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J Virol. Dec 2009; 83(23): 12378–12387.
Published online Sep 16, 2009. doi:  10.1128/JVI.01486-09
PMCID: PMC2786733

Mixed Infections of Pepino Mosaic Virus Strains Modulate the Evolutionary Dynamics of this Emergent Virus [down-pointing small open triangle]

Abstract

Pepino mosaic virus (PepMV) is an emerging pathogen that causes severe economic losses in tomato crops (Solanum lycopersicum L.) in the Northern hemisphere, despite persistent attempts of control. In fact, it is considered one of the most significant viral diseases for tomato production worldwide, and it may constitute a good model for the analysis of virus emergence in crops. We have combined a population genetics approach with an analysis of in planta properties of virus strains to explain an observed epidemiological pattern. Hybridization analysis showed that PepMV populations are composed of isolates of two types (PepMV-CH2 and PepMV-EU) that cocirculate. The CH2 type isolates are predominant; however, EU isolates have not been displaced but persist mainly in mixed infections. Two molecularly cloned isolates belonging to each type have been used to examine the dynamics of in planta single infections and coinfection, revealing that the CH2 type has a higher fitness than the EU type. Coinfections expand the range of susceptible hosts, and coinfected plants remain symptomless several weeks after infection, so a potentially important problem for disease prevention and management. These results provide an explanation of the observed epidemiological pattern in terms of genetic and ecological interactions among the different viral strains. Thus, mixed infections appear to be contributing to shaping the genetic structure and dynamics of PepMV populations.

Pepino mosaic virus (PepMV; genus Potexvirus, family Flexiviridae) was identified in 1974 as the agent responsible for a viral disease of pepino crops (Solanum muricatum) in Peru (30). PepMV in tomato (Solanum lycopersicum) was first reported in The Netherlands in 1999 (74) but has since spread rapidly in Europe (3, 11, 38, 48, 51, 57) and beyond (20, 35, 36, 42, 68), causing epidemics and severe economic losses (27, 29, 36, 51, 67, 69). The PepMV host range is limited mainly to the Solanaceae (59), and the virus is easily transmitted from plant to plant by contact (30), vectored by bumblebees (65), or seedborne-transmitted (37). PepMV infections in tomato are associated with a wide range of leaf symptoms: mild and severe mosaics, bubbling, laminal distortions, and stunting (26, 27, 51). Fruit symptoms occur with or without leaf symptoms, and the main impact of PepMV is on fruit quality (irregular lycopene distribution [26]) but not on yield (69). Therefore, PepMV is currently considered a dangerous pathogen and is included in the European Plant Protection Organization alert list (15) as one of the most important tomato viruses worldwide (27, 51, 57, 68, 69).

The PepMV genome consists of a single, positive-sense, ~6,400-nucleotide (nt) RNA strand containing five open reading frames (ORFs). ORF1 encodes the putative viral polymerase (RdRp) (3). ORFs 2, 3, and 4 encode the triple gene block (TGB) proteins TGBp1, TGBp2, and TGBp3, which are essential for virus movement (46, 75, 78). Potato virus X TGBp1 is a multifunctional protein that induces plasmodesmal gating, moves from cell to cell, has ATPase and RNA helicase activities, binds viral RNAs, and acts as suppressor of RNA silencing (39, 76-78). ORF5 encodes the coat protein (CP) which, in addition to its structural role, is required for cell-to-cell and long-distance movement (12). Finally, two short untranslated sequences flank the coding regions, and there is a poly(A) tail at the 3′ end of the genomic RNA (3, 11, 48).

