title: Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus.
abstract: Infectious bronchitis virus (IBV) is a Gammacoronavirus that causes a highly contagious respiratory disease in chickens. A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. Thirteen open reading frames (ORFs) in the order 5'-UTR-1a-1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3'UTR were predicted. The relative frequencies of missense: silent SNPs were calculated to obtain a comparative measure of variability in specific genes. The most variable ORFs in descending order were E, 3b, 5'UTR, N, 1a, S, 1ab, M, 4c, 5a, 6b. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5'UTR did not alter the predicted secondary structure. The frequency of SNPs in the Spike (S) protein ORF of 0.67% was below the genomic average of 0.76%. Only three SNPS were identified in the S1 subunit, none of which were located in hypervariable region (HVR) 1 or HVR2. The S2 subunit was considerably more variable containing 87% of the polymorphisms detected across the entire S protein. The S2 subunit also contained a previously unreported multi-A insertion site and a stretch of four consecutive mutated amino acids, which mapped to the stalk region of the spike protein. Template-based protein structure modelling produced the first theoretical model of the IBV spike monomer. Given the lack of diversity observed at the sub-consensus level, the tenet that the HVRs in the S1 subunit are very tolerant of amino acid changes produced by genetic drift is questioned.
authors.affiliation: Poultry Section, Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa. Electronic address: celia.abolnik@up.ac.za.
authors.forename: Celia
authors.initials: C
authors.lastname: Abolnik
mesh_terms: D000818:Animals; D001208:Asia / Q000453:epidemiology; D001991:Bronchitis / Q000453:epidemiology / Q000662:veterinary / Q000821:virology*; D002645:Chickens / Q000821:virology; D018352:Coronavirus Infections / Q000453:epidemiology / Q000662:veterinary*; D005060:Europe / Q000453:epidemiology; D016679:Genome, Viral; D023281:Genomics; D001351:Infectious bronchitis virus / Q000235:genetics*; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011201:Poultry Diseases / Q000453:epidemiology / Q000821:virology*; D017433:Protein Structure, Secondary; D059370:RNA Folding; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D013019:South Africa / Q000453:epidemiology; D013020:South America / Q000453:epidemiology; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins
keywords: Coronavirus; HVR; Infectious bronchitis; SNP; Spike
references.citation: Adv Virus Res. 1997;48:1-100
references.pmid: 9233431
references.citation: Dev Comp Immunol. 2000 Mar-Apr;24(2-3):187-200
references.pmid: 10717287
references.citation: RNA Biol. 2011 Mar-Apr;8(2):270-9
references.pmid: 21593585
references.citation: Avian Dis. 2014 Mar;58(1):102-10
references.pmid: 24758121
references.citation: J Virol. 2008 Feb;82(4):2013-24
references.pmid: 18045937
references.citation: Avian Pathol. 2005 Dec;34(6):439-48
references.pmid: 16537157
references.citation: Virus Genes. 2013 Jun;46(3):454-64
references.pmid: 23355072
references.citation: mBio. 2014 Apr 29;5(3):e01146-14
references.pmid: 24781747
references.citation: Vet Microbiol. 2013 Mar 23;162(2-4):408-418
references.pmid: 23159091
references.citation: J Virol. 2004 Jun;78(11):6048-54
references.pmid: 15141003
references.citation: Avian Pathol. 2001 Aug;30(4):411-21
references.pmid: 19184926
references.citation: Vet Res. 2007 Mar-Apr;38(2):281-97
references.pmid: 17296157
references.citation: Arch Virol. 2011 Feb;156(2):245-52
references.pmid: 21049275
references.citation: Avian Pathol. 2004 Dec;33(6):550-7
references.pmid: 15763721
references.citation: Virology. 1996 Mar 1;217(1):311-22
references.pmid: 8599216
references.citation: J Virol. 2013 Feb;87(4):2128-36
references.pmid: 23221558
references.citation: Avian Pathol. 2012 Oct;41(5):451-8
