Abstract
Avian infectious bronchitis is a highly contagious disease caused by infectious bronchitis virus (IBV) that affects poultry production worldwide. The absence of vaccine cross-protection and the frequent emergence of new variant strains complicate control of IBV. Here we designed a study to measure the evolution dynamics of IBV strains in China. One hundered and seven complete sequences and 1022 S1-region sequences of Chinese IBVs isolated between 1994 and 2014 were analysed by using MEGA 5.0 software and the Bayesian analysis sampling trees (BEAST) method, and selection pressure on different proteins was assessed. The phylogenetic dissimilarity of different gene trees in the data set indicated possible recombination. Fourteen isolates were identified as recombinants, possibly generated from vaccines of the Massachusetts serotype in recombination with circulating viruses. The earliest IBV in China was found to have existed in the early 1900s, and continues to evolve at a rate of approximately 10− 5 substitutions per site per year. We found that purifying selection was the main evolutionary pressure in the protein-coding regions, while the S1 gene bears the greatest positive selection pressure. The proportion of QX-like genotype strains increased over time. These results indicate that the genotypes of Chinese IBVs have undergone a remarkable transition during the past 20 years.
Highlights
Infectious bronchitis virus (IBV) is a coronavirus that causes acute, highly contagious, respiratory disease in poultry worldwide (Cavanagh, 2007)
To understand the population dynamics of the dominant IBV genotypes in China, we investigated the evolutionary trends of the main endemic QX genotype and the Mass vaccine-like genotype in China during the 1990s– 2010s by analysing a data set of 1022 complete sequences of segment 1 of the spike gene (S1) from viruses isolated at different times
Our study of the evolution of Chinese IBV strains, using available full-length genome sequences and spike 1 (S1) protein-coding sequences, demonstrated an inconsistency between genotype affiliations based on individual genes versus concatenated full-length genomes, indicating that recombination events exist widely in the IBV populations and influence the topology of phylogenetic trees
Summary
Infectious bronchitis virus (IBV) is a coronavirus that causes acute, highly contagious, respiratory disease in poultry worldwide (Cavanagh, 2007). IBV belongs to the gamma coronaviruses, with the other two genera being mammalian viruses, including those responsible for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) (Drexler et al, 2014). IBV outbreaks were first reported in the USA during the 1930s; within a few years they were recognized throughout the world (Cook et al, 2012). These outbreaks continue to cause great losses to the poultry industry worldwide, despite the widespread use of vaccines.
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