Recombinational histories of avian infectious bronchitis virus and turkey coronavirus

Abstract

Phylogenetic analysis of complete genomes of the avian coronaviruses avian infectious bronchitis (AIBV) and turkey coronavirus (TCoV) supported the hypothesis that numerous recombination events have occurred between these viruses. Although the two groups of viruses differed markedly in the sequence of the spike protein, the gene (S) encoding this protein showed no evidence of positive selection or of an elevated mutation rate. Rather, the data suggested that recombination events have homogenized the portions of the genome other than the S gene between the two groups of viruses, while continuing to maintain the two distinct, anciently diverged versions of the S gene. The latter hypothesis was supported by a phylogeny of S proteins from representative coronaviruses, in which S proteins of AIBV and TCoV fell in the same clade.

Fig. 1

(A) Neighbor-joining tree of non-overlapping portions of the S gene based on MCL distance at 3310 aligned nucleotide sites. (B) Neighbor-joining tree of the 3′ end of the b portion of the 1 ab gene based on MCL distance at 123 aligned nucleotide sites. Numbers on the branches represent the percentage of 1000 bootstrap samples supporting the branch; only values ≥50% are shown

Fig. 2

Neighbor-joining tree of non-overlapping portions of the 1 a, the b portion of 1ab (excluding the 3′ end; A), 3 a, 3 b, and Env sequences, based on MCL distance at 20,022 aligned sites. Numbers on the branches represent the percentage of 1000 bootstrap samples supporting the branch; only values ≥50% are shown

Fig. 3

(A) Neighbor-joining tree of the non-overlapping portion of the M gene based on MCL distance at 668 aligned nucleotide sites. (B) Neighbor-joining tree of non-overlapping portions of N gene sequences based on MCL distance at 1170 aligned nucleotide sites. Numbers on the branches represent the percentage of 1000 bootstrap samples supporting the branch; only values ≥50% are shown

Fig. 4

(A) Neighbor-joining tree of the non-overlapping portion of the 5a gene based on MCL distance at 198 aligned nucleotide sites. (B) Neighbor-joining tree of non-overlapping portion of the 5b gene based on MCL distance at 180 aligned nucleotide sites. Numbers on the branches represent the percentage of 1000 bootstrap samples supporting the branch; only values ≥50% are shown

Fig. 5

Neighbor-joining tree of S protein sequences of coronaviruses from avian and mammalian hosts based on the JJT distance at 796 aligned amino acid sites. Sequences are identified by accession number and host. Numbers on the branches represent the percentage of 1000 bootstrap samples supporting the branch; only values ≥50% are shown