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.

Molecular and biological characteristics of the infectious bronchitis virus TC07-2/GVI-1 lineage isolated in China

“…Despite the different sites of recombination in the genomes of the IBV strains that have been reported, the recombination events that occurred in the IBV gene encoding the spike protein may potentially cause antigenic, pathogenic, and tissue tropism changes, possibly even a host shift event, which could lead to the emergence of a novel IBV genotype or avian coronaviruses. It has been proposed that the emergence of coronaviruses in turkeys (Hughes, 2011;Jackwood et al, 2010) and guinea fowl (Brown et al, 2016) resulted from recombination events involving IBVs and an unidentified coronavirus that donated a spike gene that encoded a protein of low amino acid identity to those of IBVs. These recombinations have resulted in a host shift from chickens to turkeys and guinea fowl, respectively.…”

First characterization of a Middle-East GI-23 lineage (Var2-like) of infectious bronchitis virus in Europe

“…We also found interesting branching out of phylogenetic tree based on ORF1ab region (7684-18905 nt, File S5) which contained Polish GI-23 strain and European TCoV, GfCoV and IBVs of GI-19 lineage (ITA/90254/2005 and CK/SWE/0658946/10). Such correlation in the genome fragment recently raised the hypothesis that GfCoV could be the ancestor of Italian QX strain (Brown et al, 2016). Guinea fowl are native birds to Africa, the continent neighboring the Middle East and it could not be ruled out that the viruses infecting these animals were also the ancestors of Polish representative of GI-23 lineage of IBV, gammaCoV/Ck/Poland/G052/2016 strain.…”

Genetic, antigenic and pathogenic characterization of avian coronaviruses isolated from pheasants (Phasianus colchicus) in China

“…The S1 gene sequences of 213 reference AvCoV strains were used for phylogenetic analysis, together with those of the two new isolates I0623/17 and I0710/17. The 213 viruses included 199 reference IBV strains reported by Valastro et al (2016), three IBV GI-28 strains , three IBV GI-29 strains (Jiang et al, 2018), two IBV GVII-1 strains (Ma et al, 2019), two additional IBV GI-19 strains, ck/CH/LDL/091022 (LDL/091022) and ck/CH/LJL/140734 (LJL/140734) which were used the virus-neutralization (VN) test, three TCoVs and one guinea fowl CoV (Brown et al, 2016).…”

“…The hypothesis that different introductions of the viruses from chickens to pheasants and the independent evolution of the resulting PhCoVs may account for the inconsistent phenotypes of the PhCoVs. The emergence of CoVs in turkeys was proposed to have resulted from recombination events involving IBVs and an as-yet-unidentified CoV, which donated an S gene encoding a protein with low amino acid identity to IBV (35%) (Jackwood et al, 2010;Brown et al, 2016). This is suspected to have resulted in a host shift from chickens to turkeys, as well as switching the tissue tropism of the virus from the upper respiratory to the intestinal tract.…”

“…Most viruses in the genus Gammacoronavirus are isolated from birds, including Galliformes (chicken, turkey, quail, guinea fowl, pheasant, and peafowl) (Brown et al, 2016;Cavanagh et al, 2002;Guy, 2008;Liu et al, 2005;Sun et al, 2007;Torres et al, 2017), Anseriformes (duck, goose, teal, swan, and pintail) (Liu et al, 2005;Papineau et al, 2019), Columbiformes (pigeon) (Jonassen et al, 2005), Pelecaniformes (spoonbill and heron), Suliformes (cormorant), Charadriiformes (red knot, oystercatcher, and blackheaded gull), and Passeriformes (bulbul) (Chu et al, 2011), although they have also been identified in the beluga whale (Mihindukulasuriya et al, 2008) and in bottlenose dolphins (Woo et al, 2014). Infectious bronchitis virus (IBV) and turkey coronavirus (TCoV) are among the most economically important avian coronaviruses (AvCoVs).…”