A recombinant infectious bronchitis virus from a chicken with a spike gene closely related to that of a turkey coronavirus

Abstract

Using viral metagenomics, the complete genome sequence of an infectious bronchitis virus (IBV) strain (named ahysx-1) from a fecal sample from a healthy chicken in Anhui province, China, was determined. The genome sequence of ahysx-1 was found to be very similar to that of IBV strain ck/CH/LLN/131040 (KX252787), except for the spike gene region, which is similar to that of a turkey coronavirus strain (EU022526), suggesting that ahysx-1 is a recombinant. Recombination analysis and phylogenetic analysis based on the genomic sequences of ahysx-1 and other related strains confirmed that ahysx-1 appears to be a recombinant resulting from a recombination event that occurred between a chicken coronavirus and a turkey coronavirus. Further studies need to be performed to determine whether this recombinant IBV strain is pathogenic and whether it is transmitted between chickens and turkeys.

Keywords: Coronavirus; Genome recombination; Infectious bronchitis virus; Viral metagenomics.

Fig. 1

Recombination and phylogenetic analysis of the infectious bronchitis virus from chicken. a Genome organization of the infectious bronchitis virus strain ahysx-1. b BOOTSCAN evidence for the recombination origin on the basis of pairwise distance, modeled with a window size 200, step size 20, and 100 Bootstrap replicates. c Neighbor joining tree constructed using the nucleotide sequence of gene 1a and 1b. d Neighbor joining tree constructed using the S gene. e Neighbor joining tree constructed using the nucleotide sequence of gene 3, 4, 5, and 6. f The overlapping reads coverage across the boundaries of S gene. The S gene region was highlighted in black, while the sequences flanking the boundaries of S gene were marked with dark gray. The coverage depth is shown in blue