Insights on molecular characterization and on methods of detection of Infectious Bursal Disease virus and Avian Mycoplasmas

Among the diseases that threaten the health of poultry, immunosuppressive and respiratory infections play a major role. The first part of this thesis focuses on the phylogenetic analysis of an emerging genotype of the Infectious Bursal Disease virus (IBDV), denominated ITA. Sequence alignments revealed that the virus shared residues with either very virulent IBDVs or low-virulence strains, confirming its distinctive genetic characteristics. Moreover, no evidences of recombination and reassortant phenomena were found in the ITA genotype. Substantial economic losses are caused in poultry by Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) infections. In Chapter IV, the influences of swab type and storage temperatures on the detection of MG and MS, by both culturing and conventional or qPCR, were evaluated. The results suggest that swabs with a plastic shaft should be preferred for MG/MS detection via culture and PCR. While a lower storage temperature at 4°C was optimal for culture recovery, room temperature was adequate for molecular detection. In chapter V, molecular characterisation of MG strains from Middle East and South Asia was attempted by gene-targeted sequencing (GTS) of the MG surface-protein genes MGA_0319, mgc2, gapA and pvpA. In Chapter VI, molecular characterisation of MG and/or MS strains from Italian backyard flocks was attempted. The MS strains were typed by sequencing of the vlhA gene and mostly assigned to types C, D and F. An MS sequence showed peculiar characteristics, thereby not allowing assignment to known MS types. Different subclusters of MG were found by GTS analysis. The circulation of different mycoplasma strains in Italian backyard flocks constitutes a severe risk for commercial poultry production.