Identification of two novel avian influenza a (H5N6) viruses in wild birds, Shanghai, in 2016

•Two novel influenza A (H5N6) viruses were detected in migratory waterfowl in Shanghai, 2016.•These viruses were genetically similar to the recent South Korea and Japan H5N6 viruses collected in 2016 and 2017.•The study might provide the direct evidence for that migratory waterfowl in the dissemination of the H5N6 viruses along the migratory flyways. The H5N6 avian influenza virus (AIV) has been continuously reported in wild birds, which may contribute to further geographical spread during their long-distance migrations. Active AIV surveillance in wild birds was conducted during October and November 2016 in Shanghai, China. Two novel influenza A (H5N6) viruses were detected in samples from migratory waterfowl that are genetically similar to recent South Korea and Japan H5N6 viruses collected in 2016 and 2017, highlighting the role of migratory waterfowl in the dissemination of H5N6 viruses along migratory flyways.