Recombinant turkey coronavirus: are some S gene structures of gammacoronaviruses especially prone to exchange?

Abstract

The objective of the present study was to characterize the atypical turkey coronavirus strain detected in a commercial meat turkey farm in Poland. Using the viral metagenomics approach, we obtained a complete genome sequence of coronavirus, isolated from duodenum samples of animals suffering from acute enteritis. The nearly full-length genome consisted of 27,614 nucleotides and presented a typical genetic organization similar to that of Polish infectious bronchitis virus ( IBV ) or French turkey coronavirus/guinea fowl coronavirus strains. Phylogenetic analysis based on both the full-length genome and the whole S gene suggested that gCoV/Tk/Poland/G160/2016 is related to turkey and guinea fowl coronavirus and not IBV strains. Sequence analysis of the genome revealed unique genetic characteristics of the present strain, demonstrating that the virus emerged as a result of the exchange of the S gene of IBV GI-19 lineage with the S gene related to the North American turkey coronaviruses and French guinea fowl coronaviruses. Analysis of earlier, similar recombinations suggests that both the S gene structures may be particularly mobile, willingly switching between different gammacoronavirus genomic backbones. The identified recombinant caused a severe course of the disease, which may imply that it is in the first phase of breaking the barriers between different bird species.

Molecular Detection and Characterization of Coronaviruses in Migratory Ducks from Portugal Show the Circulation of Gammacoronavirus and Deltacoronavirus

“…Several viruses, including zoonotic and economically significant pathogens, are known to circulate among wild birds [ 2 , 30 ]. The main representative of avian coronavirus is the infectious bronchitis virus (IBV) [ 31 ], which is a Gammacoronavirus , a highly contagious viral disease that is considered responsible for significant economic losses in the poultry industry worldwide (Moreno et al, 2017). IBV control has been hampered by the intricate IBV evolution over the years, by the emergence of many different antigenic or genotypic types, commonly referred to as variants, that are likely to be facilitated by the spillover through migratory birds [ 32 ]; hence, continued monitoring of CoVs in migratory birds is key to mitigating potential outbreaks.…”

Molecular Epidemiology of Turkey Coronaviruses in Poland

“…In 2016, the presence of an atypical TCoV strain was also detected. Molecular studies of a complete genome sequence of TCoV isolated from the duodenum of turkeys suffering from acute enteritis revealed its unique characteristics: the genomic backbones of IBV GI-19 lineage and the S gene related to the North American TCoVs and French guinea fowl coronaviruses [ 20 ]. The objective of the present study was to estimate the relationship between the TCoV strains detected in a Polish turkey farm during a twelve-year period, between 2009 and 2019, by the full-length S gene.…”

Poult Enteritis and Mortality Syndrome in Turkey Poults: Causes, Diagnosis and Preventive Measures

“…Like other ACoVs, the genome of ACoV consists of 15 non-structural proteins, encoded by open reading frame (ORF) 1a/b at the 5'-end, and four structural proteins (spike (S), envelope (E), membrane (M) and nucleocapsid (N), encoded by other ORF at the 3'-end [21,[31][32][33]. Generally, ACoVs have similar phylogenetic relationships and genomic structures and close nucleotide identities.…”

“…Additionally, an atypical TCoV strain was isolated from duodenum of 5-week-old turkey poults suffering from acute enteritis in Poland. Molecular analysis revealed recombination between different γCoV genomic backbones, suggested potential transmission of coronaviruses between different bird species [32].…”