Origin and evolution of LX4 genotype infectious bronchitis coronavirus in China

Abstract

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.

Keywords: Clade I; Clade II; Evolution; Infectious bronchitis virus (IBV); LX4 genotype (QX-like); Topology.

Fig. 1

Phylogenic tree inferred from the S amino acid sequences of 110 LX4 genotype IBV strains and five reference strains. The trees were constructed using the neighbor-joining method and bootstrap values calculated from 1000 trees. The IBV strains used for comparison of amino acid similarities are in bold.

Fig. 2

Phylogenic tree inferred from the complete genomic sequences of 110 LX4 genotype IBV strains and five reference strains. The trees were constructed using the neighbor-joining method and bootstrap values calculated from 1000 trees.

Fig. 3

SimPlot analysis of our 110 LX4 IBV strains. The complete genomic sequence of the H120 strain was used as the query sequence. 101 out of 110 LX4 strains showed similar topology and are indicated in grey. Those with different topologies are indicated in different colors with the name of the virus. The position from the N gene to the 3′ UTR is also indicated.

Fig. 4

Phylogenic tree inferred from the nucleotide sequence from the N gene to the 3′ UTR of 110 LX4 IBV strains and five reference strains. The trees were constructed using the neighbor-joining method and bootstrap values calculated from 1000 trees.

Fig. 5

Recombination analysis of the IBV strains ck/CH/LHLJ/130744 (A and B) and ck/CH/LJL/140734 (C and D). SimPlot using H120 as the query sequence. The dotted lines show the deduced recombination breakpoints (A and C). The hollow arrows show the different fragments similar to those of the parental viruses. Multiple sequence alignments of the predicted breakpoints and flanking sequences among 4/91, ck/CH/LHLJ/130822 and ck/CH/LHLJ/130744 (B), and H120, ck/CH/LHLJ/130822 and ck/CH/LJL/140734 (D). The numbers on the right of each alignment show the nucleotide positions in the genome of each virus. The sequences of ck/CH/LHLJ/130744 (B) and ck/CH/LJL/140734 (D) are listed, respectively, and only the nucleotides differing from those of these two strains are depicted. The regions where the template switches (breakpoint) have taken place are in bold.