Search Results (22)

Porcine epidemic diarrhea virus (PEDV) presents a substantial challenge to the global swine industry. However, the origin, host range, and potential cross-species transmission of PEDV remain poorly understood. This study characterizes a novel PEDV strain, CHFJFQ, isolated from diarrheic piglets in Fuqing, Fujian, China. Through sequencing and phylogenetic analysis, we determined that CHFJFQ belongs to the GIIa subgroup and is a recombinant with CH/HNXX/2016 as the major parent and NW17 as the minor parent. Compared to CV777, CHFJFQ exhibits multiple base deletions and insertions across the 5′UTR, ORF1a/b, S, and ORF3 genes. Phylogenetic analysis indicates shared ancestry with bat coronaviruses, though a direct zoonotic origin remains uncertain. Interestingly, CHFJFQ demonstrated its ability to infect human and mouse cell lines in vitro and, more significantly, caused in vivo infection in both pigs and mice. The primary target organs were the intestines, lungs, and spleen, resulting in 100% mortality in suckling piglets. PEDV CHFJFQ was detected in mouse tissues, but no clinical signs were observed, indicating limited cross-species pathogenicity. Overall, these findings offer crucial insights into the epidemiology, genetics, infectivity, and pathogenicity of PEDV and provide valuable information for vaccine development. Full article

Caliciviruses including noro- and sapoviruses of family Caliciviridae are important enteric human and swine pathogens, while others, like valoviruses, are less known. In this study, we developed a detection and typing pipeline for the most prevalent swine enteric caliciviruses—sapovirus GIII (Sw-SaV), norovirus GII (Sw-NoV), and valovirus GI (Sw-VaV). The pipeline integrates triplex RT-qPCR, 3′RACE semi-nested PCR, and next-generation sequencing (NovaSeq, Illumina) techniques. A small-scale epidemiological investigation was conducted on archived enteric and, for the first time, on oral fluid/saliva samples of diarrheic and asymptomatic swine of varying ages from Hungary and Slovakia. In enteric samples, Sw-SaV was the most prevalent, detected in 26.26% of samples, primarily in diarrheic pigs with low Cq values, followed by Sw-NoV (2.53%) in nursery pigs. In oral fluid samples, Sw-NoV predominated (7.46%), followed by Sw-SaV (4.39%). Sw-VaVs were sporadically found in both sample types. A natural, asymptomatic Sw-SaV outbreak was retrospectively detected where the transient shedding of the virus was <2 weeks. Complete capsid sequences (n = 59; 43 Sw-SaV, 13 Sw-NoV, and 3 Sw-VaV) including multiple (up to five) co-infecting variants were identified. Sw-SaV sequences belong to seven genotypes, while Sw-NoV and Sw-VaV strains clustered into distinct sub-clades, highlighting the complex diversity of these enteric caliciviruses in swine. Full article

Porcine stool-associated RNA virus (Posavirus) is an unclassified virus with sequence similarity to viruses in the order of Picornaviridae. In China, lineage 1 Posavirus (Posavirus 1) has been circulating in the field since its initial emergence in 2014 however no other lineages have been reported. To investigate the genetic diversity of Posavirus in China, 1200 diarrheic samples were collected from pigs in China. Following high-throughput and Sanger sequencing, one complete genome sequence of a Posavirus (designated SC01) strain was obtained. The genome of SC01 strain was 10217 nucleotides in length and encoded a polyprotein of 3346 amino acids. Genome comparative analysis revealed that SC01 shared 85.6% nucleotide similarity to Posavirus 2 strains, but only 35.2–58.0% sequence identity with Posavirus 1 and 3–12 strains. Phylogenetic analysis showed that the SC01 was classified in Posavirus 2 and clustered into a separate branch with the American Posavirus 2 isolates, indicating that the SC01 is a Posavirus 2 strain. Notably, a novel 1-amino acid deletion was observed in polyprotein at amino acid position 147. This is the first report of the presence of Posavirus 2 in China, and the genomic data of SC01 provides insights into the genetic diversity and evolution of Posavirus in the region. Full article

