First identification and whole genome characterization of rotavirus C in pigs in Zambia

Abstract

Background Rotavirus C (RVC) is a causative agent of gastroenteritis in suckling neonatal piglets. The increased prevalence of RVC infection in pig populations, and the higher genetic diversity of porcine RVC strains influence the productivity in the pig industry. Despite the clinical importance, the distribution and prevalence of RVC infection in pigs in most African countries remains unknown. In this study, we investigated the prevalence of RVC infection in pigs in Zambia. Results RVC genomes were detected in fecal samples from pigs in Zambia by metagenomic analyses. The full genome sequence of the RVC revealed two different sequences of the VP4 gene segment, implying that two different RVC strains (ZP18-77-c1 and ZP18-77-c2) were present in the same sample. Genetic analyses revealed that all segments of ZP18-77-c1 and ZP18-77-c2 showed high nucleotide sequence identities (87.7–94.5%) to reported porcine RVC strains in Asia, Africa, Europe, and North America. ZP18-77-c1 and ZP18-77-c2 strains were assigned to genotype constellations, G1-P[4]-I13-R5-C5-M1-A7-N9-T10-E5-H1 and G1-P[14]-I13-R5-C5-M1-A7-N9-T10-E5-H1, respectively, according to the whole genome classification for RVC. We further screened RVC genomes among fecal samples collected from pigs in Zambia (n = 147) by RT-qPCR. Of these, 78 samples (53.1%) were positive, and RVC genomes were detected in all the examined farms, suggesting widespread infection in Zambia. Conclusions This study demonstrated the first full genome sequence of RVC strains in Africa with a relatively high prevalence of RVC in the pig populations in Zambia. Considering the limited genetic and epidemiological information of RVC infection in African countries, further RVC surveillance is required to improve productivity in pig industry as well as to assess the potential zoonotic risk to humans and animals.