First Report of Tomato Yellow Leaf Curl Virus in Réunion Island

Distribution of invasive versus native whitefly species and their pyrethroid knock-down resistance allele in a context of interspecific hybridization

The invasion success of a species in an agrosystem is greatly influenced by environmental factors such as the use of insecticides, by the intrinsic evolutionary capabilities of the species, and also by interactions with resident species. On the island of La Réunion, the successive invasions of MEAM1 and MED whitefly species over the last 20 years have not only led an increased use of insecticides, but have also challenged the resident IO species. To trace the evolution of the 3 species, and the distribution of the kdr mutation (resistance to pyrethroid) in the para-type voltage-gated sodium channel, we genotyped 41 populations (using neutral nuclear markers) and look at the prevalence of the kdr allele. MEAM1 was predominantly present in agrosystems showing quasi fixation of the resistant kdr allele whereas IO was mainly in natural environments and did not have any resistant allele. Hybridization between the two former species was detected in low frequency but has not led to introgression of resistant alleles in the resident species so far. MED showed a limited distribution in agrosystems but all individuals displayed a resistant allele. These highly contrasting patterns of distribution and resistant mutations between invasive and resident whitefly species are further discussed.

Ongoing geographical spread of Tomato yellow leaf curl virus

Tomato yellow leaf curl virus (TYLCV) seriously impacts tomato production throughout tropical and sub-tropical regions of the world. It has a broad geographical distribution and continues to spread to new regions in the Indian and Pacific Oceans including Australia, New Caledonia and Mauritius. We undertook a temporally-scaled, phylogeographic analysis of all publicly available, full genome sequences of TYLCV, together with 70 new genome sequences from Australia, Iran and Mauritius. This revealed that whereas epidemics in Australia and China likely originated through multiple independent viral introductions from the East-Asian region around Japan and Korea, the New Caledonian epidemic was seeded by a variant from the Western Mediterranean region and the Mauritian epidemic by a variant from the neighbouring island of Reunion. Finally, we show that inter-continental scale movements of TYLCV to East Asia have, at least temporarily, ceased, whereas long-distance movements to the Americas and Australia are probably still ongoing.

Biological invasions of geminiviruses: case study of TYLCV and Bemisia tabaci in Reunion Island

In the last 20 years, molecular ecology approaches have proven to be extremely useful to identify and assess factors associated with viral emerging diseases, particularly in economically and socially important tropical crops such as maize (maize streak disease) and cassava (cassava mosaic disease). Molecular ecology approaches were applied in Reunion Island to analyze the epidemic of tomato yellow leaf curl disease, which has been affecting the island since the end of the 1990s. Before the invasive biotype B (currently known as Middle East-Asia Minor 1 cryptic species) of Bemisia tabaci spread across the world, Reunion Island (South West Indian Ocean) only hosted an indigenous biotype of B. tabaci, Ms (currently known as Indian Ocean cryptic species). Wild hybrids between invasive and indigenous species were subsequently characterized over multiple generations. Endosymbiont analysis of the hybrid population indicated that matings were non-random. Similarly, while no indigenous begomoviruses have ever been reported on Reunion Island, the two main strains of one of the most damaging and emerging plant viruses in the world, the Mild and Israel strains of the Tomato yellow leaf curl virus (TYLCV-Mld and TYLCV-IL), were introduced in 1997 and 2004 respectively. While these introductions extensively modified the agricultural landscape of Reunion Island, they also provided an invaluable opportunity to study the ecological and genetic mechanisms involved in biological invasion and competition.

