Detection and genetic characterization of a novel pig astrovirus: relationship to other astroviruses

Impact of duck astrovirus on susceptibility to infection across duck ages

An outbreak of duck astrovirus (DAstV) has occurred in duck farming regions of China, causing substantial economic setbacks in the duck industry. This investigation aimed to examine the variations in DAstV pathogenicity among ducks at different age intervals. Infections were induced in ducks at distinct age groups (1, 7, 14, 21, and 28 d) utilizing the DAstv-1-GDB-2022 strain. The results indicate increased pathogenicity of the DAstv-1-GDB-2022 strain in ducklings aged 21 to 28 d, manifesting as liver and kidney enlargement, severe bleeding, and potential fatalities. Conversely, ducklings aged 1 and 14 d displayed milder symptoms postinfection. Notably, viral shedding continued in ducks of diverse age groups even 21 d postinfection (Dpi). Moreover, DAstV replicates in various tissues, predominantly affecting the liver. Immunohistochemical tests using rabbit anti-DAstV antibodies revealed robust positive signals in both the liver and kidneys, which correlated with the clinical symptom severity observed through macroscopic and microscopic examinations. Serum biochemical assays and indirect ELISA demonstrated a consistent response to DAstV infection across different age groups, with older ducklings exhibiting increased sensitivity. In conclusion, this study successfully replicated clinical symptoms similar to those of natural DAstV infection using the DAstv-1-GDB-2022 strain. Importantly, we systematically delineated the differences in susceptibility to DAstV among ducks at various ages, laying the foundation for further research into the pathogenic mechanisms of DAstV and potential vaccine development.

Replication of Porcine Astrovirus Type 1-Infected PK-15 Cells In Vitro Affected by RIG-I and MDA5 Signaling Pathways

The interferon (IFN) system is an extremely powerful antiviral response in animal cells. The subsequent effects caused by porcine astrovirus type 1 (PAstV1) IFN activation are important for the host's response to viral infections. Here, we show that this virus, which causes mild diarrhea, growth retardation, and damage of the villi of the small intestinal mucosa in piglets, induces an IFN response upon infection of PK-15 cells. Although IFN-β mRNA was detected within infected cells, this response usually occurs during the middle stages of infection, after genome replication has taken place. Treatment of PAstV1-infected cells with the interferon regulatory factor 3 (IRF3) inhibitor BX795 decreased IFN-β expression, whereas the nuclear factor kappa light chain enhancer of activated B cells (NF-κB) inhibitor BAY11-7082 did not. These findings indicate that PAstV induced the production of IFN-β via IRF3-mediated rather than NF-κB-mediated signaling pathways in PK-15 cells. Moreover, PAstV1 increased the protein expression levels of retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5) in PK-15 cells. The knockdown of RIG-I and MDA5 decreased the expression levels of IFN-β and the viral loads and increased the infectivity of PAstV1. In conclusion, PAstV1 induced the production of IFN-β via the RIG-I and MDA5 signaling pathways, and the IFN-β produced during PAstV1 infection inhibited viral replication. These results will help provide new evidence that PAstV1-induced IFNs may protect against PAstV replication and pathogenesis. IMPORTANCE Astroviruses (AstVs) are widespread and can infect multiple species. Porcine astroviruses produce mainly gastroenteritis and neurological diseases in pigs. However, astrovirus-host interactions are less well studied, particularly with respect to their antagonism of IFN. Here, we report that PAstV1 acts via IRF3 transcription pathway activation of IFN-β. In addition, the knockdown of RIG-I and MDA5 attenuated the production of IFN-β induced by PAstV1 in PK-15 cells and increased efficient viral replication in vitro. We believe that these findings will help us to better understand the mechanism of how AstVs affect the host IFN response.

Multiplex gel-based PCR assay for the simultaneous detection of 5 genotypes of porcine astroviruses

Porcine astrovirus (PAstV) has been associated experimentally with diarrhea in piglets, but much more knowledge is needed about this virus. PAstV has high genetic variability, and 5 genotypes have been identified, namely PAstV1-5. To obtain information on the epidemiology of PAstV, we established a multiplex PAstV PCR assay to detect and differentiate the 5 PAstV genotypes simultaneously. The assay utilized specific primers for each genotype, producing fragments of 307, 353, 205, 253, and 467 bp, representing PAstV1-5, respectively. Our multiplex PCR assay amplified all 5 DNA fragments from single or mixed viral genomes without cross-reactions with other PAstV genotypes or other viruses in pigs. The limit of detection of the multiplex PCR assay was 5 × 102 copies/μL for PAstV1 and PAstV4, and 5 × 103 copies/μL for PAstV2, PAstV3, and PAstV5. We examined 76 pig fecal specimens with our multiplex PCR assay. PAstV was detected in 36 of 76 (47.4%) samples; ≥2 PAstVs were found in 20 of 76 (26.3%) samples. The multiplex PCR assay results were essentially the same as the results using a monoplex PAstV PCR assay, with a coincidence rate of >96%. Our multiplex PCR method provides a simple, sensitive, and specific detection tool for PAstV detection and epidemiologic surveys.

Diversity of Astrovirus in Goats in Southwest China and Identification of Two Novel Caprine Astroviruses

A total of 232 goat fecal samples (124 diarrheic and 108 nondiarrheic) collected from 12 farms in Southwest China were tested for astrovirus using RT-PCR. A total of 16.9% (21/124) of diarrheic and 20.4% (22/108) of nondiarrheic samples were astrovirus-positive, and no statistical difference was found in the detection rate between healthy and sick goats. Furthermore, 28 obtained complete ORF2 sequences could be classified into six genotypes according to the species classification criteria of the International Committee on Taxonomy of Viruses (ICTV). It is worth noting that, in addition to four known caprine astrovirus genotypes (MAstV-33, MAstV-34, Caprine Astrovirus G5.1, and Caprine Astrovirus G3.1), MAstV-13 and MAstV-24 genotypes were identified in goats. Interestingly, five of 19 ORF2 sequences in the Caprine Astrovirus G3.1 genotype showed possible intragenotypic recombination events. Furthermore, nearly complete caprine astrovirus genomes of MAstV-13 and MAstV-24 genotypes were obtained. The genome of the SWUN/ECJK3/2021 strain shared the highest similarity (62.0% to 73.9%) with astrovirus in MAstV-13, and clustered in the so-called human-mink-ovine (HMO) clade, which contained the majority of the neurotropic astrovirus strains. Moreover, the SWUN/LJK2-2/2020 strain showed the highest similarity (69.7% to 78.6%) and the closest genetic relationship to the known porcine and bovine astroviruses in MAstV-24. In conclusion, this study confirmed six genotypes of astrovirus circulating among goats in Southwest China, including MAstV-13 and MAstV-24 genotypes. These findings enhance our knowledge of the prevalence and diversity of astroviruses. IMPORTANCE Caprine astrovirus is a newly emerging virus, and information regarding its prevalence and molecular characteristics remains limited. In this study, six genotypes of astrovirus, including MAstV-13 and MAstV-24, were identified in goats, adding two novel caprine astrovirus genotypes to the four previously known genotypes, thereby enriching the diversity of the caprine astrovirus. Moreover, genomes of MAstV-13 SWUN/ECJK3/2021 and MAstV-24 SWUN/LJK2-2/2020 strains were obtained from goats, which aids in the understanding of the infection spectrum and host range of the two genotypes. This study is the first to demonstrate the presence of neurotropic-like astrovirus (MAstV-13) in goats, which has significant implications for the diagnosis of neurological diseases in goats.

