Molecular investigation of S2-3a/3b-E-M-4b/4c-5a/5b-N gene of QX-like and variant genotype infectious bronchitis virus isolated in Thailand reveals a distinct E gene.

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The QX-like infectious bronchitis virus (IBV) and variant genotype have been discovered worldwide including Thailand. In order to know the origin of QX-like and variant genotype IBV in Thailand, the genetic analysis on multiple genes was investigated. Seven IBVs including four QX-like and three variant genotype were randomly selected from IBVs isolated in Thailand during 2008 and 2010. Phylogenetic analysis of the S2-3a/3b-E-M-4b/4c-5a/5b-N gene showed that Thai QX-like and variant genotype IBV were grouped together in a separate branch from other IBV strains. The isolated IBVs shared nucleotide identities of 96-99.9% with each other. They exhibited a high level of similarity (93.8%) with KM91 strain in South Korea. Phylogenetic analysis of the S2 and 3a/3b gene showed a relationship to KM91 strain. The E gene was distinct from other IBV strains. The M, 4a/4b and 5a/5b gene were closely related to Massachusetts type. The N gene was classified into two groups which were a group of unique to Thailand (variant genotype) and a relationship with Massachusetts type (QX-like). Recombination analysis identified the occurrence of recombination events in the genome of viruses. These findings demonstrated that the QX-like IBV and variant genotype isolates in Thailand were the recombinant viruses. Thai QX-like IBV had a genetic relationship with KM91 strain, Massachusetts type and unknown IBV whereas variant genotype had a genetic relationship with Thai QX-like IBV and Connecticut strain.