Phylogenetic and genome-wide deep-sequencing analyses of canine parvovirus reveal co-infection with field variants and emergence of a recent recombinant strain.

Ruben Pérez,Lucía Carrau,Gregorio Iraola,Lucía Calleros,Marco Vignuzzi,Lourdes Francia,Sofia Grecco,Katia Sosa,Martín Hernández,Ana Marandino,Yanina Panzera,Noam Shomron,Gonzalo Tomás,Ofer Isakov,Hervé Blanc,Nicolás Sarute,Eduard Ayuso

doi:10.1371/journal.pone.0111779

Ruben Pérez, Lucía Carrau + Show 15 more

Open Access

https://doi.org/10.1371/journal.pone.0111779

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Abstract

Canine parvovirus (CPV), a fast-evolving single-stranded DNA virus, comprises three antigenic variants (2a, 2b, and 2c) with different frequencies and genetic variability among countries. The contribution of co-infection and recombination to the genetic variability of CPV is far from being fully elucidated. Here we took advantage of a natural CPV population, recently formed by the convergence of divergent CPV-2c and CPV-2a strains, to study co-infection and recombination. Complete sequences of the viral coding region of CPV-2a and CPV-2c strains from 40 samples were generated and analyzed using phylogenetic tools. Two samples showed co-infection and were further analyzed by deep sequencing. The sequence profile of one of the samples revealed the presence of CPV-2c and CPV-2a strains that differed at 29 nucleotides. The other sample included a minor CPV-2a strain (13.3% of the viral population) and a major recombinant strain (86.7%). The recombinant strain arose from inter-genotypic recombination between CPV-2c and CPV-2a strains within the VP1/VP2 gene boundary. Our findings highlight the importance of deep-sequencing analysis to provide a better understanding of CPV molecular diversity.

Highlights

Members of the Parvoviridae family are small (18–22 nm), nonenveloped icosahedral viruses that cause a wide range of diseases in animals [1,2,3] and humans [1,4]
To gain insight into the variability of Canine parvovirus (CPV) strains in sample 370, we performed deep sequencing using Illumina technology and obtained,206 million high-quality DNA bases with a median coverage of 446103 sequence reads per base
Our findings indicate that Uruguayan CPV-2c and CPV-2a are two divergent phylogenetic groups that are differentiated by both VP1/VP2 and NS sequences

Summary

Introduction

Members of the Parvoviridae family are small (18–22 nm), nonenveloped icosahedral viruses that cause a wide range of diseases in animals [1,2,3] and humans [1,4]. Canine parvovirus (CPV) is an extremely relevant member of the Parvoviridae family because it is the causative agent of one of the most dangerous infectious disease in young dogs and is responsible for large numbers of animal deaths worldwide [5]. The N-terminal regions of NS1 and NS2 are identical in sequence, whereas the Cterminal region of NS2 is derived from differential splicing of the mRNA and is translated from a different reading frame than NS1. VP1 and VP2 are splice variants and are identical in sequence, except for a 143-amino-acid (aa) N-terminal region that is unique to VP1. At both ends of the CPV genome, there are non-translated regions with hairpin structures that are necessary for priming replication [6]

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