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

Maria Dolores Fernandez-Garcia,Ousmane Kebe,Kader Ndiaye,Etienne Simon-Loriere,A Sakuntabhai

doi:10.1038/s41598-020-63467-w

Maria Dolores Fernandez-Garcia, Ousmane Kebe + Show 3 more

Open Access

https://doi.org/10.1038/s41598-020-63467-w

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Journal: Scientific Reports	Publication Date: Apr 21, 2020
Citations: 5	License type: open-access

Affiliation: Institut Pasteur de Dakar, Institut Pasteur

Abstract

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.

Highlights

Human parechoviruses (HPeVs) are non-enveloped viruses that belong to one of the four species of genus Parechovirus within the Picornaviridae family
The study strain human parechovirus type 15 (HPeV15) NIG13194 was isolated in 2013 from a stool sample from a child with acute flaccid paralysis (AFP) living in the district of Mirriah, in the Zinder region of Niger
Retrospective analysis of non-polio enterovirus (NPEV) isolates obtained through routine poliomyelitis surveillance activities by partial VP1 typing revealed isolate NIG13194 as an EV-A7112

Summary

Introduction

Human parechoviruses (HPeVs) are non-enveloped viruses that belong to one of the four species of genus Parechovirus within the Picornaviridae family. HPeV infections are common throughout the world and most often cause asymptomatic or mild gastrointestinal or respiratory symptoms[1,2]. Because specific types could be missed or underdiagnosed using viral isolation, molecular identification methods are highly recommended for the routine detection of HPeVs in clinical samples[3,4]. The HPeV15 prototype strain BAN-11614 was first reported from Bangladesh from a non-human primate sampled between 2007 and 20089 Since it was detected in children from Pakistan in 2008–2010 (seven cases with acute dehydrating gastroenteritis)[4,10] and from Ghana in 2007–2008 (one case with diarrhea and two healthy controls)[11]. Increased access to molecular detection and sequencing methods are needed to expand the number of complete HPeV genomes. We present the identification and analysis of the first complete genome sequence of a HPeV15 strain (hereafter referred to as NIG13194)

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Conclusion