Introduction: Wild migratory birds are global distributors of pathogens. Sardinia, Italy, is the second largest Island in the Mediterranean and is a land bridge between Europe and Africa.
Methodology: We designed a surveillance protocol to investigate wild migratory birds for presence, frequency, and type of avian influenza viruses. We collected over 4,000 avian samples and compared three sampling methods, fecal, cloacal, and tracheal, to determine the most productive for virus identification. To determine frequency of infection, RNA was extracted and RT-PCRs for avian influenza virus genes were run. Positive samples were cultivated for live virus, sub typed and sequenced.
Results: Forty-four samples were positive for influenza nucleoprotein gene. We identified two previously unidentified H3 subtype strains and found cloacae to have the highest rate of virus identification and fecal sampling to provide quality RNA and repeatable results for determination of virus presence.
Conclusion: Our investigation provides information on the frequency of Mediterranean avian influenza viruses, and validates the initiation of an avian influenza surveillance protocol. Taken together with global avian influenza findings, these results give insight into infectious disease distributions which is important for viral pandemic monitoring and design of preventative measures.