Porcine Sapoviruses Research Articles

Discovery and Genomic Characterization of a Novel Bat Sapovirus with Unusual Genomic Features and Phylogenetic Position

Sapovirus is a genus of caliciviruses that are known to cause enteric disease in humans and animals. There is considerable genetic diversity among the sapoviruses, which are classified into different genogroups based on phylogenetic analysis of the full-length capsid protein sequence. While several mammalian species, including humans, pigs, minks, and dogs, have been identified as animal hosts for sapoviruses, there were no reports of sapoviruses in bats in spite of their biological diversity. In this report, we present the results of a targeted surveillance study in different bat species in Hong Kong. Five of the 321 specimens from the bat species, Hipposideros pomona, were found to be positive for sapoviruses by RT-PCR. Complete or nearly full-length genome sequences of approximately 7.7 kb in length were obtained for three strains, which showed similar organization of the genome compared to other sapoviruses. Interestingly, they possess many genomic features atypical of most sapoviruses, like high G+C content and minimal CpG suppression. Phylogenetic analysis of the viral proteins suggested that the bat sapovirus descended from an ancestral sapovirus lineage and is most closely related to the porcine sapoviruses. Codon usage analysis showed that the bat sapovirus genome has greater codon usage bias relative to other sapovirus genomes. In summary, we report the discovery and genomic characterization of the first bat calicivirus, which appears to have evolved under different conditions after early divergence from other sapovirus lineages.

RT-PCR test for detecting porcine sapovirus in weanling piglets in Hunan Province, China

The prevalence of porcine sapovirus infection in weanling pigs was investigated in Hunan Province, China, between August 2006 and October 2007. A total of 153 diarrheic fecal samples from ten intensive pig farms from ten representative administrative regions in Hunan province were examined for porcine sapoviruses using RT-PCR. Twenty-two of 153 (14.37 %) samples were found to contain porcine sapoviruses. Phylogenetic analysis showed that all the porcine sapovirus isolates in Hunan Province belonged to the porcine sapovirus genogroup III. The results of the present investigation have implications for the control of porcine sapovirus infection in pigs in Hunan Province, China.

Emerging and Re-emerging Swine Viruses

In the past two decades or so, a number of viruses have emerged in the global swine population. Some, such as porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2), cause economically important diseases in pigs, whereas others such as porcine torque teno virus (TTV), now known as Torque teno sus virus (TTSuV), porcine bocavirus (PBoV) and related novel parvoviruses, porcine kobuvirus, porcine toroviruses (PToV) and porcine lymphotropic herpesviruses (PLHV), are mostly subclinical in swine herds. Although some emerging swine viruses such as swine hepatitis E virus (swine HEV), porcine endogenous retrovirus (PERV) and porcine sapovirus (porcine SaV) may have a limited clinical implication in swine health, they do pose a potential public health concern in humans due to zoonotic (swine HEV) or potential zoonotic (porcine SaV) and xenozoonotic (PERV, PLHV) risks. Other emerging viruses such as Nipah virus, Bungowannah virus and Menangle virus not only cause diseases in pigs but some also pose important zoonotic threat to humans. This article focuses on emerging and re-emerging swine viruses that have a limited or uncertain clinical and economic impact on pig health. The transmission, epidemiology and pathogenic potential of these viruses are discussed. In addition, the two economically important emerging viruses, PRRSV and PCV2, are also briefly discussed to identify important knowledge gaps.

Development and application of a SYBR green RT-PCR for first line screening and quantification of porcine sapovirus infection

BackgroundSapoviruses are single stranded positive sense RNA viruses belonging to the family Caliciviridae. The virus is detected in different species including the human and the porcine species as an enteric pathogen causing asymptomatic to symptomatic enteritis. In this study, we report the development of a rapid real time qRT-PCR based on SYBR Green chemistry for the diagnosis of porcine sapovirus infection in swine.ResultsThe method allows the detection of porcine sapoviruses and the quantification of the genomic copies present in stool samples. During its development, the diagnostic tool showed good correlation compared with the gold standard conventional RT-PCR and was ten-fold more sensitive. When the method was applied to field samples, porcine noroviruses from genogroup 2 genotype 11b were also detected. The method was also applied to swine samples from the Netherlands that were positive for PoSaV infection. Phylogenetic results obtained from the samples showed that PoSaV sequences were genetically related to the currently described genogroup III, to the proposed genogroup VII and also to the MI-QW19 sequence (close to the human SaV sequences).ConclusionsA rapid, sensitive, and reliable diagnosis method was developed for porcine sapovirus diagnosis. It correlated with the gold standard conventional RT-PCR. Specificity was good apart for genogroup 2 genotype 11b porcine noroviruses. As a first line screening diagnosis method, it allows a quicker and easier decision on doubtful samples.

