Analysis of the excretion dynamics and genotypic characteristics of rotavirus A during the lives of pigs raised on farms for meat production

Genomic diversity of group A rotaviruses from wild boars and domestic pigs in Japan: wide prevalence of NSP5 carrying the H2 genotype

Group A rotavirus (RVA) sequences were detected in 10.8% (23/212) and 20.7% (87/421) of fecal samples collected in 2017-2022 from wild boars and domestic pigs, using next-generation sequencing. Complete genome sequence analysis of one wild boar and 13 domestic pig RVAs revealed that six of them carried the rare H2 NSP5 genotype. Out of the 39 samples for which the NSP5 genotype could be determined, 23 (59.0%) were of genotype H2. H2 porcine RVAs consist exclusively of Japanese porcine RVAs and exhibit sequence diversity in each segment, suggesting that H2 porcine RVAs may have evolved through reassortment within the Japanese pig population.

Temporal variations of human and animal Rotavirus A genotypes in surface water used for drinking water production

Rotavirus is a major cause of gastroenteritis among infants and children. In this study, nested PCR assays were developed to amplify partial regions of the VP7, VP4, and VP6 genes of Rotavirus A (RVA) for amplicon-based Illumina MiSeq sequencing to investigate RVA genotypes in environmental water samples. Eight sets of inner primers were first designed and screened for use in the nested PCR assays, and four sets of them could produce amplicons. Six sets of outer primers were then designed and combined with the four sets of inner primers that worked. The assays were evaluated for sensitivity using raw water samples collected from one drinking water treatment plant between April 2019 and March 2020 (Sample Set 1; N = 12) and seven DWTPs between 2018 and 2020 (Sample Set 2; N = 18). In total, 43 amplicons from Set 1 were sequenced and diverse sequences from human, porcine, bovine, equine, and feline RVA were observed. Human G8, G3, and G2 genotypes were obtained, with G8 predominant (relative abundance, 36–87%) in samples taken during the rotavirus epidemic season between April and June. Porcine G5, G11, and G4, and bovine G10 and G6 genotypes were also detected. VP4 sequence analysis revealed that the human P[8] genotype was present throughout the year, whereas P[4] and P[9] were present only in the epidemic season. The vaccine strains P[5] and P[8] (RotaTeq®) were also detected. Our approach enables the identification of prevalent human and animal RVA genotypes and their host species that potentially caused fecal contamination in water sources.

High genetic diversity of species A rotaviruses detected in swine farms in Chile

Rotavirus A is one of the main causative agents of diarrhoea in lactating and weaned pigs worldwide. Its impact in the swine industry is well documented. However, in Chile, the current epidemiological status of rotavirus on porcine farms is unknown. This study evaluated the current epidemiologic status of rotavirus A infection in Chile using on-farm detection techniques, electrophoretic confirmation, genotyping and phylogenetic clustering by analysis of partial sequences of VP4 and VP7 genes. Rotavirus A was detected in four out of five farms with an overall prevalence of 17.7 % in diarrhoeic pigs. The average age of diarrhoea onset was at 32±6.2 days, corresponding to weaning pigs, and rotavirus was not detected in lactating piglets. Molecular characterization indicated that genotypes G5, G3, P[7] and P[13] are currently the most widely represented on these pigs farms. The phylogenetic analysis showed that farms shared similar G types (VP7), which might denote a common origin. Meanwhile, [P] types (VP4) showed considerable genetic diversity, and this might represent a high rate of reassortment of this genetic segment in rotavirus circulating in the researched area. These findings demonstrate the importance of considering both the geographical and production factors to accurately determine rotavirus prevalence status at the national level, and have relevant implications in determining effective strategies for rotavirus infection control on porcine farms.

Efficacy of disinfectants against porcine rotavirus in the presence and absence of organic matter

Rotavirus is an enteric pathogen that causes morbidity and mortality in young mammals, including pigs. Outbreaks of rotavirus on commercial farms have a significant economic impact in terms of losses in production. Effective cleaning and disinfection along with good farm management can reduce rotavirus contamination in the environment, and decrease the chance of outbreaks of disease. This study investigated the efficacy of six commercial disinfectants against MS2 bacteriophage and Group A porcine rotavirus, in the presence of high and low levels of organic matter to simulate the farm environment. A phenolic-based disinfectant (Bi-OO-cyst) was effective at all levels of organic matter concentrations. Iodophore-based disinfectants did not have a significant virucidal effect against rotavirus under any conditions. For peroxygen compound-based disinfectants and glutaraldehyde-based disinfectants, organic matter load made a significant difference in reducing efficacy. This highlights the importance of thorough cleaning with detergent before disinfection to reduce viral contamination on the farm and decrease rotavirus disease incidence in pigs.