Case Report: First Report and Phylogenetic Analysis of Porcine Astroviruses in Chile

Porcine Astrovirus (PoAstV) causes mild diarrhea in young pigs and is considered an emerging virus in the swine industry worldwide. PoAstV has high genetic diversity and has been classified into five genetic lineages, PoAstV1–5. In Chile, only human astroviruses have been reported. This study aimed to determine the presence and genetic diversity of PoAstV circulating in intensive pig farms in Chile. Seventeen Chilean intensive swine farms from Valparaíso, Metropolitana, O'Higgins, Ñuble and Araucanía regions were sampled. A selection of oral fluid and fecal material samples from 1–80 days-old pigs were collected and analyzed using next-generation sequencing. The circulation of PoAstV was confirmed in all studied farms. We obtained complete or partial sequences of PoAstV-2 (n = 3), PoAstV-4 (n = 2), and PoAstV-5 (n = 7). In 15 out of 17 farms, we detected more than one lineage co-circulating. Phylogenetic analyses grouped the seven PoAstV-5 strains in a monophyletic cluster, closely related to the United States PoAstV-5 strains. The three PoAstV-2 were located into two separate sub-clusters. PoAstV-4 sequences are also grouped in two different clusters, all related to Japanese strains. Thus, our results indicate that PoAstV circulates in Chile with high frequency and diversity. However, the lack of reference sequences impairs local evolution patterns establishment and regional comparisons. This is the first contribution of PoAstV genomes in Latin America; more studies are needed to understand the diversity and impact of PoAstV on swine health.

Epidemiological investigation and genetic characterization of porcine astrovirus genotypes 2 and 5 in Yunnan province, China

Astroviruses (AstVs) are among the most important viruses causing diarrhea in human infants and many animals, posing a threat to public health safety and a burden on the economy. Five porcine AstV (PAstV) genotypes have been identified in various countries, including China. However, the epidemiology of PAstV in Yunnan province, China, remains unknown. In this study, 489 fecal samples from pigs in all 16 prefectures/cities of Yunnan were collected between April and August of 2020 for epidemiological investigation. The total infection rate of PAstV-2 or PAstV-5 was 39.9%, with suckling piglets having the highest infection rate (62.3%). The ORF2 genes of seven PAstV-2 and 10 PAstV-5 isolates were sequenced and phylogenetically analyzed. In addition to coinfections with PAstV-2 and PAstV-5, coinfections of PAstV with other diarrhea-inducing viruses (e.g., porcine bocavirus) were also discovered. A comparison of ORF2-encoded capsid protein sequences revealed that there were multiple insertions and deletions in the seven Yunnan PAstV-2 sequences, while point mutations, but no deletions or insertions, were found in the 10 Yunnan PAstV-5 sequences, which were very similar to the reference sequences. This is the first epidemiological investigation and genetic characterization of PAstV-2 and PAstV-5 in Yunnan province, China, demonstrating the current PAstV infection situation in Yunnan.

Molecular detection and characterization reveals circulation of multiple genotypes of porcine astrovirus in Haryana, India

Porcine astrovirus (PAstV) is distributed worldwide and has been reported to cause diarrhea in pigs. PAstV belongs to the family Astroviridae and genus Mamastrovirus. PAstVs are divided into five diverse genotypes (PAstV1-PAstV5) on the basis of phylogenetic analysis of a part of the RNA-dependent RNA polymerase (RdRp) gene and the capsid gene. However, knowledge regarding the clinical significance and molecular characteristics of PAstV in Haryana, India, is limited. In this study, we investigated the presence of PAstV by RT-PCR of the partial RdRp gene in 110 rectal swabs collected from diarrheic pigs in different parts of Haryana, India. Of these, 35 samples (31.8%) tested positive for PAstV, with the highest positivity observed among weaning piglets 3 to 9 weeks of age (47.7%, 21/44), followed by fattening pigs 9 to 24 weeks of age (28.5%, 8/28). Phylogenetic analysis of the partial RdRp gene revealed circulation of four different genotypes (PAstV1, PAstV2, PAstV4, and PAstV5) in Haryana, with PAstV1 being the predominant genotype. To the best of our knowledge, this is the first report of the presence of PAstV1 and PAstV5 in the pig population of India. The PAstV sequences revealed high genetic variability and genetic heterogeneity in a relatively confined area.

Scoping review on the epidemiology, diagnostics and clinical significance of porcine astroviruses

Porcine astroviruses (PoAstVs) have been reported globally and are divided into at least five distinct lineages (PoAstV1-PoAsV5). The primary objective of this review was to summarize the scientific literature about the frequency of detection, associated clinical presentations and type of samples and diagnostic tools used for the detection of porcine astroviruses. The secondary objective was to summarize the body of knowledge about the causal role in disease of PoAstVs using the Bradford Hill framework. A search was conducted using Centre for Biosciences and Agriculture International (CABI), MEDLINE, American Association of Swine Veterinarians (AASV) Swine Information Library (SIL) abstracts, swine conferences including American College of Veterinary Pathologists (ACVP) and American Association of Veterinary Laboratory Diagnosticians (AAVLD). From 168 studies identified by the search, 29 studies were eligible. Results indicated that 69% (20/29) of the literature on PoAstVs have been published between 2011 and 2018. Of 29 papers, 52% were detection studies (15 of 29) and 48% (14 of 29) were case-control studies. Seventy-two per cent (21 of 29) reported differential diagnosis and 10% (3 of 29) reported histologic lesions, out of which 67% (2 of 3) associated the detection of PoAstV3 with development of polioencephalomyelitis. PCR-based assays were the most common diagnostic tools.

