Abstract
The proposed viral genus human Cosavirus (HCoSV) consists of diverse picornaviruses found at high prevalence in the feces of children from developing countries. We sequenced four near-full length genomes and 45 partial VP1 region from HCoSV in human feces from healthy children and children with acute flaccid paralysis in Pakistan, Nigeria and Tunisia and from healthy and diarrhetic adults in Nepal. Genetic analyses of the near-full length genomes revealed presence of a new candidate cosavirus species provisionally labelled as species F (HCoSV-F). A HCoSV genome showed evidence of recombination between species D and E viruses at the P1/P2 junction indicating that these viruses may be reclassified as a single highly diverse species. Based on genetic distance criteria for assigning genotypes corresponding to neutralization serotypes in enteroviruses we identified 26 new HCoSV genotypes belonging to species A, D, and E. The detection of a large number of HCoSV genotypes based on still limited geographic sampling indicates that the phenotypic effects of cosaviruses on infected subjects are likely to be as highly diverse as those of human enteroviruses.
Highlights
Cosavirus is a proposed new genus in the family Picornaviridae originally identified in 2008 in the feces of South Asian children with non-polio acute flaccid paralysis (AFP) [1]
A 6656 bases long section without polyA tail of a new human Cosavirus (HCoSV) genome was obtained from a stool sample from a Pakistani child with non-polio acute flaccid paralysis including 182 bp of the 59UTR, the entire predicted polyprotein of 2128 aa and 110 bp at the 39 UTR (PK5006, GenBank: JN867758)
Based on VP1* sequences, HCoSV-A appears to be the most common species followed by HCoSV-D a result similar to that seen with 59UTR and 3D sequencing [1]
Summary
Cosavirus is a proposed new genus in the family Picornaviridae (www.picornaviridae.com) originally identified in 2008 in the feces of South Asian children with non-polio acute flaccid paralysis (AFP) [1]. A 904 bases amplicon was generated (from nucleotide position 2628 to 3531 on cosavirus reference genome HCoSV-A1, accession number NC_012800.1) and directly sequenced.
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