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Identification and complete genome characterization of a novel picornavirus in turkey (Meleagris gallopavo).

ABSTRACT: Members of the family Picornaviridae are important pathogens of humans and animals, although compared with the thousands of known bird species (>10?000), only a few (n?=?11) picornaviruses have been identified from avian sources. This study reports the metagenomic detection and complete genome characterization of a novel turkey picornavirus from faecal samples collected from eight turkey farms in Hungary. Using RT-PCR, both healthy (two of three) and affected (seven of eight) commercial turkeys with enteric and/or stunting syndrome were shown to be shedding viruses in seven (88?%) of the eight farms. The viral genome sequence (turkey/M176/2011/HUN; GenBank accession no. JQ691613) shows a high degree of amino acid sequence identity (96?%) to the partial P3 genome region of a picornavirus reported recently in turkey and chickens from the USA and probably belongs to the same species. In the P1 and P2 regions, turkey/M176/2011/HUN is related most closely to, but distinct from, the kobuviruses and turdivirus 1. Complete genome analysis revealed the presence of characteristic picornaviral amino acid motifs, a potential type II-like 5' UTR internal ribosome entry site (first identified among avian-origin picornaviruses) and a conserved, 48 nt long 'barbell-like' structure found at the 3' UTR of turkey/M176/2011/HUN and members of the picornavirus genera Avihepatovirus and Kobuvirus. The general presence of turkey picornavirus - a novel picornavirus species - in faecal samples from healthy and affected turkeys in Hungary and in the USA suggests the worldwide occurrence and endemic circulation of this virus in turkey farms. Further studies are needed to investigate the aetiological role and pathogenic potential of this picornavirus in food animals.

SUBMITTER: Boros A

PROVIDER: S-EPMC3541788 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

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Identification and complete genome characterization of a novel picornavirus in turkey (Meleagris gallopavo).

Boros Ákos Á Nemes Csaba C Pankovics Péter P Kapusinszky Beatrix B Delwart Eric E Reuter Gábor G

The Journal of general virology 20120808 Pt 10

Members of the family Picornaviridae are important pathogens of humans and animals, although compared with the thousands of known bird species (>10 000), only a few (n = 11) picornaviruses have been identified from avian sources. This study reports the metagenomic detection and complete genome characterization of a novel turkey picornavirus from faecal samples collected from eight turkey farms in Hungary. Using RT-PCR, both healthy (two of three) and affected (seven of eight) commercial turkeys ...[more]

PMID: 22875254

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Project description:BackgroundThe turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world's poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome.ResultsAlignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles.ConclusionThe turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey.

Dataset Information

Identification and complete genome characterization of a novel picornavirus in turkey (Meleagris gallopavo).

Publications

Identification and complete genome characterization of a novel picornavirus in turkey (Meleagris gallopavo).

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