Isolation and Characterization of Porcine Astrovirus 5 from a Classical Swine Fever Virus-Infected Specimen

Many new astroviruses have been identified in humans and other animals in recent years, but only a few have been successfully isolated for extensive biological study. Here, we report an unusual isolation of a porcine astrovirus 5 (PAstV5) strain from a clinical classical swine fever virus (CSFV)-infected tissue sample. Incubation of porcine PK-15 cells with an extract of the CSFV-positive tissue resulted in unexpected cytopathic effects (CPEs), and high-throughput viromic sequencing identified PAstV5 and porcine circovirus type 2 (PCV2) as well as CSFV in the culture. After clearance of CSFV and PCV2, a pure PAstV5 strain, named PAstV5-AH29-2014, was obtained. Analysis revealed virus of typical astroviral morphology with a genome of 6,448 nucleotides, sharing 84.3 to 88.9% nucleotide identity with previously published PAstV5 strains. A mechanistic study showed that CSFV coinfection was likely an important factor for successful isolation by significantly enhancing PAstV5 replication in PK-15 cells via suppression of a type I interferon response. Altogether, PAstV5-AH29-2014, as the first isolated PAstV5 strain, will provide critical material for the investigation of the biological and pathogenic properties of this virus as well as for future development of relevant biological and diagnostic reagents.IMPORTANCE Porcine astroviruses are mainly associated with gastroenteritis and neurological diseases in pigs, and five genotypes have been identified (PAstV1-5). However, the clinical manifestations of genotypes other than PAstV1 have not yet been determined because of the failure of in vitro virus isolation. Here, we report a surprising isolation of a PAstV5 strain from a clinical classical swine fever virus (CSFV)-infected tissue sample, which can stably passage in PK-15 cells, and coinfection with CSFV significantly enhanced the replication of PAstV5, possibly through suppression of beta interferon production. Thus, the first isolated PAstV5 strain will be useful for investigating the biological and pathogenic properties of this virus, and the findings obtained in this study provide new insights into defining the interaction mechanism between CSFV and PAstV5.

Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms

Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.

Ecology of Porcine Astrovirus Type 3 in a Herd with Associated Neurologic Disease

Astroviruses (AstVs) cause disease in a wide variety of species. Porcine AstVs are highly genetically diverse and conventionally assigned to five genetic lineages (PoAstV1-5). Due to the increasing evidence that porcine astrovirus type 3 (PoAstV3) is a cause of encephalomyelitis in swine and to elucidate important ecologic characteristics, the infection dynamics and environmental distribution of PoAstV3 were investigated in a herd with PoAstV3-associated neurologic disease. Over a 22 week period, the frequency of PoAstV3 fecal shedding varied by pig and age. The peak detection by RT-qPCR of PoAstV3 on fecal swabs (95%; 61 of 64) occurred at 3 weeks of age. The lowest frequency of detection was at 21 weeks of age (4%; 2 of 47); however, the frequency increased to 41% (19 of 46) at the final sampling time point (25 weeks of age). Viremia was rare (0.9%: 4 of 433). Detection in oral fluid was consistent with 75% to 100% of samples positive at each time point. Pens and feeders also had a high rate of detection with a majority of samples positive at a majority of sampling time points. Based on the data presented, PoAstV3 can be consistently detected in the environment with a majority of pigs being infected and a subset intermittently shedding the virus in feces out to 25 weeks of age. These findings suggest the importance of as-yet unidentified risk factors associated with the development of PoAstV3-associated polioencephalomyelitis.

Increased viral read counts and metagenomic full genome characterization of porcine astrovirus 4 and Posavirus 1 in sows in a swine farm with unexplained neonatal piglet diarrhea

Neonatal diarrhea in piglets may cause major losses in affected pig herds. The present study used random high-throughput RNA sequencing (metagenomic next generation sequencing, mNGS) to investigate the virome of sows from a farm with persistent neonatal piglet diarrhea in comparison to two control farms without diarrhea problems. A variety of known swine gastrointestinal viruses was detected in the control farms as well as in the problem farm (Mamastrovirus, Enterovirus, Picobirnavirus, Posavirus 1, Kobuvirus, Proprismacovirus). A substantial increase in normalized viral read counts was observed in the affected farm compared to the control farms. The increase was attributable to a single viral species in each of the sampled sows (porcine astrovirus 4 and Posavirus 1). The complete genomes of a porcine astrovirus 4 and two co-infecting Posavirus 1 were de novo assembled and characterized. The 6734 nt single-stranded RNA genome of porcine astrovirus 4 (PoAstV-4) strain Belgium/2019 contains three overlapping open reading frames (nonstructural protein 1ab, nonstructural protein 1a, capsid protein). Posavirus 1 strains Belgium/01/2019 and Belgium/02/2019 have a 9814 nt single-stranded positive-sense RNA genome encoding a single open reading frame (polyprotein precursor) containing the five expected Picornavirales-conserved protein domains. The study highlights the potential of mNGS workflows to study unexplained neonatal diarrhea in piglets and contributes to the scarce availability of both PoAstV-4 and Posavirus-1 whole genome sequences from Western Europe.

Molecular epidemiology and viremia of porcine astrovirus in pigs from Guangxi province of China

BACKGROUND

Porcine astroviruses (PAstVs) are common in pigs worldwide. There are five distinct lineages with each lineage representing a different ancestral origin. Recently, multiple reports have demonstrated the evidence of extra-intestinal infection of PAstVs, but little is known about viremia.

RESULTS

In this study, a total of 532 fecal samples and 120 serum samples from healthy pigs were collected and tested from 2013 to 2015 in Guangxi province, China; of these 300/532 (56.4%) and 7/120 (5.8%) of fecal samples tested positive for PAstVs, respectively. Our study revealed that there was wide genetic diversity and high prevalence of the virus in the pig population. All five of the known PAstVs genotypes (1-5) prevailed in the pig population of Guangxi province and were distributed in all age groups of pigs, from suckling piglets to sows, with PAstV2 (47.7%), PAstV1 (26.2%) and PAstV5 (21.5%) seen predominantly. Phylogenetic analysis of partial ORF1b and partial capsid sequences from fecal and serum samples revealed that they were divided into the five lineages. Among these genotypes, based on partial ORF2 genes sequencing 23 strains were grouped as PAstV1, including 6 serum-derived strains, and were regarded as the causative agents of viremia in pigs.

CONCLUSIONS

Due to the information regarding the types of PAstV in blood is limit. This is the first report for the presence of PAstV1 in blood and PAstV3 in the feces of nursery pigs of China. This study provides a reference for understanding the prevalence and genetic evolution of PAstVs in pigs in Guangxi province, China. It also provides a new perspective for understanding of the extra-intestinal infection of PAstVs in pigs.

Polioencephalomyelitis in Domestic Swine Associated With Porcine Astrovirus Type 3

In the past decade, different members of the genus Mamastrovirus have been associated with outbreaks of neurologic disease in humans, cattle, sheep, mink, and, most recently, porcine astrovirus 3 (PoAstV3) in swine. We performed a retrospective analysis of 50 cases of porcine neurologic disease of undetermined cause but with microscopic lesions compatible with a viral encephalomyelitis to better understand the role and pathogenesis of PoAstV3 infection. Nucleic acid was extracted from formalin-fixed paraffin-embedded (FFPE) tissue for reverse transcription quantitative polymerase chain reaction (RT-qPCR) testing for PoAstV3. In addition, 3 cases with confirmed PoAstV3-associated disease were assayed by RT-qPCR to investigate PoAstV3 tissue distribution. PoAstV3 was detected in central nervous system (CNS) tissue via RT-qPCR and in situ hybridization in 13 of 50 (26%) FFPE cases assayed. PoAstV3 was rarely detected in any tissues outside the CNS. Positive cases from the retrospective study included pigs in various production categories beginning in 2010, the earliest year samples were available. Based on these results, PoAstV3 appears to be a recurring putative cause of viral encephalomyelitis in swine that is rarely detected outside of the CNS at the time of clinical neurologic disease, unlike other common viral causes of neurologic disease in swine.

High genetic diversity and recombination events of porcine astrovirus strains identified from ill and asymptomatic pigs in 2017, Hunan Province, China

Astroviruses (AstV) are associated with enteric and systemic disease in mammals and birds. Astroviruses have received increased attention recently as they have been found to be associated with sporadic neurologic disease in mammals including humans. In pigs, porcine astrovirus (PoAstV) can be widely detected and has been grouped in five genotypes (PoAstV1 to PoAstV5). In the present study, we detected multiple PoAstVs in serum samples, nasal swabs, and fecal swabs collected from pigs suffering from respiratory disease or diarrhea but also from asymptomatic pigs, indicating a wide tissue tropism of the identified PoAstV genotypes. Coinfection of different genotypes in the same pig was commonly observed, and within an individual pig a high genetic diversity was observed for viruses belonging to the same PoAstV genotype. Two complete genomes of PoAstV2-WG-R2/2017 and PoAstV4-WG-R2/2017 were successfully obtained and characterized, with genome sizes of 6396 and 6643 nucleotides, respectively. The PoAstV2-WG-R2/2017 genome showed identities of 67.2-77.4% to other known PoAstV2 genomes, and the PoAstV4-WG-R2/2017 genome showed identities of 72.8-80.5% to other known PoAstV4 genomes. The predicted spike domain of open reading frame 2 (ORF2) of these strains showed the highest genetic heterogeneity, with amino acid identities of 13.7-70.9% for PoAstV2-WG-R2/2017 to other known PoAstV2 strains, and identities of 24.4-63.3% for the PoAstV4-WG-R2/2017 to other known PoAstV4 strains. Possible recombination events were identified in each of the two sequences. Two subclades of PoAstV2 and three subclades of PoAstV4 were defined in the present analyses. The obtained data provide further evidence for extraintestinal infectivity of PoAstVs, and confirmed the high genetic diversity of PoAstVs and the coinfection potential of different PoAstV types in a single pig.

Molecular detection of enteric viruses and the genetic characterization of porcine astroviruses and sapoviruses in domestic pigs from Slovakian farms

Background

Surveillance and characterization of pig enteric viruses such as transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), rotavirus, astrovirus (PAstV), sapovirus (PSaV), kobuvirus and other agents is essential to evaluate the risks to animal health and determination of economic impacts on pig farming. This study reports the detection and genetic characterization of PAstV, PSaV in healthy and diarrheic domestic pigs and PEDV and TGEV in diarrheic pigs of different age groups.

Results

The presence of PAstV and PSaV was studied in 411 rectal swabs collected from healthy (n = 251) and diarrheic (n = 160) pigs of different age categories: suckling (n = 143), weaned (n = 147) and fattening (n = 121) animals on farms in Slovakia. The presence of TGEV and PEDV was investigated in the diarrheic pigs (n = 160). A high presence of PAstV infections was detected in both healthy (94.4%) and diarrheic (91.3%) pigs. PSaV was detected less often, but also equally in clinically healthy (8.4%) and diarrheic (10%) pigs. Neither TGEV nor PEDV was detected in any diarrheic sample. The phylogenetic analysis of a part of the RdRp region revealed the presence of all five lineages of PAstV in Slovakia (PAstV-1 – PAstV-5), with the most frequent lineages being PAstV-2 and PAstV-4. Analysis of partial capsid genome sequences of the PSaVs indicated that virus strains belonged to genogroup GIII. Most of the PSaV sequences from Slovakia clustered with sequences originating from neighbouring countries.

Conclusions

Due to no significant difference between healthy and diarrheic pigs testing of the presence of PAstV and PSaV provides no diagnostic value. Genetic diversity of PAstV was very high as all five lineages were identified in pig farms in Slovakia. PSaV strains were genetically related to the strains circulating in Central European region.

The Expanding Field of Mammalian Astroviruses: Opportunities and Challenges in Clinical Virology

Astroviruses are best known as being one of the leading causes of diarrhea in infants and were first described in this context in 1975. In its first years, astrovirus research was mainly restricted to electron microscopy and serology studies. The ability to culture some of these viruses in vitro allowed a first consequent step forward, especially at the molecular level. Since the emergence of more powerful genetic methods, though, the face of this research field has dramatically changed and evolved. From the exponential number of discoveries of new astrovirus strains in the most varied of animal species to their association with atypical diseases, these viruses revealed a lot of surprises, and many more are probably still waiting to be uncovered. This chapter summarizes the most important knowledge about astroviruses and discusses the implication of the latest findings in this area of research.

Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs

Diarrhea outbreaks in pig farms have raised major concerns in Europe and USA, as they can lead to dramatic pig losses. During a suspected outbreak in Belgium of porcine epidemic diarrhea virus (PEDV), we performed viral metagenomics to assess other potential viral pathogens. Although PEDV was detected, its low abundance indicated that other viruses were involved in the outbreak. Interestingly, a porcine bocavirus and several enteroviruses were most abundant in the sample. We also observed the presence of a porcine enterovirus genome with a gene insertion, resembling a C28 peptidase gene found in toroviruses, which was confirmed using re-sequencing, bioinformatics, and proteomics approaches. Moreover, the predicted cleavage sites for the insertion suggest that this gene was being expressed as a single protein, rather than a fused protein. Recombination in enteroviruses has been reported as a major mechanism to generate genetic diversity, but gene insertions across viral families are rather uncommon. Although such inter-family recombinations are rare, our finding suggests that these events may significantly contribute to viral evolution.

Bat Astroviruses: Towards Understanding the Transmission Dynamics of a Neglected Virus Family

Bats belong to the order Chiroptera that represents the second largest order of mammals with more than 1200 species and an almost global distribution. Environmental changes and deforestation have severely influenced many ecosystems, intensifying the contact between wildlife and humans. In recent years, bats have been found to harbor a number of different viruses with zoonotic potential, as well as a great diversity of astroviruses, for which the question of zoonotic potential remains unanswered to date. Human astroviruses have been identified as the causative agent for diarrhea in children and immunocompromised patients. For a long time, astroviruses have been considered to be strictly species-specific. However, a great genetic diversity has recently been discovered among animal and human astroviruses that might indicate the potential of these viruses to cross species barriers. Furthermore, our knowledge about the tissue tropism of astroviruses has been expanded to some neurotropic strains that have recently been shown to be responsible for encephalitis in humans and livestock. This review gives an overview on what is known about astroviruses in bats, humans and livestock, especially bovines and pigs. Future research activities are suggested to unravel astrovirus infection dynamics in bat populations to further assess the zoonotic potential of these viruses.

Whole genome analysis of porcine astroviruses detected in Japanese pigs reveals genetic diversity and possible intra-genotypic recombination

Porcine astroviruses (PoAstVs) are ubiquitous enteric virus of pigs that are distributed in several countries throughout the world. Since PoAstVs are detected in apparent healthy pigs, the clinical significance of infection is unknown. However, AstVs have recently been associated with a severe neurological disorder in animals, including humans, and zoonotic potential has been suggested. To date, little is known about the epidemiology of PoAstVs among the pig population in Japan. In this report, we present an analysis of nearly complete genomes of 36 PoAstVs detected by a metagenomics approach in the feces of Japanese pigs. Based on a phylogenetic analysis and pairwise sequence comparison, 10, 5, 15, and 6 sequences were classified as PoAstV2, PoAstV3, PoAstV4, and PoAstV5, respectively. Co-infection with two or three strains was found in individual fecal samples from eight pigs. The phylogenetic trees of ORF1a, ORF1b, and ORF2 of PoAstV2 and PoAstV4 showed differences in their topologies. The PoAstV3 and PoAstV5 strains shared high sequence identities within each genotype in all ORFs; however, one PoAstV3 strain and one PoAstV5 strain showed considerable sequence divergence from the other PoAstV3 and PoAstV5 strains, respectively, in ORF2. Recombination analysis using whole genomes revealed evidence of multiple possible intra-genotype recombination events in PoAstV2 and PoAstV4, suggesting that recombination might have contributed to the genetic diversity and played an important role in the evolution of Japanese PoAstVs.

Dynamics of Virus Distribution in a Defined Swine Production Network Using Enteric Viruses as Molecular Markers

Modern swine production systems represent complex and dynamic networks involving numerous stakeholders. For instance, livestock transporters carry live animals between fattening sites, abattoirs, and other premises on a daily basis. This interconnected system may increase the risk of microbial spread within and between networks, although little information is available in that regard. In the present study, a swine network composed of 10 finishing farms, one abattoir, and three types of stakeholders (veterinarians, livestock transporters, and nutritional technicians) in Quebec, Canada, was selected to investigate specific vectors and reservoirs of enteric viruses. Environmental samples were collected from the premises over a 12-month period. Samples were screened using targeted reverse transcription-PCR and sequencing of two selected viral markers, group A rotaviruses (RVA) and porcine astroviruses (PoAstV), both prevalent and genetically heterogeneous swine enteric viruses. The results revealed frequent contamination of farm sites (21.4 to 100%), livestock transporter vehicles (30.6 to 68.8%) and, most importantly, the abattoir yard (46.7 to 94.1%), depending on the sample types. Although high levels of strain diversity for both viruses were found, identical PoAstV and RVA strains were detected in specific samples from farms, the abattoir yard, and the livestock transporter vehicle, suggesting interconnections between these premises and transporters. Overall, the results from this study underscore the potential role of abattoirs and livestock transport as a reservoir and transmission route for enteric viruses within and between animal production networks, respectively.

IMPORTANCE

Using rotaviruses and astroviruses as markers of enteric contamination in a swine network has revealed the potential role of abattoirs and livestock transporters as a reservoir and vectors of enteric pathogens. The results from this study highlight the importance of tightening biosecurity measures. For instance, implementing sanitary vacancy between animal batches and emphasizing washing, disinfection, and drying procedures on farms and for transportation vehicles, as well as giving limited access and circulation of vehicles throughout the production premises, are some examples of measures that should be applied properly. The results also emphasize the need to closely monitor the dynamics of enteric contamination in the swine industry in order to better understand and potentially prevent the spread of infectious diseases. This is especially relevant when a virulent and economically damaging agent is involved, as seen with the recent introduction of the porcine epidemic diarrhea virus in the country.

Identification and characterization of multiple porcine astrovirus genotypes in Hunan province, China

Astroviruses (AstVs) can infect a variety of hosts, including mammalian and avian species, and are commonly associated with enteric infections. Recently, mammalian AstVs have been linked to extra-intestinal manifestations, including neurologic disorders in humans, cattle and minks, demonstrating zoonotic potential. So far, five porcine AstV (PAstV) genotypes have been identified, with PAstV1, PAstV2, PAstV3 and PAstV5 implicated in cross-species transmission. Our knowledge about PAstV epidemiology in China is still limited. In this study, two duplex differential RT-PCR assays were developed to investigate the distribution and prevalence of PAstV1, PAstV2, PAstV4 and PAstV5. Two hundred eighteen samples were collected from 33 farms and pigs with known diarrhea status in nine regions of Hunan province in China. Specifically, 126 small intestines, 51 fecal swabs, 20 lungs, 19 spleens and two kidneys were obtained. PAstVs were detected in all nine regions and in 81.8% (27/33) of the pig farms investigated. The overall prevalence of PAstV was 46.3% (101/218), with PAstV5 as the predominant type, with a positive rate of 24.8% (54/218). The prevalence of PAstV4, PAstV1 and PAstV2 was 16.1% (35/218), 14.7% (32/218) and 10.1% (22/218), respectively. Besides being present in intestines and fecal swabs, PAstV RNA was also detected in lungs, spleens and kidneys. Sequencing revealed a high level of genetic divergence within each genotype, and a higher positive rate of PAstV5 was associated with pigs with diarrhea compared to pigs without diarrhea. This study revealed for the first time that PAstV4 is circulating in China, and that PAstV5 is the dominant genotype in pig herds in Hunan province in China.

