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1.
Arch Virol ; 166(8): 2311-2313, 2021 Aug.
Article in English | MEDLINE | ID: mdl-34028605

ABSTRACT

A virus tentatively named "snake melon asteroid mosaic virus" (SMAMV) was found in Sudan in cucurbit crops (10% of 600 samples) between 1992 and 2003. Biological and cytological properties as well as sequence data on a 345-nt fragment suggested that SMAMV was a member of the genus Sobemovirus. However, no complete sequence had been obtained, and the relationship between SMAMV and the acknowledged sobemoviruses had not been ascertained. In this work, we obtained the full-length sequence of an SMAMV isolate. The sequence was 4225 nt long, with a typical sobemovirus genetic organization. Sequence identity to other sobemoviruses was below 50%, both for the full-length genome and for individual proteins. These data confirm that SMAMV belongs to a novel sobemovirus species.


Subject(s)
Cucurbitaceae/virology , Mosaic Viruses/classification , Whole Genome Sequencing/methods , Genome Size , Genome, Viral , Mosaic Viruses/genetics , Mosaic Viruses/isolation & purification , Open Reading Frames , Phylogeny , Sudan
2.
Sci Rep ; 11(1): 7058, 2021 03 29.
Article in English | MEDLINE | ID: mdl-33782446

ABSTRACT

Where and when alien organisms are successfully introduced are central questions to elucidate biotic and abiotic conditions favorable to the introduction, establishment and spread of invasive species. We propose a modelling framework to analyze multiple introductions by several invasive genotypes or genetic variants, in competition with a resident population, when observations provide knowledge on the relative proportions of each variant at some dates and places. This framework is based on a mechanistic-statistical model coupling a reaction-diffusion model with a probabilistic observation model. We apply it to a spatio-temporal dataset reporting the relative proportions of five genetic variants of watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) in infections of commercial cucurbit fields. Despite the parsimonious nature of the model, it succeeds in fitting the data well and provides an estimation of the dates and places of successful introduction of each emerging variant as well as a reconstruction of the dynamics of each variant since its introduction.


Subject(s)
Models, Biological , Plant Diseases/virology , Potyvirus/classification , France , Potyvirus/isolation & purification , Probability
3.
Arch Virol ; 166(6): 1779-1782, 2021 Jun.
Article in English | MEDLINE | ID: mdl-33772644

ABSTRACT

Cucurbit-infecting tobamoviruses known so far belong to six acknowledged or tentative species. Except for cucumber green mottle mosaic virus (CGMMV), which is present worldwide, they are geographically restricted, mostly to Asia, and have not been observed in Africa so far. A tobamovirus isolate infecting a wild Coccinia grandis plant was collected in central Sudan in 2012. Its host range appeared to be mostly limited to cucurbits. Its full-length genome sequence was determined and found to be 85% identical to those of isolates of cucumber fruit mottle mosaic virus (CFMMV) described in Israel and Korea, whereas the aa sequence identity to CFMMV isolates was 92 to 95%, depending on the protein. Based on its biological and molecular properties, we suggest that the Sudanese isolate should be considered a divergent isolate of CFMMV. This is the first description of CFMMV in Africa. Its high divergence from isolates from Israel and Korea suggests a lack of recent exchanges between CFMMV from Sudan and the other known populations.


Subject(s)
Cucurbitaceae/virology , Genome, Viral , Mosaic Viruses/genetics , Mosaic Viruses/isolation & purification , Sudan
4.
Philos Trans R Soc Lond B Biol Sci ; 374(1775): 20180258, 2019 06 24.
Article in English | MEDLINE | ID: mdl-31056055

