Full Genome Sequence Analysis of a Newly Emerged QX-Like Infectious Bronchitis Virus. Full Genome Sequence Analysis of a Newly Emerged QX-Like Infectious Bronchitis Virus

Infectious bronchitis virus (IBV) infection continues to cause economically important diseases in poultry where 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 with up to 98% amino acid similarity with Chinese origin QX and other QX-like viruses. QX-like viruses have not been detected in Sudan before and that will pose further problems to control IBV by vaccination.To gain insights into the possible origin of these viruses comprehensive genetic information was established by complete genome analysis of the IBV/ck/Sudan/AR251-15/2014 isolate. A genome size of 27,542 nucleotides was found with a gene order typical of IBV (13 open reading frames: 5´-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3´). Highest nucleotide sequence identity for the whole genome was 93% with Chinese IBV strain ck/CH/LHLJ/140906, Italian IBV isolate ITA/90254/2005 and the 4/91 vaccine strain. Using full length genome sequences for phylogenetic analysis, the Sudanese isolate did not reveal distinct clustering with any reference IBV genotype. Recombination analysis gave evidence for distinct patterns of origin of RNA in the Sudanese isolate in multiple genes. Several sites of recombination were identified in a scattered pattern throughout the genome suggesting that the Sudan-QX-like strain emerged as a unique recombinant from multiple recombination events of parental viruses from QX-like, M41 and 4/91 genotypes. The Sudanese QX-like isolate is genetically different from IBV strains previously reported in Africa and other parts of the world.