Identification and molecular characterization of the first complete genome sequence of Human Parechovirus type 15

• Published in: Scientific reports Vol. 10; no. 1; p. 6759
• Main Authors: Fernandez-Garcia, Maria Dolores, Simon-Loriere, Etienne, Kebe, Ousmane, Sakuntabhai, A., Ndiaye, Kader
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 21.04.2020; Nature Publishing Group
• Subjects: 13; 13/106; 631/181/757; 631/208/514/2254; 631/326/596; Amino acids; Biodiversity; Comparative analysis; Epidemiology; Genome, Viral - genetics; Genomes; Genomics; Humanities and Social Sciences; Humans; Life Sciences; Metagenomics; Metagenomics - methods; Microbiology and Parasitology; Molecular Sequence Annotation; multidisciplinary; Nucleotide sequence; Open Reading Frames - genetics; Paralysis; Paralysis - genetics; Paralysis - virology; Parechovirus - genetics; Parechovirus - isolation & purification; Parechovirus - pathogenicity; Phylogenetics; Phylogeny; Recombination; Santé publique et épidémiologie; Science; Science (multidisciplinary); Sequence Analysis, DNA; Virology; VP1 protein; Whole Genome Sequencing
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-63467-w

Using a metagenomics approach, we have determined the first full-length genome sequence of a human parechovirus type 15 (HPeV15) strain, isolated from a child with acute flaccid paralysis and co-infected with EV-A71. HPeV15 is a rarely reported type. To date, no full-length genome sequence of HPeV15 is available in the GenBank database, where only limited VP1 sequences of this virus are available. Pairwise comparisons of the complete VP1 nucleotide and deduced amino acid sequences revealed that the study strain belongs to type 15 as it displayed 79.6% nucleotide and 93.4% amino acid identity with the HPeV15 prototype strain. Comparative analysis of available genomic regions and phylogenetic analysis using the P2 and P3 coding regions revealed low nucleotide identity to HPeV reference genomes. Phylogenetic and similarity plot analyses showed that genomic recombination events might have occurred in the UTRs and nonstructural region during HPeV15 evolution. The study strain has high similarity features with different variants of HPeV3 suggesting intertypic recombination. Our data contributes to the scarce data available on HPeVs in Africa and provides valuable information for future studies that aim to understand the evolutionary history, molecular epidemiology or biological and pathogenic properties of HPeV15.