Molecular characterization of a porcine sapovirus strain isolated from a piglet with diarrhoea: a case report

Porcine sapoviruses, members of the family Caliciviridae, have been considered as an aetiological agent of gastroenteritis in pigs. In this study, we analysed 251 faecal samples obtained from 3 to 90 day-old diarrhoeic pigs in the Czech Republic between January 2005 and June 2010 and tested them by negative staining electron microscopy for the presence of sapoviruses. Only one sample showed the presence of viral particles with characteristic sapovirus morphology. The presence of sapovirus (SaV) was confirmed by an RT-PCR assay with primers specific for the sapoviral RNA polymerase and capsid genes. Phylogenetic analysis based on a partial sequence of the RNA polymerase gene placed the new Czech isolate into the GVII genogroup of porcine sapoviruses; however, analysis of a portion of the capsid gene sequence classified the isolate as GIII of the genus Sapovirus. These contradictory findings indicate that recombinant porcine sapovirus was identified. According to our knowledge this is the first description of porcine sapovirus in domestic pigs in the Czech Republic

Identification of genetic diversity of porcine Norovirus and Sapovirus in Korea

It is well known that Norovirus (NoV) and Sapovirus (SaV) identified in humans and pigs have heterogeneous genome sequences. In this study, a total of three strains of NoV and 37 strains of SaV were detected in 567 porcine fecal samples by RT-PCR, corresponding detection rates of 0.5 and 6.5%, respectively. Phylogenetic analyses were conducted using amino acid sequences of the partial RNA-dependent RNA polymerase (RdRp) and complete capsid proteins of both viruses to determine their genogroups. Analysis with the RdRp sequences indicated that all three NoV strains HW41, DG32, and DO35 detected in this study were classified into genogroup II (GII). A further analysis with the complete capsid sequence demonstrated that the DO35 strain belonged to subgenotype b in GII-21 (GII-21b) along with the SW918 strain. A total of 26 strains out of 27 strains that were selected from the 37 porcine SaVs were classified into genogroup III when they were analyzed with the RdRp sequences. The remaining strain (DO19) was not clustered with any of the previously classified SaV strains, thereby suggesting the advent of a new genogroup virus. Additional analyses with the amino acid sequence of the capsid and the nucleotide sequence of the RdRp and capsid junction region supported the notion that the DO19 strain belonged to a novel genogroup of SaV. To the best of our knowledge, this is the first report to describe a novel porcine SaV belonging to an unknown genogroup in Korea.

Characterization of novel porcine sapoviruses

Sapoviruses are common caliciviruses known to cause enteric diseases in humans and animals. SaVs are genetically highly heterogeneous and are presently classified in five genogroups that are further subdivided in a number of genotypes. In recent years, a number of novel animal SaV strains, mostly of swine origin, have been partially characterized and proposed to represent novel genogroups or genotypes. We previously reported the detection and partial characterization of a wide range of variable and novel SaV strains of uncertain taxonomic status in Canadian swine. We now report on further genomic characterization of two novel strains to clarify their taxonomic relationship to other swine and human SaVs. Detailed analysis of different regions of their genomes, including determination of their complete capsid sequence, did not permit clear taxonomic assignment according to current criteria. This situation appears reminiscent of that of a number of SaV strains of swine origin and calls for a classification update for this calicivirus genus. We also report the detection of swine GIII SaVs for the first time in Canada.

Incidence, Diversity, and Molecular Epidemiology of Sapoviruses in Swine across Europe