Porcine epidemic diarrhea virus (PEDV), porcine transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and porcine rotavirus-A (PoRVA) are the four main pathogens that cause viral diarrhea in pigs, and they often occur in mixed infections, which are difficult to distinguish only according to clinical symptoms. Here, we developed a multiplex TaqMan-probe-based real-time RT-PCR method for the simultaneous detection of PEDV, TGEV, PDCoV, and PoRVA for the first time. The specific primers and probes were designed for the M protein gene of PEDV, N protein gene of TGEV, N protein gene of PDCoV, and VP7 protein gene of PoRVA, and corresponding recombinant plasmids were constructed. The method showed extreme specificity, high sensitivity, and excellent repeatability; the limit of detection (LOD) can reach as low as 2.18 × 10² copies/μL in multiplex real-time RT-PCR assay. A total of 97 clinical samples were used to compare the results of the conventional reverse transcription PCR (RT-PCR) and this multiplex real-time RT-PCR for PEDV, TGEV, PDCoV, and PoRVA detection, and the results were 100% consistent. Subsequently, five randomly selected clinical samples that tested positive were sent for DNA sequencing verification, and the sequencing results showed consistency with the detection results of the conventional RT-PCR and our developed method in this study. In summary, this study developed a multiplex real-time RT-PCR method for simultaneous detection of PEDV, TGEV, PDCoV, and PoRVA, and the results of this study can provide technical means for the differential diagnosis and epidemiological investigation of these four porcine viral diarrheic diseases. Full article

Postweaning diarrhea (PWD) is a multifactorial concern in the swine industry that leads to high antibiotic consumption, usually without testing susceptibility, increasing the risk of the selection of Escherichia coli-resistant strains. In this study, 251 E. coli strains isolated from fecal samples of diarrheic (n = 148) and apparently healthy piglets (n = 103) in farms in Catalonia were tested against their susceptibility to fourteen different antimicrobials. The phenotypic antimicrobial resistance (AMR) testing revealed high levels of AMR, with 41.4% of the isolates presenting a multidrug-resistant (MDR) profile. More specifically, resistance to class D (prudence) antimicrobials such as erythromycin (99.6%), amoxicillin (95.2%), streptomycin (91.6%), tetracycline (88.8%), lincospectin (64.5%), and sulfamethoxazole/trimethoprim (60%) was very high, as well as to class C (caution) antimicrobials such as florfenicol (45%). A special concern was observed for antimicrobial category B (restrict), like quinolones and colistin, that both presented a high rate of resistance. Colistin use was substantially reduced in Spain, but resistance is still present in weaned pigs, presenting a MIC90 of 4 μg/mL. This suggests that reducing antibiotic use is not enough to eliminate this AMR. Finally, it was found that piglets suffering diarrhea were more commonly carriers of MDR strains than the healthy ones (49.3% vs. 35%, p = 0.031). Therefore, given the high rates of resistance to the most commonly used antimicrobials, especially in diseased pigs, a new non-antibiotic-based approach should be implemented for the management of PWD. Full article

Porcine kobuvirus (PKV) is an enteric virus commonly detected in both diarrheic and healthy pigs. Little is known about the role of PKV in enteric diseases. In this study, an epidemiological investigation based on 324 intestinal samples collected from six provinces of China during the period of 2018 to 2022 was performed, and showed that PKV has an overall 65.43% (212/324) positive rate. Noticeably, 89.47% (17/19) of PKV and porcine epidemic diarrhea virus (PEDV) double-positive pigs were clinically diseased, while 91.71% (177/193) of PKV-positive but PEDV-negative pigs were clinically healthy, suggesting that PKV infection in itself is unlikely to cause enteric diseases. In addition, three PKV genomes were obtained from both diseased and healthy pigs. Phylogenetic analysis showed that Chinese PKV strains could be divided into three groups (SH-W-CHN-like, S-1-HUN-like and JXAT2015-like strains). All three obtained PKV genomes belong to SH-W-CHN-like strains and JSYZ1806-158 was detected as a recombinant virus. Furthermore, multiple comparisons showed that nucleotide similarities are clearly lower than amino acid similarities for PKV polyproteins. Selective pressure analysis indicated that Chinese PKV polyproteins are predominantly under negative selection. Overall, this study provided new insights into the prevalence and evolution of PKV in both diarrheic and healthy pigs in China. Full article

