Determination of the complete nucleotide sequence of a lupine potyvirus isolate from the Czech Republic reveals that it belongs to a new member of the genus Potyvirus.

The complete nucleotide sequence of the ssRNA genome of a lupine potyvirus (LP) isolate was determined. It comprised 10,113 nucleotides excluding the poly(A) tail. Phylogenetic analysis of CP protein sequences identified pepper veinal mottle virus, narcissus yellow stripe virus, and chili veinal mottle virus as the closest relatives, sharing coat protein amino acid sequence identities of only about 64% with the LP isolate. Thus, LP can be regarded as a member of a newly described potyvirus species, for which the name Lupine mosaic virus (LuMV) is proposed.

An epidemiological model for externally sourced vector-borne viruses applied to Bean yellow mosaic virus in lupin crops in a Mediterranean-type environment.

A hybrid mechanistic/statistical model was developed to predict vector activity and epidemics of vector-borne viruses spreading from external virus sources to an adjacent crop. The pathosystem tested was Bean yellow mosaic virus (BYMV) spreading from annually self-regenerating, legume-based pastures to adjacent crops of narrow-leafed lupin (Lupinus angustifolius) in the winter-spring growing season in a region with a Mediterranean-type environment where the virus persists over summer within dormant seed of annual clovers. The model uses a combination of daily rainfall and mean temperature during late summer and early fall to drive aphid population increase, migration of aphids from pasture to lupin crops, and the spread of BYMV. The model predicted time of arrival of aphid vectors and resulting BYMV spread successfully for seven of eight datasets from 2 years of field observations at four sites representing different rainfall and geographic zones of the southwestern Australian grainbelt. Sensitivity analysis was performed to determine the relative importance of the main parameters that describe the pathosystem. The hybrid mechanistic/statistical approach used created a flexible analytical tool for vector-mediated plant pathosystems that made useful predictions even when field data were not available for some components of the system.

Forecasting aphid outbreaks and epidemics of Cucumber mosaic virus in lupin crops in a Mediterranean-type environment.

Cucumber mosaic virus (CMV) causes a serious disease of narrow-leafed lupin (Lupinus angustifolius). It is seed-borne in lupin and seed-infected plants act as the primary virus source for secondary spread by aphid vectors within crops. Infection with CMV causes yield losses of up to 60% in epidemic years, but has little impact on yield in years when spread is limited. Aphids also cause sporadic yield losses due to direct feeding damage. A simulation model was developed to forecast aphid outbreaks and epidemics of CMV in lupin crops growing in the 'grainbelt' of south-west Australia, which has a Mediterranean-type climate. The model uses rainfall during summer and early autumn to calculate an index of aphid build-up on weeds, crop volunteers and self-regenerating annual pastures in each 'grainbelt' locality before the growing season commences in late autumn. The index is used to forecast the timing of aphid immigration into crops. The subsequent aphid build-up and movement within the crop, spread of CMV from virus-infected source plants within the crop, yield losses and percentage of harvested seed-infected are then calculated. The model evaluates the effects of different sowing dates, percentages of CMV infection in seed sown and plant population densities on virus spread. The model simulations were validated with 14 years' field data from six different sites in the 'grainbelt', representing a wide range of pre-growing season rainfall scenarios, sowing dates, percentages of infection in seed sown and plant population densities. The model was incorporated into a decision support system (DSS) for use by lupin farmers and agricultural consultants in planning CMV management and targeting sprays against aphids to prevent direct feeding damage. The inputs required from the user are lupin cultivar, anticipated emergence date, percentage CMV infection in seed sown, plant density and location. The output consists of a personalised risk forecast for the user and includes predictions for date of first aphid arrival, aphid numbers, CMV spread, final virus incidence, yield loss due to infection and percentage infection in harvested seed. Predictions from the DSS are accessible via an Internet site and from other information sources. The model can serve as a template for modelling similar virus/aphid vector pathosystems in other regions of the world, especially those with Mediterranean-type climates.

Plant virology and next generation sequencing: experiences with a Potyvirus.

