Genetic characterization of infectious bronchitis viruses in Thailand, 2014-2016: identification of a novel recombinant variant

Abstract

Infectious bronchitis (IB) causes severe economic losses to the poultry industry worldwide owing to frequent emergence of novel infectious bronchitis virus (IBV) variants, which potentially affect the effectiveness of the currently used IBV vaccine. Therefore, continuous monitoring of IBV genotypes and lineages recently circulating in chickens worldwide is essential. In this study, we characterized the complete S1 gene from 120 IBVs circulating in chickens in Thailand from 2014 to 2016. Phylogenetic analysis of the complete S1 gene of 120 Thai IBVs revealed that the 2014-2016 Thai IBVs were divided into 3 lineages (GI-1, GI-13, and GI-19) and a novel IBV variant. Our results also showed that GI-19 lineage has become the predominant lineage of IBV circulating in chicken flocks in Thailand from 2014 to 2016. It is interesting to note that a novel IBV variant, which was genetically different from the established IBV lineages, was identified in this study. The recombination analysis demonstrated that this novel IBV variant was a recombinant virus, which was originated from the GI-19 and GI-13 lineage viruses. In conclusion, our data demonstrate the circulation of different lineages of IBV and the presence of a novel recombinant IBV variant in chicken flocks in Thailand. This study highlights the high genetic diversity and continued evolution of IBVs in chickens in Thailand, and the importance of continued IBV surveillance for effective control and prevention of IB.

Keywords: Thailand; chicken; genetic characterization; infectious bronchitis virus.

Figure 1

Geographic distribution of infectious bronchitis virus (IBV) in Thailand from 2014 to 2016.

Figure 2

Phylogenetic tree of the complete S1 genes of the 2014–2016 Thai IBVs, the previously reported Thai IBVs, and 89 selected reference IBV strains from genotype I (GI-1-29), GII, GIII, GIV, GV, GVI, GVII, and unique variants (UV). A phylogenetic tree was constructed in MEGA v.6.0 using the maximum-likelihood algorithm (Tamura et al., 2013). A similar result was observed when applying the neighbor-joining algorithm. The countries, year of detection, genotypes, and lineages of IBVs are labeled behind the strain names. Dark blue, green, and yellow circles indicate the 2014, 2015, and 2016 Thai IBVs, respectively, whereas black squares indicate the previously reported Thai IBVs.

Figure 3

Recombination analysis of a novel recombinant IBV variant (TH/IBV/2014/CU-179 and TH/IBV/2016/CU-92). The results from RDP4 showing the possible recombination events in TH/IBV/2014/CU-179 (A) and TH/IBV/2016/CU-92 (B). The positions of recombination break point are shown as black arrows.