Determination of molecular epidemiology of Fowl Aviadenoviruses isolated from broiler chickens in Turkey

Fowl Aviadenoviruses (FAdVs), found among adenoviruses affecting poultry, are viral agents causing significant economic losses in broiler chicken farming. Given their ability to transmit vertically and horizontally, understanding the epidemiological characteristics of factors in the control of FAdV-related diseases in breeder and broiler chicken flocks is crucial. FAdVs lead to varying mortalities, reaching up to 80% in broiler chickens, causing Inclusion Body Hepatitis (IBH), Hepatitis-Hydropericardium Syndrome (HHS), and Adenoviral Gizzard Erosion (AGE). These viruses predominantly affect young broiler chickens. Due to the dominance of different genotypes of FAdVs in various geographical regions, targeted studies focusing on genotypes are essential in protection-control programs. The aim of this thesis is to determine the circulating field serotypes of FAdVs in regions with intensive broiler chicken farming in Turkey, revealing the dominant genotypes and molecular epidemiologies. To achieve this goal, samples were taken, considering epidemiologically important parameters such as breeding vaccination status, age, and transmission routes. Viral DNA obtained from liver and cloacal swab samples was diagnosed for FAdV using PCR with primers targeting the hexon loop-1 gene region. The results indicated that 30% of the sampled flocks over two breeding periods were FAdV positive, with 50% positivity in non-vaccinated flocks and 10% in vaccinated ones. Hexon gene sequence analysis was conducted to identify the circulating serotypes in FAdV-positive flocks. The analysis revealed that all isolated FAdVs from both liver and cloacal swabs resembled the FAdV-8b serotype, showing 100% homology among themselves. FAdV diagnosis was five times more frequent in the offspring lines derived from non-vaccinated breeders compared to those from vaccinated breeders. The obtained hexon loop-1 gene sequences were entered into the GenBank database, and phylogenetic analysis demonstrated a high homology between FAdV-8b serotypes from Turkey and those previously reported from Indonesia and worldwide, with percentages ranging from 96.48% to 96.72%. To gain a deeper understanding of the genetic structure of FAdV-8b, a random positive sample was selected for whole-genome sequencing analysis, resulting in a consensus genome of 45,995 base pairs. For the first time, the FAdV whole-genome sequence from this thesis was deposited in the GenBank database under the accession number SUB14015087. The consensus genome from whole-genome sequencing provided a comprehensive data output for a better understanding of the genetic structure of FAdVs. In conclusion, this thesis has provided extensive insights into the epidemiology of FAdVs through the examination of molecular data using various phylogenetic analyses. The entry of hexon gene sequences and whole-genome sequences into the GenBank database is a crucial step in serving as a valuable resource for future studies. By offering valuable molecular epidemiological information, this thesis underscores the importance of understanding the molecular epidemiology of FAdVs for organizing protective and control measures against FAdV-related diseases. Emphasizing the need to comprehend the molecular epidemiology of FAdVs is essential for mitigating economic losses and effectively implementing protection and control programs.