Detection and characterization of two co-infection variant strains of avian orthoreovirus (ARV) in young layer chickens using next-generation sequencing (NGS)

Abstract

Using next-generation sequencing (NGS) for full genomic characterization studies of the newly emerging avian orthoreovirus (ARV) field strains isolated in Pennsylvania poultry, we identified two co-infection ARV variant strains from one ARV isolate obtained from ARV-affected young layer chickens. The de novo assembly of the ARV reads generated 19 contigs of two different ARV variant strains according to 10 genome segments of each ARV strain. The two variants had the same M2 segment. The complete genomes of each of the two variant strains were 23,493 bp in length, and 10 dsRNA segments ranged from 1192 bp (S4) to 3958 bp (L1), encoding 12 viral proteins. Sequence comparison of nucleotide (nt) and amino acid (aa) sequences of all 10 genome segments revealed 58.1–100% and 51.4–100% aa identity between the two variant strains, and 54.3–89.4% and 49.5–98.1% aa identity between the two variants and classic vaccine strains. Phylogenetic analysis revealed a moderate to significant nt sequence divergence between the two variant and ARV reference strains. These findings have demonstrated the first naturally occurring co-infection of two ARV variants in commercial young layer chickens, providing scientific evidence that multiple ARV strains can be simultaneously present in one host species of chickens.

Molecular and Antigenic Characterization of Piscine orthoreovirus (PRV) from Rainbow Trout (Oncorhynchus mykiss)

“…The occurrence of PRV-1 and PRV-3 infected fish in the dense and highly populated farming situations increase the risk of interactions between these PRV subtypes. The high level of sequence similarities, and the fact that PRV-3 can infect Atlantic salmon [ 6 ], increases the probability that new variants of PRV may evolve through the compatible reassortment of gene segments following a co-infection, as observed for ARV and MRV [ 47 ].…”

Genetic and pathogenic characterisation of 11 avian reovirus isolates from northern China suggests continued evolution of virulence

“…Thus, the full genomic characterisation of emerging ARV field strains will provide more detailed molecular data to better understand ARV mutations and/or recombination events that may influence the epidemiology and pathogenicity of the virus. We are currently sequencing the full genome of the MS01 strain using the MiSeq next-generation sequencing system (Illumina, San Diego, CA, USA) 32 33 34 . The full genome sequence will allow us to determine the locations of mutated sites in the complete sequences of all 10 genome segments by comparison with reference strain S1133.…”

In vitro study on role of σB protein in avian reovirus pathogenesis

“…Previously, it was reported that ARV and σC protein induces DNA damage and this process involves ROS intermediates and signaling pathways associated with DDIT-3 and GADD45α using microarray [ 31 ]. Another high throughput next generation sequencing study revealed whole genome sequence of two ARV isolates and established that the two co-infection strains showed close relationships in σA, σB and σNS genes [ 32 ]. Most recently a report identified that Wnt14 plays a pivotal role in initiating synovial joint formation in the chick limb, but the researchers were unable to determine the specific pathway that is responsible for the joint pathogenesis of ARV [ 39 ].…”

“…Further, a number of high throughput sequencing studies came in recent past. Identification and complete genome sequencing of two naturally occurring ARV variant strain co-infections having same M2 segment but were distantly evolved nine other segments in layer chickens using NGS was achieved [ 32 ]. Most recently, a gene expression RNA-Seq study showed that inoculation of chicken fibroblast DF-1 cells lines with ARV stimulates a prolonged antiviral response in host cells and interferes with cell growth and cell death pathways [ 33 ].…”