(1) Background: Piglet diarrhea is one of the most serious diseases in pigs and has brought great economic losses to the pig industry. Alteration of the gut microbiota is an important factor in the etiology of piglet diarrhea. Therefore, this study aimed to analyze the differences in the gut microbial structures and fecal metabolic profile between post-weaning diarrhea and healthy Chinese Wannan Black pigs. (2) Methods: An integrated approach of 16S rRNA gene sequencing combined with LC/MS-based metabolomics was employed in this study. (3) Results: We found an increase in the relative abundance of the bacterial genus Campylobacter and a decrease in phylum Bacteroidetes and the species Streptococcus gallolyticus subsp. macedonicus. (S. macedonicus) in piglet diarrhea. Meanwhile, obvious changes in the fecal metabolic profile of diarrheic piglets were also detected, particularly higher levels of polyamines (spermine and spermidine). Moreover, there were substantial associations between the disturbed gut microbiota and the altered fecal metabolites, especially a strong positive relationship between spermidine and Campylobacter. (4) Conclusions: These observations may provide novel insights into potential etiologies related to post-weaning diarrhea and further enhance our understanding of the role of gut microbiota in host homeostasis and in modulating gut microbial structure. Full article

Porcine epidemic diarrhea virus (PEDV) is a major causative pathogen of diarrheic disease. In this study, the prevalence and evolution of PEDV was evaluated using intestinal samples collected from six provinces of China in 2019–2022. PEDV could not only be detected in diarrheic piglets but also in adult pigs without enteric diseases. The complete genomes of five temporal and geographical representative PEDV strains were determined. Genome-based phylogenetic analysis indicated that XJ1904-700 belongs to the G2-a subgroup, while the other strains are clustered within the S-INDEL subgroup. Recombination analyses supported that JSNJ2004-919 is an inter-subgroup recombinant from SD2014-like (G2-b), CHZ-2013-like (G2-b) and CV777-like (G1-b) isolates, while FJFZ2004-1017 is an intra-subgroup recombinant from XM1-2-like (S-INDEL) and LYG-2014-like (S-INDEL) isolates. Both JSNJ2004-919 and FJFZ2004-1017 were from adult pigs, providing evidence that adult pigs may also serve as the host of PEDV reservoirs for virus evolution. Overall, this study provides new insights into PEDV’s prevalence and evolution in both diseased piglets and clinically healthy adult pigs. Full article

Since porcine kobuvirus (PKV) was first described in 2008, researchers have speculated whether the virus is of clinical importance. This systematic literature review answers the question: Is porcine kobuvirus a cause of gastrointestinal disease in young pigs? A case-control study showed that PKV was not associated with neonatal diarrhea. A cohort study suffered from a very small sample size (n = 5), and in an experimental trial, the effect of PKV inoculation could not be separated from the effect of being inoculated with porcine epidemic diarrhea virus. In 13 poorly defined observational studies, more than 4000 young pigs had been assigned a diarrhea status and their feces analyzed for PKV. Unfortunately, the studies lacked well-characterized unbiased samples, and thus the strongest possible inference from these studies was that a very strong association between PKV and diarrhea is unlikely. PKV was commonly detected in non-diarrheic pigs, and this could indicate that PKV is not a sufficient cause in itself or that reinfection of individuals with some immunological protection due to previous infections is common. Conclusively, there is a lack of good evidence of PKV being a cause of gastrointestinal disease, but the sparse available evidence suggests that PKV is of limited clinical importance. Full article

