First complete genome sequence of European turkey coronavirus suggests complex recombination history related with US turkey and guinea fowl coronaviruses

Abstract

A full-length genome sequence of 27,739 nt was determined for the only known European turkey coronavirus (TCoV) isolate. In general, the order, number and size of ORFs were consistent with other gammacoronaviruses. Three points of recombination were predicted, one towards the end of 1a, a second in 1b just upstream of S and a third in 3b. Phylogenetic analysis of the four regions defined by these three points supported the previous notion that European and American viruses do indeed have different evolutionary pathways. Very close relationships were revealed between the European TCoV and the European guinea fowl coronavirus in all regions except one, and both were shown to be closely related to the European infectious bronchitis virus (IBV) Italy 2005. None of these regions of sequence grouped European and American TCoVs. The region of sequence containing the S gene was unique in grouping all turkey and guinea fowl coronaviruses together, separating them from IBVs. Interestingly the French guinea fowl virus was more closely related to the North American viruses. These data demonstrate that European turkey and guinea fowl coronaviruses share a common genetic backbone (most likely an ancestor of IBV Italy 2005) and suggest that this recombined in two separate events with different, yet related, unknown avian coronaviruses, acquiring their S-3a genes. The data also showed that the North American viruses do not share a common backbone with European turkey and guinea fowl viruses; however, they do share similar S-3a genes with guinea fowl virus.

Fig. 1.

Fr TCoV genome organization (not drawn to scale). Above the graphic the names (bold and underlined) of each ORF are shown, followed by their nucleotide positions (start–stop codons included). Arrows below the graphic correspond to the predicted positions of the most likely recombination sites (positions 8658, 20 280 and 24 058, from left to right).

Fig. 2.

Phylogenetic relationships of the Fr TCoV genomic sequence assessed in four separate phylogenetic trees. Diagrams of the genome are provided above each tree and contain black shading to depict the segment of sequence used for that tree.

Fig. 2.

Phylogenetic relationships of the Fr TCoV genomic sequence assessed in four separate phylogenetic trees. Diagrams of the genome are provided above each tree and contain black shading to depict the segment of sequence used for that tree.

Fig. 3.

Bootscan analysis of the full-length genomic sequences of Fr TCoV, GfCoV/Fr/2011, US TCoV (TX-GL) and IBV (Italy 2005). In SimPlots (a) and (b) the query sequences are Fr TcoV and GfCoV respectively. Arrows above SimPlot (a) indicate putative breakpoints, which were predicted from analysis using the 69 full-length sequences. In (a) the yellow line corresponds to FN430414_ITA_90254_2005 – Turkey_GQ427174_TCoV_TX-GL_01; blue, FN430414_ITA_90254_2005 – Fr-TCoV-080385d_; purple, Turkey_GQ427174_TCoV_TX – GL_01 -Fr-TCoV-080385d_. In (b) the yellow line corresponds to FN430414_ITA_90254_2005 – Turkey_GQ427174_TCoV_TX-GL_01; blue, FN430414_ITA_90254_2005 – GfCoV/FR/2011_; purple, Turkey_GQ427174_TCoV_TX – GL_01 -GfCoV/FR/2011_. The dotted lines show bootstrap cut-offs of 80 %. Very similar plots were observed for FrTCoV and GfCoV in that both viruses were grouped with Italy 2005 for the majority of the sequences leading up to the S gene and after the S gene to the end of the genome.

Fig. 4.

TMRCA analysis for different regions of the Fr TCoV and Gf CoV/Fr/2011 genomes. Black squares represent median values, and bars 95 % HPD intervals. Zero on the y-axis indicates the year when the most recent virus was isolated.

Fig. 5.

Hypothetical evolution of Fr TCoV, GfCoV/Fr/2011 and US TCoV. (a) From left to right: (i) IBV and AvCoV donor ancestors would have evolved to produce IBV EU and US plus AvCoV donors 1 and 2 respectively. (ii, iii) Three recombination events R1, R2 and R3 (iii) would have resulted in viruses Fr TCoV, GfCoV/Fr/2011 and US TCoV (iii). (b) From left to right: a recombination event (R1) between IBV EU and an AvCoV donor would have produced Fr TCoV/GfCoV/Fr/2011 ancestor, which would have evolved into FrTCoV and GfCoV/Fr/2011. Here, a recombination event (R2) between GfCoV/Fr/2011 and IBV US would have generated US TCoV.