Diversity of dicotyledenous-infecting geminiviruses and their associated DNA molecules in southern Africa, including the South-west Indian ocean islands

The family Geminiviridae comprises a group of plant-infecting circular ssDNA viruses that severely constrain agricultural production throughout the temperate regions of the world, and are a particularly serious threat to food security in sub-Saharan Africa. While geminiviruses exhibit considerable diversity in terms of their nucleotide sequences, genome structures, host ranges and insect vectors, the best characterised and economically most important of these viruses are those in the genus Begomovirus. Whereas begomoviruses are generally considered to be either monopartite (one ssDNA component) or bipartite (two circular ssDNA components called DNA-A and DNA-B), many apparently monopartite begomoviruses are associated with additional subviral ssDNA satellite components, called alpha- (DNA-αs) or betasatellites (DNA-βs). Additionally, subgenomic molecules, also known as defective interfering (DIs) DNAs that are usually derived from the parent helper virus through deletions of parts of its genome, are also associated with bipartite and monopartite begomoviruses. The past three decades have witnessed the emergence and diversification of various new begomoviral species and associated DI DNAs, in southern Africa, East Africa, and proximal Indian Ocean islands, which today threaten important vegetable and commercial crops such as, tobacco, cassava, tomato, sweet potato, and beans. This review aims to describe what is known about these viruses and their impacts on sustainable production in this sensitive region of the world.

A novel synthetic quantification standard including virus and internal report targets: application for the detection and quantification of emerging begomoviruses on tomato

BACKGROUND

Begomovirus is a genus of phytopathogenic single-stranded DNA viruses, transmitted by the whitefly Bemisia tabaci. This genus includes emerging and economically significant viruses such as those associated with Tomato Yellow Leaf Curl Disease, for which diagnostic tools are needed to prevent dispersion and new introductions. Five real-time PCRs with an internal tomato reporter gene were developed for accurate detection and quantification of monopartite begomoviruses, including two strains of the Tomato yellow leaf curl virus (TYLCV; Mld and IL strains), the Tomato leaf curl Comoros virus-like viruses (ToLCKMV-like viruses) and the two molecules of the bipartite Potato yellow mosaic virus. These diagnostic tools have a unique standard quantification, comprising the targeted viral and internal report amplicons. These duplex real-time PCRs were applied to artificially inoculated plants to monitor and compare their viral development.

RESULTS

Real-time PCRs were optimized for accurate detection and quantification over a range of 2 × 10(9) to 2 × 10(3) copies of genomic viral DNA/μL for TYLCV-Mld, TYLCV-IL and PYMV-B and 2 × 10(8) to 2 × 10(3) copies of genomic viral DNA/μL for PYMV-A and ToLCKMV-like viruses. These real-time PCRs were applied to artificially inoculated plants and viral loads were compared at 10, 20 and 30 days post-inoculation. Different patterns of viral accumulation were observed between the bipartite and the monopartite begomoviruses. Interestingly, PYMV accumulated more viral DNA at each date for both genomic components compared to all the monopartite viruses. Also, PYMV reached its highest viral load at 10 dpi contrary to the other viruses (20 dpi). The accumulation kinetics of the two strains of emergent TYLCV differed from the ToLCKMV-like viruses in the higher quantities of viral DNA produced in the early phase of the infection and in the shorter time to reach this peak viral load.

CONCLUSIONS

To detect and quantify a wide range of begomoviruses, five duplex real-time PCRs were developed in association with a novel strategy for the quantification standard. These assays should be of a great interest for breeding programs and epidemiological surveys to monitor viral populations.

Distribution of the phenotypic effects of random homologous recombination between two virus species

Recombination has an evident impact on virus evolution and emergence of new pathotypes, and has generated an immense literature. However, the distribution of phenotypic effects caused by genome-wide random homologous recombination has never been formally investigated. Previous data on the subject have promoted the implicit view that most viral recombinant genomes are likely to be deleterious or lethal if the nucleotide identity of parental sequences is below 90%. We decided to challenge this view by creating a bank of near-random recombinants between two viral species of the genus Begomovirus (Family Geminiviridae) exhibiting 82% nucleotide identity, and by testing infectivity and in planta accumulation of recombinant clones randomly extracted from this bank. The bank was created by DNA-shuffling-a technology initially applied to the random shuffling of individual genes, and here implemented for the first time to shuffle full-length viral genomes. Together with our previously described system allowing the direct cloning of full-length infectious geminivirus genomes, it provided a unique opportunity to generate hundreds of "mosaic" virus genomes, directly testable for infectivity. A subset of 47 randomly chosen recombinants was sequenced, individually inoculated into tomato plants, and compared with the parental viruses. Surprisingly, our results showed that all recombinants were infectious and accumulated at levels comparable or intermediate to that of the parental clones. This indicates that, in our experimental system, despite the fact that the parental genomes differ by nearly 20%, lethal and/or large deleterious effects of recombination are very rare, in striking contrast to the common view that has emerged from previous studies published on other viruses.

