Analysis of the genome of grapevine red blotch virus and related grabloviruses indicates diversification prior to the arrival of Vitis vinifera in North America

Abstract

In this study 163 complete whole-genome sequences of the emerging pathogen grapevine red blotch virus (GRBV; genus Grablovirus, family Geminiviridae) were used to reconstruct phylogenies using Bayesian analyses on time-tipped (heterochronous) data. Using different combinations of priors, Bayes factors identified heterochronous datasets (3×200 million chains) generated from strict clock and exponential tree priors as being the most robust. Substitution rates of 3.2×10−5 subsitutions per site per year (95% HPD 4.3–2.1×10−5) across the whole of the GRBV genome were estimated, suggesting ancestral GRBV diverged from ancestral wild Vitis latent virus 1 around 9 000 years ago, well before the first documented arrival of Vitis vinifera in North America. Whole-genome analysis of GRBV isolates in a single infected field-grown grapevine across 12 years identified 12 single nucleotide polymorphisms none of which were fixed substitutions: an observation not discordant with the in silico estimate. The substitution rate estimated here is lower than those estimated for other geminiviruses and is the first for a woody-host-infecting geminivirus.

Cassava brown streak virus evolves with a nucleotide-substitution rate that is typical for the family Potyviridae

“…4 ). This unusually low rate is from a multiple-species analysis, looking at the diversification of grabloviruses over a much longer time frame than the other BEAST analyses included here, and therefore isn't perfectly comparable to studies looking at just the most recent common ancestor of a single species ( Thompson 2022 ). The unequal sampling times also makes it more difficult to compare across studies.…”

Grapevine red blotch disease: A comprehensive Q&A guide

“…Despite analyses with existing related viruses suggesting divergence from its most common recent ancestor occurred over 6,000 years ago [ 18 ], GRBV remained unnoticed in North American vineyards probably due to its symptoms being mistaken for those of leafroll viruses [ 2 ]. Given the epidemiological uncertainties of red blotch disease, the primary control measures currently advised are focused on the use of GRBV-free planting material [ 14 ].…”

The Three-Cornered Alfalfa Hopper, Spissistilus festinus, Is a Vector of Grapevine Red Blotch Virus in Vineyards

“…Its single-stranded, circular DNA genome is composed of seven bi-directional open reading frames (ORFs). GRBV was recently speculated to have emerged from wild Vitis latent virus 1, a closely related geminivirus, about 9000 years ago [14]. Analyses of the genetic diversity of GRBV isolates revealed two statistically supported, distinct phylogenetic clades with up to 8.5% nucleotide sequence divergence [15].…”