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

Yi Tang,Aswathy Sebastian,Lin Lin,Huaguang Lu

doi:10.1038/srep24519

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.

Highlights

Strains can lead to the generation of recombinant viruses, confirmed through experimental co-infections of chicken embryonic fibroblast cells with two Avian orthoreovirus (ARV) strains[15]
We described two co-infection ARV variant strains detected in one ARV field isolate obtained from ARV-affected young layer chickens in PA
ARV-affected viral arthritis/tenosynovitis syndrome in domestic poultry was observed and described as a highly pathogenic and contagious poultry disease as early as over half a century ago in the 1950 s22–24, and continued studies were performed in 1960–70 s25–27

Summary

Introduction

Strains can lead to the generation of recombinant viruses, confirmed through experimental co-infections of chicken embryonic fibroblast cells with two ARV strains[15]. The diagnosis of two or multiple ARV strain co-infections is difficult in field cases, reflecting the limitations of physically isolating genome segments and high-frequency reassortment in some ARV segments[14]. Until recently, field cases of ARV co-infections have not been reported. NGS has made revolutionary changes and offered new perspectives in complete genome sequencing studies[18]. We described two co-infection ARV variant strains detected in one ARV field isolate obtained from ARV-affected young layer chickens in PA. These research findings provide scientific data for the confirmation of the naturally occurring co-infection of two ARV variant strains in layer chickens

Methods

Results

Conclusion