The complete nucleotide sequence and development of a differential detection assay for a pepper mild mottle virus (PMMoV) isolate that overcomes L3 resistance in pepper.

The complete nucleotide sequence of the RNA genome of a Pepper Mild Mottle Virus (PMMoV) isolate that overcomes L3 resistance in pepper (Capsicum sp.) was determined and compared with the sequence of other Tobamoviruses. The RNA genome consists of 6357 nucleotides and contains four open reading frames. The 5' proximal ORF encodes a 128 kDa product that terminates in an amber codon which may be readthrough to produce a 180 kDa replication-associated protein (ORF 2). ORF 3 codes for the 28 kDa protein assumed to be involved in cell to cell spread of the virus. The last ORF encodes the coat protein (CP). Amino acid sequence comparison of the CP of this and other PMMoV isolates showed the same substitution (Met to Asn) as found in the Italian isolate of PMMoV and which is assumed to be responsible for L3-resistance breaking. RT-PCR using a common primer pair for PMMoV followed by restriction enzyme analysis with EcoRI allowed the discrimination of resistance breaking from non-L3 resistance breaking virus isolates.