Detection and characterization of a novel genotype of porcine astrovirus 4 from nasal swabs from pigs with acute respiratory disease

Metagenomic sequencing of three nasal swabs collected from 10- to 21-day-old pigs exhibiting unexplained acute respiratory disease from two different commercial production facilities in Oklahoma identified a novel genotype of porcine astrovirus 4 (PAstV-4). The genomes had only ~75 % nucleotide sequence identity to previously characterized PAstV-4 isolates, while the capsid-encoding ORF2 had only ~53 % amino acid sequence identity to reference strains. A TaqMan assay targeting the novel ORF2 gene found 21 % and 19 % incidence in nasal and fecal swabs, respectively, submitted for unrelated diagnostic testing. PAstV-4 RNA levels were significantly higher (P = 0.04) in nasal swabs, suggesting a possible atypical respiratory tropism.

Molecular detection of Porcine astrovirus in Sichuan Province, China

Background

Porcine astrovirus (PoAstV) is widely distributed worldwide, and is highly prevalent among piglets with or without diarrhea, existing as at least five distinct lineages (PoAstV1–PoAstV5) within the genus Mamastrovirus. However, our knowledge of the diversity and epidemiology of PoAstV in China is limited.

Results

In this study, fecal samples from 21/120 (17.5 %) domestic pigs, including 18/100 (18 %) diarrheic and 3/20 (15 %) healthy pigs, and from 1/9 (11.1 %) healthy wild boars tested in Sichuan Province were positive for PoAstV on reverse transcription–PCR. Of the 22 positive samples, 13.6 % were positive for PoAstV only, whereas 40.9 % also contained Porcine epidemic diarrhea virus (PEDV), 22.7 % also contained porcine group A rotavirus (PRoVA), and 22.7 % also contained PEDV and PRoVA. A phylogenetic analysis of the RdRp gene revealed genetic heterogeneity among the PoAstV sequences and two lineages were detected in this study, with PoAstV-2 predominant. PoAstV-5 was detected in wild boars for the first time.

Conclusions

PoAstV infections exist in Sichuan Province regardless of the disease status in the pig population, either alone or in combination with other enteric viruses, and may be associated with diarrhea.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-015-0462-6) contains supplementary material, which is available to authorized users.

Molecular investigations on the prevalence and viral load of enteric viruses in pigs from five European countries

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Porcine astrovirus type 4 was prevalent in the 49 European farms with a high viral load.

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Rotaviruses were mainly found in diarrheic pigs.

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Kobuvirus and porcine circovirus 2 were ubiquitous.

Enteric viral infections in pigs may cause diarrhea resulting in ill-thrift and substantial economic losses. This study reports the enteric infections with porcine astrovirus type 4 (PAstV4), porcine group A rotavirus (GARV), porcine group C rotavirus (GCRV), porcine circovirus type 2 (PCV2) and porcine kobuvirus (PKoV) in 419 pigs, comprising both healthy and diarrheic animals, from 49 farms in five European countries (Austria, Germany, Hungary, Spain and Sweden). Real-time RT-PCR assays were developed to test fecal samples and to compare the prevalence and viral load in relation to health status, farms of origin and age groups. The results showed that PAstV4 (70.4%) was the dominant virus species, followed by PKoV (56.7%), PCV2 (42.2%), GCRV (3%) and GARV (0.9%). Diarrheic pigs had a higher viral load of PAstV4 in the nursery and growing-finishing groups. Rotaviruses were mainly detected in diarrheic pigs, whereas PCV2 was more often detected in clinically healthy than in diarrheic pigs, suggesting that most PCV2 infections were subclinical. PAstV4, PCV2 and PKoV were considered ubiquitous in the European pig livestock and co-infections among them were frequent, independently of the disease status, in contrast to a low prevalence of classical rotavirus infections.

Spatiotemporal trends in the discovery of new swine infectious agents

A literature review was conducted to assess the spatiotemporal trend and diversity of infectious agents that were newly found in pigs between 1985 and 2010. We identified 173 new variants from 91 species, of which 73 species had not been previously described in pigs. These new species, of which one third was zoonotic, were taxonomically diverse. They were identified throughout the study period, predominantly in the main pork producing countries, with the rate of discovery of new virus variants doubling within the last 10 years of the study period. Whilst infectious agent species newly detected in high-income countries were more likely to be associated with higher virulence, zoonotic agents prevailed in low- and middle-income countries. Although this trend is influenced by factors conditioning infectious agent detection – diagnostic methods, surveillance efforts, research interests –, it may suggest that different scales and types of production systems promote emergence of certain types of infectious agents. Considering the rapid transformation of the swine industry, concerted efforts are needed for improving our understanding of the factors influencing the emergence of infectious agents. This information then needs to inform the design of risk-based surveillance systems and strategies directly mitigating the risk associated with these factors.

Identification and genetic characterization of two porcine astroviruses from domestic piglets in China

Porcine astrovirus are divided into five genotypes. In this study, we identified two porcine astroviruses (AstV-LL-1 and AstV-LL-2) by using sequence-independent single-primer amplification (SISPA) on faecal specimens of healthy domestic piglets younger than 15 days. The detection rate for both was 2.82% (14/497). AstV-LLs were then sequenced and characterised. Phylogenetic analysis revealed that they have the characteristics of porcine astrovirus (PastV) 2 and 5 and have some unique genetic features. Our findings show that the two astroviruses are novel lineages of PAstV2 and 5. The findings may be helpful in evaluating the ecology and evolution of astroviruses in pigs.