Previous studies have shown that Spanish PepMV populations sampled between 2000 and 2004 were genetically very homogeneous (~99% nucleotide identity), most comprising isolates highly similar to the so-called European tomato strain (PepMV-EU). However, a few isolates sampled in 2004 in the Murcia region (Southeastern Spain) were distinct and highly similar to the US2 strain reported in the United States (51). U.S. isolates (US1 and US2) and a Chilean isolate from infected tomato seeds (CH2) share only 79 to 86% nucleotide identity with European (EU) isolates (36, 42). The CH2 type has been reported recently in greenhouses for tomato production in Poland (29) and Belgium (27). In this last study, CH2 was predominant in single infections and also frequent in mixed infections with isolates of the EU type (27). However, all PepMV types (EU, US1, US2, and CH2) have been found in United States, where the PepMV-EU type has been the most prevalent, and mixed infections were found in samples collected from Arizona, Colorado, and Texas (35).

Several studies of plant virus populations have reported a reduced genetic diversity of populations separated in time or space (19, 40, 56) with high virus genetic stability (23). Nevertheless, how genetic and ecological factors modulate the evolutionary dynamics of viruses and determine epidemiological patterns is still poorly understood (25, 47).

We have characterized the population genetic structure of PepMV in infected samples of commercial tomato crops in the Murcia region (southeastern Spain) between 2005 and 2008. Phylogenetic analysis was performed, and genetic diversity values among PepMV isolates were estimated to determine the structure of the population and the strength and direction of selection. In addition, the biological properties (host range, fitness, and virulence) of two cloned isolates of the CH2 and EU types were studied to understand the evolutionary dynamics of natural PepMV populations.

MATERIALS AND METHODS

Surveys of tomato crops and PepMV detection.

During 2005, 2006, 2007, and 2008, we carried out surveys in greenhouses from two areas of the Murcia region (southeastern Spain), Mazarrón and Águilas. A collection of 334 samples of young leaves from the apices of symptomatic tomato plants was prepared. Total RNA was extracted from samples by using Tri-Reagent (Sigma Chemical Co., St. Louis, MO), dissolved in 25 μl of RNase-free water, and stored at −80°C. PepMV was identified by RNA-RNA molecular hybridization in dot blots using probes that discriminate between the EU and CH2 isolates. Probes were complementary to positions 1387 to 1711 and 4693 to 5191 of the PepMV-EU and PepMV-CH2 replicase genes, respectively (Fig. (Fig.1)1) (3, 36). Probes were prepared by transcription with digoxigenin (60) from plasmids pepSP0.5 (5) and pep104-53 (CH2) and used as previously described (41).

FIG. 1.
The PepMV RNA genome consists of a single-stranded, positive-sense, ~6,400-nt RNA containing five ORFs flanked by two untranslated regions. The ORFs are indicated by boxes. Segments correspond to the specific probes for PepMV-EU and PepMV-CH2, ...

Nucleotide sequencing and accession numbers.

The variability and genetic structure of PepMV populations were analyzed by sequencing a 2,223-nt genomic fragment, which included the complete TGB and CP genes. Twelve isolates from each year, from 2005 to 2008, were selected randomly. The cDNAs were generated by reverse transcription-PCR (RT-PCR) by using the primers 5′-GGGGTACCGCGGGCCCGGGd(T)20VN-3′ (CE-43) and 5′-GACATGAARCATTCATACCAAATGGG-3′ (CE-403). Purification of cDNAs, ligation into pGEM-T Easy and transformation of TOP10 electrocompetent Escherichia coli cells were carried out according to the manufacturer's instructions (Promega, Madison, WI). Two clones were sequenced from each isolate. In all cases, sequences of these two clones were identical, except for two isolates of 2006, for which we obtained sequences differing significantly and, most probably (see Results) corresponding to mixed infections; both clones were included in the present study. The 50 cDNAs were sequenced by an external custom service (Secugen, Madrid, Spain).

Phylogenetic and diversity analysis.

