Acute diarrhea in West African children: diverse enteric viruses and a novel parvovirus genus

Abstract

Parvoviruses cause a variety of mild to severe symptoms or asymptomatic infections in humans and animals. During a viral metagenomic analysis of feces from children with acute diarrhea in Burkina Faso, we identified in decreasing prevalence nucleic acids from anelloviruses, dependoviruses, sapoviruses, enteroviruses, bocaviruses, noroviruses, adenoviruses, parechoviruses, rotaviruses, cosavirus, astroviruses, and hepatitis B virus. Sequences from a highly divergent parvovirus, provisionally called bufavirus, were also detected whose NS1 and VP1 proteins showed <39% and <31% identities to those of previously known parvoviruses. Four percent of the fecal samples were PCR positive for this new parvovirus, including a related bufavirus species showing only 72% identity in VP1. The high degree of genetic divergence of these related genomes from those of other parvoviruses indicates the presence of a proposed new Parvoviridae genus containing at least two species. Studies of the tropism and pathogenicity of these novel parvoviruses will be facilitated by the availability of their genome sequences.

Fig 1

Bufavirus genome and phylogeny. (A) Organization of the bufavirus genome. The PLA₂ similarity region, including the calcium-binding region and catalytic residues, is shown. Theoretical splicing for expression of VP1 is shown. nt, nucleotides. (B) Pairwise sliding window of percent nucleotide identity of bufavirus aligned with representatives of other parvovirus genera and bufavirus 2. (C) Phylogenetic analyses of the NS1, VP1, and VP2 proteins of bufavirus and related parvoviruses. Genetic distances were calculated by Kimura's two-parameter method (PHYLIP), and a phylogenetic tree with 100 bootstrap resampling of the alignment data sets was generated using the neighbor-joining method. Each scale indicates the number of amino acid substitutions per position. Proposed and official Parvoviridae genera are labeled. The names and accession numbers of the taxa used are listed in Table S1 in the supplemental material.