Genome Characterisation of Enteroviruses 117 and 118: A New Group within Human Enterovirus Species C

Antonio Piralla,Fausto Baldanti,Vytautas Usonis,Susanna Esposito,Alessia Scala,David Greenberg,Cristina Daleno,Nicola Principi,Patrick C Y Woo

doi:10.1371/journal.pone.0060641

Abstract

The more than 120 genotypes of human enteroviruses (HEVs) reflect a wide range of evolutionary divergence, and there are 23 currently classified as human enterovirus C species (HEV-C). Two new HEV-C (EV-C117 and EV-C118) were identified in the Community-Acquired Pneumonia Pediatric Research Initiative (CAP-PRI) study, and the present paper describes the characterisation of the complete genome of one EV-C117 strain (LIT22) and two EV-C118 (ISR38 and ISR10) strains. The EV-C117 and EV-C118 5′UTR sequences were related to those of EV-C104, EV-C105 and EV-C109, and were slightly shorter than those of other HEV A-D species. Similarity plot analyses showed that EV-C117 and EV-C118 have a P1 region that is highly divergent from that of the other HEV-C, and phylogenetic analyses highly supported a monophyletic group consisting of EV-C117, EV-C118, EV-C104, EV-C105 and EV-C109 strains. Phylogenetic, Simplot and Bootscan analyses indicated that recombination was not the main mechanism of EV-C117 and EV-C118 evolution, thus strengthening the hypothesis of the monophyletic origin of the coding regions, as in the case of other HEV-C. Phylogenetic analysis also revealed the emergence of a new group within HEV-C that is divided into two subgroups. Nucleotide and amino acid identity in VP1 sequences have been established as useful criteria for assigning new HEV types, but analysis of the complete P1 region improves resolution.

Highlights

Human enteroviruses (HEVs) belong to the Picornaviridae family and cause a wide range of clinical conditions, ranging from asymptomatic or mild infections to more severe diseases such as acute hemorrhagic conjunctivitis, aseptic meningitis, severe community-acquired pneumonia (CAP), gastroenteritis, acute flaccid paralysis, myocarditis, and neonatal sepsis-like disease [1]
The phylogenetic tree constructed on the basis of the 59UTR sequences showed that EV-C117 and EV-C118 clustered in a group that was different from that of the other human enterovirus C species (HEV-C) prototype strains (Fig. 1A), and consisted of EVC104, EV-C105, EV-C109, EV-C117 and EV-C118 strains
Over the last ten years, a number of new HEVs have been described as being responsible for respiratory syndromes, including EV-68, EV-C104, EV-C105, EV-C109, and EV-C116

Summary

Introduction

Human enteroviruses (HEVs) belong to the Picornaviridae family and cause a wide range of clinical conditions, ranging from asymptomatic or mild infections to more severe diseases such as acute hemorrhagic conjunctivitis, aseptic meningitis, severe community-acquired pneumonia (CAP), gastroenteritis, acute flaccid paralysis, myocarditis, and neonatal sepsis-like disease [1]. HEVs are non-enveloped viruses characterised by a single positivestrand RNA genome that consists of approximately 7,500 nucleotides (nt) and contains a single open reading frame (ORF) flanked by untranslated regions (UTRs) at each end. The ORF encodes a polyprotein that is post-translationally cleaved to yield four structural (VP4, VP2, VP3 and VP1) and seven nonstructural proteins (2A, 2B, 2C, 3A, 3B, 3C and 3D) [2]. Enterovirus typing is based on comparing the sequences encoding the VP1 capsid protein: viruses of different genotypes have ,75% nucleotide identity, and ,85% amino acid identity [3,4]. HEVs are currently divided into four species (HEV-A to HEV-D) depending on their sequence similarities and biological properties. Twenty-three types of HEV-C have so far been identified Twenty-three types of HEV-C have so far been identified (www.picornaviridae.com/enterovirus/hev-c/hev-c. htm), a number of which have been identified in the last decade

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