ABSTRACT

Pathogen sequence data have been exploited to infer who infected whom, by using empirical and model-based approaches. Most of these approaches exploit one pathogen sequence per infected host (e.g. individual, household, field). However, modern sequencing techniques can reveal the polymorphic nature of within-host populations of pathogens. Thus, these techniques provide a subsample of the pathogen variants that were present in the host at the sampling time. Such data are expected to give more insight on epidemiological links than a single sequence per host. In general, a mechanistic viewpoint to transmission and micro-evolution has been followed to infer epidemiological links from these data. Here, we investigate an alternative approach grounded on statistical learning. The idea consists of learning the structure of epidemiological links with a pseudo-evolutionary model applied to training data obtained from contact tracing, for example, and using this initial stage to infer links for the whole dataset. Such an approach has the potential to be particularly valuable in the case of a risk of erroneous mechanistic assumptions, it is sufficiently parsimonious to allow the handling of big datasets in the future, and it is versatile enough to be applied to very different contexts from animal, human and plant epidemiology. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.


Subject(s)
Animal Diseases/epidemiology , Communicable Diseases/epidemiology , Communicable Diseases/veterinary , Plant Diseases/statistics & numerical data , Viruses/genetics , Animal Diseases/virology , Animals , Communicable Diseases/virology , Databases, Genetic , High-Throughput Nucleotide Sequencing , Humans , Models, Statistical , Molecular Sequence Annotation , Viruses/classification , Viruses/isolation & purification
5.
Arch Virol ; 164(1): 297-301, 2019 Jan.
Article in English | MEDLINE | ID: mdl-30302581

ABSTRACT

A mechanically transmissible virus tentatively named "melon chlorotic spot virus" (MeCSV) was isolated in southeastern France from a melon plant showing chlorotic spots and yellowing of the older leaves. Its complete sequence was obtained by Illumina and Sanger sequencing. The genome comprises eight RNAs for a total size of 20,079 nt and is distantly related to Ramu stunt virus and maize yellow stunt virus, two tentative tenuiviruses. MeCSV differs from other tenuiviruses by its number of genomic fragments, by being readily mechanically transmissible, and by infecting only dicotyledonous hosts. MeCSV should thus be considered a member of a tentative new species related to tenuiviruses.


Subject(s)
Magnoliopsida/virology , Plant Diseases/virology , Tenuivirus/genetics , Tenuivirus/isolation & purification , Petunia/virology , Phylogeny , Plant Leaves/virology
6.
Virus Res ; 241: 88-94, 2017 09 15.
Article in English | MEDLINE | ID: mdl-28669763

ABSTRACT

The "Papaya ringspot virus (PRSV) cluster" of cucurbit-infecting potyviruses contains five acknowledged species that have similar biological, serological and molecular properties. Additional data suggest there are other uncharacterized species from various locations in the world that likely belong to the PRSV cluster including a new PRSV-like virus reported from Sudan in 2003. Molecular and biological data indicated that the virus from Sudan belongs to a new species, tentatively named wild melon vein banding virus (WMVBV). The complete nucleotide sequence of a second virus from Sudan revealed it was a divergent relative of Moroccan watermelon mosaic virus (MWMV). Based on sequence similarity this virus was determined to be a distinct species and tentatively named Sudan watermelon mosaic virus (SuWMV). Molecular analyses indicate that SuWMV is a recombinant between WMVBV- and MWMV-related viruses. Based on surveys performed in Sudan between 1992 and 2012, SuWMV appeared 10 times more frequent than WMVBV in that country (14.6% vs. 1.5% of the samples tested). The geographic structure and molecular diversity patterns of the putative and acknowledged species suggest that the PRSV-like cluster originated in the Old World about 3600 years ago, with an important diversification in Africa.


Subject(s)
Cucurbita/virology , Plant Diseases/virology , Potyvirus/genetics , Base Sequence/genetics , Capsid Proteins/genetics , Host Specificity/genetics , Potyvirus/classification , RNA, Viral/genetics , Recombination, Genetic/genetics , Sequence Analysis, DNA , Sequence Homology, Nucleic Acid , Sudan
7.
Sci Rep ; 7: 41045, 2017 01 25.
Article in English | MEDLINE | ID: mdl-28120868

