THE INCIDENCE AND STRAIN VARIATION OF APPLE STEM GROOVING AND APPLE STEM PITTING VIRUSES IN AUSTRALIAN POME FRUIT

A recent survey of the key pome fruit growing districts of Australia for Apple stem pitting foveavirus (ASPV) and Apple stem grooving capillovirus (ASGV) indicated that each virus is widespread in Australia. By using RT-PCR, ASPV and ASGV were detected in 152/173 (87.9%) and 121/173 (69.9%) of trees tested, respectively. Significant variation was observed between isolates of each virus and these isolates were distinct from isolates reported in other countries. Sequence analysis of a 1.2 kb region of the of the 3’ end of ORF1 and ORF2 of the ASPV genome of five Australian isolates identified a sequence variation ranging from 76−96% sequence similarity. A comparison of the 3’ terminal end of ORF1 and ORF2 regions of the ASPV genome indicates that the 3’ terminal end of ORF1 is generally less conserved than ORF2. A 2.5 kb region of the ASGV genome, which encodes the 3’ end of ORF1 as well as ORFs 2 and 3, of five Australian isolates indicated that all the isolates are very closely related having 98% or greater sequence similarity. Alignment of the published ASGV sequences and several Australian isolates identified in this survey showed that ORF3 (coat protein) and the 3’ terminal region of the ASGV genome are more highly conserved (greater than 90% similarity) than the 3’ end of ORF 1 and ORF2 (less than 86% similarity). Our results show that the genetic variation between viral strains can affect the reliability of the molecular tests for ASGV and ASPV and it is essential that PCR assays are adequately validated. For certification of pome fruit material it may be useful to continue to use a bioassay such as woody indexing in combination with the RT-PCR tests to accurately test for ASPV and ASGV.