title: Complete genomic sequence analysis of infectious bronchitis virus Ark DPI strain and its evolution by recombination.
abstract: An infectious bronchitis virus Arkansas DPI (Ark DPI) virulent strain was sequenced, analyzed and compared with many different IBV strains and coronaviruses. The genome of Ark DPI consists of 27,620 nucleotides, excluding poly (A) tail, and comprises ten open reading frames. Comparative sequence analysis of Ark DPI with other IBV strains shows striking similarity to the Conn, Gray, JMK, and Ark 99, which were circulating during that time period. Furthermore, comparison of the Ark genome with other coronaviruses demonstrates a close relationship to turkey coronavirus. Among non-structural genes, the 5'untranslated region (UTR), 3C-like proteinase (3CLpro) and the polymerase (RdRp) sequences are 100% identical to the Gray strain. Among structural genes, S1 has 97% identity with Ark 99; S2 has 100% identity with JMK and 96% to Conn; 3b 99%, and 3C to N is 100% identical to Conn strain. Possible recombination sites were found at the intergenic region of spike gene, 3'end of S1 and 3a gene. Independent recombination events may have occurred in the entire genome of Ark DPI, involving four different IBV strains, suggesting that genomic RNA recombination may occur in any part of the genome at number of sites. Hence, we speculate that the Ark DPI strain originated from the Conn strain, but diverged and evolved independently by point mutations and recombination between field strains.
authors.affiliation: Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, 701 East Pratt Street, Baltimore, Maryland 21202-3101, USA. ammayapp@umbi.umd.edu
authors.forename: Arun
authors.initials: A
authors.lastname: Ammayappan
authors.forename: Chitra
authors.initials: C
authors.lastname: Upadhyay
authors.forename: Jack
authors.initials: J
authors.lastname: Gelb
authors.forename: Vikram N
authors.initials: VN
authors.lastname: Vakharia
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D000818:Animals; D002645:Chickens / Q000821:virology*; D000086782:Coronavirus 3C Proteases; D018352:Coronavirus Infections / Q000662:veterinary* / Q000821:virology; D003546:Cysteine Endopeptidases / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D019143:Evolution, Molecular; D016679:Genome, Viral; D001351:Infectious bronchitis virus / Q000145:classification / Q000235:genetics*; D008562:Membrane Glycoproteins / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D011201:Poultry Diseases / Q000821:virology*; D011995:Recombination, Genetic; D017423:Sequence Analysis, RNA; D017385:Sequence Homology; D064370:Spike Glycoprotein, Coronavirus; D014759:Viral Envelope Proteins / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics; D015678:Viral Structural Proteins / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; D008562:Membrane Glycoproteins; D064370:Spike Glycoprotein, Coronavirus; D014759:Viral Envelope Proteins; D014764:Viral Proteins; D015678:Viral Structural Proteins; D012321:DNA-Directed RNA Polymerases; D003546:Cysteine Endopeptidases; C000706208:3C-like proteinase, Avian infectious bronchitis virus; D000086782:Coronavirus 3C Proteases