Full genome analysis of bovine astrovirus from fecal samples of cattle in Japan: identification of possible interspecies transmission of bovine astrovirus

A viral metagenomics approach was used to investigate fecal samples of Japanese calves with and without diarrhea. Of the different viral pathogens detected, read counts gave nearly complete astrovirus-related RNA sequences in 15 of the 146 fecal samples collected in three distinct areas (Hokkaido, Ishikawa, and Kagoshima Prefectures) between 2009 and 2015. Due to the lack of genetic information about bovine astroviruses (BoAstVs) in Japan, these sequences were analyzed in this study. Nine of the 15 Japanese BoAstVs were closely related to Chinese BoAstVs and clustered into a lineage (tentatively named lineage 1) in all phylogenetic trees. Three of 15 strains were phylogenetically separate from lineage 1, showing low sequence identities, and clustered instead with an American strain isolated from cattle with respiratory disease (tentatively named lineage 2). Interestingly, two of 15 strains clustered with lineage 1 in the open reading frame (ORF)1a and ORF1b regions, while they clustered with lineage 2 in the ORF2 region. Remarkably, one of 15 strains exhibited low amino acid sequence similarity to other BoAstVs and was clustered separately with porcine astrovirus type 5 in all trees, and ovine astrovirus in the ORF2 region, suggesting past interspecies transmission.

Complete genome sequence of a porcine astrovirus from South Korea

Porcine astrovirus (PAstV) is broadly distributed in pigs in several countries worldwide. PAstVs belong to the genus Mamastrovirus and are divided into five genetically divergent types. This study presents a molecular characterization of PAstV identified in diarrheic piglets in South Korea. The complete genome of the Korean PAstV strain KOR/KNU14-07/2014 was sequenced and analyzed to characterize PAstV circulating in South Korea. The full-length genomic sequence of KNU14-07 was determined to be 6,337 nucleotides in length and consisted of three major open reading frames (5'-ORF1a-ORF1b-ORF2-3'). The overall degree of nucleotide sequence identity was 40.8 to 72.5% between KUN14-07 and other reported PAstVs, indicating high heterogeneity among PAstVs. Genetic and phylogenetic analyses showed that the KNU14-07 strain was most closely related to the PAstV2 lineage, which is the second most common type in South Korea.

Astrovirus as a possible cause of congenital tremor type AII in piglets?

BACKGROUND

Congenital tremor is associated with demyelination of the brain and spinal cord and is clinically noted as outbreaks of trembling and shaking in newborn piglets during a limited time-period. Six forms of the disease have been described, where form AII may be caused by an, as yet, unidentified viral infection. This study aimed to investigate the presence of astrovirus and circovirus by sequencing and polymerase chain reaction (PCR) analysis and by relating the findings to the occurrence of disease and lesions in the brain, in 4-6 days-old piglets obtained from a clinical outbreak of congenital tremor.

RESULTS

In piglets with congenital tremor, there were mild to moderate vacuolar changes of the white matter in the cerebrum, brain stem and cerebellum. In healthy piglets, less conspicuous vacuolar changes were detected. One healthy and one diseased piglet were positive for porcine circovirus type 2. The nested pan-PCR showed the presence of astrovirus in at least one brain region in all piglets and by sequencing, two different porcine astrovirus lineages were identified.

CONCLUSIONS

The results do not support previous studies identifying porcine circovirus type 2 as the cause of congenital tremor. The demonstration of astrovirus in the brain of piglets suffering from congenital tremor is interesting. However, astrovirus was demonstrated in both healthy and diseased individuals and therefore, further studies are warranted to determine the possible involvement of astrovirus in the pathogenesis of congenital tremor in pigs.

Human astroviruses

Human astroviruses (HAtVs) are positive-sense single-stranded RNA viruses that were discovered in 1975. Astroviruses infecting other species, particularly mammalian and avian, were identified and classified into the genera Mamastrovirus and Avastrovirus. Through next-generation sequencing, many new astroviruses infecting different species, including humans, have been described, and the Astroviridae family shows a high diversity and zoonotic potential. Three divergent groups of HAstVs are recognized: the classic (MAstV 1), HAstV-MLB (MAstV 6), and HAstV-VA/HMO (MAstV 8 and MAstV 9) groups. Classic HAstVs contain 8 serotypes and account for 2 to 9% of all acute nonbacterial gastroenteritis in children worldwide. Infections are usually self-limiting but can also spread systemically and cause severe infections in immunocompromised patients. The other groups have also been identified in children with gastroenteritis, but extraintestinal pathologies have been suggested for them as well. Classic HAstVs may be grown in cells, allowing the study of their cell cycle, which is similar to that of caliciviruses. The continuous emergence of new astroviruses with a potential zoonotic transmission highlights the need to gain insights on their biology in order to prevent future health threats. This review focuses on the basic virology, pathogenesis, host response, epidemiology, diagnostic assays, and prevention strategies for HAstVs.

Detection and characterization of avastrovirus associated with diarrhea isolated from minks in China

Astroviruses are becoming a growing concern in veterinary and public health. Many astrovirus species are associated with enteric diseases have been described in both mammalian and avian hosts. In the present study, 23 fecal samples from diarrheic minks were collected in Liaoning and Shandong Province, and an investigation of astrovirus was performed using biochemical methods and RT-PCR assay with specific primers. A total of four mink astroviral isolates were detected from sick minks with diarrhea problems. Further sequencing and characterization of the partial ORF1b gene and ORF2 gene segments revealed low sequence identities (20.0-85.3 and 31.8-87.2%) with known astroviral strains, indicating the emergence of a novel clade of astroviruses. Some new features of the astroviral genome have also been discovered. The phylogenetic tree revealed that all samples were distantly related to mink astrovirus and were closely related to chicken astroviruses and turkey astroviruses. MK/DL-1, MK/DL-2, MK/SD-1, and MK/SD-2 formed a new clade and were found to be more closely related to astroviruses from birds than to other mink strains, indicating past cross-species transmission and considerable zoonotic potential.

Molecular detection and genetic characterization of kobuviruses and astroviruses in asymptomatic local pigs in East Africa

In this study, swine fecal specimens (n = 251) collected from nursing and weaned piglets raised under smallholder production systems were screened for the presence of kobuviruses by RT-PCR. Porcine kobuviruses were detected in 13.1 % (33/251) of the samples. We demonstrated that porcine kobuvirus infections exist in indigenous pigs in Kenya and Uganda and that the prevalence was higher in young piglets than older pigs: nursing piglets (15 %), post-weaning (3-month-old) pigs (17 %), 4-month-old pigs (10 %). Genetic analysis of the partial RNA-dependent RNA polymerase (RdRp) region (690 nt) revealed that kobuviruses circulating in East Africa are diverse, sharing nucleotide sequence identities ranging from 89.7 to 99.1 % and 88 to 92.3 % among them and with known porcine kobuviruses, respectively. The nucleotide sequence identities between our kobuvirus strains and those of human, bovine and canine kobuviruses were 69.4-70.7 %, 73.1-74.4 % and 67-70.7 %, respectively. Additionally, upon sequencing selected samples that showed consistent 720-bp RT-PCR bands while using the same primer set, we detected porcine astroviruses in our samples belonging to type 2 and type 3 mamastroviruses. To our knowledge, this study reports the first detection and molecular analysis of both porcine kobuviruses and astroviruses in an African region. Further studies are required to determine the role of these viruses in gastrointestinal infections of pigs in this region and to determine the genetic diversity of the circulating strains to develop accurate diagnostic tools and implement appropriate control strategies.

