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

Tang Y, Lin L, Sebastian A, Lu H - Sci Rep (2016)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Wiley Lab/Avian Virology, Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, United States.

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.

No MeSH data available.


Related in: MedlinePlus

Pie chart illustrating the homology search results for NGS reads.(A) Total NGS reads homology search results; (B) Orthoreovirus NGS reads homology search results.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4835796&req=5

f1: Pie chart illustrating the homology search results for NGS reads.(A) Total NGS reads homology search results; (B) Orthoreovirus NGS reads homology search results.

Mentions: From the total RNA sample of the layer ARV isolate after propagation in LMH cell cultures, a total of 842,235 sequencing reads were generated, resulting in 251 Mb of fastq format sequence data. After default quality control (QC) filter processing on the MiSeq platform, the sequencing reads were aligned to the reference sequences of chicken genomic DNA and rRNA databases, followed by quality trimming to remove low-quality reads and to exclude reads with similarities to chicken mRNA or rRNA sequences. As a result, 573,669 reads (68.1%) were identified as chicken rRNA, 189,132 reads (22.4%) as chicken mRNA, and 12,161 reads (1.4%) as sequencing adapters (Fig. 1A). The remaining 76,689 reads (9.1%) were considered clean reads and were further analyzed using BLASTN, revealing 35,321 reads (4.2%) as no hits and 41,368 reads (4.9%) as orthoreovirus-origin (Fig. 1B).


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

Tang Y, Lin L, Sebastian A, Lu H - Sci Rep (2016)

Pie chart illustrating the homology search results for NGS reads.(A) Total NGS reads homology search results; (B) Orthoreovirus NGS reads homology search results.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4835796&req=5

f1: Pie chart illustrating the homology search results for NGS reads.(A) Total NGS reads homology search results; (B) Orthoreovirus NGS reads homology search results.
Mentions: From the total RNA sample of the layer ARV isolate after propagation in LMH cell cultures, a total of 842,235 sequencing reads were generated, resulting in 251 Mb of fastq format sequence data. After default quality control (QC) filter processing on the MiSeq platform, the sequencing reads were aligned to the reference sequences of chicken genomic DNA and rRNA databases, followed by quality trimming to remove low-quality reads and to exclude reads with similarities to chicken mRNA or rRNA sequences. As a result, 573,669 reads (68.1%) were identified as chicken rRNA, 189,132 reads (22.4%) as chicken mRNA, and 12,161 reads (1.4%) as sequencing adapters (Fig. 1A). The remaining 76,689 reads (9.1%) were considered clean reads and were further analyzed using BLASTN, revealing 35,321 reads (4.2%) as no hits and 41,368 reads (4.9%) as orthoreovirus-origin (Fig. 1B).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Wiley Lab/Avian Virology, Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, United States.

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.

No MeSH data available.


Related in: MedlinePlus