Methods of identifying animals infected with a vvIBDV are provided. The methods comprise contacting a
nucleic acid sample obtained from the animal or a
nucleic acid product obtained by amplifying
RNA obtained from the animal with one or more probe pairs, each of which comprises a
mutation probe and an anchor probe, and then determining the
melting temperature of any hybridization complex that is formed when the one or more probe pairs hybridize with a
nucleic acid in the sample. Such determination is made using FRET analysis. In one embodiment the
mutation probe comprises a sequence identical to a first mutated target sequence of SEQ ID NO: 1 in which the
cytosine at position 827 is substituted with a
thymidine, the
cytosine at position 830 is substituted with a
thymidine, and the
thymidine at position 833 is substituted with a
cytosine, or the reverse complement thereof. In another embodiment, the
mutation probe comprises a sequence identical to a second mutated target sequence of SEQ ID NO: 1 in which the
guanine at position 897 is substituted with an adenine, the cytosine at position 905 is substituted with a thymidine, and the cytosine at position 908 is substituted with an thymidine. Also, provided herein are kits containing
nucleotide probe pairs that can be used in the present methods.