title: Full genome sequence analysis of a newly emerged QX-like infectious bronchitis virus from Sudan reveals distinct spots of recombination.
abstract: Infectious bronchitis virus (IBV) infection continues to cause economically important diseases in poultry while different geno- and serotypes continue to circulate globally. Two infectious bronchitis viruses (IBV) were isolated from chickens with respiratory disease in Sudan. Sequence analysis of the hypervariable regions of the S1 gene revealed a close relation to the QX-like genotype which has not been detected in Sudan before. Whole genome analysis of IBV/Ck/Sudan/AR251-15/2014 isolate by next generation sequencing revealed a genome size of 27,646 nucleotides harbouring 13 open reading frames: 5'-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3'. Highest nucleotide sequence identity of 93% for the whole genome was found with the Chinese IBV strain Ck/CH/LHLJ/140906, the Italian IBV isolate ITA/90254/2005 and the 4/91 vaccine strain. Phylogenetic analysis of the S1 gene revealed that the IBV/Ck/Sudan/AR251-15/2014 isolate clustered together with viruses of the GI-19 lineage. Recombination analysis gave evidence for distinct patterns of origin of RNA in the Sudanese isolate in multiple genes. Several sites of recombination were scattered throughout the genome suggesting that the Sudan-QX-like strain emerged as a unique recombinant from multiple recombination events of parental viruses from 4/91, H120 and ITA/90254/2005 genotypes. The Sudanese QX-like isolate is plausibly genetically different from IBV strains previously reported in Africa and elsewhere.
authors: The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Greifswald, Insel-Riems 17493, Germany; National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza 12618, Egypt.
authors: Mahmoud M
authors: MM
authors: Naguib
authors: The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Greifswald, Insel-Riems 17493, Germany.
authors: Dirk
authors: D
authors: Höper
authors: National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza 12618, Egypt.
authors: Abdel-Satar
authors: AS
authors: Arafa
authors: Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt; Ceva Santé Animale, Egypt; Ceva Santé Animale, Sudan.
authors: Ahmed M
authors: AM
authors: Setta
authors: Ceva Santé Animale, Egypt; Ceva Santé Animale, Sudan.
authors: Mohamed
authors: M
authors: Abed
authors: Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padua, Italy.
authors: Isabella
authors: I
authors: Monne
authors: The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Greifswald, Insel-Riems 17493, Germany.
authors: Martin
authors: M
authors: Beer
authors: The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Greifswald, Insel-Riems 17493, Germany. Electronic address: timm.harder@fli.bund.de.
authors: Timm C
authors: TC
authors: Harder
mesh_terms: D000818:Animals; D002645:Chickens; D018352:Coronavirus Infections / Q000662:veterinary / Q000821:virology; D016679:Genome, Viral / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D001351:Infectious bronchitis virus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D012367:RNA, Viral / Q000032:analysis / Q000235:genetics; D011995:Recombination, Genetic / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013397:Sudan
chemical_list: D012367:RNA, Viral
keywords: Infectious bronchitis virus; QX-like; Recombination; Sudan; Whole genome