ABSTRACT

Deformed wing virus (DWV) is considered one of the most damaging pests in honey bees since the spread of its vector, Varroa destructor. In this study, we sequenced the whole genomes of two virus isolates and studied the evolutionary forces that act on DWV genomes. The isolate from a Varroa-tolerant bee colony was characterized by three recombination breakpoints between DWV and the closely related Varroa destructor virus-1 (VDV-1), whereas the variant from the colony using conventional Varroa management was similar to the originally described DWV. From the complete sequence dataset, nine independent DWV-VDV-1 recombination breakpoints were detected, and recombination hotspots were found in the 5' untranslated region (5' UTR) and the conserved region encoding the helicase. Partial sequencing of the 5' UTR and helicase-encoding region in 41 virus isolates suggested that most of the French isolates were recombinants. By applying different methods based on the ratio between non-synonymous (dN) and synonymous (dS) substitution rates, we identified four positions that showed evidence of positive selection. Three of these positions were in the putative leader protein (Lp), and one was in the polymerase. These findings raise the question of the putative role of the Lp in viral evolution.


Subject(s)
Evolution, Molecular , RNA Viruses/classification , RNA Viruses/genetics , Recombination, Genetic , Selection, Genetic , 5' Untranslated Regions , Animals , Bees/virology , Genome, Viral , Mutation, Missense , Point Mutation , RNA Helicases/genetics , Viral Proteins/genetics , Whole Genome Sequencing
8.
Arch Virol ; 161(6): 1651-5, 2016 Jun.
Article in English | MEDLINE | ID: mdl-26935919

ABSTRACT

During a survey conducted in Sudan in 2012, a virus with spherical particles was isolated from a squash plant showing chlorotic leaf spots. The virus was transmitted mechanically and by two whitefly species, but not by aphids. RT-PCR with generic torradovirus primers yielded a band of expected size from total RNA of a symptomatic plant. Next-generation sequencing confirmed that this is tentatively a new torradovirus, for which we propose the name 'squash chlorotic leaf spot virus'. Using specific RT-PCR primers, the virus was detected in cucurbit samples collected since 1992 at different locations in Sudan.


Subject(s)
Cucurbita/virology , Picornaviridae/classification , Picornaviridae/genetics , Plant Diseases/virology , Animals , Disease Vectors , Hemiptera/virology , Phylogeny , Picornaviridae/isolation & purification , Plant Leaves/virology , RNA, Plant/genetics , Sudan
9.
Virus Res ; 186: 135-43, 2014 Jun 24.
Article in English | MEDLINE | ID: mdl-24486486

ABSTRACT

Zucchini yellow mosaic virus (ZYMV, genus Potyvirus) causes important crop losses in cucurbits worldwide. In France, ZYMV epidemics are sporadic but occasionally very severe. This contrasts with Watermelon mosaic virus (WMV, genus Potyvirus) which causes regular and early epidemics. Factors influencing ZYMV epidemiology are still poorly understood. In order to gain new insights on the ecology and epidemiology of this virus, a 5-year multilocation trial was conducted in which ZYMV spread and populations were studied in each of the 20 plot/year combinations and compared with WMV. Search for ZYMV alternative hosts was conducted by testing weeds growing naturally around one plot and also by checking ZYMV natural infections in selected ornamental species. Although similar ZYMV populations were observed occasionally in the same plot in two successive years suggesting the occurrence of overwintering hosts nearby, only two Lamium amplexicaule plants were found to be infected by ZYMV of 3459 weed samples that were tested. The scarcity of ZYMV reservoirs contrasts with the frequent detection of WMV in the same samples. Since ZYMV and WMV have many aphid vectors in common and are transmitted with similar efficiencies, the differences observed in ZYMV and WMV reservoir abundances could be a major explanatory factor for the differences observed in the typology of ZYMV and WMV epidemics in France. Other potential ZYMV alternative hosts have been identified in ornamental species including begonia. Although possible in a few cases, exchanges of populations between different plots located from 500 m to 4 km apart seem uncommon. Therefore, the potential dissemination range of ZYMV by its aphid vectors seems to be rather limited in a fragmented landscape.


