Genomic characterization of a turkey reovirus field strain by Next-Generation Sequencing

Tang, Yi; Lu, Huaguang; Sebastian, Aswathy; Yeh, Yu‐Yan; Praul, Craig A.; Albert, István; Zheng, Shan

doi:10.1016/j.meegid.2015.03.029

Cited by 23 publications

(13 citation statements)

References 51 publications

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“…ARVs are important pathogens of domestic poultry and wild avian species, causing a variety of clinical diseases, with viral arthritis/tenosynovitis as the primary infection 2 8 . ARV-associated viral arthritis is an important disease problem in meat-type chickens, turkeys 9 and layer chickens 10 . Newly emerging ARV variants or novel ARV strains have occurred, causing severe lameness and arthritis diseases in Pennsylvania (PA) poultry since 2011 until the present 9 11 .…”

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confidence: 99%

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

Tang

Lin

Sebastian

et al. 2016

Sci Rep

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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.

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confidence: 99%

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

Tang

Lin

Sebastian

et al. 2016

Sci Rep

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“…We extracted swollen spleen tissue from the ducks, homogenized the tissues by centrifuging them, and then froze and thawed the extracted supernatant three times. Then, we isolated the virus in LMH (Leghorn Male‐chicken Hepatocellular‐carcinoma, ATCC CRL‐2013) cell after which the cultures were incubated at 37℃ with 5% CO 2 and checked daily for giant or bloom‐like cytopathic effects (CPEs; Tang et al, ). When we observed more than 75% CPEs, we collected the virus cultures and sub‐culture them until a stable CPE could be harvested (Sterner, Rosenberger, Margolin, & Ruff, ).…”

Section: Methodsmentioning

confidence: 99%

“…We compared sequence similarities between the N‐DRV‐XT18 genome segment and published sequences using the BLASTN online searching program in GenBank (http://blast.ncbi.nlm.nih.gov/Blast.cgi). We constructed phylogenetic trees of all gene segments with MEGA V7.0 program using the neighbour‐joining method and a bootstrap value selected for 1,000 replications (Tang & Lu, ; Teng et al, ). We performed the analysis and visualization of entire genome alignment using the mVISTA online platform (http://genome.lbl.gov/vista/mvista/submit.shtml) and the GenBank accession numbers of the reference strains (Table ).…”

Section: Methodsmentioning

confidence: 99%

Isolation and characterization of a variant duck orthoreovirus causing spleen necrosis in Peking ducks, China

Wang

Gao

Chen

et al. 2019

Transbound Emerg Dis

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Since December 2017, an infectious disease has caused economic hardship for duck farms and breeding ducks in many regions of China. This disease characterized by spleen necrosis and swelling, is due to a variant strain of duck orthoreovirus (DRV) (Duck/N‐DRV‐XT18/China/2018), which we isolated from the spleen of diseased ducks. After isolating the virus, we used next‐generation sequencing technology to determine the entire genomic of the virus. Our phylogenetic analysis of 10 genomic segments showed that the N‐DRV‐XT18 strain is closely related to orthoreovirus isolates derived from ducks and geese, with nucleotide sequence identities for 10 genomic fragments ranging between 49.8% and 99.3%. In contract, the nucleotide sequence of N‐DRV‐XT18 genomic fragments are only 38.6% to 78.8% similar to the chicken orthoreovirus isolate. Therefore, we determined that this pathogen, causing duck spleen necrosis, is a new variant of a duck orthoreovirus that is significantly different from any previously reported waterfowl‐derived othoreovirus.

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“…DMSO has been successfully used to improve the performance of RT-PCR [10] and Sanger Sequencing [11]. However, to our knowledge DMSO has not been used for next-generation sequencing approaches and many dsRNA sequencing studies omit DMSO treatment [6,12,13,14].…”

Section: Theory and Implementationmentioning

confidence: 99%

Next-generation sequencing of double stranded RNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO

Wilcox

Delwart

Díaz‐Muñoz

2019

Preprint

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Double stranded RNA (dsRNA) is the genetic material of important viruses and a key component of RNA interference-based immunity in eukaryotes. Previous studies have noted difficulties in determining the sequence of dsRNA molecules that have affected studies of immune function and estimates of viral diversity in nature. Dimethyl sulfoxide (DMSO) has been used to denature dsRNA prior to the reverse transcription stage to improve RT-PCR and Sanger sequencing. We systematically tested the utility of DMSO to improve sequencing yield of a dsRNA virus (Φ6) in a short-read next generation sequencing platform. DMSO treatment improved sequencing read recovery by over two orders of magnitude, even when RNA and cDNA concentrations were below the limit of detection. We also tested the effects of DMSO on a mock eukaryotic viral community and found that dsRNA virus reads increased with DMSO treatment. Furthermore, we provide evidence that DMSO treatment does not adversely affect recovery of reads from a single-stranded RNA viral genome (Influenza A/California/07/2009). We suggest that up to 50% DMSO treatment be used prior to cDNA synthesis when samples of interest are composed of or may contain dsRNA.

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Genomic characterization of a turkey reovirus field strain by Next-Generation Sequencing

Cited by 23 publications

References 51 publications

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

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

Isolation and characterization of a variant duck orthoreovirus causing spleen necrosis in Peking ducks, China

Next-generation sequencing of double stranded RNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO

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