Using nested RT-PCR analyses to determine the prevalence of avian influenza viruses in passerines in western Slovakia, during summer 2007

The prevalence of avian influenza virus (AIV), together with the distribution of different AIV subtypes, was studied in migratory waterfowl and terrestrial birds caught in western Slovakia during summer 2007. Both oropharyngeal and cloacal swabs were collected. Screening of samples revealed that 18% of oropharyngeal and 18% of cloacal samples were positive for AIV. Samples from both the oropharynx and cloaca were positive in only 6.6% of cases. A total of 10 different subtypes of haemagglutinin (H2, H3, H4, H6, H7, H9, H10, H11, H12, and H13) and 4 different subtypes of neuraminidase (N1, N2, N3, and N5) were detected in 32 samples from this location. The most abundant subtypes of HA in the samples were H12 and H9 (25% each), followed by H11 and H10 (15% each), and H13 (9%). There were 3 cases where different AIV infections were detected in oropharyngeal and cloacal samples originating from the same bird (H13N1 and H12N5; H13N3 and H9N5; H10N2 and H9N5 in the oropharynx and cloaca, respectively).