Subject(s)
Citrullus/virology , Cucurbita/virology , Phylogeny , Plant Diseases/virology , Potyvirus/genetics , RNA, Viral/genetics , Animals , Aphids/physiology , Behavior, Animal , Citrullus/parasitology , Cucurbita/parasitology , Feeding Behavior , France , Haplotypes , Host Specificity , Host-Parasite Interactions , Insect Vectors/physiology , Molecular Epidemiology , Phylogeography , Plant Diseases/parasitology , Plant Weeds/parasitology , Plant Weeds/virology , Potyvirus/classification , Potyvirus/isolation & purification
10.
Arch Virol ; 159(2): 277-89, 2014 Feb.
Article in English | MEDLINE | ID: mdl-23979176

ABSTRACT

In recent years, three new potyviruses have been described in the papaya ringspot virus (PRSV) cluster. In addition, two types of PRSV are recognized, type W, infecting cucurbit plants, and type P, infecting papaya and also cucurbits. A third type, PRSV-T, was also partially described in Guadeloupe. Complete genome sequencing of four PRSV-T isolates showed that this virus is a related virus that is distinct from PRSV, and the name zucchini tigré mosaic virus (ZTMV) is proposed, in reference to the typical symptoms observed in zucchini squash. Eleven other viral isolates from different geographic origins were confirmed as ZTMV isolates using the complete sequence of the cylindrical inclusion (CI) coding region, whereas pairwise sequence similarities in the coat protein (CP) coding region did not unambiguously distinguish ZTMV isolates from PRSV isolates. The use of the CI coding region for species demarcation appears more suitable than the CP coding region for closely related viruses. Principal coordinates analysis based on the biological behavior of the viral isolates studied clustered PRSV-P, PRSV-W and ZTMV isolates into three different groups. Therefore, ZTMV is different from PRSV in its molecular and biological properties.


Subject(s)
Cucurbita/virology , Genome, Viral , Plant Diseases/virology , Potyvirus/classification , Potyvirus/genetics , RNA, Viral/genetics , Sequence Analysis, DNA , Cluster Analysis , Molecular Sequence Data , Open Reading Frames , Phylogeny , Potyvirus/isolation & purification , Sequence Homology
11.
Plant Dis ; 97(11): 1515, 2013 Nov.
Article in English | MEDLINE | ID: mdl-30708468

ABSTRACT

Watermelon mosaic virus (WMV, Potyvirus) is an important virus of cucurbit crops worldwide, although it is rarely found in tropical regions. Cucumis anguria L. is a native species from tropical regions of Africa and can be found as a volunteer or cultivated plant in the Neotropic (1). In Venezuela, C. anguria is a ubiquitous volunteer cucurbit that grows in crop fields year round and may serve as reservoir for viruses. In 2009 and 2010, during surveys for viruses in cultivated and wild cucurbits, WMV was found at a low frequency (3 out of 284 samples) and two out of three positive samples were C. anguria. One of these samples was used to mechanically inoculate WMV to melon (Cucumis melo L.) and zucchini squash (Cucurbita pepo L.) plants. Typical symptoms of WMV were observed 2 weeks after inoculation and viral identification was confirmed by double antibody sandwich (DAS)-ELISA. Based on whole genome sequences, three phylogenetic groups of WMV, namely groups G1 to G3, are defined (2). Since molecular characterization of this virus is scarce in South America, the complete sequence of a WMV isolate recovered from C. anguria (hereafter, VE10-99) was obtained. RNA extractions, amplification procedures, and sequencing analyses were performed according to Desbiez and Lecoq (2). The total sequence length of VE10-99 isolate was 10,039 nucleotides, excluding the polyadenylated tail (GenBank Accession No. KC292915). This isolate had the typical potyviral genome organization, exhibiting a unique large ORF with 9 putative cleavage sites. In a BLAST analysis, the isolate most closely related to VE10-99 was the Chilean isolate CHI87-620 (EU660580), sharing 96% nucleotide identity. Phylogenetic analyses showed that VE10-99 belongs to group G2 of WMV. No evidence for recombination was found in the genome of VE10-99. Although recombination events have been noticed between members of G1 and G3, recombinant isolates between members of G2 and G1 are more frequent (2). In fact, the isolate CHI87-620 had been the only bona fide member of G2 until the sequencing of VE10-99. G2/G1 recombinants seem to have almost completely replaced the parental isolates throughout the world, probably due to a better fitness (2). To our knowledge, WMV natural infections in C. anguria had not been described before. The finding of a bona fide G2 member in Venezuela raises the question about the origin of G2 group. Currently, the prevalence of WMV appears reduced compared to the previous survey performed in Venezuela in 1966 (16 WMV-positive plants out of 95 samples) (3). References: (1) F. Chitty and R. Lopez. Acta Bot. Venez. 30:19, 2007. (2) C. Desbiez and H. Lecoq. Arch. Virol. 153:1749, 2008. (3) R. Lastra. Plant Dis. Rep. 52:171, 1968. ERRATUM: A correction was made to this Disease Note on June 9, 2014. The author R. Gustavo was changed to G. Romay.

