Recombination analysis of genomic sequences of infectious bronchitis viruses from 2002−2016 in China

Abstract:

[Objective] Infectious bronchitis virus (IBV) that causes respiratory and nephritic diseases in chicken is one of the important viral pathogens in poultry industry. To understand the epidemiology and recombination of IBV in China. [Methods] S1 gene sequences of 92 IBV strains and the genomic sequences of 55 strains isolated during 2002?2016 in China were collected from GenBank and analyzed by bioinformatics. [Results] Thirteen genotypes of IBV, including QX, 4/91, Mass, tl/CH/LDT3/03, CK/CH/LSC/99I, TW-I, TW-II, TC07-2, Ck/CH/LDL/97I, N1/62-associated, Arkansas, New-I and a newly emerging genotype New-II, were found co-circulation in China during 2002?2016 based on phylogenetic analysis of S1 gene. It was notable that ck/CH/LSD/110712 belonging USA branch was found in China in this study. Recombination analysis revealed the S1 gene of New-II genotype IBVs was originated from recombination between tl/CH/LDT3/03- and QX-type IBVs. With analysis of whole genomes of 55 IBV isolates, 52 recombinants were identified through RDP4. The partial sequence of vaccine strains were found in 25 of 52 IBV isolates. The recombination events were further confirmed by SimPlot bioinformatics analysis. [Conclusion] Bioinformatics analysis results demonstrated that multiple genotypes of IBV were co-circulated in China during 2002?2016, and novel IBV genotypic clusters and variants could be emerged through recombination which frequently occurring between field and vaccine strains. It indicates the adverse effects of IBV vaccine on controlling IB in China should be paid more attention.