Porcine sapovirus is an enteric calicivirus in domestic pigs that belongs to the family Caliciviridae. Some porcine sapoviruses are genetically related to human caliciviruses, which has raised public health concerns over animal reservoirs and the potential cross-species transmission of sapoviruses. We report on the incidence, genetic diversity, and molecular epidemiology of sapoviruses detected in domestic pigs in a comprehensive study conducted in six European countries (Denmark, Finland, Hungary, Italy, Slovenia, and Spain) between 2004 and 2007. A total of 1,050 swine fecal samples from 88 pig farms were collected and tested by reverse transcription-PCR for sapoviruses, and positive findings were confirmed by sequencing. Sapoviruses were detected in 80 (7.6%) samples collected on 39 (44.3%) farms and in every country. The highest prevalence was seen among piglets aged 2 to 8 weeks, and there was no significant difference in the proportion of sapovirus-positive findings for healthy animals and animals with diarrhea in Spain and Denmark (the only countries where both healthy animals and animals with diarrhea were tested). On the basis of the sequence of the RNA polymerase region, highly heterogeneous populations of viruses representing six different genogroups (genogroups III, VI, VII, and VIII, including potential new genogroups IX and X) were identified, with a predominance of genogroup GIII (50.6%). Genogroup VIII, found in five of the six countries, had the highest degree of homology (up to 66% at the amino acid level) to human sapovirus strains. Sapoviruses are commonly circulating and endemic agents in swine herds throughout Europe. Highly heterogeneous and potential new genogroups of sapoviruses were found in pigs; however, no "human-like" sapoviruses were detected.

Porcine noroviruses and sapoviruses on Korean swine farms

Porcine noroviruses (NoVs) and sapoviruses (SaVs), which belong to the family Caliciviridae, have been considered potential zoonotic agents for human infection, and several cases have been reported in Asian countries. In this study, a total of 537 porcine fecal samples collected from 64 swine farms in Korea were tested. Among 537 samples, porcine NoVs were detected by semi-nested RT-PCR in ten samples (1.9%), and porcine SaVs were detected by RT-PCR in 60 samples (11.2%), showing their circulation in Korea. The porcine NoVs were genetically related to strains of genotypes 11 and 18, of genogroup II (GII) of the genus Norovirus. The porcine SaV strains were genetically related to the porcine enteric calicivirus Cowden strain and to the previously identified Korean porcine strains in genogroup III (GIII) of the genus Sapovirus. In no case was co-infection with both NoV and SaV observed in one pig. This is the first report describing porcine NoVs identified in Korea.

Detection and characterization of porcine sapoviruses from asymptomatic animals in Irish farms

Caliciviruses are an important cause of gastroenteritis in humans and animals. Molecular analysis of the polymerase and capsid genes of porcine caliciviruses, sapoviruses (SaVs) and noroviruses (NoVs), has demonstrated a broad range of genetic diversity but information on their epidemiology and pathogenic role in pigs is limited. In this study, 292 faecal samples were obtained from 4–5 to 8–9 week old asymptomatic pigs from four porcine herds in Ireland during 2005–2007 and were screened by RT-PCR using calicivirus-specific primers. Only seven samples from two porcine herds tested positive for porcine calicivirus. By sequence analysis of the partial RNA-dependent RNA polymerase (RdRp) fragment, six samples from one such herd were closely related to each other (>98% nucleotide identity) and were characterised as genogroup (GG) III (Cowden-like) porcine SaVs. These viruses demonstrated an amino acid (aa) identity of 81.3–98.6% to GGIII SaVs. Conversely, one calicivirus strain, 9/07/Ire (identified from a different herd in 2007), was distantly related to GIII SaVs and displayed 94.6–98.6% aa identity to rare K7-like porcine caliciviruses, representatives of a potential novel SaV genogroup (GGVII), described previously in Japan and the USA. Circulation of SaVs in asymptomatic animals might be a mechanism of virus persistence in porcine populations and should be considered with respect to understanding the epidemiology of these viruses in porcine herds.

Candidate New Species ofKobuvirusin Porcine Hosts

Candidate New Species of<i>Kobuvirus</i>in Porcine Hosts

Noroviruses and sapoviruses in pigs in Belgium

Porcine noroviruses and sapoviruses belong to the family Caliciviridae and are rarely reported in European countries. In this study, swine stools from a region representative of northern Europe were screened for these viruses by RT-PCR. Both porcine noroviruses and sapoviruses were detected, showing their circulation in this region. The porcine norovirus strains were genetically related to genotype 19 strains in the genogroup II of the genus Norovirus. The porcine sapovirus strains were genetically related to the porcine enteric calicivirus Cowden reference strain and to newly described porcine strains in the genus Sapovirus.