Complete genome sequence of a newly identified porcine astrovirus genotype 3 strain US-MO123

Astrovirus (AstV) infections are among the most common causes of gastroenteritis and are also associated with extraintestinal manifestations in humans and many animals. Herein, for the first time, the complete genome sequence of newly identified porcine astrovirus genotype 3 (PAstV3) strain US-MO123 was determined. Sequence comparison and phylogenetic analysis showed that PAstV3 has the closest relationship with mink AstV and the human AstV strains VA1, VA2, and SG, indicating the same ancestral origin and zoonotic potential of the virus.

Porcine astrovirus viremia and high genetic variability in pigs on large holdings in Croatia

Astroviruses are emerging viral agents, primarily enteropathogenic in mammals, but recently have been acknowledged to have extra-intestinal implications in humans and mink. Porcine astrovirus is thought to be widely distributed and highly prevalent among pigs, nevertheless its clinical significance remains doubtful as it can be detected in diarrheic as well as in healthy pigs. Recent reports imply the immense genetic variability among porcine astrovirus strains with five distinct lineages being characterized so far. Herein, we report porcine astrovirus circulation in the blood of healthy pigs in different age categories bred on two large industrial holdings in Croatia, with viral RNA seroprevalence of 3.89%. These are the first extra-intestinal findings of astrovirus in pigs, indicating a more complex pathogenesis than previously thought. Partial polymerase sequences of serum-derived strains provisionally clustered into porcine astrovirus lineages 2 and 4, sharing high genetic identity with previously described porcine astrovirus strains. The results were supported by detecting porcine astrovirus strains in composite fecal samples, regardless of pig category or holding tested. Phylogenetic analysis of derived strains suggested the presence of porcine astrovirus lineages previously detected in pig sera with an additional highly genetically divergent lineage 5, reported for the first time in Europe. Moreover, the existence of possible sub lineages should not be excluded. The results obtained in the present study, contribute to knowledge of porcine astrovirus pathogenesis; even though it's possible clinical significance remains unclear. High fecal prevalence accompanied with vast genetic diversity on a relatively confined area, underscores the importance of pigs as porcine astrovirus reservoirs with eventual recombination events as a possible outcome.

Identification and characterization of novel porcine astroviruses (PAstVs) with high prevalence and frequent co-infection of individual pigs with multiple PAstV types

Many astrovirus (AstV) species are associated with enteric disease, although extraintestinal manifestations in mammalian and avian hosts have also been described. In this study, the prevalence rates of porcine AstV types 1-5 (PAstV1-PAstV5) were investigated using faecal samples from 509 pigs of which 488 (95.9%) came from farms with a history of diarrhoea. All of the five known PAstV types were found to circulate in pigs in the USA, and co-infection of a single pig with two or more PAstV types was frequently observed. A high overall prevalence of 64.0% (326/509) of PAstV RNA-positive samples was detected, with 97.2% (317/326) of the PAstV RNA-positive pigs infected with PAstV4. Further genomic sequencing and characterization of the selected isolates revealed low sequence identities (49.2-89.0%) with known PAstV strains, indicating novel types or genotypes of PAstV2, PAstV4 and PAstV5. Some new features of the genomes of the PAstVs were also discovered. The first complete genome of a PAstV3 isolate was obtained and showed identities of 50.5-55.3% with mink AstV and the novel human AstVs compared with 38.4-42.7% with other PAstV types. Phylogenetic analysis revealed that PAstV1, PAstV2 and PAstV3 were more closely related to AstVs from humans and other animals than to each other, indicating past cross-species transmission and the zoonotic potential of these PAstVs.

Phylogenetic analysis of porcine astrovirus in domestic pigs and wild boars in South Korea

Porcine astrovirus (PAstV) belongs to genetically divergent lineages within the genus Mamastrovirus. In this study, 25/129 (19.4 %) domestic pig and 1/146 (0.7 %) wild boar fecal samples tested in South Korea were positive for PAstV. Positive samples were mainly from pigs under 6 weeks old. Bayesian inference (BI) tree analysis for RNA-dependent RNA polymerase (RdRp) and capsid (ORF2) gene sequences, including Mamastrovirus and Avastrovirus, revealed a relatively geographically divergent lineage. The PAstVs of Hungary and America belong to lineage PAstV 4; those of Japan belong to PAstV 1; and those of Canada belong to PAstV 1, 2, 3, and 5, but not to 4. This study revealed that the PAstVs of Korea belong predominantly to lineage PAstV 4 and secondarily to PAstV 2. It was also observed that PAstV infections are widespread in South Korea regardless of the disease state in domestic pigs and in wild boars as well.

Detection and molecular characterization of Porcine astrovirus strains associated with swine diarrhea

Astrovirus has been reported to be associated with diarrhea in pigs. The current study was conducted for the detection and molecular characterization of astroviruses in diarrheic pigs submitted to the Veterinary Diagnostic Laboratory, University of Minnesota. Intestinal contents from 269 pigs were examined by reverse transcription polymerase chain reaction (RT-PCR), and 62% were found positive for astroviruses. Of the positive samples, 20% were positive for astrovirus alone while astrovirus with rotavirus was detected in 58% of the samples. The remaining 22% revealed the presence of astrovirus along with Porcine hemagglutinating encephalomyelitis virus, Transmissible gastroenteritis virus, or Porcine circovirus-2. Sequencing the capsid gene of 56 randomly selected samples confirmed them to be Porcine astrovirus type 4 (PAstV-4) with 58-100% nucleotide identity within these viruses. Phylogenetic analysis revealed 2 possible subgroups. The results indicate that PAstV is present on swine farms in the United States and that it may be associated with diarrhea either alone or in combination with other enteric viruses. Further studies are needed to determine strain diversity among porcine astroviruses so that appropriate control strategies can be devised and implemented.