Detection and molecular characterization of selected swine enteric viruses in smallholder farms in Kenya and Uganda.
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Virus induced enteritis is one of the serious problems accounting for maximum deaths in neonatal animals and human throughout the world. The absence of appropriate surveillance programs and laboratory facilities have resulted in scarcity of accessible data on virus associated diarrheas in pigs in the region. This study reports the incidence of selected enteric viral infections in nursing and weaned pigs on smallholder farms. A total of 251 swine fecal samples were screened for rotaviruses (RV), caliciviruses (CaV) and kobuviruses (KoV) using RT-PCR assay. Rotaviruses, CaV and KoV were detected in 42.6%, 12.7% and 13.1% of the samples, respectively. There were incidences of mixed infections involving RV, CaV and KoV. These viruses were detected in almost equal proportions in Kenya and Uganda, an indication of their endemicity on the tested farms. More nursing piglets shed RV (85.4%) and CaV (29.3%) than weaned piglets. However, KoV was more prevalent in post weaned pigs. More pigs that were either housed & free-range (82.4%) or tethered & free-range (45.1%) were RV positive than tethered (38.3%) or free-range (12.5%) or housed (33.3%) pigs. Pigs that were entirely housed shed more KoV (33.3%) while those that were housed & tethered shed more CaV(33.3%). Age and management system affected the prevalence of viral infections with nursing and confinement presenting higher risk for enteric viral infections. Partial sequencing of VP4 gene of selected positive samples revealed that different P genotypes (P, P and P) are circulating in the study region. The P and P RV genotypes detected were genetically closely related to human strains suggesting the possibility of interspecies transmission. Genetic analysis of the kobuvirus sequence revealed that they are more variable, sharing nucleotide identity ranging from 89.7-99.1% among them. Porcine astroviruses belonging to type 2 and type 3 Mamastroviruses were detected in 3 samples sequenced. This study reports the first detection and molecular analysis of porcine rotaviruses, caliciviruses, kobuviruses and astroviruses in Africa. The presence of these gastroenteritis-producing viruses in clinically healthy pigs represents a source of infection to pigs and possibly to humans. Further research is needed to determine their role in gastrointestinal infections of pigs in this region and to determine their genetic diversity in-order to develop accurate diagnostic tools and implement appropriate control strategies to improve pig health.