Tang Yi, Lin Lin, Sebastian Aswathy, Lu Huaguang
Wiley Lab/Avian Virology, Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, United States.
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States.
Sci Rep. 2016 Apr 19;6:24519. doi: 10.1038/srep24519.
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.
利用下一代测序（NGS）对宾夕法尼亚州家禽中分离出的新出现的禽正呼肠孤病毒（ARV）田间毒株进行全基因组特征研究，我们从一株从受ARV感染的年轻蛋鸡中获得的ARV分离株中鉴定出两种共感染的ARV变异株。根据每个ARV毒株的10个基因组片段，对ARV reads进行从头组装，产生了两种不同ARV变异株的19个重叠群。这两种变异株具有相同的M2片段。两种变异株的完整基因组长度均为23,493 bp，10个双链RNA片段长度从1192 bp（S4）到3958 bp（L1）不等，编码12种病毒蛋白。对所有10个基因组片段的核苷酸（nt）和氨基酸（aa）序列进行比较，发现两种变异株之间的氨基酸同一性为58.1 - 100%和51.4 - 100%，两种变异株与经典疫苗株之间的氨基酸同一性为54.3 - 89.4%和49.5 - 98.1%。系统发育分析表明，两种变异株与ARV参考毒株之间存在中度到显著的核苷酸序列差异。这些发现首次证明了商业年轻蛋鸡中两种ARV变异株的自然共感染，提供了科学证据表明多种ARV毒株可同时存在于鸡的一个宿主物种中。