Prevalence of hepatitis E virus and sapovirus in post-weaning pigs and identification of their genetic diversity

Hepatitis E virus (HEV) and sapovirus (SaV) induce acute hepatitis and gastroenteritis, respectively, in humans. As pigs have been recognized as an important reservoir for these viruses, we evaluated the infection rates of both viruses using fecal samples collected from post-weaning pigs via RT-PCR methods. In the five swine farms assessed in this study, 3 farms were found to be HEV-positive and 4 farms were SaV-positive. The overall prevalence of HEV and SaV in the pigs was 17.0 and 23.1%, respectively. Phylogenetic tree analysis revealed that the isolated swine HEVs belonged to genotype 3 and the porcine SaVs belonged to genogroup III. This study proved that both HEV and SaV are prevailing in post-weaning pigs in Korea.

Effects of Different Animal Waste Treatment Technologies on Detection and Viability of Porcine Enteric Viruses

Enteric pathogens in animal waste that is not properly processed can contaminate the environment and food. The persistence of pathogens in animal waste depends upon the waste treatment technology, but little is known about persistence of porcine viruses. Our objectives were to characterize the porcine enteric viruses (porcine noroviruses [PoNoVs], porcine sapoviruses [PoSaVs], rotavirus A [RV-A], RV-B, and RV-C) in fresh feces or manure and to evaluate the effects of different candidate environmentally superior technologies (ESTs) for animal waste treatment on the detection of these viruses. Untreated manure and samples collected at different stages during and after treatment were obtained from swine farms that used conventional waste management (CWM) and five different candidate ESTs. The RNA from porcine enteric viruses was detected by reverse transcription-PCR and/or seminested PCR; PoSaV and RV-A were also detected by enzyme-linked immunosorbent assay. Cell culture immunofluorescence (CCIF) and experimental inoculation of gnotobiotic (Gn) pigs were used to determine RV-A/C infectivity in posttreatment samples. The PoSaV and RV-A were detected in pretreatment samples from each farm, whereas PoNoV and RV-C were detected in pretreatment feces from three of five and four of five farms using the candidate ESTs, respectively. After treatment, PoSaV RNA was detected only in the samples from the farm using CWM and not from the farms using the candidate ESTs. RV-A and RV-C RNAs were detected in four of five and three of four candidate ESTs, respectively, after treatment, but infectious particles were not detected by CCIF, nor were clinical signs or seroconversion detected in inoculated Gn pigs. These results indicate that only RV-A/C RNA, but no viral infectivity, was detected after treatment. Our findings address a public health concern regarding environmental quality surrounding swine production units.

Genetic diversity of porcine sapoviruses

Sapoviruses (SaVs) within the Caliciviridae family are an important cause of gastroenteritis in both humans and animals. Although the widespread occurrence of divergent human SaV strains has been reported, there have only been a few studies of porcine SaVs examining their genetic diversity. The aim of this study was to assess the genetic diversity of porcine SaVs in piglets with diarrhea in South Korea. Two hundred and thirty-seven fecal specimens from piglets with diarrhea were examined from 78 farms over a 2-year period from six provinces in South Korea. Overall, 69 (29.1%) of the samples from five provinces tested positive for porcine SaVs by either RT-PCR or nested PCR with the primer pairs specific to porcine SaVs. An analysis of the partial capsid gene (757 bp) of 12 porcine SaVs detected from fecal samples showed genetic divergence, not only among the Korean porcine SaVs (67.7–99.1%), but also between Korean and American porcine SaVs (69.1–90.2%). Interestingly, one strain (Po/SaV/JN-MA113/05/Korea), formed a second porcine SaV/GIII genotype, and is tentatively called GIII/2. This strain had a 0.236–0.405 inter-cluster distance with the other strains in the same genogroup, which is comparable to the distances between the established GI and GII SaVs. Furthermore, two potential recombinant porcine SaVs were identified. In conclusion, porcine SaV infections are common in diarrheic piglets in South Korea. The infecting strains are genetically diverse, and include a newly recognized genotype and recombinant viruses within genogroup III.

Porcine enteric caliciviruses: Genetic and antigenic relatedness to human caliciviruses, diagnosis and epidemiology

Porcine enteric caliciviruses include sapoviruses and noroviruses. Porcine sapoviruses infect pigs of all ages and cause diarrhea in young pigs, whereas porcine noroviruses were detected exclusively from adult pigs without clinical signs. Importantly, certain porcine norovirus strains were genetically and antigenically related to human noroviruses. This raises public health concerns that pigs may be reservoirs for emergence of epidemic human norovirus strains. This article reviews the discovery of porcine noroviruses and sapoviruses, their classification, diagnosis, epidemiology and genetic and antigenic relatedness to human caliciviruses.