12.
J Virol Methods ; 183(1): 94-7, 2012 Jul.
Article in English | MEDLINE | ID: mdl-22498260

ABSTRACT

The availability of an infectious cDNA clone is a prerequisite for genetic studies on RNA viruses. However, despite important improvement in molecular biology techniques during the last decades, obtaining such clones often remains tedious, time-consuming and rather unpredictable. In the case of potyviruses, cDNA clones are frequently unstable due to the toxicity of some viral proteins for bacteria. The problem can be overcome by inserting introns into the viral sequence but this requires additional steps in the cloning process and depends on the availability of suitable restriction sites in the viral sequence or adjunction of such sites by mutagenesis. Homologous recombination in yeast rather than in vitro restriction and ligation can be used to build infectious clones or other viral constructs. This paper describes how, by using recombination in yeast and fusion PCR, infectious intron-containing clones were obtained within a few weeks for two strains of watermelon mosaic virus (WMV, Potyvirus), whereas previous attempts using "classical" cloning techniques had failed repeatedly. Using the same approach, intronless infectious clones of two other potyviruses, zucchini yellow mosaic virus (ZYMV) and papaya ringspot virus (PRSV), were obtained in less than two weeks.


Subject(s)
Molecular Biology/methods , Potyvirus/genetics , Potyvirus/pathogenicity , Virology/methods , Bacteria , Carica/virology , Citrullus/virology , Cucurbita/virology , DNA, Complementary/genetics , Introns , Potyvirus/isolation & purification , RNA, Viral/genetics , Recombination, Genetic , Yeasts/genetics
13.
Virus Res ; 159(2): 115-23, 2011 Aug.
Article in English | MEDLINE | ID: mdl-21605606

ABSTRACT

Watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) was reported for the first time in France in 1974, and it is now the most prevalent virus in cucurbit crops. In 2000, new strains referred as 'emerging' (EM) strains were detected in South-eastern France. EM strains are generally more severe and phylogenetically distinct from those previously reported in this country and referred as 'classic' (CL) strains. Since 2000, EM strains have been progressively replacing CL strains in several areas where they co-exist. In order to explain this rapid shift in virus populations, the biological properties of a set of 17 CL and EM WMV isolates were compared. No major differences were observed when comparing a limited host range including 48 different plant species or cultivars. Only two species were differential; Chenopodium quinoa was systemically infected by CL and not by EM isolates whereas Ranunculus sardous was systemically infected by EM and not by CL isolates. A considerable variability was observed in aphid transmission efficiencies but this could not be correlated to the CL or EM types. Two subsets of five isolates of each group were used to compare aphid transmission efficiencies from single and double (CL-EM) infections using six different cucurbit and non-cucurbit hosts. EM isolates were generally better transmitted from mixed CL-EM infections than CL isolates and CL transmission rates were significantly lower from double than from single infections. Cross-protection was only partial between CL and EM strains leading to frequent double infections, and only a slight asymmetry was observed in cross-protection efficiencies. Since double infections occur very commonly in fields, the preferential transmission of EM from mixed CL-EM infections could be one of the factors leading to the displacement of CL isolates by EM isolates.


