Origin and evolution of LX4 genotype infectious bronchitis coronavirus in China

•LX4 is one the most important genotypes of infectious bronchitis coronavirus worldwide.•Two LX4 genotype viruses have novel genomic organizations which lacked 3a and 5b gene, respectively.•Recombination events may be responsible for the emergence of the LX4 genotype.•Most of these viruses disappeared likely because they were not “fit” to adaptation in chickens.•The “fit” viruses continued to evolve and have become widespread and predominant in commercial poultry. We investigated the genomic characteristics of 110 LX4 genotype strains of infectious bronchitis viruses (IBVs) isolated between 1995 and 2005 in China. The genome of these IBVs varies in size from 27596bp to 27790bp. Most IBV strains have the typical genomic organization of other gamacoronaviruses, however, two strains lacked 3a and 5b genes as a result of a nucleotide change within the start codon in the 3a or 5b genes. Analysis of our 110 viruses revealed that recombination events may be responsible for the emergence of the LX4 genotype with different topologies. Most of these viruses disappeared (before mid-2005) because they were not “fit” to adaptation in chickens. Finally, those of the “fit” viruses (after mid-2005) continued to evolve and have become widespread and predominant in commercial poultry. In addition, few of these viruses experienced recombination with those of the vaccine strains at the 3′ end of the genome.