The increasing detection of Porcine circovirus 3 (PCV3, family Circoviridae) in clinically ill pigs worldwide has raised concerns on the implications of the virus on porcine health and the pork industry. Although pork production constitutes an important component of the livestock economy and is a major source of animal protein in the Caribbean Islands, there are no reports on PCV3 in pigs from the region so far. In the present study, PCV3 was detected in 21% (21/100) of diarrheic pigs (sampled at three farms) from the Caribbean nation of the Dominican Republic (DR). Although the sample size varied between porcine age groups, the highest PCV3 detection rates (35.3% each, respectively) were observed in piglets and growers. Co-infections with PCV2 and porcine adenovirus were observed in 38.09% and 9.52% of the PCV3 positive samples, respectively. The complete genomes of 11 DR PCV3 strains were analyzed in the present study, revealing a unique deletion (corresponding to nucleotide residue at position 1165 of reference PCV3 sequences) in one of the DR PCV3 sequences. Based on sequence identities and phylogenetic analysis (open reading frame 2 and complete genome sequences), the DR PCV3 strains were assigned to genotype PCV3a, and shared high sequence homologies (>98% identities) between themselves and with those of other PCV3a (Clade-1) strains, corroborating previous observations on the genetic stability of PCV3 worldwide. To our knowledge, this is the first report on the detection and molecular characterization of PCV3 in pigs from the Caribbean region, providing important insights into the expanding global distribution of the virus, even in isolated geographical regions (the Island of Hispaniola). Our findings warrant further investigations on the molecular epidemiology and economic implications of PCV3 in pigs with diarrhea and other clinical conditions across the Caribbean region. Full article

Human rotavirus (HRV) is a leading cause of gastroenteritis in children under 5 years of age. Licensed vaccines containing G1P[8] and G1-4P[8] strains are less efficacious against newly emerging P[6] strains, indicating an urgent need for better cross protective vaccines. Here, we report our development of a new gnotobiotic (Gn) pig model of P[6] HRV infection and disease as a tool for evaluating potential vaccine candidates. The Arg HRV (G4P[6]) strain was derived from a diarrheic human infant stool sample and determined to be free of other viruses by metagenomic sequencing. Neonatal Gn pigs were orally inoculated with the stool suspension containing 5.6 × 10⁵ fluorescent focus units (FFU) of the virus. Small and large intestinal contents were collected at post inoculation day 2 or 3. The virus was passaged 6 times in neonatal Gn pigs to generate a large inoculum pool. Next, 33–34 day old Gn pigs were orally inoculated with 10⁻², 10³, 10⁴, and 10⁵ FFU of Arg HRV to determine the optimal challenge dose. All pigs developed clinical signs of infection, regardless of the inoculum dose. The optimal challenge dose was determined to be 10⁵ FFU. This new Gn pig model is ready to be used to assess the protective efficacy of candidate monovalent and multivalent vaccines against P[6] HRV. Full article

Porcine group A rotavirus (PoRVA; family, Reovirideae) strains cause acute viral gastroenteritis in piglets (especially suckling and weaned pigs), resulting in significant economic losses. In this study, we analyzed the VP7 and VP4 genes of PoRVA isolated between 2014 and 2018 from domestic pigs in South Korea to investigate the prevalence of predominant circulating genotypes (G and P types). The prevalence of the PoRVA antigen in the diarrheic fecal samples was 14.1% (53/377). Further genetic characterization of the VP7 and VP4 genes of 53 PoRVA isolates identified six different G-genotypes and five different P genotypes. The G4 and G9 genotypes were the most common (each 39.6%) in PoRVA-positive pigs, followed by P[7] and P[6] (33.9% and 30.1%, respectively). Because the G5 and G9 genotype vaccines are currently mainly used in South Korea, this result provides valuable epidemiological information about the genetic characteristics of PoRVA circulating on domestic pig farms. Development of a novel PoRVA vaccine that targets the current strains circulating in South Korea may be required for more effective virus control on pig farms. Full article

