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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

Phylogenetic trees constructed with avian orthoreoviruses (ARVs) based on nucleotide sequences of the L-, M- and σ-class homologous genome segments or genes.Note: The two co-infection variant strains are indicated with colored dots: red indicates Reo/PA/Layer/01224a/14, and blue indicates Reo/PA/Layer/01224b/14.
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f3: Phylogenetic trees constructed with avian orthoreoviruses (ARVs) based on nucleotide sequences of the L-, M- and σ-class homologous genome segments or genes.Note: The two co-infection variant strains are indicated with colored dots: red indicates Reo/PA/Layer/01224a/14, and blue indicates Reo/PA/Layer/01224b/14.

Mentions: To examine the evolutionary relationships of the two co-infection variant strains with other ARV members, both variant strains of PA01224a and PA01224b were subjected to phylogenetic-tree analysis (Fig. 3). Rooted maximum likelihood phylogenetic trees were generated based on the nt sequence alignments of six genome segments and four σ-class genes. For the L-class segment analysis, the two co-infection variant and reference strains formed 4 host-related groups in all three segments (L1–L3), of which two groups were chicken-origin, and the other two variants were, respectively turkey- and waterfowl-origin. The two variant strains of PA01224a and PA01224b were divided into different chicken-origin ARV groups in L1 and L2 segments (Fig. 3, L1 and L2). Although the two co-infection variant strains were in the same group in the L3 tree, strain PA01224b showed a closer evolutionary relationship with AVS-B and 138 strains compared with PA01224a (Fig. 3, L3). For the M-class segments analysis, host-related groups were also observed in M1 and M3 trees, and the two co-infection variant strains evolved into separated groups in these two segments (Fig. 3, M1 and M3). Four genotyping lineages were formed through different combinations of ARVs of different species origins in the M2 tree. The same M2 segment of the two co-infection variant strains belonged to lineage 2, together with other two PA ARV field strains (PA05682 and PA15511)1121 and one classic ARV strain 138 (Fig. 3). The phylogenetic trees of σ-class genes illustrated a close relationship between the two co-infection variant strains of PA01224a and PA01224b, particularly in the σA, σB and σNS genes (Fig. 3). Genes σA and σNS evolved distantly from all vaccine strains and formed a separated genotyping group with the pathogenic ARV strains. In contrast, the σB genes of the two co-infection variant strains were closely related with the vaccine strains, suggesting the possibility of the reassortment of S3 segments between the co-infection variant strains and vaccine strains. Gene σC was the most diverse among all 10 ARV segment genes, and the construction of a σC phylogenetic tree using co-infection variant strains and reference strains generated five genotyping clusters, showing more than 70% identity within each cluster. The two co-infection variant strains were grouped into genotyping cluster 3 (PA01224a) and cluster 5 (PA01224b), respectively, exhibiting markedly higher divergence with vaccine strains than with other segments, as indicated in the sequence comparisons.


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)

Phylogenetic trees constructed with avian orthoreoviruses (ARVs) based on nucleotide sequences of the L-, M- and σ-class homologous genome segments or genes.Note: The two co-infection variant strains are indicated with colored dots: red indicates Reo/PA/Layer/01224a/14, and blue indicates Reo/PA/Layer/01224b/14.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Phylogenetic trees constructed with avian orthoreoviruses (ARVs) based on nucleotide sequences of the L-, M- and σ-class homologous genome segments or genes.Note: The two co-infection variant strains are indicated with colored dots: red indicates Reo/PA/Layer/01224a/14, and blue indicates Reo/PA/Layer/01224b/14.
Mentions: To examine the evolutionary relationships of the two co-infection variant strains with other ARV members, both variant strains of PA01224a and PA01224b were subjected to phylogenetic-tree analysis (Fig. 3). Rooted maximum likelihood phylogenetic trees were generated based on the nt sequence alignments of six genome segments and four σ-class genes. For the L-class segment analysis, the two co-infection variant and reference strains formed 4 host-related groups in all three segments (L1–L3), of which two groups were chicken-origin, and the other two variants were, respectively turkey- and waterfowl-origin. The two variant strains of PA01224a and PA01224b were divided into different chicken-origin ARV groups in L1 and L2 segments (Fig. 3, L1 and L2). Although the two co-infection variant strains were in the same group in the L3 tree, strain PA01224b showed a closer evolutionary relationship with AVS-B and 138 strains compared with PA01224a (Fig. 3, L3). For the M-class segments analysis, host-related groups were also observed in M1 and M3 trees, and the two co-infection variant strains evolved into separated groups in these two segments (Fig. 3, M1 and M3). Four genotyping lineages were formed through different combinations of ARVs of different species origins in the M2 tree. The same M2 segment of the two co-infection variant strains belonged to lineage 2, together with other two PA ARV field strains (PA05682 and PA15511)1121 and one classic ARV strain 138 (Fig. 3). The phylogenetic trees of σ-class genes illustrated a close relationship between the two co-infection variant strains of PA01224a and PA01224b, particularly in the σA, σB and σNS genes (Fig. 3). Genes σA and σNS evolved distantly from all vaccine strains and formed a separated genotyping group with the pathogenic ARV strains. In contrast, the σB genes of the two co-infection variant strains were closely related with the vaccine strains, suggesting the possibility of the reassortment of S3 segments between the co-infection variant strains and vaccine strains. Gene σC was the most diverse among all 10 ARV segment genes, and the construction of a σC phylogenetic tree using co-infection variant strains and reference strains generated five genotyping clusters, showing more than 70% identity within each cluster. The two co-infection variant strains were grouped into genotyping cluster 3 (PA01224a) and cluster 5 (PA01224b), respectively, exhibiting markedly higher divergence with vaccine strains than with other segments, as indicated in the sequence comparisons.

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