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.

Comparative features of infections of two Massachusetts (Mass) infectious bronchitis virus (IBV) variants isolated from Western Canadian layer flocks

“…To our knowledge this is the first study, which investigated the full genome of Canadian IBV isolates. Although, IBV strains circulating in other countries have been characterized and changes in the IBV genome due to mutations and recombination have been shown [40,[55][56][57][58][59], our whole genome sequencing data shows that mutations are more common than the recombination and genes other than S1 have been affected by mutations. These changes in the genome of these two IBV isolates reflected in the differences in the pathogenicity although host response characterized by macrophage recruitment into the respiratory tract were similar.…”

Phylodynamic analysis and molecular diversity of the avian infectious bronchitis virus of chickens in Brazil

“…These events could be responsible for the emergence of this diverse number of variant strains in the field (Jackwood, 2012). Due to the advance of the bioinformatics programs for recombination screening, several studies have been performed in order to evaluate if the recombinant events could be the source of these variant isolates described worldwide (Kiss et al, 2016;Naguib et al, 2016;Quinteros et al, 2016). Moreover, the high prevalence of avian coronaviruses circulating in birds other than chicken suggests that wild and synanthropic birds are potential disseminators and could play a role in the emergence of recombinant strains and the dissemination of IBV among distant regions (Durães-Carvalho et al, 2015).…”

Pathogenic characteristics of a QX-like infectious bronchitis virus strain SD in chickens exposed at different ages and protective efficacy of combining live homologous and heterologous vaccination

“…Among the numerous genotypes, QX-like IBVs have emerged and gradually evolved into the predominant circulating genotype worldwide since the 1990s [18,[23][24][25][26]. Analyses of genetic evolution, antigenicity and pathogenicity reveal many major differences among QX-like IBVs and other serotypes [17,[27][28][29].…”