Prevalence of Noroviruses and Sapoviruses in Swine of Various Ages Determined by Reverse Transcription-PCR and Microwell Hybridization Assays

Noroviruses (NoVs) and sapoviruses (SaVs) are emerging enteric pathogens that cause diarrhea in humans and animals. Porcine genogroup II (GII) NoVs replicate in pigs, but their pathogenesis is undefined. The porcine SaV/GIII/Cowden/80/US strain causes diarrhea and intestinal lesions in pigs. Recently, genetically diverse porcine NoVs (genotypes 11, 18, and 19 within GII) and SaVs comprising at least two genogroups (GIII and GVI?/JJ681-like) and two unclassified strains (G?/QW19 and G?/LL26) were identified; however, their prevalence has not been reported. To investigate the prevalence of porcine NoVs and SaVs, 621 fecal samples were collected from swine of various ages from seven swine farms and one slaughterhouse in three states in the United States. Fecal samples were tested by reverse transcription-PCR and microwell hybridization assays with porcine NoV- and SaV-specific primers and probes, respectively. Porcine GII NoVs were detected exclusively from finisher pigs with an overall prevalence of 20%. Porcine GIII SaVs were detected in 62% of pigs, with the highest prevalence in postweaning pigs and lowest in nursing pigs. Porcine GVI?/JJ681-like SaVs and the G?/QW19-like SaVs were detected infrequently in pigs. The G?/LL26-like SaVs were detected mainly in younger pigs. Because some porcine NoVs and SaVs are genetically or antigenically related to human strains and recombinants within NoVs or SaVs occur for human and pig strains, the high prevalence and subclinical infection rate of these viruses in pigs raise questions of whether pigs may be reservoirs for human strains or for the emergence of new human and porcine recombinants.

Genetic Diversity and Recombination of Porcine Sapoviruses

Sapoviruses (SaVs) are emerging enteric pathogens that cause diarrhea in humans and animals. Human SaVs are genetically variable and have been classified into four genogroups (GI, -II, -IV, and -V). To date, only two genetically similar porcine SaV strains have been reported that belong to GIII. To investigate the genetic diversity of porcine SaVs and their genetic relatedness to human strains, we sequenced 286 nucleotides (nt) of the RNA-dependent RNA polymerase (RdRp) region of nine porcine SaVs detected from field pig fecal samples collected in U.S. swine farms during the period from 1999 to 2003. One strain (Po/SaV/MI-QW19/2002/US) was most closely related to human GII SaVs. We also sequenced 3 kb of the viral genome, including the partial RdRp (766 to 790 nt), the complete capsid, the ORF2 and the 3'-untranslated region of four strains representative for the positive farms or for the distinct genetic clusters. From the sequence analysis of the complete capsid, we identified a potential new genogroup of porcine SaVs, with Po/SaV/OH-JJ681/00/US as the representative strain. Furthermore, two potential porcine SaV recombinants were identified. To our knowledge this is the first report of a porcine SaV strain more closely related genetically to human SaVs and the occurrence of porcine SaV recombinants. The presence of porcine SaVs more similar to human SaVs is a significant finding because of the potential for zoonotic infections or generation of porcine/human recombinants if intragenogroup human strains exist.

Development of a new microwell hybridization assay and an internal control RNA for the detection of porcine noroviruses and sapoviruses by reverse transcription-PCR

Recently, genetically diverse porcine noroviruses (NoV) and sapoviruses (SaV) were identified from field pig fecal samples. Reverse transcription (RT)-PCR is the primary method used for detection of human NoVs and SaVs. However, RT-PCR inhibitors frequently cause false-negative results. In this study, a competitive internal control (IC) RNA, specific for use in the SaV RT-PCR assay, was developed to monitor inhibition of RT-PCR; primers for detection of genetically diverse porcine NoVs and SaVs were designed; and microwell hybridization assays to confirm the specific RT-PCR products were developed. The primer pairs and the RT-PCR–hybridization combinations were compared using representative porcine NoV and SaV strains, positive pig fecal samples and a panel of 30 field pig fecal samples. Extracted RNA from 3 of 30 samples failed to amplify the IC RNA. However, this inhibition was not present after a 10-fold dilution of the extracted RNA. The five different RT-PCR–hybridization combinations developed specifically detected all three genotypes of porcine NoVs, all GIII porcine SaVs, unclassified JJ681-like, QW19 and LL26-like porcine SaVs, respectively. These RT-PCR–hybridization assays are specific, less time consuming and economical and particularly applicable to testing large number of samples for porcine NoVs and SaVs.