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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research Unit » Research » Publications at this Location » Publication #237405
Title: Molecular Diversity and Recombination in a Foveavirus Infecting Grapevine

Author
item ALABI,, O - WASHINGTON STATE UNIV
item Martin, Robert
item NAIDU, R - WASHINGTON STATE UNIV

Submitted to: Phytopathology
Publication Type: Abstract Only
Publication Acceptance Date: 6/2/2009
Publication Date: 7/27/2009
Citation: Alabi,, O.J., Martin, R.R., Naidu, R.A. 2009. Molecular Diversity and Recombination in a Foveavirus Infecting Grapevine. Phytopathology.

Interpretive Summary:

Technical Abstract: Rupestris stem-pitting associated virus (RSPaV; genus Foveavirus; family Flexiviridae) is widely distributed in grape-growing countries worldwide. We studied the genetic diversity of RSPaV in Pacific Northwest (PNW) vineyards. The coat protein (CP) and a portion of the replicase (Rep) from seventy three isolates were amplified, cloned, sequenced and phylogenetically compared with corresponding sequences of RSPaV isolates deposited in GenBank from other countries. In pair wise comparisons, the CP sequences from 53 isolates showed nucleotide sequence identities ranging from 79 to 100% and amino acid sequence identities ranging from 86-100%. The Rep sequences from 53 isolates also showed similar range of identity values. Seven of the 53 isolates showed within-isolate genetic diversity in the CP, indicating mixed infection of diverging viral variants within a single grapevine. This was observed most frequently in grafted vines. Phylogenetic analysis showed that several individual sequenced isolates had Rep and CP sequences from multiple RSPaV variants. Further analysis of these isolates by Recombination Detection Program version 3 (RDP3) Beta 27 indicated more recombination events occurred in the CP sequences than in the Rep sequences. These results indicate the quasispecies nature of RSPaV and provide evidence for the first time of the occurrence of recombination in the genus Foveavirus.