Since the first report on isolation of porcine adenovirus serotype 5 (PAdV-5, species Porcine mastadenovirus C (PAdV-C)) from pigs with respiratory illness in Japan in 1987, PAdV-5 have been detected in a few fecal samples from healthy pigs and in some environmental samples. To date, only a single PAdV-5 strain (isolate HNF-70 from 1987) has been analyzed for the complete genome. We report here high detection rates of PAdV-5 (25.74%, 26/101 fecal samples) in diarrheic pigs at 3 different farms in the Caribbean country of Dominican Republic. After a long gap, the complete deduced amino acid sequences of the DNA-dependent DNA polymerase (pol) and hexon of two PAdV-5 strains (GES7 and Z11) were determined, revealing >99% sequence identities between PAdV-5 strains (HNF-70, GES7 and Z11) detected in different parts of the world and during different time periods (1987, and 2020–2021). By phylogenetic analysis, the putative hexon and pol of HNF-70, GES7 and Z11 exhibited similar clustering patterns, with the PAdV-5 strains forming a tight cluster near ruminant AdVs, distinct from the species PAdV-A and -B. GES7 and Z11 retained the various conserved features present in the putative pol and major late promoter region of HNF-70. Considering the paucity of data on current epidemiological status and genetic diversity of PAdV in porcine populations, our findings warrant similar studies on PAdV-5 and other PAdVs in clinically ill and healthy pigs. To our knowledge, this is the first report on detection and molecular characterization of PAdV-5 (PAdV-C) from diarrheic pigs. Full article

We report here high rates (47.5%, 48/101) of detection of porcine circovirus 2 (PCV2) in diarrheic pigs from three pig farms in the Dominican Republic. Seventeen of the PCV2 positive samples, representing the three pig farms, different age groups and sampling periods (2020–2021), were amplified for the complete PCV2 genome. Based on analysis of open reading frame 2 and complete genome sequences, the 17 PCV2 strains were assigned to the PCV2d genotype. Significant differences were observed in PCV2 detection rates between the vaccinated (20% (10/50)) and unvaccinated (62.5% (10/16) and 80% (28/35)) farms, corroborating previous observations that PCV2a-based vaccines confer protection against heterologous PCV2 genotypes. The present study is the first to report detection and molecular characterization of PCV2 from the Dominican Republic, warranting large-scale molecular epidemiological studies on PCV2 in pig farms and backyard systems across the country. For the first time, PCV2d was identified as the predominant PCV2 genotype in a study from the Caribbean region, suggesting that a genotype shift from PCV2b to PCV2d might be happening in the Caribbean region, which mirrored the current PCV2 genotype scenario in many other parts of the world. Besides PCV2, we also identified a pigeon circovirus-like virus, and a circular Replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus, which was characterized for the complete genome. The CRESS DNA virus shared a similar genomic organization and was related to unclassified CRESSV2 DNA viruses (belonging to the Order Cirlivirales) from porcine feces in Hungary, indicating that related unclassified CRESS DNA viruses are circulating among pigs in different geographical regions, warranting further studies on the epidemiology and biology of these novel viruses. Full article

Entamoeba spp. is a common zoonotic intestinal protozoan that can parasitize most vertebrates, including humans and pigs, causing severe intestinal diseases and posing a serious threat to public health. However, the available data on Entamoeba spp. infection in pigs are relatively limited in China. To characterize the infection of Entamoeba spp. within pigs in southern China, 1254 fecal samples of diarrheic pigs were collected from 37 intensive pig farms in Hunan, Jiangxi and Fujian provinces and the infection of Entamoeba spp. was investigated based on the small subunit rRNA (SSU rRNA) gene. The overall infection rate of Entamoeba spp. was 58.4% (732/1254), including 38.4% (118/307) in suckling piglets, 51.2% (153/299) in weaned piglets, 57.9% (55/95) in fattening pigs and 73.4% (406/553) in sows, respectively. Moreover, age and the sampling cities in Jiangxi and Fujian provinces were found to be the key factors influencing the infection of Entamoeba spp. (p < 0.05). Two subtypes (ST1 and ST3) with a zoonotic potential of Entamoeba polecki and Entamoeba suis were detected in all age groups of pigs and all sampling areas, with the predominant species and predominant subtype being E. polecki (91.3%, 668/732) and E. polecki ST1 (573/668), respectively, and E. polecki ST1 + E. polecki ST3 (78.6%, 239/304) being the most frequently detected form of mixed infection. Severe Entamoeba spp. infection and zoonotic subtypes were found in this study, exposing a large public health problem in the study area, and strategies need to be implemented to eliminate the risk in the future. Full article