Genomic analysis of two novel human enterovirus C genotypes found in respiratory samples from Peru

Abstract

We report the discovery of two enteroviruses detected in nasopharyngeal samples obtained from subjects with respiratory disease in Peru. Phylogenetic analysis indicated that both viruses belong to a clade within the species Human enterovirus C, which includes the recently characterized human enteroviruses 109 and 104. Members of this clade have undergone significant genomic rearrangement, as indicated by deletions in the hypervariable region of the 5' UTR and the VP1 protein, as well as recombination within the non-structural genes. Our findings and review of published sequences suggests that several novel human enterovirus C serotypes are currently circulating worldwide.

Fig. 1.

Phylogenetic relationship of PER153 and PER161 to other HEV-C serotypes. (a, b) Maximum-likelihood phylogenetic trees constructed from available complete (a) HEV-C P1 sequences and (b) HEV-C 3D sequences. (c) Maximum-likelihood phylogenetic tree based on a 326 nt fragment of the VP1 gene. Analysis is based on sequences in GenBank related most closely to PER153 and PER161. The branches of genotypes with deletions within the 5′ UTR are shown in black; other branches are shown in grey. For strains ROM31, BU5, BU77 and ISR10, the 5′ UTR sequence is not yet available. Strains with a 3 bp deletion are indicated in bold. In all trees, GenBank accession numbers are indicated next to the strain designation and * indicates the two genotypes identified in this study.

Fig. 2.

Alignment of the first 150 aa of VP1 from EV-C109, PER153, PER161 and EV-C104. Amino acids in the BC and DE loops are indicated in bold and boxed; ∧ indicates the deletion site in PER153. Variant residues are indicated by their letter designation.

Fig. 3.

Similarity plots and bootscanning analysis comparing PER153 (a, b) and PER161 (c, d) with EV-C104, EV-C109, CV-A1, CV-A19 and CV-A22. The EV genetic map is shown as a reference. Colour legend is shown on the right.