references.pmid: 22897690
references.citation: Virus Res. 2008 Sep;136(1-2):43-9
references.pmid: 18514348
references.citation: Virus Res. 2013 Nov 6;177(2):127-37
references.pmid: 24041648
references.citation: Virus Res. 2014 Dec 19;194:124-37
references.pmid: 25093995
references.citation: J Virol. 2004 Jan;78(2):669-82
references.pmid: 14694098
references.citation: J Virol. 2012 Apr;86(7):3995-4008
references.pmid: 22278237
references.citation: Protein Cell. 2013 Dec;4(12):951-61
references.pmid: 24318862
references.citation: RNA Biol. 2011 Mar-Apr;8(2):237-48
references.pmid: 21378501
references.citation: J Interferon Cytokine Res. 2001 Dec;21(12):1071-7
references.pmid: 11798465
references.citation: Onderstepoort J Vet Res. 2014 Sep 09;81(1):
references.pmid: 25685887
references.citation: BMC Syst Biol. 2010 Apr 13;4:43
references.pmid: 20385029
references.citation: BMC Bioinformatics. 2010 Sep 07;11:451
references.pmid: 20822531
references.citation: Avian Pathol. 2012;41(3):239-50
references.pmid: 22702451
references.citation: Viruses. 2014 Aug 07;6(8):2991-3018
references.pmid: 25105276
references.citation: mBio. 2014 Sep 23;5(5):e01704-14
references.pmid: 25249281
references.citation: J Gen Virol. 1990 Sep;71 ( Pt 9):1929-35
references.pmid: 1698920
references.citation: Br Vet J. 1980 Jul-Aug;136(4):349-6
references.pmid: 6250665
references.citation: Infect Genet Evol. 2014 Apr;23:189-95
references.pmid: 24613433
references.citation: Br Poult Sci. 2010 Feb;51(1):1-11
references.pmid: 20390564
references.citation: J Immunol. 1989 Oct 15;143(8):2692-8
references.pmid: 2477454
references.citation: Avian Dis. 2005 Dec;49(4):614-8
references.pmid: 16405010
references.citation: J Gen Virol. 1991 Dec;72 ( Pt 12):2915-22
references.pmid: 1722501
references.citation: Adv Virus Res. 2011;81:85-164
references.pmid: 22094080
references.citation: Avian Pathol. 2002 Jun;31(3):229-36
references.pmid: 12396345
references.citation: J Virol. 2015 Jan 15;89(2):1156-67
references.pmid: 25378498
references.citation: J Virol. 2005 Jul;79(13):8065-78
references.pmid: 15956552
references.citation: Arch Virol. 2000;145(2):291-300
references.pmid: 10752554
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D259-66
references.pmid: 24214962
references.citation: Vaccine. 2013 Nov 12;31(47):5524-30
references.pmid: 24099870
references.citation: PLoS One. 2013;8(1):e52752
references.pmid: 23308119
references.citation: Arch Virol. 1997;142(11):2249-56
references.pmid: 9672590
references.citation: J Virol. 2014 Sep;88(18):10525-40
references.pmid: 24965472
references.citation: Arch Virol. 1979;61(3):227-38
references.pmid: 227344
references.citation: Vet Res. 2014 Jun 14;45:67
references.pmid: 24928425
references.citation: J Virol. 2012 Oct;86(19):10903-4
references.pmid: 22966194
references.citation: J Gen Virol. 2009 Nov;90(Pt 11):2679-2685
references.pmid: 19625463
references.citation: Virology. 2005 Apr 10;334(2):306-18
references.pmid: 15780881
references.citation: J Gen Virol. 1992 Mar;73 ( Pt 3):591-6
references.pmid: 1372036
references.citation: J Virol. 2007 Feb;81(3):1220-9
references.pmid: 17108045
references.citation: Avian Pathol. 1992 Sep;21(3):401-8
references.pmid: 18670955
references.citation: Avian Dis. 1997 Jul-Sep;41(3):661-9
references.pmid: 9356713
references.citation: Adv Exp Med Biol. 1995;380:551-6
references.pmid: 8830540
references.citation: Virology. 2014 Jan 5;448:26-32
references.pmid: 24314633
references.citation: Adv Exp Med Biol. 1990;276:269-73
references.pmid: 1966412
references.citation: J Virol. 2006 Jan;80(1):296-305
references.pmid: 16352554
references.citation: Avian Dis. 2014 Mar;58(1):83-9
references.pmid: 24758118
references.citation: Nat Protoc. 2012 Jul 19;7(8):1511-22
references.pmid: 22814390
references.citation: Avian Pathol. 2000 Apr;29(2):71-93
references.pmid: 19184793
references.citation: Virus Res. 1997 Jun;49(2):139-45
references.pmid: 9213388