Determination of infectious bronchitis virus genotypes in vaccinated flocks of poultry

Cilj ovog istraţivanja bio je da se izoluje, genetski karakteriše i odredi filogenetska pozicija sojeva virusa infektivnog bronhitisa otkrivenih u Srbiji u poreĊenju sa poznatim referentnim i cirkulišujućim sojevima u svetu. Prikupljeno je ukupno 480 uzoraka trahealnih briseva iz 13 razliĉitih komercijalnih jata koka nosilja. Uzorci prikupljeni tokom 2016. i 2017. godine, analizirani su molekularnim metodama realtime RT-PCR-om, multipleks nested RT-PCR te sekvencionirani. Filogenetske analize bazirane na delimiĉnim S1 sekvencama pokazale su da su šest sojeva od ukupno deset detektovanih klasifikovani kao genotip D274, dva soja kao QX genotip i dva soja kao genotip 4/91. Razlika u nukleotidnoj sliĉnosti izmeĊu naših izolata koji pripadaju D274 grupi kretala se od 0 do 1,2%. PoreĊenjem dobijenih sojeva i D274 (X15832) utvrĊene su razlike od 0 do 0,9%. Najveća nukleotidna sliĉnost detektovanih QX sojeva bila je sa kineskim sojem QXIBV (KC795604), i kretala se u rasponu od 98,8% do 99,1%. Dva naša izolata koja pripadaju genotipu 4/91 imala su 99,7% i 98,8% nukleotidne sliĉnosti sa vakcinalnim sojem 4/91 (KF377577). Ova studija je pokazala da virusi koji pripadaju genotipu D274, QX i 4/91 su cirkulisali u jatima ţivine u Srbiji tokom 2016. i 2017. godine.The aim of this study was to isolate, genetically characterize and determine phylogenetic relationship of strains of virus IB detected in Serbia in comparison to other known referent and circulating strains in the world. A total of 480 samples collected from 13 different commercial layer flocks, obtained from tracheal swabs were included. Samples are taken from 2016 to 2017 and thereafter samples were molecularly analyzed by real-time RT-PCR, multiplex nested RT-PCR, and by sequencing of the S1 gene. Phylogenetic analyses based on partial S1 sequences revealed that six strains were classified as the D274 genotype, two strains as the QX genotype and two strains as the 4/91 genotype. The difference in nucleotide similarity between the Serbian isolates belonging to the D274 group ranges from 0 to 1.2%. Comparison of the obtained strains and D274 (X15832) showed differences from 0 to 0.9%. The greatest nucleotide of detected QX strains was with Chinese QXIBV (KC795604), ranging from 98.8% to 99.1%. Two Serbian strains belonging to the 4/91 genotype had 99.7% and 98.8% nucleotide similarities with vaccine strain 4/91 (KF377577). This study has shown that viruses belonging to D274, QX, and 4/91 genotypes were circulating in poultry flocks in Serbia during 2016 and 2017