Surveillance of avian influenza virus and paramyxovirus in migratory waterfowl and shorebirds was conducted in the San-in district of western Japan from the winter of 2001 to 2008. From 4,335 fecal samples from wild birds, 41 avian influenza viruses of 12 different HA and NA combinations, including two H5N3 strains, and 13 avian paramyxoviruses were isolated. Phylogenetic analysis of HA genes revealed that H5N3 strains clustered in a different branch from the recent highly pathogenic H5N1 isolates in Japan; however, the introduction of new highly pathogenic avian influenza virus by migratory birds cannot be ignored. Therefore, it is necessary to continue surveillance of these potentially serious pathogens in waterfowl and shorebirds.
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