title: Genomic characterization of a turkey reovirus field strain by Next-Generation Sequencing.
abstract: The genome of a turkey arthritis reovirus (TARV) field strain (Reo/PA/Turkey/22342/13), isolated from a turkey flock in Pennsylvania (PA) in 2013, has been sequenced using Next-Generation Sequencing (NGS) on the Illumina MiSeq platform. The genome of the PA TARV field strain was 23,496bp in length with 10 dsRNA segments encoding 12 viral proteins. The lengths of the genomic segments ranged from 1192bp (S4) to 3959bp (L1). The 5' and 3' conserved terminal sequences of the PA TARV field strain were similar to the two Minnesota (MN) TARVs (MN9 and MN10) published recently and avian orthoreovirus (ARV) reference strains. Phylogenetic analysis of the nucleotide sequences of all 10 genome segments revealed that there was a low to significant nucleotide sequence divergence between the PA TARV field strain and reference TARV and ARV strains. Analysis of the PA TARV sequence indicates that this PA TARV field strain is a unique strain and is different from the TARV MN9 or MN10 in M2 segment genes and ARV S1133 vaccine strain.
authors.affiliation: Wiley Lab/Avian Virology, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, United States.
authors.forename: Yi
authors.initials: Y
authors.lastname: Tang
authors.affiliation: Wiley Lab/Avian Virology, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, United States. Electronic address: hxl15@psu.edu.
authors.forename: Huaguang
authors.initials: H
authors.lastname: Lu
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States.
authors.forename: Aswathy
authors.initials: A
authors.lastname: Sebastian
authors.affiliation: Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, United States.
authors.forename: Yin-Ting
authors.initials: YT
authors.lastname: Yeh
authors.affiliation: Genomics Core Facility, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, United States.
authors.forename: Craig A
authors.initials: CA
authors.lastname: Praul
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States.
authors.forename: Istvan U
authors.initials: IU
authors.lastname: Albert
authors.affiliation: Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, United States.
authors.forename: Si-Yang
authors.initials: SY
authors.lastname: Zheng
mesh_terms: D000818:Animals; D017124:Conserved Sequence / Q000235:genetics; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016366:Open Reading Frames; D030101:Orthoreovirus, Avian / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D010414:Pennsylvania; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011201:Poultry Diseases / Q000821:virology; D017423:Sequence Analysis, RNA; D014422:Turkeys / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D014764:Viral Proteins
keywords: Genome segments; Genotyping; Next-Generation Sequencing; Turkey arthritis reovirus
references.citation: Comp Immunol Microbiol Infect Dis. 1994 Aug-Nov;17(3-4):151-61
references.pmid: 8001342
references.citation: Avian Dis. 1969 May;13(2):243-51
references.pmid: 4307738
references.citation: J Virol Methods. 2006 May;133(2):146-57
references.pmid: 16337282
references.citation: Avian Dis. 2013 Mar;57(1):97-103
references.pmid: 23678736
references.citation: Avian Dis. 1986 Jul-Sep;30(3):603-8
references.pmid: 3021104
references.citation: Arch Virol. 1975;48(3):261-9
references.pmid: 170888
references.citation: Virus Genes. 2007 Oct;35(2):235-42
references.pmid: 17265142
references.citation: Bioinformatics. 2012 Dec 15;28(24):3211-7
references.pmid: 23071270
references.citation: Biochem Biophys Res Commun. 1992 Sep 30;187(3):1227-31
references.pmid: 1417798
references.citation: Ann Rech Vet. 1982;13(2):149-52
references.pmid: 6301348
references.citation: Am J Vet Res. 1957 Oct;18(69):735-9
references.pmid: 13470226
references.citation: Genome Res. 2009 Sep;19(9):1639-45
references.pmid: 19541911
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: Virus Genes. 2011 Feb;42(1):82-9
references.pmid: 21116842
references.citation: J Virol. 1994 Oct;68(10):6775-7
references.pmid: 8084013
references.citation: Avian Dis. 1972 Oct-Dec;16(5):1067-72
references.pmid: 4344861
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: J Virol. 1976 Feb;17(2):513-24
references.pmid: 176428
references.citation: Avian Pathol. 2003 Apr;32(2):129-38
references.pmid: 12745366
references.citation: Proc Natl Acad Sci U S A. 1972 Feb;69(2):490-4
references.pmid: 4621835
references.citation: J Virol. 1996 May;70(5):2974-81
references.pmid: 8627773
references.citation: Bioinformatics. 2010 Mar 1;26(5):589-95
references.pmid: 20080505
references.citation: Avian Dis. 1987 Oct-Dec;31(4):713-22
references.pmid: 2831866
references.citation: Trop Anim Health Prod. 1997 May;29(2):83-91
references.pmid: 9203308
references.citation: BMC Genomics. 2013;14:444
references.pmid: 23822119
references.citation: Infect Genet Evol. 2014 Oct;27:193-201
references.pmid: 25057811
references.citation: Avian Dis. 2005 Mar;49(1):36-42
references.pmid: 15839410
references.citation: Virol J. 2008;5:153
references.pmid: 19091125
references.citation: Avian Dis. 1993 Oct-Dec;37(4):1130-5
references.pmid: 8141744
references.citation: J Ultrastruct Res. 1972 Oct;41(1):67-79
references.pmid: 4627607
references.citation: Infect Genet Evol. 2015 Apr;31:177-82
references.pmid: 25660035
references.citation: Avian Pathol. 1973 Apr;2(2):135-52
references.pmid: 18777392
references.citation: J Virol Methods. 2012 Nov;185(2):189-92
references.pmid: 22820073
references.citation: Avian Pathol. 2010 Jun;39(3):169-70
references.pmid: 20544421
references.citation: Vet Rec. 2013 May 25;172(21):556
references.pmid: 23636701
references.citation: PLoS One. 2010;5(4):e10256
references.pmid: 20428231
references.citation: Poult Sci. 2002 Nov;81(11):1661-7
references.pmid: 12455593
references.citation: PLoS One. 2012;7(5):e36939
references.pmid: 22590638
references.citation: Avian Dis. 1989 Jul-Sep;33(3):545-54
references.pmid: 2549942
references.citation: Vet Res. 2003 Mar-Apr;34(2):203-12
references.pmid: 12657212
references.citation: Avian Dis. 2000 Jul-Sep;44(3):638-41
references.pmid: 11007012
references.citation: Avian Pathol. 1980 Jan;9(1):1-4
references.pmid: 18770233
references.citation: Arch Virol. 2013 Dec;158(12):2583-8
references.pmid: 23771766
references.citation: J Virol. 1976 Sep;19(3):968-76
references.pmid: 987252
references.citation: Avian Dis. 1974 Jul;18(3):289-96
references.pmid: 4368815
references.citation: Virus Res. 2007 Feb;123(2):105-19
references.pmid: 17018239
references.citation: J Comput Biol. 2012 May;19(5):455-77
references.pmid: 22506599
references.citation: Virology. 2014 Sep;464-465:33-44
references.pmid: 25043587
references.citation: Can Vet J. 1979 Dec;20(12):348-53
references.pmid: 231481
references.citation: Phytopathology. 1999 Apr;89(4):303-7
references.pmid: 18944775
references.citation: Avian Pathol. 1980 Jul;9(3):341-54
references.pmid: 18770272
references.citation: Avian Dis. 1966 Nov;10(4):470-6
references.pmid: 4961651
references.citation: Avian Pathol. 1989 Jul;18(3):433-40
references.pmid: 18679874