Downloaded from www.microbiologyresearch.org by IP: 54.160.81.51 On: Mon, 19 Sep 2016 17:35:49 Characterization of a new genotype and serotype of infectious bronchitis virus in Western Africa Mariette F. Ducatez, 1 3 Ana Moreno Martin, 2 Ademola A. Owoade, 3 Isaac O. Olatoye, 4 Bello R. Alkali, 5 Issoufou Maikano, 6 Chantal J. Snoeck, 1 Aurelie Sausy, 1 Paolo Cordioli 2 and Claude P. Muller 1 Correspondence Claude P. Muller claude.muller@LNS.ETAT.LU 1 Institute of Immunology, National Public Health Laboratory, CRP-Sante ´ , 20A rue Auguste Lumie ` re, L-1950 Luxembourg 2 Istituto Zooprofilattico sperimentale della Lombardia e dell’Emilia Romagna, Reparto di virologia e sierologia specializzata, Via Bianchi 9, 25124 Brescia, Italy 3 Department of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria 4 Food Safety, Drug Residues/Animal Diseases Surveillance and Intervention, Department of Veterinary Public Health and Preventive Medicine, University of Ibadan, Ibadan, Nigeria 5 Department Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Sokoto, Nigeria 6 LABOCEL, Direction des Laboratoires Ve ´ te ´ rinaires, Niamey, Niger Received 7 April 2009 Accepted 18 July 2009 Between 2002 and 2007, more than 1000 chickens from commercial farms, live bird markets and backyard farms in Nigeria and Niger were tested for the presence of the infectious bronchitis virus (IBV) genome. Phylogenetic analysis of full-length sequences of the spike 1 (S1) gene revealed a new genotype of IBV that we refer to as ‘IBADAN’. The minimum genetic distance to the closest ‘non-IBADAN’ strains (UK/7/93 at the nucleotide level; H120 and M41 at the amino acid level) reached 24 and 32 % at the nucleotide and amino acid levels, respectively. The full genome of the IBADAN reference strain (NGA/A116E7/2006) had a genetic distance of 9.7–16.4 % at the nucleotide level with all available fully sequenced strains. As IBV S1 plays a major role in antigenicity, the antigenic relatedness of NGA/A116E7/2006 was compared with strains of other serotypes. NGA/A116E7/2006 did not cross-react with antisera against IT02, M41, D274, Connecticut or 793/B strains in virus neutralization assays. NGA/A116E7/2006 cross-reacted with the QX-like strain ITA/90254/2005 but only to a low level (antigenic relatedness of 33 %), suggesting that IBADAN also represents a new serotype. A comparison of S1 sequences identified several amino acids that may play a role in IBV antigenicity. Despite the absence of obvious clinical signs in poultry infected by IBADAN strains, it is important to test the cross- protection of current vaccine strains. INTRODUCTION The recent emergence of a coronavirus variant causing severe acute respiratory syndrome (SARS) in humans has renewed interest in the virus family Coronaviridae. Coronaviruses comprise three genetic groups, two of which (groups 1 and 2) contain viruses that are pathogenic in humans. Turkeys can be infected by group 2 as well as group 3 turkey coronaviruses (Lai & Holmes, 2001). Group 3 viruses such as infectious bronchitis virus (IBV) (Cavanagh, 2000; Enjuanes et al., 2000; Lai & Holmes 2001), the first coronavirus to be discovered, occur only in birds. So far, group 3 viruses have not been found in humans, but phylogenetic analysis of SARS-coronavirus has shown that its genome contains sequences that seem to be of group 3 origin (Stavrinides & Guttman, 2004). IBV was first found in the USA in 1930 and has since been reported from most countries throughout the four continents of America (Johnson & Marquardt, 1975), Europe (Capua et al., 1994; Cavanagh & Davis, 1993; 3Present address: St Jude Children’s Research Hospital, Department of Infectious Diseases, Division of Virology, 262 Danny Thomas Place, MS330, Memphis, TN 38105, USA. The GenBank/EMBL/DDBJ accession numbers for the complete genome sequences of NGA/A116E7/2006 and ITA/90254/2005 are FN430415 and FN430414, respectively. Full S1 and N gene sequences as well as partial S2 gene sequences are under accession numbers FN182243–FN182283. Details of the PCR conditions are available with the online version of this paper. Journal of General Virology (2009), 90, 2679–2685 DOI 10.1099/vir.0.012476-0 012476 G 2009 SGM Printed in Great Britain 2679