Prevalence and genome characterization of porcine rotavirus A in southern Mozambique

Rotavirus A (RVA) is an important pathogen causing gastroenteritis in many species, including humans and pigs. The objective of this study was to determine the prevalence of RVA in pigs from smallholdings and commercial farms in southern Mozambique and characterize the complete genomes of selected strains. RVA was detected at a rate of 11.8% (n = 288), of which 7.6% was detected at commercial farms and 4.2% at smallholdings. The whole genomes of eight rotavirus strains were determined using an Illumina MiSeq platform. Seven displayed a G9P[13] and one a G4P[6] genotype combination, all with a typical porcine backbone (I1/5-R1-C1-M1-A1/8-N1-T1/7-E1-H1). Phylogenetic analysis indicated that the seven G9P[13] strains were in fact one strain that circulated on a commercial pig farm. The genome segments of this strain clustered with diverse segments of human and porcine RVA strains from various Asian countries. Analysis of the G4P[6] strain revealed four distinct genome segments (VP2, VP4, VP6 and VP7) and five genome segments closely related to South African porcine rotavirus strains (NSP1, NSP3, NSP4, NSP5 and VP1). These results suggest that both the G4P[6] and the G9P[13] strains possibly emerged through multiple reassortment events. The presence of these strains on the commercial farms and smallholdings calls for a more in-depth surveillance of rotavirus in Mozambique.

• Prevalence of porcine RVA in southern Mozambique was determined as 11.8%.

• Commercial farms had a prevalence of 12.2% and smallholdings 11.1%.

• RVA G4P[6] and G9P[13] genotypes with typical porcine backbones were identified.

• Mozambican porcine strains possibly emerged through multiple reassortment events.