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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

The mVISTA method for whole-genome nucleotide alignment.(A) Alignment results of the Reo/PA/Layer/01224a/14 variant strain in comparisons with the Reo/PA/Layer/01224b/14 variant strain and other 7 ARV reference strains (PA15511, PA05682, S1133, 1733, 138, AVS-B, MN9 and J18); (B) Alignment results of the Reo/PA/Layer/01224b/14 variant strain compared with the Reo/PA/Layer/01224a/14 variant strain and 7 other ARV reference strains (PA15511, PA05682, S1133, 1733, 138, AVS-B, MN9 and J18). The areas in pink represent ≥90% similarities, and the areas in white represent <90% similarities. The scale bar measures the approximate length of the concatenated genome.
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f4: The mVISTA method for whole-genome nucleotide alignment.(A) Alignment results of the Reo/PA/Layer/01224a/14 variant strain in comparisons with the Reo/PA/Layer/01224b/14 variant strain and other 7 ARV reference strains (PA15511, PA05682, S1133, 1733, 138, AVS-B, MN9 and J18); (B) Alignment results of the Reo/PA/Layer/01224b/14 variant strain compared with the Reo/PA/Layer/01224a/14 variant strain and 7 other ARV reference strains (PA15511, PA05682, S1133, 1733, 138, AVS-B, MN9 and J18). The areas in pink represent ≥90% similarities, and the areas in white represent <90% similarities. The scale bar measures the approximate length of the concatenated genome.

Mentions: The nt sequence similarity values of individual genome segments of the two co-infection variant strains, PA01224a and PA01224b, showed different divergence from each other and from all seven ARV reference strains (Fig. 4). The visualization of the genome in this way supported the phylogenetic results described above. High sequence similarities (>90%) were observed in most regions of L1, L3, M1, M2, S2, S3, and S4 segments between the two co-infection variant strains. In contrast, the two co-infection strains showed low identity (<85%) in the L2, L3, and S1 segments, with the lowest identity observed at the 3′ end of the S1 segment, corresponding to the σC-coding region. When compared with ARV reference strains, considerable genetic relatedness of the PA01224a variant and 138 strain was observed in 8 of the 10 genome segments, except for the most 3′ regions of the S1 segment and the most 5′ regions of the S3 segment. However, the highest identities of the S1 and S3 segments were observed between the PA01224a variant and the S1133 strain, with more than 57% and 88% nt similarities, respectively. The PA01224b variant strain showed close genetic relatedness with PA15511 strain of whole genome but more divergence from other reference strains compared with the PA01224a variant. The concatenated genome segments revealed that at least 6 reference strains (PA15511, PA05682, 1133, 1733 and AVS-B) shared high sequence similarity with the PA01224b variant in some genome segments. In addition, the M2 and S1 segments of the PA01224a and PA01224b variants, encoding the outer capsid proteins (μB and σC) of ARV, exhibited marked differences compared with vaccine strain S1133, indicating classic vaccine protection failure against the two co-infection variant strains. The duck-origin ARV strain-J18 shared low sequence identity with the two co-infection variant strains (<78.2%) throughout the entire genome, indicating no segment reassortment between the waterfowl-origin ARV and the two co-infection variant strains.


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)

The mVISTA method for whole-genome nucleotide alignment.(A) Alignment results of the Reo/PA/Layer/01224a/14 variant strain in comparisons with the Reo/PA/Layer/01224b/14 variant strain and other 7 ARV reference strains (PA15511, PA05682, S1133, 1733, 138, AVS-B, MN9 and J18); (B) Alignment results of the Reo/PA/Layer/01224b/14 variant strain compared with the Reo/PA/Layer/01224a/14 variant strain and 7 other ARV reference strains (PA15511, PA05682, S1133, 1733, 138, AVS-B, MN9 and J18). The areas in pink represent ≥90% similarities, and the areas in white represent <90% similarities. The scale bar measures the approximate length of the concatenated genome.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: The mVISTA method for whole-genome nucleotide alignment.(A) Alignment results of the Reo/PA/Layer/01224a/14 variant strain in comparisons with the Reo/PA/Layer/01224b/14 variant strain and other 7 ARV reference strains (PA15511, PA05682, S1133, 1733, 138, AVS-B, MN9 and J18); (B) Alignment results of the Reo/PA/Layer/01224b/14 variant strain compared with the Reo/PA/Layer/01224a/14 variant strain and 7 other ARV reference strains (PA15511, PA05682, S1133, 1733, 138, AVS-B, MN9 and J18). The areas in pink represent ≥90% similarities, and the areas in white represent <90% similarities. The scale bar measures the approximate length of the concatenated genome.
Mentions: The nt sequence similarity values of individual genome segments of the two co-infection variant strains, PA01224a and PA01224b, showed different divergence from each other and from all seven ARV reference strains (Fig. 4). The visualization of the genome in this way supported the phylogenetic results described above. High sequence similarities (>90%) were observed in most regions of L1, L3, M1, M2, S2, S3, and S4 segments between the two co-infection variant strains. In contrast, the two co-infection strains showed low identity (<85%) in the L2, L3, and S1 segments, with the lowest identity observed at the 3′ end of the S1 segment, corresponding to the σC-coding region. When compared with ARV reference strains, considerable genetic relatedness of the PA01224a variant and 138 strain was observed in 8 of the 10 genome segments, except for the most 3′ regions of the S1 segment and the most 5′ regions of the S3 segment. However, the highest identities of the S1 and S3 segments were observed between the PA01224a variant and the S1133 strain, with more than 57% and 88% nt similarities, respectively. The PA01224b variant strain showed close genetic relatedness with PA15511 strain of whole genome but more divergence from other reference strains compared with the PA01224a variant. The concatenated genome segments revealed that at least 6 reference strains (PA15511, PA05682, 1133, 1733 and AVS-B) shared high sequence similarity with the PA01224b variant in some genome segments. In addition, the M2 and S1 segments of the PA01224a and PA01224b variants, encoding the outer capsid proteins (μB and σC) of ARV, exhibited marked differences compared with vaccine strain S1133, indicating classic vaccine protection failure against the two co-infection variant strains. The duck-origin ARV strain-J18 shared low sequence identity with the two co-infection variant strains (<78.2%) throughout the entire genome, indicating no segment reassortment between the waterfowl-origin ARV and the two co-infection variant strains.

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