This article was downloaded by: [McMaster University] On: 06 March 2015, At: 11:04 Publisher: Taylor & Francis Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered office: Mortimer House, 37-41 Mortimer Street, London W1T 3JH, UK Avian Pathology Publication details, including instructions for authors and subscription information: http://www.tandfonline.com/loi/cavp20 First full-length sequences of the S gene of European isolates reveal further diversity among turkey coronaviruses S. Maurel a , D. Toquin a , F. X. Briand a , M. Quéguiner a , C. Allée a , J. Bertin b , L. Ravillion c , C. Retaux b , V. Turblin d , H. Morvan e & N. Eterradossi a a Anses—French Agency for Food, Environmental and Occupational Health Safety, Ploufragan-Plouzané Laboratory, Avian and Rabbit Virology , Immunology, and Parasitology Unit , B.P. 53, 22440, Ploufragan, France b Coopérative Le Gouessant , B.P. 40228, 22402, Lamballe-Cedex, France c Laboratoire BOCAVET , 79250, Nueil-Les-Aubiers, France d MC Vet Conseil , 72300, Sablé-sur-Sarthe, France e Laboratoire de Développement et d'analyse des Côtes d'Armor , B.P. 54, 22440, Ploufragan, France Published online: 15 Apr 2011. To cite this article: S. Maurel , D. Toquin , F. X. Briand , M. Quéguiner , C. Allée , J. Bertin , L. Ravillion , C. Retaux , V. Turblin , H. Morvan & N. Eterradossi (2011) First full-length sequences of the S gene of European isolates reveal further diversity among turkey coronaviruses, Avian Pathology, 40:2, 179-189, DOI: 10.1080/03079457.2011.551936 To link to this article: http://dx.doi.org/10.1080/03079457.2011.551936 PLEASE SCROLL DOWN FOR ARTICLE Taylor & Francis makes every effort to ensure the accuracy of all the information (the “Content”) contained in the publications on our platform. However, Taylor & Francis, our agents, and our licensors make no representations or warranties whatsoever as to the accuracy, completeness, or suitability for any purpose of the Content. Any opinions and views expressed in this publication are the opinions and views of the authors, and are not the views of or endorsed by Taylor & Francis. The accuracy of the Content should not be relied upon and should be independently verified with primary sources of information. Taylor and Francis shall not be liable for any losses, actions, claims, proceedings, demands, costs, expenses, damages, and other liabilities whatsoever or howsoever caused arising directly or indirectly in connection with, in relation to or arising out of the use of the Content. This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden. Terms & Conditions of access and use can be found at http:// www.tandfonline.com/page/terms-and-conditions First full-length sequences of the S gene of European isolates reveal further diversity among turkey coronaviruses S. Maurel1, D. Toquin1, F. X. Briand1, M. Que´guiner1, C. Alle´e1, J. Bertin2, L. Ravillion3, C. Retaux2, V. Turblin4$, H. Morvan5 and N. Eterradossi1* 1Anses*French Agency for Food, Environmental and Occupational Health Safety, Ploufragan-Plouzane´ Laboratory, Avian and Rabbit Virology, Immunology, and Parasitology Unit, B.P. 53, 22440 Ploufragan, France, 2Coope´rative Le Gouessant, B.P. 40228, 22402 Lamballe-Cedex, France, 3Laboratoire BOCAVET, 79250, Nueil-Les-Aubiers, France, 4MC Vet Conseil, 72300 Sable´-sur-Sarthe, France, and 5Laboratoire de De´veloppement et d’analyse des Coˆtes d’Armor, B.P. 54, 22440 Ploufragan, France An increasing incidence of enteric disorders clinically suggestive of the poult enteritis complex has been observed in turkeys in France since 2003. Using a newly designed real-time reverse transcriptase-polymerase chain reaction assay specific for the nucleocapsid (N) gene of infectious bronchitis virus (IBV) and turkey coronaviruses (TCoV), coronaviruses were identified in 37% of the intestinal samples collected from diseased turkey flocks. The full-length spike (S) gene of these viruses was amplified, cloned and sequenced from three samples. The French S sequences shared 98% identity at both the nucleotide and amino acid levels, whereas they were at most 65% and 60% identical with North American (NA) TCoVand at most 50% and 37% identical with IBVat the nucleotide and amino acid levels, respectively. Higher divergence with NATCoV was observed in the S1-encoding domain. Phylogenetic analysis based on the S gene revealed that the newly detected viruses form a sublineage genetically related with, but significantly different from, NA TCoV. Additionally, the RNA- dependent RNA polymerase gene and the N gene, located on the 5? and 3? sides of the S gene in the coronavirus genome, were partially sequenced. Phylogenetic analysis revealed that both the NA TCoV and French TCoV (Fr TCoV) lineages included some IBV relatives, which were however different in the two lineages. This suggested that different recombination events could have played a role in the evolution of the NA and Fr TCoV. The present results provide the first S sequence for a European TCoV. They reveal extensive genetic variation in TCoV and suggest different evolutionary pathways in North America and Europe. Introduction Coronaviruses (CoVs) consist of large, enveloped and positive-stranded RNA viruses within the order Nidovir- ales. They possess an approximately 30-kb-long genome from which they transcribe a set of multiple 3?-coterminal nested subgenomic mRNAs (Masters, 2006). The virions are pleomorphic enveloped particles, roughly spherical, with diameters ranging from 50 to 200 nm. They possess long petal-shaped spikes on their membrane that are responsible for the CoV typical crown-shaped morphol- ogy in electron microscopy. CoVs infect a wide variety of avian and mammalian species and cause primarily respiratory or enteric diseases, but also in some cases neurologic illness or hepatitis. In humans, the outbreak of severe acute respiratory syndrome (SARS) caused in 2003 by a CoV has led to an increased interest in family Coronaviridae and its potential animal reservoirs. Based on the latest proposals to the International Committee on the Taxonomy of Viruses, family Coronaviridae in the Nidovirales order includes two sub-families, Coronavir- inae and Torovirinae, the former comprising three genera, Alphacoronaviruses, Betacoronaviruses and Gammacoro- naviruses (deGroot et al., 2008). The proposed Gammacoronavirus genus groups mostly coronaviruses isolated from birds, with the exception of the SW1 and ALC/GX/230/06 viruses isolated from a beluga whale (Mihindukulasuriya et al., 2008), and from the Asian leopard cat or Chinese ferret badger (Dong et al., 2007), respectively. A first proposed species, avian coronavirus (AvCoV), corresponds to the former ‘‘sub- group 3a within the coronavirus genus’’. It groups isolates obtained from Galliformes (chicken, turkey, pheasant, peafowl, quail), Columbiformes (pigeon), Ana- tidae (teal, goose, duck, swan), Charadriiformes (red knot and oystercatcher) and possibly Psittaciformes (Cavanagh et al., 2002; Jonassen et al., 2005; Liu et al., 2005; Gough et al., 2006; Qian et al., 2006; Circella et al., 2007; Hughes et al., 2009). The second proposed species within the Gammacoronavirus genus is Beluga whale coronavirus SW1, and corresponds to the former 3b subgroup (Mihindukulasuriya et al., 2008). A third group of isolates (former 3c subgroup) contains viruses obtained from passerines (bulbul, munia, and thrush) (Woo et al., 2009) and from the Asian leopard cat and Chinese ferret badger (Dong et al., 2007; Who et al., $Present adress: Ceva Animal Health, 46300 Selangor, Malaysia. *To whom correspondence should be addressed. Tel: �33 2 96 01 62 88. Fax: �33 2 96 01 62 63. E-mail: