Emergence of a group 3 coronavirus through recombination

Abstract

Analyses of turkey coronavirus (TCoV), an enteric disease virus that is highly similar to infectious bronchitis virus (IBV) an upper-respiratory tract disease virus in chickens, were conducted to determine the adaptive potential, and genetic changes associated with emergence of this group 3 coronavirus. Strains of TCoV that were pathogenic in poults and nonpathogenic in chickens did not adapt to cause disease in chickens. Comparative genomics revealed two recombination sites that replaced the spike gene in IBV with an unidentified sequence likely from another coronavirus, resulting in cross-species transmission and a pathogenicity shift. Following emergence in turkeys, TCoV diverged to different serotypes through the accumulation of mutations within spike. This is the first evidence that recombination can directly lead to the emergence of new coronaviruses and new coronaviral diseases, emphasizing the importance of limiting exposure to reservoirs of coronaviruses that can serve as a source of genetic material for emerging viruses.

Fig. 1

Neighbor-Joining method used to infer evolutionary history using full genomic sequence data of the available group 3 coronaviruses. The bootstrap consensus tree was constructed from 1000 replicates (percentage of replicate trees in which associated strains clustered together are presented at nodes). The p-distance scale is presented at the bottom of the figure.

Fig. 2

Neighbor-Joining method used to infer evolutionary history using full genomic sequence data for available TCoV isolates. The bootstrap consensus sub-tree was constructed from 1000 replicates (percentage of replicate trees in which associated strains clustered together are presented at nodes). The p-distance scale is presented at the bottom of the figure. Different genetic groups are indicated at the right of the figure.

Fig. 3

Phylogenetic relationships of virus proteins. Phylogenetic trees showing amino acid sequence relatedness computed using Neighbor-Joining and the Nei-Gojobori method. (a) Main protease (3CLpro) coding region (residues 2778-3084 in the 1ab protein). (b) RNA-dependent RNA polymerase (RdRp) coding region (residues 3927-4866 in the 1ab protein). (c) Helicase coding region (residues 4867–5465 in the 1ab protein). (d) Spike glycoprotein. (e) Membrane glycoprotein. (f) Nucleocapsid protein. Viruses included in the analysis are TCoV/74 (GQ427173), TCoV/TX-GL (GQ427174), TCoV/TX-1038 (GQ427176), TCoV/IN-517 (GQ427175), TCoV/MG10 (EU095850), TCoV/540 (EU022525), TCoV/ATCC (EU022526), IBV/Ark (EU418976), IBV/Mass41 (AY851295), SW1 (NC010646), and ThCoV (FJ376621). The amino acid sequences were aligned with ClustalW (MEGA 4.0.2, Tamura et al., 2007), and the evolutionary distances are shown for each of the trees. Residue positions listed above are relative to the TCoV/TX-GL/01 strain.

Fig. 4

Simplot analysis of full-length genomic sequence for IBV/Mass 41, TCoV/VA-74/03, TCoV/TX-GL/01, TCoV/IN-517/94, and TCoV/TX-1038/98 showing recombination between nucleotides 20,173 and 23,849. The query sequence is TCoV/VA-74/03. Bars at the top represent relative position of the coding regions for 1a, 1ab, spike, membrane (M), and nucleocapsid (N).