Next generation sequencing is quickly emerging as the go-to tool for plant virologists when sequencing whole virus genomes, and undertaking plant metagenomic studies for new virus discoveries. This study aims to compare the genomic and biological properties of Bean yellow mosaic virus (BYMV) (genus Potyvirus), isolates from Lupinus angustifolius plants with black pod syndrome (BPS), systemic necrosis or non-necrotic symptoms, and from two other plant species. When one Clover yellow vein virus (ClYVV) (genus Potyvirus) and 22 BYMV isolates were sequenced on the Illumina HiSeq2000, one new ClYVV and 23 new BYMV sequences were obtained. When the 23 new BYMV genomes were compared with 17 other BYMV genomes available on Genbank, phylogenetic analysis provided strong support for existence of nine phylogenetic groupings. Biological studies involving seven isolates of BYMV and one of ClYVV gave no symptoms or reactions that could be used to distinguish BYMV isolates from L. angustifolius plants with black pod syndrome from other isolates. Here, we propose that the current system of nomenclature based on biological properties be replaced by numbered groups (I-IX). This is because use of whole genomes revealed that the previous phylogenetic grouping system based on partial sequences of virus genomes and original isolation hosts was unsustainable. This study also demonstrated that, where next generation sequencing is used to obtain complete plant virus genomes, consideration needs to be given to issues regarding sample preparation, adequate levels of coverage across a genome and methods of assembly. It also provided important lessons that will be helpful to other plant virologists using next generation sequencing in the future.

Split personality of a Potyvirus: to specialize or not to specialize?

Bean yellow mosaic virus (BYMV), genus Potyvirus, has an extensive natural host range encompassing both dicots and monocots. Its phylogenetic groups were considered to consist of an ancestral generalist group and six specialist groups derived from this generalist group during plant domestication. Recombination was suggested to be playing a role in BYMV's evolution towards host specialization. However, in subsequent phylogenetic analysis of whole genomes, group names based on the original hosts of isolates within each of them were no longer supported. Also, nine groups were found and designated I-IX. Recombination analysis was conducted on the complete coding regions of 33 BYMV genomes and two genomes of the related Clover yellow vein virus (CYVV). This analysis found evidence for 12 firm recombination events within BYMV phylogenetic groups I-VI, but none within groups VII-IX or CYVV. The greatest numbers of recombination events within a sequence (two or three each) occurred in four groups, three which formerly constituted the single ancestral generalist group (I, II and IV), and group VI. The individual sequences in groups III and V had one event each. These findings with whole genomes are consistent with recombination being associated with expanding host ranges, and call into question the proposed role of recombination in the evolution of BYMV, where it was previously suggested to play a role in host specialization. Instead, they (i) indicate that recombination explains the very broad natural host ranges of the three BYMV groups which infect both monocots and dicots (I, II, IV), and (ii) suggest that the three groups with narrow natural host ranges (III, V, VI) which also showed recombination now have the potential to reduce host specificity and broaden their natural host ranges.

Complete nucleotide sequence of Nootka lupine vein-clearing virus.

The complete genome sequence of Nootka lupine vein-clearing virus (NLVCV) was determined to be 4,172 nucleotides in length containing four open reading frames (ORFs) with a similar genetic organization of virus species in the genus Carmovirus, family Tombusviridae. The order and gene product size, starting from the 5'-proximal ORF consisted of: (1) polymerase/replicase gene, ORF1 (p27) and ORF1RT (readthrough) (p87), (2) movement proteins ORF2 (p7) and ORF3 (p9), and, (3) the 3'-proximal coat protein ORF4, (p37). The genomic 5'- and 3'-proximal termini contained a short (59 nt) and a relatively longer 405 nt untranslated region, respectively. The longer replicase gene product contained the GDD motif common to RNA-dependent RNA polymerases. Phylogenetically, NLVCV formed a subgroup with the following four carmoviruses when separately comparing the amino acids of the coat protein or replicase protein: Angelonia flower break virus (AnFBV), Carnation mottle virus (CarMV), Pelargonium flower break virus (PFBV), and Saguaro cactus virus (SgCV). Whole genome nucleotide analysis (percent identities) among the carmoviruses with NLVCV suggested a similar pattern. The species demarcation criteria in the genus Carmovirus for the amino acid sequence identity of the polymerase (<52%) and coat (<41%) protein genes restricted NLVCV as a distinct species, and instead, placed it as a tentative strain of CarMV, PFBV, or SgCV when both the polymerase and CP were used as the determining factors. In contrast, the species criteria that included different host ranges with no overlap and lack of serology relatedness between NLVCV and the carmoviruses, suggested that NLVCV was a distinct species. The relatively low cutoff percentages allowed for the polymerase and CP genes to dictate the inclusion/exclusion of a distinct carmovirus species should be reevaluated. Therefore, at this time we have concluded that NLVCV should be classified as a tentative new species in the genus Carmovirus, family Tombusviridae.