Detection and genetic diversity of porcine rotavirus A, B and C in eastern Australian piggeries

The use of oral fluids and sock samples for monitoring key pathogens in pig populations for surveillance purposes

Despite the prevalence of co-infections and the association of over 50 viral and 46 bacterial pathogens with pig diseases, little is known about their simultaneous occurrence, particularly in commercial pig farming environments where health programs are in place. To address this knowledge gap, this study aimed to evaluate the pathogen threshold of respiratory and enteric pathogens in pig herds using the Pork MultiPath™ (PMP1 and PMP2, respiratory and enteric respectively) technology, which detects multiple pathogens simultaneously in a single reaction with high sensitivity and specificity. In this study the most prevalent respiratory pathogens, Mycoplasma hyrohinis, Pasteurella multocida, and Haemophilus parasuis detected by PMP1 were effectively controlled during the nursery stage through strategic treatment with tiamulin. Even though the major respiratory incidences were reduced, the recorded coughing and sneezing rates were associated with the levels of H. parasuis and M. hyrohinis, which were set at 1356 and 1275 copies/reaction, respectively. In addition, one of the identified co-infection patterns indicated a strong relationship between the occurrence of H. parasuis and M. hyorhinis at the sample and pen levels, highlighting the high likelihood of detecting these two pathogens together. Testing with enteric panel PMP2 revealed that the most frequently detected virulence factors during the early nursery stage were Escherichia coli genes for toxins - ST1, ST2, and fimbriae - F4 and F18. Moreover, a co-infection with Rotavirus B and C was often observed during the nursery stage, and a strong positive correlation between these two markers has been identified. Additionally, the levels of several markers, namely E. coli F4, F5, F18, LT, ST1, and ST2, have been associated with a higher likelihood of sickness in pig populations. In addition, the onset of Brachyspira pilosicoli during the nursery and grower stages was found to be associated with an increased risk of diarrhoea, with a set threshold at around 500 copies/reaction. Although simultaneous detection of multiple pathogens is not yet widely used in the pig industry, it offers a significant advantage in capturing the diversity and interactions of co-infections. Testing pooled samples with Pork MultiPath™ is cost-effective and practical to regularly monitor the health status of pig populations.

Isolation and characterization of a G9P[23] porcine rotavirus strain AHFY2022 in China

Rotavirus group A (RVA) is a main pathogen causing diarrheal diseases in humans and animals. Various genotypes are prevalent in the Chinese pig herd. The genetic diversity of RVA lead to distinctly characteristics. In the present study, a porcine RVA strain, named AHFY2022, was successfully isolated from the small intestine tissue of piglets with severe diarrhea. The AHFY2022 strain was identified by cytopathic effects (CPE) observation, indirect immunofluorescence assay (IFA), electron microscopy (EM), high-throughput sequencing, and pathogenesis to piglets. The genomic investigation using NGS data revealed that AHFY2022 exhibited the genotypes G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1, using the online platform the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) (https://www.bv-brc.org/). Moreover, experimental inoculation in 5-day-old and 27-day-old piglets demonstrated that AHFY2022 caused severe diarrhea, fecal shedding, small intestinal villi damage, and colonization in all challenged piglets. Taken together, our results detailed the virological features of the porcine rotavirus G9P[23] from China, including the whole-genome sequences, genotypes, growth kinetics in MA104 cells and the pathogenicity in suckling piglets.

The vaccination changed the profile of rotavirus infection with the increase of non-rotavirus A species diagnosis in one-week-old diarrheic piglets

Porcine rotavirus (RV) is a major viral agent associated with severe diarrhea in newborn piglets. RVA, RVB, RVC, and RVH are RV species that have already been identified in pigs. RVA is considered the most prevalent and relevant virus in pig production worldwide. This study aimed to evaluate the frequency of RV infection associated with diarrhea in suckling piglets from regular RVA-vaccinated Brazilian pig herds between 2015 and 2021. Therefore, 511 diarrheic fecal samples were collected from suckling piglets aged up to 3 weeks from 112 pig farms located in three main Brazilian pork production regions. All piglets were born to RVA-vaccinated sows. The nucleic acids of RVA, RVC, and RVH were investigated by RT-PCR assays and RVB by semi-nested RT-PCR assay. Of the diarrheic fecal samples analyzed, 221/511 (43.3%) were positive for at least one of the RV species. Regarding the distribution of RV species among the positive fecal samples that presented with only one RV species, 99 (44.8%), 63 (28.5%), and 45 (20.4%) were identified as RVB, RVC, and RVA, respectively. RVH was not identified in diarrheic piglets with a single infection. More than one RV species was identified in 14/221 (6.3%) of the diarrheic fecal samples evaluated. Co-detection of RVB + RVH (11/221; 5.0%), RVA + RVB (1/221; 0.4%), RVA + RVC (1/221; 0.4%), and RVB + RVC (1/221; 0.4%) was identified in fecal samples. The results demonstrated a significant increase in the RVC and, mainly, RVB detection rates in single infections. This study allowed us to characterize the importance of other RV species, in addition to RVA, in the etiology of neonatal diarrhea in piglets from pig herds with a regular vaccination program for RVA diarrhea control and prophylaxis.