The spread of tomato yellow leaf curl virus from the Middle East to the world

The ongoing global spread of Tomato yellow leaf curl virus (TYLCV; Genus Begomovirus, Family Geminiviridae) represents a serious looming threat to tomato production in all temperate parts of the world. Whereas determining where and when TYLCV movements have occurred could help curtail its spread and prevent future movements of related viruses, determining the consequences of past TYLCV movements could reveal the ecological and economic risks associated with similar viral invasions. Towards this end we applied Bayesian phylogeographic inference and recombination analyses to available TYLCV sequences (including those of 15 new Iranian full TYLCV genomes) and reconstructed a plausible history of TYLCV's diversification and movements throughout the world. In agreement with historical accounts, our results suggest that the first TYLCVs most probably arose somewhere in the Middle East between the 1930s and 1950s (with 95% highest probability density intervals 1905-1972) and that the global spread of TYLCV only began in the 1980s after the evolution of the TYLCV-Mld and -IL strains. Despite the global distribution of TYLCV we found no convincing evidence anywhere other than the Middle East and the Western Mediterranean of epidemiologically relevant TYLCV variants arising through recombination. Although the region around Iran is both the center of present day TYLCV diversity and the site of the most intensive ongoing TYLCV evolution, the evidence indicates that the region is epidemiologically isolated, which suggests that novel TYLCV variants found there are probably not direct global threats. We instead identify the Mediterranean basin as the main launch-pad of global TYLCV movements.

Begomovirus 'melting pot' in the south-west Indian Ocean islands: molecular diversity and evolution through recombination

During the last few decades, many virus species have emerged, often forming dynamic complexes within which viruses share common hosts and rampantly exchange genetic material through recombination. Begomovirus species complexes are common and represent serious agricultural threats. Characterization of species complex diversity has substantially contributed to our understanding of both begomovirus evolution, and the ecological and epidemiological processes involved in the emergence of new viral pathogens. To date, the only extensively studied emergent African begomovirus species complex is that responsible for cassava mosaic disease. Here we present a study of another emerging begomovirus species complex which is associated with serious disease outbreaks in bean, tobacco and tomato on the south-west Indian Ocean (SWIO) islands off the coast of Africa. On the basis of 14 new complete DNA-A sequences, we describe seven new island monopartite begomovirus species, suggesting the presence of an extraordinary diversity of begomovirus in the SWIO islands. Phylogenetic analyses of these sequences reveal a close relationship between monopartite and bipartite African begomoviruses, supporting the hypothesis that either bipartite African begomoviruses have captured B components from other bipartite viruses, or there have been multiple B-component losses amongst SWIO virus progenitors. Moreover, we present evidence that detectable recombination events amongst African, Mediterranean and SWIO begomoviruses, while substantially contributing to their diversity, have not occurred randomly throughout their genomes. We provide the first statistical support for three recombination hot-spots (V1/C3 interface, C1 centre and the entire IR) and two recombination cold-spots (the V2 and the third quarter of V1) in the genomes of begomoviruses.

