Sequencing of the genomic RNA of Grapevine leafroll associated virus (GLRaV) -4 and -6 was continued in 2005. In this effort 4692 and 3832 nucleotides (nt), respectively, for GLRaV-4 and -6 were sequenced. Open reading frames (ORF) identified and the genome organization for each virus included: partial sequence of ORF 1a followed by ORF 1b encoding for a protein recognized as viral RdRp domain. ORF 2 encodes for a small hydrophobic protein followed by ORF 3 encoding for HSP70 homologue protein of 533 aa in length for both viruses. ORF 4 encodes for a putative protein of 539 aa long (P60). ORF 5 encodes for the viral coat protein of estimated molecular mass of 29.5 and 29.2 kDa, and OFR 6, a possible CP minor (CPm) gene, encodes for a putative product of 23.1, and 22.9 kDa, respectively for GLRaV- and -6.
The sequence information revealed that these two viruses are closely related to each other. They have 81%amino acid sequence similarities at the CP region and 78%at the HSP70 region. The phylogenetic analysis using the CP nucleotide sequences of these two viruses compared with other viruses in the family Closteroviridae (the family includes all other known leafroll associated viruses) showed that these two viruses have closer relationship to GLRaV-5 and -9. Specific PCR detection primers have been designed and evaluated.