Pekin and Muscovy ducks respond differently to vaccination with a H5N1 highly pathogenic avian influenza (HPAI) commercial inactivated vaccine

► Muscovy ducks respond less well to H5N1 avian influenza vaccination than Pekin ducks. ► Muscovy ducks are affected more severely after infection with an H5N1 HPAI virus. ► Differences in innate immunity were observed between infected Pekin and Muscovy ducks.