Identification and characterisation of the genomic segment 7 of the infectious salmon anaemia virus genome.

The isolation and characterisation of a gene encoding the putative matrix proteins of infectious salmon anaemia virus (ISAV) is reported. Following identification of an ISAV-specific sequence from a cDNA library, RACE-PCR was used to identify a mRNA transcript of approximately 1.2 kb containing the ISAV consensus sequence GCTAAGA at the 5' end. Although the cDNA transcript and its putative protein product did not possess high homology with other orthomyxoviral sequences, similarity to a paramyxovirus fusion glycoprotein and viral cell surface proteins was identified. The size of this transcript suggested that it was derived from segment 7 of the ISAV genome and encoded the matrix proteins. Like syntenic segments of other orthomyxoviruses, this segment was shown to encode at least two matrix proteins, M1 and M2. The existence of M1 and M2 ISAV mRNA was demonstrated by RT-PCR and sequencing, with the M1 transcript being more abundant than the M2 in infected cell cultures, as is found in other orthomyxoviruses. Nucleotide sequence comparison of segment 7 of the ISAV genome from isolates of different geographic origin indicated it to be the one of the most variable of the ISAV genes characterised to date.