitative RT‐PCR was developed to detect these pathogens simultaneously. The PPgV strain Minnesota‐1/2016 had a 95.5%–96.3% nucleotide identity and clustered with the recently identified US PPgV strains, which is a distant clade from the German PPgV strains. The APPV strain Minnesota‐1/2016 shared an 87.3%–92.0% nucleotide identity with the other global APPV strains identity but only shared an 82.8%–83.0% nucleotide identity with clade II consisting of strain identified in China. Detection of both PPgV and APPV was 9.0% of the diagnostic cases. Co‐infection of PPgV and APPV was identified in 7.5% of the diagnostic cases. The occurrence and genetic characterization of PPgV and APPV further enhance our knowledge regarding these new pathogens in the United States.     

Kidney transplant graft outcomes in 379 257 recipients on 3 continents

Kidney transplant outcomes that vary by program or geopolitical unit may result from variability in practice patterns or health care delivery systems. In this collaborative study, we compared kidney graft outcomes among 4 countries (United States, United Kingdom, Australia, and New Zealand) on 3 continents. We analyzed transplant and follow‐up registry data from 1988‐2014 for 379 257 recipients of first kidney‐only transplants using Cox regression. Compared to the United States, 1‐year adjusted graft failure risk was significantly higher in the United Kingdom (hazard ratio [HR] 1.22, 95% confidence interval [CI] 1.18‐1.26, P < .001) and New Zealand (hazard ratio [HR] 1.29, 95% confidence interval [CI] 1.14‐1.46, P < .001), but lower in Australia (HR 0.90, 95% CI 0.84‐0.96, P = .001). In contrast, long‐term adjusted graft failure risk (conditional on 1‐year function) was significantly higher in the United States compared to Australia, New Zealand, and the United Kingdom (HR 0.74, 0.75, and 0.74, respectively; each P < .001). Thus long‐term kidney graft outcomes are approximately 25% worse in the United States than in 3 other countries with well‐developed kidney transplant systems. Case mix differences and residual confounding from unmeasured factors were found to be unlikely explanations. These findings suggest that identification of potentially modifiable country‐specific differences in care delivery and/or practice patterns should be sought.     

Detection and phylogenetic analysis of porcine circovirus type 3 in central China

Porcine circovirus type 3 (PCV3) is the pathogen responsible for a new infectious disease that was first reported in 2016 in the United States. To further investigate the epidemic profile and genetic diversity of the virus, one hundred and seventy clinical samples (110 tissue samples and 60 serum samples) were collected from 41 different pig farms in 14 cities in central China, and a SYBR Green I‐based quantitative real‐time PCR method was developed to detect PCV3. The partial cap genes of four field strains from four different farms were sequenced and analysed. The results showed the detection limit was 2.19 × 10¹ genome copies/μl. Fifty‐three of 170 samples were detected as positive for PCV3, giving a PCV3‐positive rate of 31.18%, with 48.78% (20/41) of pig farms harbouring PCV3, which varied from 20% to 42.86% between 2013 and 2017. PCV3 could be detected in samples from pigs with different clinical presentations, and the PCV3‐positive rates varied for these different clinical presentations. The partial capsid genes of four PCV3 strains (designated YZ, LY‐03, NY and SP) shared 96.3%–99.4% nucleotide identity with those available in GenBank. Phylogenetic analysis based on the capsid gene of 32 PCV3 strains showed that the four PCV3 strains in this study were clustered with the China/GD2016 and South Korea Ku‐1606 strains. The results of this study will aid our understanding of the molecular epidemiology of PCV3.