First description and phylogenetic analysis of coxsackie virus A non‐polio enteroviruses and parechoviruses A in South Sudanese children

Abstract

AbstractEnteroviruses (EV) and parechoviruses A (PeV‐A) are commonly circulating viruses able to cause severe disease. Surveillance studies from sub‐Saharan Africa are limited and show high but variable infection rates and a high variation in genotypes. This is the first study to describe EV and PeV‐A circulation in children in South Sudan. Of the fecal samples collected, 35% and 10% were positive for EV and PeV‐A, respectively. A wide range of genotypes were found, including several rarely described EV and PeV‐A types. Coxsackie virus A (CVA) EV‐C types, particularly CVA13, were the most dominant EV types. The CVA13 types had a high diversity with the majority belonging to four different previously described clusters. PeV‐A1 and ‐A14 were the most common PeV‐A genotypes. A lack of representative data from our and other studies from sub‐Saharan Africa demonstrates the need for more systematic surveillance of non‐polio EV and PeV‐A types in this region.