A highly prevalent and genetically diversified Picornaviridae genus in South Asian children

Abstract

Viral metagenomics focused on particle-protected nucleic acids was used on the stools of South Asian children with nonpolio acute flaccid paralysis (AFP). We identified sequences distantly related to Seneca Valley virus and cardioviruses that were then used as genetic footholds to characterize multiple viral species within a previously unreported genus of the Picornaviridae family. The picornaviruses were detected in the stools of >40% of AFP and healthy Pakistani children. A genetically diverse and highly prevalent enteric viral infection, characteristics similar to the Enterovirus genus, was therefore identified substantially expanding the genetic diversity of the RNA viral flora commonly found in children.

Fig. 1.

Sequence similarity detection and phylogenetic relationships of cosaviruses with other picornaviridae genera. (A) Mean divergence calculated for a sliding window of pairwise translated protein p distances between HCoSV-A1 and members of the 5 most closely related Picornaviridae genera; a separate plot of the other genera is provided in Fig. S1A. (B) Phylogenetic analysis of 3Dpol region with a representative of each picornavirus genera (2 sequences per species or genus) by neighbor-joining using amino acid p distances. Phylogenetic analysis of the 2C and P1 regions are shown in Fig. S1 B and C.

Fig. 2.

Comparisons of cosavirus and HEV diversity. Mean divergences sliding window of pairwise translated protein p distances between cosaviruses (A) and HEVs (B). Cosavirus sequences were compared with those of the 2 most closely related genera, SVV and Cardiovirus (A, blue lines). HEV sequences were compared with those of its most closely related Sapelovirus genus (B, blue line). For cosaviruses divergence were compared between species HCoSVA-D (green) and between genotypes of HCoSV-A species (red). For enteroviruses divergence was compared between species HEVA-D (green) and between genotypes of HEV-B species (red). For HEV intragenotype divergence is shown in yellow.