Subject(s)
Cucurbita/virology , Genetic Variation , Phylogeography , Plant Diseases/virology , Potyvirus/genetics , Potyvirus/pathogenicity , Animals , Aphids/virology , Cross Protection , Disease Vectors , France , Host Specificity , Potyvirus/classification
14.
J Gen Virol ; 92(Pt 8): 1939-1948, 2011 Aug.
Article in English | MEDLINE | ID: mdl-21471312

ABSTRACT

Since their introduction in south-eastern France around 1999, new, 'emerging' (EM) strains of watermelon mosaic virus (WMV) coexist with the 'classic' (CL) strains present for more than 40 years. This situation constitutes a unique opportunity to estimate the frequency of recombinants appearing in the few years following introduction of new strains of a plant RNA virus. Molecular analyses performed on more than 1000 isolates from epidemiological surveys (2004-2008) and from experimental plots (2009-2010), and targeting only recombinants that became predominant in at least one plant, revealed at least seven independent CL/EM or EM/EM recombination events. The frequency of recombinants involving at least one EM parent in the natural populations tested was on the order of 1 %. No new recombinant was detected for more than 1 year, and none but one in more than one location. In tests comparing host range and aphid transmissibility, the new recombinants did not display a better fitness than their 'parental' isolates. No recombinant was detected from artificial mixed infections of CL and EM isolates of various hosts after testing more than 1500 subcultures obtained after single-aphid transmission. These results constitute one of the first estimations of the frequency of recombinants in natural conditions for a plant RNA virus. This suggests that although viable recombinants of WMV are not rare, and although recombination may potentially lead to new highly damaging strains, the new recombinants observed so far had a lower fitness than the parental strains and did not emerge durably in the populations.


Subject(s)
Citrullus/virology , Plant Diseases/virology , Potyvirus/genetics , Recombination, Genetic , France , Host Specificity , Molecular Sequence Data , Potyvirus/classification , Potyvirus/isolation & purification , Potyvirus/physiology
15.
Infect Genet Evol ; 11(5): 812-24, 2011 Jul.
Article in English | MEDLINE | ID: mdl-21382520

ABSTRACT

All viruses are obligatory parasites that must develop tight interactions with their hosts to complete their infectious cycle. Viruses infecting plants share many structural and functional similarities with those infecting other organisms, particularly animals and fungi. Quantitative data regarding their evolutionary mechanisms--generation of variability by mutation and recombination, changes in populations by selection and genetic drift have been obtained only recently, and appear rather similar to those measured for animal viruses.This review presents an update of our knowledge of the phylogenetic and evolutionary characteristics of plant viruses and their relation to their plant hosts, in comparison with viruses infecting other organisms.


Subject(s)
Biological Evolution , Plant Viruses/genetics , Plants/virology , Genetic Variation , Host-Pathogen Interactions , Selection, Genetic
16.
Phytopathology ; 100(12): 1373-9, 2010 Dec.
Article in English | MEDLINE | ID: mdl-20879843

ABSTRACT

Since 1999, "emerging" (EM) strains of Watermelon mosaic virus (WMV) have been detected in cucurbit crops of southeastern France, probably as a result of recent introductions. Population genetic approaches were used to study the structure of EM isolates in southeastern France and to identify factors involved in their spatial distribution. A population clustering method (SAMOVA) and a maximum-difference algorithm (Monmonier's algorithm) were combined to visualize and quantify barriers to gene flow between populations. Both methods yielded similar results and two main barriers were identified. A North/South oriented barrier may be related to physical obstacles to gene flow (Rhône River, presence of an area with few cucurbit crops). Although the barrier was very strong, some "crossing" events were detected. A second barrier, oriented Northwest to Southeast, was not correlated with obvious geographical features. The two methods used here are complementary and confirm the limited spread of WMV-EM isolates. This approach can be useful in epidemiology studies to characterize the structure of viral populations and identify barriers to gene flow.