Multiple sequence alignments were generated by using CLUSTAL W (72) and, whenever necessary, manually adjusted to maximize similarity while maintaining consistency in the reading frames. Phylogenetic and other molecular evolution analyses were conducted with MEGA4 (70). Phylogenetic trees were constructed by the minimum-evolution method (58) using the close-neighbor-interchange algorithm (50) at a search level of 1, using the corresponding best model of nucleotide substitution (see below) to estimate branch lengths by maximum likelihood (71). The statistical reliability of the resulting trees was evaluated by the bootstrap method (1,000 pseudoreplicates) (17). The genetic distances within each year were computed by using the Pamilo-Bianchi-Li method (52) and were expressed as the number of synonymous (dS) and nonsynonymous (dN) substitutions per synonymous and nonsynonymous sites, respectively.

In addition, the evolutionary distances per nucleotide site for each viral type (EU and CH2) were estimated among all sequence pairs by using a maximum-likelihood-based method (24, 49). The best substitution model (based on Akaike's information criterion) was chosen for each ORF: for TGBp1 this was K81 (32), whereas for TGBp2, TGBp3, and CP it was HKY85 (28). The difference between dN and dS substitution rates was used as a proxy to determine the direction and intensity of natural selection acting on different amino acid sites. This difference was estimated for each codon position in the alignments by using the single-likelihood ancestor counting method implemented in the HYPHY package and available online (www.datamonkey.org) (33). Standard errors were computed by the bootstrap method (based on 1,000 pseudoreplicates). A value dNdS > 0 is taken as evidence for positive or directional selection operating on a given amino acid, whereas values of <0 are a signature for negative or purifying selection.

Virus inoculation.

Isolates PepMV-Sp13 (EU type) and PepMV-PS5 (CH2 type) were used to generate agroinfectious clones (to be described elsewhere). Nicotiana benthamiana plants were agroinoculated (60) using these clones. Virions were purified from N. benthamiana leaves after extraction and PEG precipitation with two cycles of differential centrifugation (2, 30). Virus concentration was estimated by optical density readings at 260 nm, with an extinction coefficient epsilon0.1% = 2.9 (2). Virus inoculations were carried out by rubbing carborundum-dusted cotyledons of young but fully expanded leaves with purified virions at 100 μg/ml or at 50 + 50 μg/ml in single or mixed infections, respectively, in 30 mM sodium phosphate buffer (pH 8).

Host range.

A panel of 19 potential host species from different families was characterized using at least five plants from each host species. Plants were mechanically inoculated with purified virions of isolates PepMV-Sp13 and PepMV-PS5 in single and mixed infections. Symptoms in inoculated and uninoculated leaves were recorded 25 days postinoculation (dpi). Infections were determined by molecular hybridization in dot blot s for all plants at 28 dpi. Three independent replicates were carried out for this experiment. In addition, a RT-PCR/restriction fragment length polymorphism (RFLP) analysis was performed in order to determine whether recombinant viruses could have arisen and be responsible of infections after mixed inoculations. RTs and subsequent PCRs were carried out by using Expand High Fidelity PCR enzyme blend (Roche Diagnostics, Ltd., United Kingdom), oligo(dT)20, and 5′-GAYCTWGCTCGTGCWTATGCTG-3′ (CE-204) as primers and total RNA extracts from symptomatic uninoculated leaves as a template (31); the restriction enzyme AluI (New England Biolabs, Ltd., United Kingdom) was used to digest the PCR products and distinguish between both PepMV types.

Viral fitness.