SIGNIFICANCE AND IMPACT OF THE STUDY

Infection of rotavirus has a negative impact on the health and growth of pigs in production. Given that the virus is transmitted faecal-orally, use of an effective disinfectant on farm, which works even in high organic matter, has the potential to save costs in terms of outbreaks of disease and viral contamination. Here, we test a number of commercial disinfectants of which one a phenolic compound, Bio-OO-cyst, shows effectivity even in high organic matter, implying its use could have a huge impact in reducing viral contamination and preventing losses in production.

Great genetic diversity of rotaviruses detected in piglets with diarrhea in Thailand

A total of 491 fecal specimens collected from diarrheic piglets in Thailand from January 2011 to March 2014 were screened for group A rotavirus by RT-PCR assay. The G and P genotypes of the detected rotaviruses were determined by multiplex PCR or nucleotide sequencing. Group A rotaviruses were detected in 113 out of 491 (23.0 %) fecal specimens. A wide variety of G-P genotype combinations were identified, and G4P[13] was the most prevalent genotype combination (29.2 %), followed by G4P[23] (14.1 %), G5P[23] (11.5 %), G4P[6] (9.7 %), G3P[23] (7.0 %), G5P[13] (6.1 %), G3P[13] (4.4 %), G3P[6] (2.7 %), and G5P[6] (2.7 %). In addition, the other G-P combinations were also detected at a low percentage, including G3P[19], G4P[7], G9P[19], G9P[23], G9P[7], G4P[19], and G11P[13] strains. This study indicated that group A rotaviruses are a common causes of diarrhea in piglets and a great diversity of G and P genotype combinations are circulating in piglets in Thailand.

Persistence of clinical signs associated with rotavirus following an outbreak of porcine epidemic diarrhea (PED) on a farrow-to-grow swine operation in southwestern Ontario

Clinical signs attributed to porcine epidemic diarrhea (PED) persisted for several months in a southwestern Ontario farm following an outbreak of PED. Extensive testing revealed rotavirus infection and absence of PED in nursing and nursery pigs, highlighting the importance of repeated diagnostic testing following a disease outbreak.

Isolation of an unusual G26P[13] group A rotavirus strain from piglets with diarrhea in Brazil

This report describes the identification of an unusual G26P[13] genotype combination in a porcine group A rotavirus (RVA) strain. In a retrospective study, the VP7 (G type) and VP4 (P type) genes of porcine RVA Brazilian field strains identified in two diarrheic suckling piglets were amplified by RT-PCR and subjected to sequencing. The sequence analysis revealed the G26P[13] RVA genotype in one strain (BRA381) and G26P[X] in the other (BRA382). This study presents evidence of porcine RVA G26 genotype circulating in a Brazilian pig herd.

Diversity of group A rotavirus on a UK pig farm

Group A rotaviruses (GARV) are a significant cause of enteritis in young pigs. The aim of this study was to extend our understanding of the molecular epidemiology of porcine GARV in the UK by investigating the genetic diversity of GARV on a conventional farrow-to-finish farm. Faecal samples were obtained from six batches of pigs in 2009 and 8 batches in 2010, when the pigs were 2, 3 (time point omitted in 2009), 4, 5, 6 and 8 weeks of age. Presence of rotavirus was detected by reverse transcriptase-polymerase chain reaction (RT-PCR) in 89% and 80% of samples from 2009 and 2010, respectively. A combination of multiplex PCRs and sequencing identified four VP7 genotypes (G2, G3, G4 and G5) and three VP4 genotypes (P[6], P[7] and P[32]) present in almost every combination over the 2 years. The predominant genotype combination was G5P[32] in 2009 and G4P[32] in 2010. Conservation among the P[32] sequences between 2009 and 2010 suggests that reassortment may have led to the different genotype combinations. There were significant changes in the predominant VP7 genotype prior to weaning at 4 weeks, and post weaning when pigs were moved to a different building. Phylogenetic analysis indicated that introduction of new viruses onto the farm was limited. Taken together, these findings suggest that genetically diverse GARV strains persist within the farm environment.

