Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias

Background. Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ∼10-4 substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered. Results. We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained in planta for up to five years and displayed evolution rates of between 7.4 × 10-4 and 7.9 × 10-4 subs/site/year. Conclusion. These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules. © 2008 Walt et al; licensee BioMed Central Ltd

Exploring the Diversity of Plant DNA Viruses and Their Satellites Using Vector-Enabled Metagenomics on Whiteflies

Current knowledge of plant virus diversity is biased towards agents of visible and economically important diseases. Less is known about viruses that have not caused major diseases in crops, or viruses from native vegetation, which are a reservoir of biodiversity that can contribute to viral emergence. Discovery of these plant viruses is hindered by the traditional approach of sampling individual symptomatic plants. Since many damaging plant viruses are transmitted by insect vectors, we have developed “vector-enabled metagenomics” (VEM) to investigate the diversity of plant viruses. VEM involves sampling of insect vectors (in this case, whiteflies) from plants, followed by purification of viral particles and metagenomic sequencing. The VEM approach exploits the natural ability of highly mobile adult whiteflies to integrate viruses from many plants over time and space, and leverages the capability of metagenomics for discovering novel viruses. This study utilized VEM to describe the DNA viral community from whiteflies (Bemisia tabaci) collected from two important agricultural regions in Florida, USA. VEM successfully characterized the active and abundant viruses that produce disease symptoms in crops, as well as the less abundant viruses infecting adjacent native vegetation. PCR assays designed from the metagenomic sequences enabled the complete sequencing of four novel begomovirus genome components, as well as the first discovery of plant virus satellites in North America. One of the novel begomoviruses was subsequently identified in symptomatic Chenopodium ambrosiodes from the same field site, validating VEM as an effective method for proactive monitoring of plant viruses without a priori knowledge of the pathogens. This study demonstrates the power of VEM for describing the circulating viral community in a given region, which will enhance our understanding of plant viral diversity, and facilitate emerging plant virus surveillance and management of viral diseases

Addressing emerging plant viruses in Florida

Vegetable and ornamental crops produced in the subtropical/tropical state of Florida have experienced a number of emerging viruses over the last 2 decades. Most of these viruses belong to one of the following plant virus families: Betaflexiviridae, Bunyaviridae, Closteroviridae, Geminiviridae or Potyviridae. Emerging viruses have appeared in Florida through different routes or mechanisms, and their effects on hosts have also varied. The viruses that have caused the biggest concerns are those transmitted by either a single species of whitefly (Bemisia tabaci MEAM1) or various species of thrips. The response to these emerging plants viruses has varied with the type of virus. These range from the standard responses (development of virus-specific assays, surveys, testing cultivar susceptibility, and identification of host range, development or modification of insect management guidelines) to metagenomic studies to identify viruses before they emerge in epidemics. The metagenomic approach is the newest and has allowed the identification of plant viruses before they became problematic. Metagenomes can be constructed from the plants in question, or from the vectors. Metagenomes from vectors are particularly helpful when the vector is both polyphagous and highly mobile. Specific emerging viruses, their impacts and responses will be discussed

Addressing emerging plant viruses in Florida

Vegetable and ornamental crops produced in the subtropical/tropical state of Florida have experienced a number of emerging viruses over the last 2 decades. Most of these viruses belong to one of the following plant virus families: Betaflexiviridae, Bunyaviridae, Closteroviridae, Geminiviridae or Potyviridae. Emerging viruses have appeared in Florida through different routes or mechanisms, and their effects on hosts have also varied. The viruses that have caused the biggest concerns are those transmitted by either a single species of whitefly (Bemisia tabaci MEAM1) or various species of thrips. The response to these emerging plants viruses has varied with the type of virus. These range from the standard responses (development of virus-specific assays, surveys, testing cultivar susceptibility, and identification of host range, development or modification of insect management guidelines) to metagenomic studies to identify viruses before they emerge in epidemics. The metagenomic approach is the newest and has allowed the identification of plant viruses before they became problematic. Metagenomes can be constructed from the plants in question, or from the vectors. Metagenomes from vectors are particularly helpful when the vector is both polyphagous and highly mobile. Specific emerging viruses, their impacts and responses will be discussed

Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias

Background: Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ~10-4 substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered. Results: We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained in planta for up to five years and displayed evolution rates of between 7.4 × 10-4 and 7.9 × 10-4 subs/site/year. Conclusion: These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules