Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant

Detectable episodic positive selection in the virion strand a-strain Maize streak virus genes may have a role in its host adaptation

Maize streak virus (MSV) has four genes: cp, encoding the coat protein; mp, the movement protein; and repA and rep, encoding two distinct replication-associated proteins from an alternatively spliced transcript. These genes play roles in encapsidation, movement, replication, and interactions with the external environment, making them prone to stimuli-driven molecular adaptation. We accomplished selection studies on publicly available curated, recombination-free, complete coding sequences for representative A-strain maize streak virus (MSV-A) cp and mp genes. We found evidence of gene-wide selection in these two MSV genes at specific sites within the genes (cp 1.23% and mp 0.99%). Positively selected sites have amino acids that are 60% hydrophilic and 40% hydrophobic in nature. We found significant evidence of positive selection at branches (cp: 0.76 and mp:1.66%) representing the diversity of MSV-A-strain in South Africa, which is related to the MSV-A-matA isolate (GenBank accession number: AF329881), well disseminated and adapted to the maize plant in sub-Saharan Africa. In the mp gene, selection significantly intensified for the overall diversities of the MSV-A sequences and those more related to the MSV-Mat-A isolate. These findings reveal that despite predominantly undergoing non-diversifying selection, the detectable diversifying positive selection observed in these genes may play a major role in MSV-A host adaptive evolution, ensuring sufficient pathogenicity for onward transmission without killing the host.

Movement of the A-strain maize streak virus in and out of Madagascar

The maize streak virus belongs in the genus Mastrevirus, in the family Geminiviridae. The A-strain of the virus (MSV-A) is recognised as the principal causative agent of the most severe manifestation of maize streak disease (MSD). This disease continues to be a persistent limitation on maize output across sub-Saharan Africa and the nearby Indian Ocean islands. Irrespective of the causes behind the spread of MSV-A, we can determine the paths and speeds with which MSV-A spreads by analysing MSV genome sequence data along with information on when and where samples were taken. This information is valuable for identifying the geographical origins of viral strains that cause sporadic MSD epidemics in specific places and the geographical regions where viruses remain in reservoirs and contribute to prolonged epidemics during outbreaks. Our aim is to utilise these analyses to estimate the timing and origin of the MSV-A that arrived on the island of Madagascar in the Indian Ocean. Specifically, we employ model-based phylogeographic analyses on 524 complete MSV-A genome sequences, which consist of 56 newly obtained genomes from infected maize plants collected in Madagascar. These studies allow us to reconstruct the most likely paths of MSV-A to Madagascar. We found strong evidence for the existence of at least four separate movements of MSV-A variants from East and southern Africa to Madagascar. These movements took place between roughly 1979 (with a 95% highest probability density interval [HPD] ranging from 1976 to 1982) and 2003 (with a 95% HPD ranging from 2002 to 2003). While we inferred that MSV-A variants are spreading at an average rate of 38.9 km/year (with a 95% highest posterior density interval of 34.0-44.4) across their geographical range. Since their arrival in Madagascar, MSV-A variants have been migrating at an average rate of 47.6 km/year (with a 95% highest posterior density interval of 36.05-61.70). Human influences are likely significant contributors to both sporadic long-range movements of MSV-A between mainland Africa and Madagascar, as well as shorter to medium range movements within the island.

Molecular identification and phylogenetic characterization of A-strain isolates of maize streak virus from western Ethiopia

The A-strain of maize streak virus (MSV) causes maize streak disease (MSD), which is a major biotic threat to maize production in sub-Saharan Africa. Previous studies have described different MSV strains of economic importance from southern and eastern African countries and how eastern African regions are hubs for MSV diversification. Despite these efforts, due to a lack of extensive sampling, there is limited knowledge about the MSV-A diversity in Ethiopia. Here, field sampling of maize plants and wild grasses with visible MSD symptoms was carried out in the western Ethiopian regions of Gambela, Oromia, and Benishangul-Gumuz during the maize-growing season of 2019. The complete genomes of MSV isolates (n = 60) were cloned and sequenced by the Sanger method. We used a model-based phylogenetic approach to analyse 725 full MSV genome sequences available in the GenBank database together with newly determined genome sequences from Ethiopia to determine their subtypes and identify recombinant lineages. Of the 127 fields accessed, MSD prevalence was highest, at 96%, in the Gambela region and lowest in Oromia, at 66%. The highest mean symptom severity of 4/5 (where 5 is the highest and 1 the lowest) was observed in Gambela and Benishangul-Gumuz. Our results show that these newly determined MSV isolates belong to recombinant lineage V of the A₁ subtype, with the widest dissemination and greatest economic significance in sub-Saharan Africa and the adjacent Indian Ocean islands.

Banana bunchy top virus genetic diversity in Pakistan and association of diversity with recombination in its genomes

Banana Bunchy top virus (BBTV) is a multipartite circular single strand DNA virus that belongs to genus Babuvirus and family Nanoviridae. It causes significant crop losses worldwide and also in Pakistan. BBTV is present in Pakistan since 1988 however, till now only few (about twenty only) sequence of genomic components have been reported from the country. To have insights into current genetic diversity in Pakistan fifty-seven genomic components including five complete genomes (comprises of DNA-R, -U3, -S, -M, -C and -N components) were sequenced in this study. The genetic diversity analysis of populations from Pakistan showed that DNA-R is highly conserved followed by DNA-N, whereas DNA-U3 is highly diverse with the most diverse Common Region Stem-loop (CR-SL) in BBTV genome, a functional region, which previously been reported to have undergone recombination in Pakistani population. A Maximum Likelihood (ML) phylogenetic analysis of entire genomes of isolates by using sequence of all the components concatenated together with the reported genomes around the world revealed deeper insights about the origin of the disease in Pakistan. A comparison of the genetic diversity of Pakistani and entire BBTV populations around the world indicates that there exists a correlation between genetic diversity and recombination. Population genetics analysis indicated that the degree of selection pressure differs depending on the area and genomic component. A detailed analysis of recombination across various components and functional regions suggested that recombination is closely associated with the functional parts of BBTV genome showing high genetic diversity. Both genetic diversity and recombination analyses suggest that the CR-SL is a recombination hotspot in all BBTV genomes and among the six components DNA-U3 is the only recombined component that has extensively undergone inter and intragenomic recombination. Diversity analysis of recombinant regions results on average one and half fold increase and, in some cases up to four-fold increase due to recombination. These results suggest that recombination is significantly contributing to the genetic diversity of BBTV populations around the world.

Bioecology of fall armyworm Spodoptera frugiperda (J. E. Smith), its management and potential patterns of seasonal spread in Africa

Fall armyworm, Spodoptera frugiperda (J. E. Smith) has rapidly spread in sub-Saharan Africa (SSA) and has emerged as a major pest of maize and sorghum in the continent. For effective monitoring and a better understanding of the bioecology and management of this pest, a Community-based Fall Armyworm Monitoring, Forecasting, Early Warning and Management (CBFAMFEW) initiative was implemented in six eastern African countries (Ethiopia, Kenya, Tanzania, Uganda, Rwanda and Burundi). Over 650 Community Focal Persons (CFPs) who received training through the project were involved in data collection on adult moths, crop phenology, cropping systems, FAW management practices and other variables. Data collection was performed using Fall Armyworm Monitoring and Early Warning System (FAMEWS), a mobile application developed by the Food and Agricultural Organization (FAO) of the United Nations. Data collected from the CBFAMFEW initiative in East Africa and other FAW monitoring efforts in Africa were merged and analysed to determine the factors that are related to FAW population dynamics. We used the negative binomial models to test for effect of main crops type, cropping systems and crop phenology on abundance of FAW. We also analysed the effect of rainfall and the spatial and temporal distribution of FAW populations. The study showed variability across the region in terms of the proportion of main crops, cropping systems, diversity of crops used in rotation, and control methods that impact on trap and larval counts. Intercropping and crop rotation had incident rate 2-times and 3-times higher relative to seasonal cropping, respectively. The abundance of FAW adult and larval infestation significantly varied with crop phenology, with infestation being high at the vegetative and reproductive stages of the crop, and low at maturity stage. This study provides an understanding on FAW bioecology, which could be vital in guiding the deployment of FAW-IPM tools in specific locations and at a specific crop developmental stage. The outcomes demonstrate the relevance of community-based crop pest monitoring for awareness creation among smallholder farmers in SSA.

Molecular analysis of maize (Zea mays L.)-infecting mastreviruses in Ethiopia reveals marked diversity of virus genomes and a novel species

Maize (Zea mays L.) is host for more than 50 virus species worldwide with Maize streak virus (MSV) (genus Mastrevirus) causing significant yield losses in Africa. A survey for viruses infecting maize was conducted in major growing regions of Ethiopia. To test for DNA viruses, in particular mastreviruses, rolling circle amplification was performed for the analysis of virus composition in assayed samples. Following the analysis of the entire virus genomes, three genetic groups, each representing distinct virus species, were identified. The first group was almost identical with the A-strain of MSV. The next sequence-cluster shared 96-98% identity with isolates of Maize streak reunion virus (MSRV) confirming the presence of this virus also in continental East Africa. Sequence analysis of additional virus genomes (each 2846 nt) in length revealed only a limited 70-71% nt identity with MSRV isolates and an even lower identity (< 64%) with sequences of mastreviruses described elsewhere. Our analysis suggests a novel virus species, which is tentatively named maize streak dwarfing virus (MSDV). The pairwise comparison of capsid protein and replication-associated protein (Rep) of the novel species revealed a limited identity of 63% and 68% with the respective protein sequences of MSRV. The incidence of the virus species in the maize regions of Ethiopia was studied across 89 samples collected during four growing seasons. PCR analysis with general and specific mastrevirus primers showed that MSV is the most incident virus (39.3%) followed by MSRV (14.6%) and MSDV (12.4%). Identification of three different mastrevirus species in a confined geographical location on the same host, maize, is unprecedented, and suggests that Ethiopia may be one of the potential hot spots for diversity of maize-infecting mastreviruses.

Recurrent speciation of a tomato yellow leaf curl geminivirus in Portugal by recombination

Recurrent evolution can involve interspecific interactions, recognized to play a primary role in the diversification and organization of life. Both in the plant and animal kingdoms, the recurrent formation of allopolyploid species has been described. In the virosphere, recombination between isolates of different species has been shown to be a source of speciation. In this work, complete genome analysis showed that speciation through recombination of an emergent DNA plant virus, tomato yellow leaf curl Malaga virus (genus Begomovirus, family Geminiviridae), has occurred independently in Portugal and Spain, confirming previous observations with tomato yellow leaf curl Axarquia virus, also originated independently in Spain and Italy. These results will guide future research to discover new cases of recurrent emergence of recombinant virus species in geographical areas where the putative parents co-exist or can be introduced. This will reveal the role that recurrent speciation through recombination plays in the evolution of the virosphere and will help to understand the consequences of this phenomenon on the diversification of life.

Molecular diversity, geographic distribution and host range of monocot-infecting mastreviruses in Africa and surrounding islands

Maize streak virus (MSV), an important pathogen of maize in Africa, is the most extensively studied member of the Mastrevirus genus in the family Geminiviridae. Comparatively little is known about other monocot-infecting African mastreviruses, most of which infect uncultivated grasses. Here we determine the complete sequences of 134 full African mastrevirus genomes from predominantly uncultivated Poaceae species. Based on established taxonomic guidelines for the genus Mastrevirus, these genomes could be classified as belonging to the species Maize streak virus, Eragrostis minor streak virus, Maize streak Reunion virus, Panicum streak virus, Sugarcane streak Reunion virus and Sugarcane streak virus. Together with all other publicly available African monocot-infecting mastreviruses, the 134 new isolates extend the known geographical distributions of many of these species, including MSV which we found infecting Digitaria sp. on the island of Grand Canaria: the first definitive discovery of any African monocot-infecting mastreviruses north-west of the Saharan desert. These new isolates also extend the known host ranges of both African mastrevirus species and the strains within these. Most notable was the discovery of MSV-C isolates infecting maize which suggests that this MSV strain, which had previously only ever been found infecting uncultivated species, may be in the process of becoming adapted to this important staple crop.

The role of Kenya in the trans-African spread of maize streak virus strain A

Maize streak virus (MSV), the causal agent of maize streak disease (MSD), is the most important viral pathogen of Africa's staple food crop, maize. Previous phylogeographic analyses have revealed that the most widely-distributed and common MSV variant, MSV-A₁, has been repeatedly traversing Africa over the past fifty years with long-range movements departing from either the Lake Victoria region of East Africa, or the region around the convergence of Zimbabwe, South Africa and Mozambique in southern Africa. Despite Kenya being the second most important maize producing country in East Africa, little is known about the Kenyan MSV population and its contribution to the ongoing diversification and trans-continental dissemination of MSV-A₁. We therefore undertook a sampling survey in this country between 2008 and 2011, collecting MSD prevalence data in 119 farmers' fields, symptom severity data for 170 maize plants and complete MSV genome sequence data for 159 MSV isolates. We then used phylogenetic and phylogeographic analyses to show that whereas the Kenyan MSV population is likely primarily derived from the MSV population in neighbouring Uganda, it displays considerably more geographical structure than the Ugandan population. Further, this geographical structure likely confounds apparent associations between virus genotypes and both symptom severity and MSD prevalence in Kenya. Finally, we find that Kenya is probably a sink rather than a source of MSV diversification and movement, and therefore, unlike Uganda, Kenya probably does not play a major role in the trans-continental dissemination of MSV-A₁.

Global-scale computational analysis of genomic sequences reveals the recombination pattern and coevolution dynamics of cereal-infecting geminiviruses

Genetic diversity and recombination patterns were evaluated for 229 isolates of Wheat dwarf virus (WDV), which are important cereal-infecting geminiviruses. Recombination hot spots were concentrated at the boundary of the genes encoding for the replication protein (Rep), the coat protein (cp) and the movement protein (mp), as well as inside Rep and cp and in the short intergenic regions (SIR). Phylogenomic analyses confirmed that the global population of WDV clustered into two groups according to their specific host: wheat and barley, and the crucial regions for the division of two groups were mp and the large intergenic regions (LIR). The computationally inferred pattern of coevolution between amino acid residues and the predicted 3D structure for the viral proteins provided further differences among the strains or species at the genome and protein level. Pervasive interaction between Rep and Rep A proteins in WDV-wheat-specific group reflected their important and complex function in the replication and transcription of WDV. Furthermore, significant predicted interactions between CP and Rep and CP and Rep A proteins in the WDV-wheat-specific group are thought to be crucial for successful encapsidation and movement of the virus during infection.

Mapping the distribution of maize streak virus genotypes across the forest and transition zones of Ghana

Throughout sub-Saharan Africa, maize streak virus strain A (MSV-A), the causal agent of maize streak disease (MSD), is an important biological constraint on maize production. In November/December 2010, an MSD survey was carried out in the forest and transition zones of Ghana in order to obtain MSV-A virulence sources for the development of MSD-resistant maize genotypes with agronomic properties suitable for these regions. In 79 well-distributed maize fields, the mean MSD incidence was 18.544 % and the symptom severity score was 2.956 (1 = no symptoms and 5 = extremely severe). We detected no correlation between these two variables. Phylogenetic analysis of cloned MSV-A isolates that were fully sequenced from samples collected in 51 of these fields, together with those sampled from various other parts of Africa, indicated that all of the Ghanaian isolates occurred within a broader cluster of West African isolates, all belonging to the highly virulent MSV-A1 subtype. Besides being the first report of a systematic MSV survey in Ghana, this study is the first to characterize the full-genome sequences of Ghanaian MSV isolates. The 51 genome sequences determined here will additionally be a valuable resource for the rational selection of representative MSV-A variant panels for MSD resistance screening.

Analysis of complete genomes of isolates of the Wheat dwarf virus from new geographical locations and descriptions of their defective forms

Recently, the importance of the Geminiviruses infecting cereal crops has been appreciated, and they are now being studied in detail. Barley and wheat strains of Wheat dwarf virus are recorded in most European countries. Information on complete sequences of isolates from the United Kingdom, Spain, and Austria are reported here for the first time. Analysis revealed that their sequences are very stable. Recombination between strains was recorded only for the barley strain. We identified several defective forms of the barley strain from barley and wheat, which do not influence symptom expression. Sequences of barley isolates infecting wheat were obtained that did not differ from the isolates from barley. Based on specific features of the SIR of the barley strains, it is suggested that they are assigned to one of the two proposed new clusters, A1 or A2.

Extensive recombination-induced disruption of genetic interactions is highly deleterious but can be partially reversed by small numbers of secondary recombination events

Although homologous recombination can potentially provide viruses with vastly more evolutionary options than are available through mutation alone, there are considerable limits on the adaptive potential of this important evolutionary process. Primary among these is the disruption of favorable coevolved genetic interactions that can occur following the transfer of foreign genetic material into a genome. Although the fitness costs of such disruptions can be severe, in some cases they can be rapidly recouped by either compensatory mutations or secondary recombination events. Here, we used a maize streak virus (MSV) experimental model to explore both the extremes of recombination-induced genetic disruption and the capacity of secondary recombination to adaptively reverse almost lethal recombination events. Starting with two naturally occurring parental viruses, we synthesized two of the most extreme conceivable MSV chimeras, each effectively carrying 182 recombination breakpoints and containing thorough reciprocal mixtures of parental polymorphisms. Although both chimeras were severely defective and apparently noninfectious, neither had individual movement-, encapsidation-, or replication-associated genome regions that were on their own "lethally recombinant." Surprisingly, mixed inoculations of the chimeras yielded symptomatic infections with viruses with secondary recombination events. These recombinants had only 2 to 6 breakpoints, had predominantly inherited the least defective of the chimeric parental genome fragments, and were obviously far more fit than their synthetic parents. It is clearly evident, therefore, that even when recombinationally disrupted virus genomes have extremely low fitness and there are no easily accessible routes to full recovery, small numbers of secondary recombination events can still yield tremendous fitness gains. Importance: Recombination between viruses can generate strains with enhanced pathological properties but also runs the risk of producing hybrid genomes with decreased fitness due to the disruption of favorable genetic interactions. Using two synthetic maize streak virus genome chimeras containing alternating genome segments derived from two natural viral strains, we examined both the fitness costs of extreme degrees of recombination (both chimeras had 182 recombination breakpoints) and the capacity of secondary recombination events to recoup these costs. After the severely defective chimeras were introduced together into a suitable host, viruses with between 1 and 3 secondary recombination events arose, which had greatly increased replication and infective capacities. This indicates that even in extreme cases where recombination-induced genetic disruptions are almost lethal, and 91 consecutive secondary recombination events would be required to reconstitute either one of the parental viruses, moderate degrees of fitness recovery can be achieved through relatively small numbers of secondary recombination events.

A high degree of African streak virus diversity within Nigerian maize fields includes a new mastrevirus from Axonopus compressus

The A-strain of maize streak virus (MSV-A; genus Mastrevirus, family Geminiviridae), the causal agent of maize streak disease, places a major constraint on maize production throughout sub-Saharan Africa. In West-African countries such as Nigeria, where maize is not cultivated year-round, this MSV strain is forced to overwinter in non-maize hosts. In order to both identify uncultivated grasses that might harbour MSV-A during the winter season and further characterise the diversity of related maize-associated streak viruses, we collected maize and grass samples displaying streak symptoms in a number of Nigerian maize fields. From these we isolated and cloned 18 full mastrevirus genomes (seven from maize and 11 from various wild grass species). Although only MSV-A isolates were obtained from maize, both MSV-A and MSV-F isolates were obtained from Digitaria ciliaris. Four non-MSV African streak viruses were also sampled, including sugarcane streak Reunion virus and Urochloa streak virus (USV) from Eleusine coacana, USV from Urochloa sp., maize streak Reunion virus (MSRV) from both Setaria barbata and Rottboellia sp., and a novel highly divergent mastrevirus from Axonopus compressus, which we have tentatively named Axonopus compressus streak virus (ACSV). Besides the discovery of this new mastrevirus species and expanding the known geographical and host ranges of MSRV, we have added D. ciliaris to the list of uncultivated species within which Nigerian MSV-A isolates are possibly able to overwinter.

Genetic diversity and recombination analysis of sweepoviruses from Brazil

BACKGROUND

Monopartite begomoviruses (genus Begomovirus, family Geminiviridae) that infect sweet potato (Ipomoea batatas) around the world are known as sweepoviruses. Because sweet potato plants are vegetatively propagated, the accumulation of viruses can become a major constraint for root production. Mixed infections of sweepovirus species and strains can lead to recombination, which may contribute to the generation of new recombinant sweepoviruses.

RESULTS

This study reports the full genome sequence of 34 sweepoviruses sampled from a sweet potato germplasm bank and commercial fields in Brazil. These sequences were compared with others from public nucleotide sequence databases to provide a comprehensive overview of the genetic diversity and patterns of genetic exchange in sweepoviruses isolated from Brazil, as well as to review the classification and nomenclature of sweepoviruses in accordance with the current guidelines proposed by the Geminiviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV). Co-infections and extensive recombination events were identified in Brazilian sweepoviruses. Analysis of the recombination breakpoints detected within the sweepovirus dataset revealed that most recombination events occurred in the intergenic region (IR) and in the middle of the C1 open reading frame (ORF).

CONCLUSIONS

The genetic diversity of sweepoviruses was considerably greater than previously described in Brazil. Moreover, recombination analysis revealed that a genomic exchange is responsible for the emergence of sweepovirus species and strains and provided valuable new information for understanding the diversity and evolution of sweepoviruses.

A novel maize-infecting mastrevirus from La Réunion Island

Despite extensive sampling, only one virus belonging to the genus Mastrevirus of the family Geminiviridae, maize streak virus (MSV), has until now been detected in maize with maize streak disease (MSD) symptoms. Here, we report for the first time a second, highly divergent, mastrevirus isolated from two maize plants displaying characteristic MSD-like symptoms, sampled on the South-west Indian Ocean Island, La Réunion. The two isolates shared <57 % genome-wide identity with all other known mastreviruses. We propose calling the new species Maize streak Réunion virus.

Evolution of African cassava mosaic virus by recombination between bipartite and monopartite begomoviruses

Background

Cassava mosaic disease (CMD) is a major constraint on cassava cultivation in Africa. The disease is endemic and is caused by seven distinct cassava mosaic geminiviruses (CMGs), some of them including several variants.

Findings

From cassava leaf samples presenting CMD symptoms collected in Burkina Faso, four DNA-A begomovirus components were cloned and sequenced, showing 99.9% nucleotide identity among them. These isolates are most closely related to African cassava mosaic virus (ACMV) but share less than 89% nucleotide identity (taxonomic threshold) with any previously described begomovirus. A DNA-B genomic component, sharing 93% nucleotide identity with DNA-B of ACMV, was also characterized. Since all genomic components have a typical genome organization of Old World bipartite begomoviruses, this new species was provisionally named African cassava mosaic Burkina Faso virus (ACMBFV). Recombination analysis of the new virus demonstrated an interspecies recombinant origin, with major parents related to West African isolates of ACMV, and minor parents related to Tomato leaf curl Cameroon virus and Cotton leaf curl Gezira virus.

Conclusion

This is the first report of an ACMV-like recombinant begomovirus arisen by interspecific recombination between bipartite and monopartite African begomoviruses.

Molecular characterisation of dicot-infecting mastreviruses from Australia

Monocotyledonous and dicotyledonous plant infecting mastreviruses threaten various agricultural systems throughout Africa, Eurasia and Australasia. In Australia three distinct mastrevirus species are known to infect dicotyledonous hosts such as chickpea, bean and tobacco. Amongst 34 new "dicot-infecting" mastrevirus full genome sequences obtained from these hosts we discovered one new species, four new strains, and various variants of previously described mastrevirus species. Besides providing additional support for the hypothesis that evolutionary processes operating during dicot-infecting mastrevirus evolution (such as patterns of pervasive homologous and non-homologous recombination, and strong purifying selection acting on all genes) have mostly mirrored those found in their monocot-infecting counterparts, we find that the Australian dicot-infecting viruses display patterns of phylogeographic clustering reminiscent of those displayed by monocot infecting mastrevirus species such as Panicum streak virus and Maize streak virus.

Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution

BACKGROUND

Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae), the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA.

RESULTS

Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots - of the breakpoints required to re-create MSV-MatA. Although the MSV-sensitive maize genotype gave rise to the greatest variety of recombinants, the measured fitness of each of these recombinants correlated with their similarity to MSV-MatA.

CONCLUSIONS

The mechanistic predispositions of different MSV genomic regions to recombination can strongly influence the accessibility of high-fitness MSV recombinants. The frequency with which the fittest recombinant MSV genomes arise also correlates directly with the escalating selection pressures imposed by increasingly MSV-resistant maize hosts.

Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks

Genetic recombination is an important process during the evolution of many virus species and occurs particularly frequently amongst begomoviruses in the single stranded DNA virus family, Geminiviridae. As in many other recombining viruses it is apparent that non-random recombination breakpoint distributions observable within begomovirus genomes sampled from nature are the product of variations both in basal recombination rates across genomes and in the over-all viability of different recombinant genomes. Whereas factors influencing basal recombination rates might include local degrees of sequence similarity between recombining genomes, nucleic acid secondary structures and genomic sensitivity to nuclease attack or breakage, the viability of recombinant genomes could be influenced by the degree to which their co-evolved protein-protein and protein-nucleotide and nucleotide-nucleotide interactions are disreputable by recombination. Here we investigate patterns of recombination that occur over 120 day long experimental infections of tomato plants with the begomoviruses Tomato yellow leaf curl virus and Tomato leaf curl Comoros virus. We show that patterns of sequence exchange between these viruses can be extraordinarily complex and present clear evidence that factors such as local degrees of sequence similarity but not genomic secondary structure strongly influence where recombination breakpoints occur. It is also apparent from our experiment that over-all patterns of recombination are strongly influenced by selection against individual recombinants displaying disrupted intra-genomic interactions such as those required for proper protein and nucleic acid folding. Crucially, we find that selection favoring the preservation of co-evolved longer-range protein-protein and protein DNA interactions is so strong that its imprint can even be used to identify the exact sequence tracts involved in these interactions.

Genetic recombination between viruses is a form of parasexual reproduction during which two parental viruses each contribute genetic information to an offspring, or recombinant, virus. Unlike with sexual reproduction, however, recombination in viruses can even involve the transfer of sequences between the members of distantly related species. When parental genomes are very distantly related, it is anticipated that recombination between them runs the risk of producing defective offspring. The reason for this is that the interactions between different parts of genomes and the proteins they encode (such as between different viral proteins or between viral proteins and the virus genomic DNA or RNA) often depend on particular co-evolved binding sites that recognize one another. When in a recombinant genome the partners in a binding site pair are each inherited from different parents there is a possibility that they will not interact with one another properly. Here we examine recombinant genomes arising during experimental mixed infections of two distantly related viruses to detect evidence that intra-genome interaction networks are broadly preserved in these genomes. We show this preservation is so strict that patterns of recombination in these viruses can even be used to identify the interacting regions within their genomes.

Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa

Maize streak virus strain A (MSV-A), the causal agent of maize streak disease, is today one of the most serious biotic threats to African food security. Determining where MSV-A originated and how it spread transcontinentally could yield valuable insights into its historical emergence as a crop pathogen. Similarly, determining where the major extant MSV-A lineages arose could identify geographical hot spots of MSV evolution. Here, we use model-based phylogeographic analyses of 353 fully sequenced MSV-A isolates to reconstruct a plausible history of MSV-A movements over the past 150 years. We show that since the probable emergence of MSV-A in southern Africa around 1863, the virus spread transcontinentally at an average rate of 32.5 km/year (95% highest probability density interval, 15.6 to 51.6 km/year). Using distinctive patterns of nucleotide variation caused by 20 unique intra-MSV-A recombination events, we tentatively classified the MSV-A isolates into 24 easily discernible lineages. Despite many of these lineages displaying distinct geographical distributions, it is apparent that almost all have emerged within the past 4 decades from either southern or east-central Africa. Collectively, our results suggest that regular analysis of MSV-A genomes within these diversification hot spots could be used to monitor the emergence of future MSV-A lineages that could affect maize cultivation in Africa.

Recombination in eukaryotic single stranded DNA viruses

Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.

A rep-based hairpin inhibits replication of diverse maize streak virus isolates in a transient assay

Maize streak disease, caused by the A strain of the African endemic geminivirus, maize streak mastrevirus (MSV-A), threatens the food security and livelihoods of subsistence farmers throughout sub-Saharan Africa. Using a well-established transient expression assay, this study investigated the potential of a spliceable-intron hairpin RNA (hpRNA) approach to interfere with MSV replication. Two strategies were explored: (i) an inverted repeat of a 662 bp region of the MSV replication-associated protein gene (rep), which is essential for virus replication and is therefore a good target for post-transcriptional gene silencing; and (ii) an inverted repeat of the viral long intergenic region (LIR), considered for its potential to trigger transcriptional silencing of the viral promoter region. After co-bombardment of cultured maize cells with each construct and an infectious partial dimer of the cognate virus genome (MSV-Kom), followed by viral replicative-form-specific PCR, it was clear that, whilst the hairpin rep construct (pHPrepΔI(662)) completely inhibited MSV replication, the LIR hairpin construct was ineffective in this regard. In addition, pHPrepΔI(662) inhibited or reduced replication of six MSV-A genotypes representing the entire breadth of known MSV-A diversity. Further investigation by real-time PCR revealed that the pHPrepΔI(662) inverted repeat was 22-fold more effective at reducing virus replication than a construct containing the sense copy, whilst the antisense copy had no effect on replication when compared with the wild type. This is the first indication that an hpRNA strategy targeting MSV rep has the potential to protect transgenic maize against diverse MSV-A genotypes found throughout sub-Saharan Africa.

Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome

Despite having single stranded DNA genomes that are replicated by host DNA polymerases, viruses in the family Geminiviridae are apparently evolving as rapidly as some RNA viruses. The observed substitution rates of geminiviruses in the genera Begomovirus and Mastrevirus are so high that the entire family could conceivably have originated less than a million years ago (MYA). However, the existence of geminivirus related DNA (GRD) integrated within the genomes of various Nicotiana species suggests that the geminiviruses probably originated >10 MYA. Some have even suggested that a distinct New-World (NW) lineage of begomoviruses may have arisen following the separation by continental drift of African and American proto-begomoviruses ∼110 MYA. We evaluate these various geminivirus origin hypotheses using Bayesian coalescent-based approaches to date firstly the Nicotiana GRD integration events, and then the divergence of the NW and Old-World (OW) begomoviruses. Besides rejecting the possibility of a<2 MYA OW-NW begomovirus split, we could also discount that it may have occurred concomitantly with the breakup of Gondwanaland 110 MYA. Although we could only confidently narrow the date of the split down to between 2 and 80 MYA, the most plausible (and best supported) date for the split is between 20 and 30 MYA--a time when global cooling ended the dispersal of temperate species between Asia and North America via the Beringian land bridge.

Genetic variability of East African cassava mosaic Cameroon virus under field and controlled environment conditions

Cassava geminiviruses occur in all cassava growing areas of Africa and are considered to be the most damaging vector-borne plant pathogens. At least seven species of these viruses have been identified. We investigated genetic variation in East African cassava mosaic cassava Cameroon virus (EACMCV) from naturally infected cassava and from experimentally infected Nicotiana benthamiana. Results showed that the populations of EACMCV in cassava and in N. benthamiana were genetically heterogeneous. Mutation frequencies in the order of 10(-4), comparable to that reported for plant RNA viruses, were observed in both hosts. We also produced an EACMCV mutant that induces reversion and second site mutations, thus suggesting that a high mutation frequency facilitates the maintenance of genome structure and function. This is direct experimental evidence showing that cassava geminiviruses exhibit a high mutation frequency and that a single clone quickly transforms into a collection of mutant sequences upon introduction into the host.

Recombination patterns in dicot-infecting mastreviruses mirror those found in monocot-infecting mastreviruses

Recombination has profoundly shaped the evolution of viruses in the family Geminiviridae and has been studied extensively in the two best characterised geminivirus lineages: the dicotyledonous plant infecting begomoviruses and the monocotyledonous plant infecting mastreviruses. Here, we demonstrate that the sizes and distributions of recombination events detectable within the members of a third major geminivirus lineage--the dicotyledonous plant infecting mastreviruses--are very similar to those of the monocot-infecting mastreviruses. This suggests that, despite host range differences, very similar biochemical, ecological and evolutionary factors must underlie recombination patterns in the dicot- and monocot-infecting mastreviruses.

The impact of HIV on agricultural livelihoods in southern Uganda and the challenges of attribution

Changes in agriculture and rural livelihoods in Africa are often attributed to the HIV epidemic. While acknowledging that the epidemic has devastated many families and communities because of excess morbidity and mortality, this review explores other causes of change in agriculture practices and production in southern Uganda. Over the past 20 years labour shortages, because of labour migration and changing aspirations (as well as HIV), crop and livestock pests and diseases, declining soil fertility, changes in commodity markets and a growing off-farm sector have contributed to the changes seen in rural southern Uganda. Policy interventions outside agriculture and health have also had an impact on households. The HIV epidemic has not happened in isolation. The perceived impacts of the epidemic cannot be addressed in isolation from these other drivers of change.

Genetic diversity of sweet potato begomoviruses in the United States and identification of a natural recombinant between sweet potato leaf curl virus and sweet potato leaf curl Georgia virus

In the United States, two sweet potato begomoviruses, sweet potato leaf curl virus (SPLCV) and sweet potato leaf curl Georgia virus (SPLCGV), were previously identified in Louisiana. In recent years, at least seven additional sweet potato begomoviruses have been identified in other parts of the world. In an effort to determine the genetic diversity and distribution of sweet potato begomoviruses in the U.S., we focused our efforts on molecular characterization of field-collected begomovirus isolates in two states: Mississippi and South Carolina. Using rolling-circle amplification, a total of 52 clones of the full genome were obtained. Initial inspection of alignments of the end sequences in these clones revealed a strong genetic diversity. Overall, 10 genotypes could be assigned. A majority of the isolates (50/52) in eight genotypes were shown to be closely related to SPLCV. A representative clone of each genotype was fully sequenced and analyzed. Among them, four genotypes from South Carolina with 91-92% sequence identity to the type member of SPLCV were considered a new strain, whereas four other genotypes from Mississippi with >95% sequence identity to SPLCV were considered variants. In addition, a member of a proposed new begomovirus species was identified after comparative sequence analysis of the isolate [US:SC:646B-9] from South Carolina with less than 89% sequence identity to any known begomovirus. Hence, the provisional name Sweet potato leaf curl South Carolina virus (SPLCSCV) is proposed. Moreover, a natural recombinant consisting of two distinct parental genomic sequences from SPLCV and SPLCGV was identified in the sample [US:MS:1B-3] from Mississippi. Two recombinant breakpoints were identified, one in the origin of replication and the other between C2 and C4. This knowledge about the genetic diversity of begomoviruses infecting sweet potato will likely have a major impact on PCR-based virus detection and on disease management practice through breeding for virus resistance.

Genetic diversity of tomato-infecting Tomato yellow leaf curl virus (TYLCV) isolates in Korea

Epidemic outbreaks of Tomato yellow leaf curl virus (TYLCV) diseases occurred in greenhouse grown tomato (Solanum lycopersicum) plants of Busan (TYLCV-Bus), Boseong (TYLCV-Bos), Hwaseong (TYLCV-Hwas), Jeju Island (TYLCV-Jeju), and Nonsan (TYLCV-Nons) in Korea during 2008-2009. Tomato disease by TYLCV has never occurred in Korea before. We synthesized the full-length genomes of each TYLCV isolate from the tomato plants collected at each area and determined their nucleotides (nt) sequences and deduced the amino acids of six open reading frames in the genomes. TYLCV-Bus and -Bos genomes shared higher nt identities with four Japanese isolates -Ng, -Omu, -Mis, and -Miy. On the other hand, TYLCV-Hwas, -Jeju, and -Nons genomes shared higher nt identities with five Chinese isolates TYLCV-AH1, -ZJ3, -ZJHZ12, -SH2, -Sh10, and two Japanese isolates -Han and -Tosa. On the basis of a neighbor-joining tree, five Korean TYLCV isolates were separated into three clades. TYLCV-Bus and -Bos formed the first clade, clustering with four Japanese isolates TYLCV-Mis, -Omu, -Ng, and -Miy. TYLCV-Jeju and -Nons formed the second clade, clustering with two Chinese isolates -ZJHZ212 and -Sh10. TYLCV-Hwas was clustered with two Japanese isolates -Han and -Tosa and three Chinese isolates -AH1, -ZJ3, and -SH2. Two fragments that had a potentially recombinant origin were identified using the RDP, GENECONV, BootScan, MaxChi, Chimaera, SiScan, and 3Seq methods implemented in RDP3.41. On the basis of RDP analysis, all TYLCV isolates could originated from the interspecies recombination between TYLCV-Mld[PT] isolated from Portugal as a major parent and TYLCTHV-MM isolated from Myanmar as a minor parent.

Molecular characterization of a distinct begomovirus species from Vernonia cinerea and its associated DNA-beta using the bacteriophage Phi 29 DNA polymerase

Vernonia cinerea plants with yellow vein symptoms were collected around crop fields in Madurai. A portion (550 bp) of the AV1 gene amplified using degenerate primers from the total DNA purified from diseased leaf sample was cloned and sequenced. Specific primers derived from the above sequence were used to amplify 2,745 nucleotides with the typical genome organization of begomoviral DNA A (EMBL Accession No. AM182232). Sequence comparison with other begomoviruses revealed the greatest identity (82.4%) with Emilia yellow vein virus (EmYVV-[Fz1]) from China and less than 80% with all other known begomoviruses. The International Committee on Taxonomy of Viruses (ICTV) has therefore recognized Vernonia yellow vein virus (VeYVV) as a distinct begomovirus species. Conventional PCR could not amplify the DNA B or DNA beta from the diseased tissue. However, the beta DNA (1364 bp) associated with the disease was obtained (Accession No. FN435836) by the rolling circle amplification-restriction fragment length polymorphism method (RCA-RFLP) using Phi 29 DNA polymerase. Sequence analysis shows that DNA beta of VeYVV has the highest identity (56.8%) with DNA beta of Sigesbeckia yellow vein Guangxi betasatellite (SibYVGxB-[CN: Gx111:05]) and 56-53% with DNA beta associated with other begomoviruses. This is the first report of the molecular characterization of VeYVV from V. cinerea in India. The complete molecular characterization, phylogenetic analysis, and putative recombination events in VeYVV are reported.

Maize streak virus: an old and complex 'emerging' pathogen

Maize streak virus (MSV; Genus Mastrevirus, Family Geminiviridae) occurs throughout Africa, where it causes what is probably the most serious viral crop disease on the continent. It is obligately transmitted by as many as six leafhopper species in the Genus Cicadulina, but mainly by C. mbila Naudé and C. storeyi. In addition to maize, it can infect over 80 other species in the Family Poaceae. Whereas 11 strains of MSV are currently known, only the MSV-A strain is known to cause economically significant streak disease in maize. Severe maize streak disease (MSD) manifests as pronounced, continuous parallel chlorotic streaks on leaves, with severe stunting of the affected plant and, usuallly, a failure to produce complete cobs or seed. Natural resistance to MSV in maize, and/or maize infections caused by non-maize-adapted MSV strains, can result in narrow, interrupted streaks and no obvious yield losses. MSV epidemiology is primarily governed by environmental influences on its vector species, resulting in erratic epidemics every 3-10 years. Even in epidemic years, disease incidences can vary from a few infected plants per field, with little associated yield loss, to 100% infection rates and complete yield loss.

TAXONOMY

The only virus species known to cause MSD is MSV, the type member of the Genus Mastrevirus in the Family Geminiviridae. In addition to the MSV-A strain, which causes the most severe form of streak disease in maize, 10 other MSV strains (MSV-B to MSV-K) are known to infect barley, wheat, oats, rye, sugarcane, millet and many wild, mostly annual, grass species. Seven other mastrevirus species, many with host and geographical ranges partially overlapping those of MSV, appear to infect primarily perennial grasses.

PHYSICAL PROPERTIES

MSV and all related grass mastreviruses have single-component, circular, single-stranded DNA genomes of approximately 2700 bases, encapsidated in 22 x 38-nm geminate particles comprising two incomplete T = 1 icosahedra, with 22 pentameric capsomers composed of a single 32-kDa capsid protein. Particles are generally stable in buffers of pH 4-8.

DISEASE SYMPTOMS

In infected maize plants, streak disease initially manifests as minute, pale, circular spots on the lowest exposed portion of the youngest leaves. The only leaves that develop symptoms are those formed after infection, with older leaves remaining healthy. As the disease progresses, newer leaves emerge containing streaks up to several millimetres in length along the leaf veins, with primary veins being less affected than secondary or tertiary veins. The streaks are often fused laterally, appearing as narrow, broken, chlorotic stripes, which may extend over the entire length of severely affected leaves. Lesion colour generally varies from white to yellow, with some virus strains causing red pigmentation on maize leaves and abnormal shoot and flower bunching in grasses. Reduced photosynthesis and increased respiration usually lead to a reduction in leaf length and plant height; thus, maize plants infected at an early stage become severely stunted, producing undersized, misshapen cobs or giving no yield at all. Yield loss in susceptible maize is directly related to the time of infection: infected seedlings produce no yield or are killed, whereas plants infected at later times are proportionately less affected.

DISEASE CONTROL

Disease avoidance can be practised by only planting maize during the early season when viral inoculum loads are lowest. Leafhopper vectors can also be controlled with insecticides such as carbofuran. However, the development and use of streak-resistant cultivars is probably the most effective and economically viable means of preventing streak epidemics. Naturally occurring tolerance to MSV (meaning that, although plants become systemically infected, they do not suffer serious yield losses) has been found, which has primarily been attributed to a single gene, msv-1. However, other MSV resistance genes also exist and improved resistance has been achieved by concentrating these within individual maize genotypes. Whereas true MSV immunity (meaning that plants cannot be symptomatically infected by the virus) has been achieved in lines that include multiple small-effect resistance genes together with msv-1, it has proven difficult to transfer this immunity into commercial maize genotypes. An alternative resistance strategy using genetic engineering is currently being investigated in South Africa.

USEFUL WEBSITES

http://www.mcb.uct.ac.za/MSV/mastrevirus.htm; http://www.danforthcenter.org/iltab/geminiviridae/geminiaccess/mastrevirus/Mastrevirus.htm.

Replicative intermediates of maize streak virus found during leaf development

Geminiviruses of the genera Begomovirus and Curtovirus utilize three replication modes: complementary-strand replication (CSR), rolling-circle replication (RCR) and recombination-dependent replication (RDR). Using two-dimensional gel electrophoresis, we now show for the first time that maize streak virus (MSV), the type member of the most divergent geminivirus genus, Mastrevirus, does the same. Although mastreviruses have fewer regulatory genes than other geminiviruses and uniquely express their replication-associated protein (Rep) from a spliced transcript, the replicative intermediates of CSR, RCR and RDR could be detected unequivocally within infected maize tissues. All replicative intermediates accumulated early and, to varying degrees, were already present in the shoot apex and leaves at different maturation stages. Relative to other replicative intermediates, those associated with RCR increased in prevalence during leaf maturation. Interestingly, in addition to RCR-associated DNA forms seen in other geminiviruses, MSV also apparently uses dimeric open circular DNA as a template for RCR.

Novel begomovirus species of recombinant nature in sweet potato (Ipomoea batatas) and Ipomoea indica: taxonomic and phylogenetic implications

Viral diseases occur wherever sweet potato (Ipomoea batatas) is cultivated and because this crop is vegetatively propagated, accumulation and perpetuation of viruses can become a major constraint for production. Up to 90 % reductions in yield have been reported in association with viral infections. About 20 officially accepted or tentative virus species have been found in sweet potato and other Ipomoea species. They include three species of begomoviruses (genus Begomovirus, family Geminiviridae) whose genomes have been fully sequenced. In this investigation, we conducted a search for begomoviruses infecting sweet potato and Ipomoea indica in Spain and characterized the complete genome of 15 isolates. In addition to sweet potato leaf curl virus (SPLCV) and Ipomoea yellowing vein virus, we identified three new begomovirus species and a novel strain of SPLCV. Our analysis also demonstrated that extensive recombination events have shaped the populations of Ipomoea-infecting begomoviruses in Spain. The increased complexity of the unique Ipomoea-infecting begomovirus group, highlighted by our results, open new horizons to understand the phylogeny and evolution of the family Geminiviridae.

Dating the origins of the maize-adapted strain of maize streak virus, MSV-A

Maize streak virus (MSV), which causes maize streak disease (MSD), is one of the most serious biotic threats to African food security. Here, we use whole MSV genomes sampled over 30 years to estimate the dates of key evolutionary events in the 500 year association of MSV and maize. The substitution rates implied by our analyses agree closely with those estimated previously in controlled MSV evolution experiments, and we use them to infer the date when the maize-adapted strain, MSV-A, was generated by recombination between two grass-adapted MSV strains. Our results indicate that this recombination event occurred in the mid-1800s, ∼20 years before the first credible reports of MSD in South Africa and centuries after the introduction of maize to the continent in the early 1500s. This suggests a causal link between MSV recombination and the emergence of MSV-A as a serious pathogen of maize.

Rapid host adaptation by extensive recombination

Experimental investigations into virus recombination can provide valuable insights into the biochemical mechanisms and the evolutionary value of this fundamental biological process. Here, we describe an experimental scheme for studying recombination that should be applicable to any recombinogenic viruses amenable to the production of synthetic infectious genomes. Our approach is based on differences in fitness that generally exist between synthetic chimaeric genomes and the wild-type viruses from which they are constructed. In mixed infections of defective reciprocal chimaeras, selection strongly favours recombinant progeny genomes that recover a portion of wild-type fitness. Characterizing these evolved progeny viruses can highlight both important genetic fitness determinants and the contribution that recombination makes to the evolution of their natural relatives. Moreover, these experiments supply precise information about the frequency and distribution of recombination breakpoints, which can shed light on the mechanistic processes underlying recombination. We demonstrate the value of this approach using the small single-stranded DNA geminivirus, maize streak virus (MSV). Our results show that adaptive recombination in this virus is extremely efficient and can yield complex progeny genomes comprising up to 18 recombination breakpoints. The patterns of recombination that we observe strongly imply that the mechanistic processes underlying rolling circle replication are the prime determinants of recombination breakpoint distributions found in MSV genomes sampled from nature.

Widely conserved recombination patterns among single-stranded DNA viruses

The combinatorial nature of genetic recombination can potentially provide organisms with immediate access to many more positions in sequence space than can be reached by mutation alone. Recombination features particularly prominently in the evolution of a diverse range of viruses. Despite rapid progress having been made in the characterization of discrete recombination events for many species, little is currently known about either gross patterns of recombination across related virus families or the underlying processes that determine genome-wide recombination breakpoint distributions observable in nature. It has been hypothesized that the networks of coevolved molecular interactions that define the epistatic architectures of virus genomes might be damaged by recombination and therefore that selection strongly influences observable recombination patterns. For recombinants to thrive in nature, it is probably important that the portions of their genomes that they have inherited from different parents work well together. Here we describe a comparative analysis of recombination breakpoint distributions within the genomes of diverse single-stranded DNA (ssDNA) virus families. We show that whereas nonrandom breakpoint distributions in ssDNA virus genomes are partially attributable to mechanistic aspects of the recombination process, there is also a significant tendency for recombination breakpoints to fall either outside or on the peripheries of genes. In particular, we found significantly fewer recombination breakpoints within structural protein genes than within other gene types. Collectively, these results imply that natural selection acting against viruses expressing recombinant proteins is a major determinant of nonrandom recombination breakpoint distributions observable in most ssDNA virus families.

Geminiviruses

Plant pathogenic geminiviruses have been proliferating worldwide and have, therefore, attracted considerable scientific interest during the past three decades. Current knowledge concerning their virion and genome structure, their molecular biology of replication, recombination, transcription, and silencing, as well as their transport through plants and dynamic competition with host responses are summarized. The topics are chosen to provide a comprehensive introduction for animal virologists, emphasizing similarities and differences to the closest functional relatives, polyomaviruses and circoviruses.

Genetic diversity and distribution of tomato-infecting begomoviruses in Iran

The incidence and severity of tomato leaf curl disease (TLCD) is increasing worldwide. Here we assess the diversity and distribution within tomato producing areas of Iran of begomoviruses that cause this disease. Tomato with typical TLCD symptoms and asymptomatic weeds were collected in 2005 and 2006 and tested for the presence of begomovirus DNA using polymerase chain reaction (PCR). Analysis of cloned and sequenced PCR products revealed that both mono- and bipartite begomoviruses are associated with TLCD in Iran. Furthermore, our results confirmed the symptomless infection with mono- and bipartite begomoviruses of two weed species, Chrozophora hierosolymitana Spreng (Euphobiaceae) and Herniaria sp. (Caryophyllaceae). Eighteen Iranian begomovirus isolates were classified into two major groups and two or three subgroups according to the 5'-proximal 200 nucleotides of the coat protein (CP) gene or the N-terminal 600 nucleotides of the Rep gene. Whereas most of the monopartite isolates showed closest similarity to tomato yellow leaf curl virus-Gezira (TYLCV-Ge), the three bipartite isolates were most similar to Tomato leaf curl New Delhi virus (ToLCNDV). Mixed mono- and a bipartite begomovirus infections were detected in both tomato and C. hierosolymitana. Our results indicate that the tomato producing areas in central, southern, and southeastern Iran are threatened by begomoviruses originating from both the Mediterranean basin and the Indian subcontinent.

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.

Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen

Maize streak virus (MSV; family Geminiviridae, genus Mastrevirus), the causal agent of maize streak disease, ranks amongst the most serious biological threats to food security in subSaharan Africa. Although five distinct MSV strains have been currently described, only one of these - MSV-A - causes severe disease in maize. Due primarily to their not being an obvious threat to agriculture, very little is known about the 'grass-adapted' MSV strains, MSV-B, -C, -D and -E. Since comparing the genetic diversities, geographical distributions and natural host ranges of MSV-A with the other MSV strains could provide valuable information on the epidemiology, evolution and emergence of MSV-A, we carried out a phylogeographical analysis of MSVs found in uncultivated indigenous African grasses. Amongst the 83 new MSV genomes presented here, we report the discovery of six new MSV strains (MSV-F to -K). The non-random recombination breakpoint distributions detectable with these and other available mastrevirus sequences partially mirror those seen in begomoviruses, implying that the forces shaping these breakpoint patterns have been largely conserved since the earliest geminivirus ancestors. We present evidence that the ancestor of all MSV-A variants was the recombinant progeny of ancestral MSV-B and MSV-G/-F variants. While it remains unknown whether recombination influenced the emergence of MSV-A in maize, our discovery that MSV-A variants may both move between and become established in different regions of Africa with greater ease, and infect more grass species than other MSV strains, goes some way towards explaining why MSV-A is such a successful maize pathogen.

Avoidance of protein fold disruption in natural virus recombinants

With the development of reliable recombination detection tools and an increasing number of available genome sequences, many studies have reported evidence of recombination in a wide range of virus genera. Recombination is apparently a major mechanism in virus evolution, allowing viruses to evolve more quickly by providing immediate direct access to many more areas of a sequence space than are accessible by mutation alone. Recombination has been widely described amongst the insect-transmitted plant viruses in the genus Begomovirus (family Geminiviridae), with potential recombination hot- and cold-spots also having been identified. Nevertheless, because very little is understood about either the biochemical predispositions of different genomic regions to recombine or what makes some recombinants more viable than others, the sources of the evolutionary and biochemical forces shaping distinctive recombination patterns observed in nature remain obscure. Here we present a detailed analysis of unique recombination events detectable in the DNA-A and DNA-A-like genome components of bipartite and monopartite begomoviruses. We demonstrate both that recombination breakpoint hot- and cold-spots are conserved between the two groups of viruses, and that patterns of sequence exchange amongst the genomes are obviously non-random. Using a computational technique designed to predict structural perturbations in chimaeric proteins, we demonstrate that observed recombination events tend to be less disruptive than sets of simulated ones. Purifying selection acting against natural recombinants expressing improperly folded chimaeric proteins is therefore a major determinant of natural recombination patterns in begomoviruses.

The exchange of genetic material between different virus species, called inter-species recombination, has the potential to generate, within a single genome replication cycle, an almost unimaginable number of genetically distinct virus strains, including many that might cause deadly new human, animal, or plant diseases. Many fear that inter-species recombination could provide viruses with quick access to evolutionary innovations such as broader host ranges, altered tissue tropisms, or increased severities. However, mounting evidence suggests that recombination is not an unconstrained process and that most inter-species recombinants that occur in nature are probably defective. It is suspected that networks of coevolved interactions between different parts of virus genomes and their encoded proteins must be kept intact for newly formed inter-species recombinants to have any chance of out-competing their parents. One category of coevolved interaction is that between contacting amino acids within the 3-D structures of folded proteins. Here we examine the distributions of recombination events across the genomes of a group of rampantly recombining plant viruses and find very good evidence that this class of interaction tends to be preserved amongst recombinant sequences sampled from nature. This indicates that selection against misfolded proteins strongly influences the survival of natural recombinants.