Sequence variability in the genome-3'-terminal region of BYDV for 10 geographically distinct PAV-like isolates of barley yellow dwarf virus: analysis of the ORF6 variation.

Nucleotide sequence of the genome terminal region 3' to the capsid-readthrough cistron were compared for 10 PAV-like isolates of barley yellow dwarf virus (BYDV) from three continents. The sequenced region varied in length from 853 to 864 nucleotides and the extent of sequence homology among the isolates ranged from 84 to 99%. Sequence variations occur mainly in two locations, one in the ORF6 coding region and the other near the genome 3' terminus. Sequence homology grouping reveals three genetically distinct clusters of PAV isolates (A, B and C). Cluster A consists of the Australian isolates, cluster B of one Canadian and three French isolates, and cluster C of the French isolate, RG. Dissimilarities with the corresponding genome-3'- terminal region of the BYDV-MAV serotype were greater than those observed between the PAV isolates alone. Comparison with the sequence of the 3' untranslated region of soybean dwarf virus revealed two stretches of nucleotide similarity, suggesting a common ancestor. Study of the coding ability revealed that the ORF6 is present in all the sequenced PAV isolates but differs in size and deduced amino acids composition. However, the fact that the majority of nucleotide changes are restricted to the third base position of the ORF6-codons suggests that ORF6 codes for a functional protein.