Molecular epidemiology of vaccine preventable viral diseases in poultry

Whole genome sequencing by using various NGS platforms has revolutionized virology research, including the molecular epidemiology of viral diseases. In our research project we proposed a routine, NGS-based virus detection and characterization approach to support virus monitoring in the area of vaccine preventable viral infections in poultry. At the beginning of the project pre-analytical sample processing (i.e. enrichment of viral genomes) was the main methodological challenge. However, we found adequate solutions for 12 virus families. Thanks to the availability of two large virus isolate collections we had sufficient amount of viruses to perform molecular epidemiological studies for nearly all major virus groups represented in these strain collections. Large number of viral genomic sequences (>100-100) were determined for poultry reoviruses, adenoviruses and coronaviruses. In these collections international isolates were also represented. In addition, the number of strains in some additional virus families (orthomyxoviruses, paramyxoviruses, polyomaviruses, CRESS DNA viruses) permitted deeper epidemiologic analyses and understanding the major driving forces of molecular evolution. Viruses new to science (within reoviruses) and new genotypes of known viruses (within adenoviruses, CRESS DNA viruses, orthobunyaviruses, coronaviruses) were alike identified.