Whole genomic characterization of a Korean human parechovirus type 1 (HPeV1) identifies recombination events

Abstract

A human parechovirus (HPeV) strain CAU10-NN was detected from a stool sample of a 2-year-old healthy female infant in South Korea using a metagenomic approach. The CAU10-NN virus was isolated using a cell culture system and its whole genome was analyzed. The RNA genome of the CAU10-NN strain consists of 7,348 nucleotides (nt), excluding a poly(A) tail. A large open reading frame of 6,540 nt that encodes a putative polyprotein precursor of 2,180 amino acids is flanked by a 5'-untranslated region (UTR) of 708 nt and 3'-UTR of 88 nt followed by a poly(A) tail. Phylogenetic analysis shows that the CAU10-NN strain belongs to HPeV1. SimPlot and Bootscan analyses reveal that the virus genome is composed of regions related to corresponding genomic regions of other HPeVs. Recombination analysis indicates that the CAU10-NN strain might be a product of more than one genomic recombination event that occurred among HPeV1, HPeV3, and HPeV4 strains.

Genome analysis revealed novel genotypes and recombination of the human parechoviruses prevalent in children in Eastern China

“…Like other picornaviruses, recombination in HPeVs has also been found, with breaking points at the capsid encoding and non-structural encoding regions [31–34], among these recombination events most belonged to intra-genotype recombination. In the present study, a recombination event was detected in the non-structural region, which was inter-genotype recombination occurred between 3 HPeV strains belong three different genotypes and led to an HPeV-1 recombinant.…”

Human Parechovirus 3

“…8 Frequent nucleic acid recombination events between the same or differing genotypes seem to be responsible for HPeV's genetic diversity, including the presence of mosaic genomes (mixtures of genetic parts from more than one strain). [9][10][11][12] Fig. 1.…”

Evolutionary and network analysis of virus sequences from infants infected with an Australian recombinant strain of human parechovirus type 3

“…However, this RGD motif is not present in HPeV3, HPeV7-16, the related rodent/zoonotic virus Ljungan virus or in some strains within HPeV types normally encoding the RGD motif, for example for HPeV4 7, 13–16 . Like other picornaviruses, recombination of HPeV often involves breakpoints at the very end of VP1 and thus may remove or add the RGD motif, or alternatively occur downstream in the nonstructural coding region 7, 17–21 .…”