Subject(s)
Citrullus/virology , Gene Flow/genetics , Potyvirus/genetics , Algorithms , Crops, Agricultural/virology , France , Genetic Variation , Mosaic Viruses/classification , Mosaic Viruses/genetics , Mosaic Viruses/isolation & purification , Plant Diseases/virology , Population Density , Potyvirus/classification , Potyvirus/isolation & purification
17.
Arch Virol ; 155(11): 1843-7, 2010 Nov.
Article in English | MEDLINE | ID: mdl-20665058

ABSTRACT

The complete sequence of a watermelon-infecting Venezuelan begomovirus was obtained; it corresponds to that of the partially characterized melon chlorotic mosaic virus (MeCMV). MeCMV is a typical bipartite New World begomovirus. A putative alphasatellite, MeCMVa1, was found associated with MeCMV. This is the first satellite detected in the New World, and the first natural association of an alphasatellite with a bipartite begomovirus. The sequence of MeCMVa1 diverged highly from those of other alphasatellites, except for two atypical ones, which, like MeCMVa1, had a putative ORF2 embedded in the Rep-encoding ORF1. These findings raise new questions about the origin and evolution of subviral agents associated with begomoviruses.


Subject(s)
Begomovirus/genetics , Citrullus/virology , DNA, Satellite/genetics , Phylogeny , Plant Diseases/virology , Sequence Alignment , Venezuela
18.
Plant Dis ; 94(11): 1378, 2010 Nov.
Article in English | MEDLINE | ID: mdl-30743639

ABSTRACT

During a field survey conducted in December 2008 and January 2009 in southern Ivory Coast, zucchini squash (Cucurbita pepo L.) and cucumber (Cucumis sativus L.) plants were observed showing severe symptoms of leaf mosaic and distortions, filiformism, and fruit deformations. Nine samples were collected from symptomatic plants in four locations (Adzopé, Songon, Ayamé, and Gagnoa) and dried over CaCl2. Double-antibody sandwich (DAS)-ELISA tests were performed directly on dried samples with antisera against nine cucurbit-infecting viruses: Zucchini yellow mosaic virus (ZYMV, Potyvirus); Papaya ringspot virus (PRSV, Potyvirus); Watermelon mosaic virus (WMV, Potyvirus); Moroccan watermelon mosaic virus (MWMV, Potyvirus); Cucumber vein yellowing virus (CVYV, Ipomovirus); Cucumber mosaic virus (CMV, Cucumovirus); Cucurbit aphid borne yellows virus (CABYV, Polerovirus); Squash mosaic virus (SqMV, Comovirus); and Cucumber green mottle mosaic virus (CGMMV, Tobamovirus). ZYMV was detected alone in four of six zucchini squash samples and in mixed infection with CMV and PRSV in two of three cucumber samples. A cucumber sample (CI09-09) collected at Songon and infected by ZYMV, CMV, and PRSV was inoculated to zucchini squash. ZYMV was separated from CMV and PRSV by inoculating zucchini squash plantlets with one Myzus persicae Sulzer per plant with 2-min acquisition and 2-h inoculation access periods. Plants infected by ZYMV only developed typical symptoms of severe mosaic, distortion, and filiformism on leaves. Total RNA was extracted from the original dried sample of CI09-09 using TRI-Reagent (Molecular Research Center Inc., Cincinnati, OH) (2). One-step reverse transcription (RT)-PCR was performed with our standard protocol and specific primers (2), yielding a 605-bp fragment corresponding to part of the polymerase (NIb) and coat protein (CP) coding regions. The nucleotide sequence of the NIb-CP fragment of Ivory Coast ZYMV isolate CI09-09 (GenBank No. HM450303) shared 98.5, 92.7, 80.5, and 75.7% identity with ZYMV isolates from France (isolate E9, HM641798), Florida (D13914), Singapore (AF014811), and Vietnam (DQ925449), respectively. Sequence comparison indicated that CI09-09 belongs to the phylogenetic cluster 1 of group A of ZYMV (2). ZYMV, first described in 1981, is now one of the most damaging viruses in cucurbit crops worldwide and is characterized by an important biological and molecular diversity (1,3). ZYMV has already been reported in several African countries, mostly in the northern and southern parts of the continent (1), but to our knowledge, this is the first report of ZYMV in Ivory Coast. Among African isolates, CI09-09 shared 97.5% identity with isolate Su06-22 from Sudan (HM641799) belonging to the phylogenetic cluster 1 of group A of ZYMV, 94 to 95% identity with isolates from neighboring Mali (HM005307-HM005312) belonging to cluster 2 of group A, and 79.6% identity with the divergent isolate R5A from Réunion Island (L29569) belonging to phylogenetic group B of ZYMV. The presence of ZYMV in four distant locations in southern Ivory Coast suggests that this virus constitutes a serious threat to cucurbit production in this country. References: (1) C. Desbiez and H. Lecoq. Plant Pathol. 46:809, 1997, (2) C. Desbiez et al. Virus Res. 85:5, 2002, (3) H. Lecoq et al. Virus Res. 141:190, 2009.

