Risk factors for rotavirus infection in pigs in Busia and Teso subcounties, Western Kenya

Abstract

We analysed data that were previously collected for molecular characterisation of rotavirus (RV) groups A and C in pigs from Teso and Busia subcounties in Kenya to determine risk factors for its infection. The data included records from 239 randomly selected piglets aged between 1 and 6 months raised in free range and backyard production systems. RV infection was confirmed by screening of fresh faecal samples by using reverse transcription polymerase chain reaction (RT-PCR); selected positive samples were subsequently sequenced and used for phylogenetic analysis. In this analysis, RV infection status was used as outcome variable, while the metadata collected at the time of sampling were used as predictors. A Bayesian hierarchical model which used integrated nested Laplace approximation (INLA) method was then fitted to the data. The model accounted for the spatial effect by using stochastic partial differential equations (SPDEs). Of the 239 samples screened, 206 were available for the analysis. Descriptive analyses showed that 27.7 % (57/206) of the samples were positive for rotaviruses groups A and C, 18.5 % were positive for group A rotaviruses, 5.3 % were positive for group C rotaviruses, while 3.9 % had co-infections from both groups of rotaviruses. The spatial effect was insignificant, and a simple (non-spatial) model showed that piglets (≤4 months) and those pigs kept in free range systems had higher risk of exposure to rotavirus infection as compared to older pigs (>4 months) and those tethered or housed, respectively. Intervention measures that will target these high-risk groups of pigs will be beneficial to farmers.

Porcine Rotaviruses: Epidemiology, Immune Responses and Control Strategies

“…Infections by RVAs are confirmed in pigs worldwide with or without association with diarrhea [63,64,65,66,67,68,69,70,71,72,73,74]. RVA prevalence rates in pigs vary from 3.3% to 67.3% without evidence of seasonality, but with spatio-temporal fluctuations and re-emergence of certain genotypes, including G9 and G1 [67,71,75,76,77,78,79,80,81,82,83,84,85,86,87], with farm-level prevalence reaching 61%–74% [73,74].…”

A G3P[13] porcine group A rotavirus emerging in China is a reassortant and a natural recombinant in the VP4 gene

“…Infections are confirmed in piglets by the association of RVAs with diarrhoea worldwide. An analysis of molecular characterization data for RVAs in Kenya showed that 18.5% of pigs were positive for RVA (Amimo, Otieno, Okoth, Onono, & Bett, ). RVA is an important pathogen for diarrhoea in Belgian suckling pigs (Amimo et al., ).…”

Co-Surveillance of Rotaviruses in Humans and Domestic Animals in Central Uganda Reveals Circulation of Wide Genotype Diversity in the Animals

“…We found a difference in rotavirus prevalence in the different sub-counties. A study in Kenya found a difference in rotavirus prevalence depending on whether the animals were free range or housed [ 29 ]. We need to carry out further studies to understand the differences in animal husbandry in the different sub-counties that may account for the difference in the observed rotavirus infection.…”

“…A subset of rotavirus ELISA negative samples (60 samples) from animals aged 2 months and below was also screened using the NSP3 real-time RT-PCR for quality control of ELISA testing. Samples from younger animals were tested because these were more likely to be positive for rotavirus, as per previous reports [ 29 ].…”