Molecular detection of novel picornaviruses in chickens and turkeys

Abstract

Fecal specimens, including swabs and litter extracts, collected from chickens, domestic ducks, turkeys, and Canadian geese were tested using degenerate primers targeting regions encoding for conserved amino acid motifs (YGDD and DY(T/S)(R/K/G)WDST) in calicivirus RNA-dependent RNA polymerases. Similar motifs are also present in other RNA viruses. Two fecal specimens and 18 litter extracts collected from chickens and turkeys yielded RT-PCR products. BLAST search and phylogenetic analysis revealed that all amplicons represented picornaviruses that clustered into two major groups. Four chicken and one turkey samples yielded 250 bp amplicons with 84-91% nucleotide identity to the recently described turkey hepatitis viruses, while 280 and 283 bp amplicons obtained from 11 chicken and 4 turkey samples represented novel picornaviruses with the closest nucleotide identity to kobuviruses (54-61%) and turdiviruses (47-54%). Analysis of 2.2-3.2 kb extended genome sequences including the partial P2 (2C) and complete P3 (3A, 3B (VPg), 3C(pro), and 3D(pol)) regions of selected strains indicated that viruses yielding the 280/283 bp amplicons represent a putative new genus of Picornaviridae. The 3'-non-translated region (NTR) of the turkey hepatitis-like viruses described in this study was significantly longer (641-654 nt) than that of any of the other piconaviruses and included a putative short open reading frame (ORF). In summary, we report the molecular detection of novel picornaviruses that appear to be endemic in both chickens and turkeys.

A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds

“…Previous metagenomic studies into the avian gut microbiome have identified multiple picornavirus species in disease-affected and healthy birds, findings which have been echoed in the present study. However, the pathogenic potential of these viruses in avian species remains relatively unknown due to the large amount of genetic variation observed among these viruses Farkas et al, 2012;Bullman et al, 2014;Zhou et al, 2015). In the present study picornaviruses were commonly found alongside the Astroviridae, Caliciviridae, Parvoviridae, and bacteriophage families (Table 1) and seem to be prevalent in growth-stunted birds.…”

Comparative Complete Genome Analysis of Chicken and Turkey Megriviruses (Family Picornaviridae): Long 3′ Untranslated Regions with a Potential Second Open Reading Frame and Evidence for Possible Recombination

“…Furthermore, the presence of a putative second ORF in partial nucleotide sequences of chicken and turkey picornaviruses has been identified in silico (5).…”

“…The largest (still incomplete) picornavirus genome is THV, a virus associated with liver necrosis and enteritis in turkeys, which belongs to the species Melegrivirus A (genus Megrivirus) and consists of Ͼ9,040 nucleotides (nt), although neither the full length of the 5= UTR nor the complete 3= UTR were determined (7). Additionally, two partial 3D/3= UTR sequence fragments (1,327 nt), closely related to THV, have been identified in turkeys and chickens (5). Recently, two novel picornaviruses (mesivirus 1 and 2) most closely related to megriviruses were identified from wild pigeons.…”

Characterization of a Novel Picornavirus Isolate from a Diseased European Eel ( Anguilla anguilla )

“…However, picornavirus taxonomy is still in flux, as next-generation sequencing technologies facilitate metagenomics studies using viral nucleic acid-containing specimens. Analysis of viral genomes without prior virus isolation led to the identification of more than 30 approved or tentative picornavirus species from humans (cosavirus [3], salivirus [4], saffold virus [5], and rhinovirus-C [6]), rodents (mosavirus, rosavirus, and murine kobuvirus [7]), pinnipeds (seal picornavirus [8] and California sea lion sapelovirus [9]), domestic cats and dogs (feline picornavirus [10], canine picornavirus [11], canine kobuvirus [12], and canine picodicistrovirus [2]), ungulates (bovine hungarovirus, ovine hungarovirus [13], swine pasivirus [14], and porcine kobuvirus [15]), birds (turdiviruses 1 to 3 [16], turkey hepatitis virus [17], pigeon picornaviruses A and B [18], quail picornavirus [19], and gallivirus [20]), and bats (bat picornaviruses 1 to 3 [21], bat kobuvirus-like virus [22], Rhinolophus affinis picornavirus, Ia io picornavirus, and Miniopterus schreibersii picornavirus [23]). …”