Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent in enteric infections

Abstract

A new species of parvovirus, tentatively named human bocavirus 4 (HBoV4), was genetically characterized. Among 641 feces samples obtained from children and adults, the most commonly detected bocavirus species were, in descending order, HBoV2, HBoV3, HBoV4, and HBoV1, with an HBoV2 prevalence of 21% and 26% in Nigerian and Tunisian children, respectively. HBoV3 or HBoV4 species were found in 12 of 192 patients with non-polio acute flaccid paralysis in Tunisia and Nigeria and 0 of 96 healthy Tunisian contacts (P = .01). Evidence of extensive recombination at the NP1 and VP1 gene boundary between and within bocavirus species was found. The high degree of genetic diversity seen among the human bocaviruses found in feces specimens, relative to the highly homogeneous HBoV1, suggest that this worldwide-distributed respiratory pathogen may have recently evolved from an enteric bocavirus after acquiring an expanded tropism favoring the respiratory tract. Elucidating the possible role of the newly identified enteric bocaviruses in human diseases, including acute flaccid paralysis and diarrhea, will require further epidemiological studies.

Table 1.

Distribution of Human Bocavirus (HBoV) Species and Genotypes in Different Countries and Cohorts

Figure 1.

Phylogenetic analysis of partial VP1 pan-bocavirus polymerase chain reaction amplicons of different species of human bocaviruses. Tree constructed by neighbor-joining of pair-wise maximum composite likelihood distances between nucleotide sequences; bootstrap values 70% are shown.

Table 2.

Genetic Distances Between and Within Human Bocavirus (HBoV) Species and Genotypes

Figure 2.

Phylogenetic analyses of nucleotide (upper panel) and inferred amino acid sequences of the 3 principal open reading frames of human bocavirus (HBoV) 1–4; bootstrap values 70% are shown. The NS1 trees used HBoV sequences spliced as described in the text.

Figure 3.

Human bocavirus (HBoV) 3 and HBoV4 have recombinant genomes. Pair-wise Jukes-Cantor corrected distance scans of HBoV3 and HBoV4 sequences against representative sequences of HBoV1 and 2A or individual sequences, as indicated in legend.

Figure 4.

Representation of genetic diversity within and between different bocavirus species. Distribution of pair-wise uncorrected p-distances in the partial VP1 region amplified using pan-bocavirus polymerase chain reaction among human bocavirus (HBoV) 1 (A), HBoV2 (B), and HBoV2–4 combined (C).

Figure 5.

Evidence for RNA splicing in human bocavirus (HBoV) genomes to generate longer NS1 proteins.A,Proposed genomic organization of HBoVs relative to that of animal bocaviruses.Black boxesrepresent exon 2 of the NS1 protein.B,Canonical sequence of the splice donor, branch site, and splice acceptor (Pu p A/G, Py p T/C). All HBoV species were aligned to show the presence of putative RNA splicing elements in the NS exon.C,Region of highest similarity between extended carboxy termini of NS1 of HBoV1–4 species and termini of animal bocavirus NS1. The amino acid positions used in the alignment are shown.