Evidence for a founder effect after introduction of Tomato yellow leaf curl virus-mild in an insular environment

Evolution of Tomato yellow leaf curl virus-Mild (TYLCV-Mld[RE]) (family Geminiviridae, genus Begomovirus) was monitored in La Réunion island from its first upsurge in 1997 until 2004. Two genome fragments, one comprising partial C4 and C1 open reading frames (ORFs), and the other comprising part of the V1 and V2 ORFs and part of the intergenic region were sequenced in 111 isolates. The very low initial diversity of TYLCV-Mld[RE] in La Réunion was followed by a quasi-linear increase in genetic diversity across years. In addition, the population effective size of TYLCV-Mld[RE] has undergone a sudden increase from 2001 to 2004, which is consistent with a founder effect due to the introduction of a small number of virus individuals in an insular environment. Surprisingly, one nucleotide substitution introducing a premature stop codon in the C4 ORF was observed in an increasing number of isolates in the population of TYLCV-Mld[RE] over time, contrasting with the other substitutions which were observed at low frequencies. This substitution which shortens the C4 protein by four amino acids may therefore have been selected during TYLCV-Mld[RE] evolution.

South West Indian Ocean islands tomato begomovirus populations represent a new major monopartite begomovirus group

Biological and molecular properties of Tomato leaf curl Madagascar virus isolates from Morondova and Toliary (ToLCMGV-[Tol], -[Mor]), Tomato leaf curl Mayotte virus isolates from Dembeni and Kahani (ToLCYTV-[Dem], -[Kah]) and a Tomato yellow leaf curl virus isolate from Reunion (TYLCV-Mld[RE]) were determined. Full-length DNA components of the five isolates from Madagascar, Mayotte and Reunion were cloned and sequenced and, with the exception of ToLCMGV-[Tol], were shown to be both infectious in tomato and transmissible by Bemisia tabaci. Sequence analysis revealed that these viruses had genome organizations of monopartite begomoviruses and that both ToLCMGV and ToLCYTV belong to the African begomoviruses but represent a distinct monophyletic group that we have tentatively named the South West islands of the Indian Ocean (SWIO). All of the SWIO isolates examined were apparently complex recombinants. None of the sequences within the recombinant regions closely resembled that of any known non-SWIO begomovirus, suggesting an isolation of these virus populations.

A new silverleaf-inducing biotype Ms of Bemisia tabaci (Hemiptera: Aleyrodidae) indigenous to the islands of the south-west Indian Ocean

Following the first detection of tomato yellow leaf curl virus (TYLCV) from Reunion (700 km east of Madagascar) in 1997 and the upsurge of Bemisia tabaci (Gennadius) on vegetable crops, two genetic types of B. tabaci were distinguished using RAPD-PCR and cytochrome oxidase I (COI) gene sequence comparisons. One type was assigned to biotype B and the other was genetically dissimilar to the populations described elsewhere and was named Ms, after the Mascarenes Archipelago. This new genetic type forms a distinct group that is sister to two other groups, one to which the B biotype is a member and one to which the Q biotype belongs. The Ms biotype is thought to be indigenous to the region as it was also detected in Mauritius, the Seychelles and Madagascar. Both B and Ms populations of B. tabaci induced silverleaf symptoms on Cucurbita sp., and were able to acquire and transmit TYLCV. Taken together these results indicate that the Ms genetic type should be considered a new biotype of B. tabaci.

Tomato yellow leaf curl virus Can Be Acquired and Transmitted by Bemisia tabaci (Gennadius) from Tomato Fruit

The whitefly Bemisia tabaci is an insect pest causing worldwide economic losses, especially as a vector of geminiviruses such as Tomato yellow leaf curl virus (TYLCV). Currently, imported and exported tomato fruit are not monitored for TYLCV infection because they are not considered to represent a potential risk as a virus source for whiteflies. A survey of tomato fruit imported into Réunion Island indicated that more than 50% of the fruit contained TYLCV as determined by DNA blot analysis. Moreover, we showed that TYLCV was present at a high titer in tomato fruit, and demonstrated that it can be acquired by whiteflies and subsequently transmitted to healthy tomato plants. Potential risk of the spread of TYLCV by tomato fruit in natural conditions needs to be further assessed.