H2 genotypes of G4P[6], G5P[7], and G9[23] porcine rotaviruses show super-short RNA electropherotypes

During group A rotavirus (RVA) surveillance of pig farms in Japan, we detected three RVA strains (G4P[6], G5P[7], and G9P[23] genotypes), which showed super-short RNA patterns by polyacrylamide gel electrophoresis, in samples from a healthy eight-day-old pig and two pigs of seven and eight days old with diarrhea from three farms. Reverse transcription PCR and sequencing revealed that the full-length NSP5 gene of these strains contained 952 or 945 nucleotides, which is consistent with their super-short electropherotypes. Due to a lack of whole genome data on Japanese porcine RVAs, we performed whole genomic analyses of the three strains. The genomic segments of these RVA strains showed typical porcine RVA constellations, except for H2 NSP5 genotype, (G4,5,9-P[6,7,23]-I5-R1-C1-M1-A8-N1-T1-E1-H2 representing VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5 genes). In phylogenetic analyses, these porcine RVA strains clustered with porcine and porcine-like human RVA strains and showed a typical porcine RVA backbone, except for the NSP5 gene; however, intra-genotype reassortment events among porcine and porcine-like human RVA strains were observed. The NSP5 gene segments of these strains were clustered within the H2b genotype with super-short human RVA strains. The H2 genotype has to date only been identified in human and lapine RVA strains. Thus, to our knowledge, this report presents the first case of H2 NSP5 genotype showing a super-short RNA pattern in porcine RVA. These data suggest the possibility of interspecies transmission between pigs and humans and imply that super-short porcine RVA strains possessing H2 genotype are circulating among both asymptomatic and diarrheic porcine populations in Japan.

Complete genome characterization of recent and ancient Belgian pig group A rotaviruses and assessment of their evolutionary relationship with human rotaviruses

Group A rotaviruses (RVAs) are an important cause of diarrhea in young pigs and children. An evolutionary relationship has been suggested to exist between pig and human RVAs. This hypothesis was further investigated by phylogenetic analysis of the complete genomes of six recent (G2P[27], G3P[6], G4P[7], G5P[7], G9P[13], and G9P[23]) and one historic (G1P[7]) Belgian pig RVA strains and of all completely characterized pig RVAs from around the globe. In contrast to the large diversity of genotypes found for the outer capsid proteins VP4 and VP7, a relatively conserved genotype constellation (I5-R1-C1-M1-A8-N1-T7-E1-H1) was found for the other 9 genes in most pig RVA strains. VP1, VP2, VP3, NSP2, NSP4, and NSP5 genes of porcine RVAs belonged to genotype 1, which is shared with human Wa-like RVAs. However, for most of these gene segments, pig strains clustered distantly from human Wa-like RVAs, indicating that viruses from both species have entered different evolutionary paths. However, VP1, VP2, and NSP3 genes of some archival human strains were moderately related to pig strains. Phylogenetic analysis of the VP6, NSP1, and NSP3 genes, as well as amino acid analysis of the antigenic regions of VP7, further confirmed this evolutionary segregation. The present results also indicate that the species barrier is less strict for pig P[6] strains but that chances for successful spread of these strains in the human population are hampered by the better adaptation of pig RVAs to pig enterocytes. However, future surveillance of pig and human RVA strains is warranted.

IMPORTANCE

Rotaviruses are an important cause of diarrhea in many species, including pigs and humans. Our understanding of the evolutionary relationship between rotaviruses from both species is limited by the lack of genomic data on pig strains. In this study, recent and ancient Belgian pig rotavirus isolates were sequenced, and their evolutionary relationship with human Wa-like strains was investigated. Our data show that Wa-like human and pig strains have entered different evolutionary paths. Our data indicate that pig P[6] strains form the most considerable risk for interspecies transmission to humans. However, efficient spread of pig strains in the human population is most likely hampered by the adaptation of some crucial viral proteins to the cellular machinery of pig enterocytes. These data allow a better understanding of the risk for direct interspecies transmission events and the emergence of pig rotaviruses or pig-human reassortants in the human population.

Phylogenetic analyses of the VP4 and VP7 genes of porcine group A rotaviruses in Sao Paulo State, Brazil: first identification of G5P[23] in piglets

This study determined the group A rotavirus occurrence in pig farms from 7 different cities in São Paulo State, Brazil. Out of 143 samples, 70 tested positive. Sequence analyses of 37 strains indicated that the strains had the G3, G5, G9, and P[6], P[13]/P[22]-like, and P[23] genotypes.