19.
Virus Res ; 141(2): 201-8, 2009 May.
Article in English | MEDLINE | ID: mdl-19152813

ABSTRACT

Severe symptoms caused by Watermelon mosaic virus (WMV) in zucchini squash leaves and fruits have been observed since 1999 in South-eastern (SE) France. Their appearance correlates with the introduction of new, "emerging" (EM) isolates distant at the molecular level from the "classic" (CL) isolates present for more than 30 years. To understand the origin and spread of EM isolates, a survey was performed between 2004 and 2007. WMV isolates collected were characterized by sequencing part of the polymerase and coat protein coding regions. This revealed the presence of EM isolates in SE France only, whereas CL isolates were widespread throughout the country. Besides, four subgroups of EM isolates were observed in SE France, suggesting multiple introductions. Recombinants between CL and EM groups, which probably arose locally, were observed during the survey. A strong geographic structure that remained stable during the 4 years was observed between different EM isolates. Our results showed that EM isolates did not spread over long distances, but rapidly replaced the pre-existing CL isolates in all sites where both groups occurred.


Subject(s)
Cucurbita/virology , Plant Diseases/virology , Potyvirus/genetics , Potyvirus/isolation & purification , France , Genetic Variation , Molecular Sequence Data , Phylogeny , Potyvirus/classification , Viral Proteins/genetics
20.
Virus Res ; 141(2): 190-200, 2009 May.
Article in English | MEDLINE | ID: mdl-19152815

ABSTRACT

Cucurbit viruses are involved in complex and changing pathosystems in France, with new virus strains or species regularly reported. Zucchini yellow mosaic virus (ZYMV) is an archetypal emerging virus that was reported in France in 1979. It has since caused sporadic but occasionally very severe economic losses and its epidemiology still remains poorly understood. Partial sequencing of the viral genome has been used to characterize ZYMV isolates that occurred over a 29-year period in experimental plots at Montfavet, France (n=227), or that were received through a national survey for cucurbit viruses conducted in France from 2004 to 2007 (n=198). A total of 34 haplotypes were differentiated belonging to five molecular groups, three including isolates already described in France and two corresponding to isolates that emerged in France within the last 5 years. Comparison of haplotypes found at one location during successive years revealed contrasting situations. When they were either the same or closely related haplotypes, this suggested the availability of overwintering hosts, whereas when they belonged to different molecular groups this indicated shifts in viral populations with possible new introductions. The contribution of molecular epidemiology in tracing the origin of ZYMV in the French West Indies is also reviewed.


Subject(s)
Cucurbita/virology , Plant Diseases/virology , Potyvirus/genetics , France , Molecular Epidemiology , Molecular Sequence Data , Phylogeny , Potyvirus/classification , Potyvirus/isolation & purification
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