The fitness of each PepMV isolate in single and mixed infections in tomato (cv. Boludo) was estimated by measuring viral RNA accumulation by real-time quantitative PCR (qPCR) with an AB7500 System (Applied Biosystems, Foster City, CA) using the Power SYBR Green RNA-to-CT 1-Step Kit (Applied Biosystems). A set of 36 tomato plants was mechanically inoculated with purified PepMV-Sp13 and PepMV-PS5 virions. The inoculated and mock-treated plants were maintained in a greenhouse under controlled conditions (16-h photoperiod, 25°C) for up to 32 dpi. All leaves from three plants from each treatment group were homogenized by using a Polytron PT 3100 (Kinematica, Lucerne, Switzerland) in 10 mM Tris-HCl, 5 mM EDTA (pH 8), and 2% sodium dodecyl sulfate. Three biological replicates were processed at 8, 16, 24, and 32 dpi. Total RNA was extracted by using Tri-Reagent (150 mg/ml). RNA concentrations were quantified in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE), adjusted to 100 ng/μl and then stored in aliquots at −80°C. Two pairs of primers were designed by using the Primer Express software (Applied Biosystems) targeting a region of the RdRp ORF (Fig. (Fig.1).1). The primers for PepMV-Sp13 were 5′-CCCAGCATTGCCACACAAG-3′ (CE-432) and 5′-GAGATTTCAAGCTCAGCAATTATGTT-3′ (CE-433), and those for PepMV-PS5 were 5′-CGGCACTAATGAAACATTGCTTA-3′ (CE-434) and 5′-TATTGGCGCCGCTTCG-3′ (CE-435). The reaction mix was prepared according to the manufacturer's instructions (Applied Biosystems). Melting-curve analysis at the amplification endpoint and no-template controls were carried out to ensure product-specific amplification and the absence of primer-dimers.

Viral RNAs were used in serial dilutions to generate external standard curves. Viral RNA was extracted for each isolate from 500 μl of purified virion by using a standard phenol-chloroform procedure (2). RNA concentration was estimated at least twice with a NanoDrop ND-1000 spectrophotometer for each preparation, and then 10-fold serial dilutions (1012 to 10) were prepared using total RNA extract (10 ng/μl) from healthy tomatoes as diluent. The slope values were estimated plotting the threshold cycle (CT) values from two independent assays with three replicates each. The CT value for PepMV-Sp13 was −3.238 with R2 = 0.997, whereas for PepMV-PS5 it was −2.364 with R2 = 0.999. RNA concentration in each sample (ng of viral RNA per 100 ng of total RNA) was estimated by interpolating individual CT values in the standard curve from two independent qPCR assays. In control experiments, no interference was found when measuring the amount of viral RNA in samples with RNAs mixed from isolates PepMV-Sp13 and PepMV-SP5 (mimicking double infections) compared to samples with RNA from only one isolate (data not shown).

In addition, the severity of viral symptoms induced by PepMV was estimated on the basis of relative growth reduction experienced by infected plants. Fresh weight (in grams) and height (18) were measured in each set of plants at 8, 16, 24, and 32 dpi.

Statistical analysis.

Data on genetic diversity among synonymous and nonsynonymous positions, viral RNA concentration, and plant fresh weight and height were analyzed by using SPSS software (v.17.0; SPSS, Inc., Chicago, IL). Model I analysis of covariance using year or dpi as covariables and the type of infection or virus as fixed factors were fitted to the data. Correlation between the accumulation levels, heights, and fresh weights of plants were tested by using Pearson correlation coefficients.

RESULTS

PepMV-CH2 prevailed in tomato crops without excluding PepMV-EU.

We examined 334 samples of symptomatic tomato plants obtained during the period from 2005 to 2008 from two areas of the Spanish region of Murcia, Mazarrón and Águilas (Table (Table1),1), which are used for intensive commercial tomato production. Samples were analyzed by molecular hybridization using probes that discriminate between PepMV-EU and PepMV-CH2. In 2005, 97% of the PepMV isolates were of the CH2 type, and no double infections were observed. In contrast, during 2006, 2007, and 2008, double infections were observed in 76, 26, and 48% of the samples, respectively, whereas single PepMV-CH2 infections were observed in 24, 74, and 48% of the samples, respectively, and PepMV-EU was almost exclusively found in mixed infections (see Fig. S1 in the supplemental material). In total, 75.5% infected samples contained PepMV-CH2 alone, 22.7% corresponded to mixed infections, and just 1.8% of the samples hybridized solely with the PepMV-EU probe. Therefore, it appears that PepMV isolates of the CH2 type, after a likely introduction in 2003 or 2004 (51), have spread to become prevalent in the region, although they have not displaced EU isolates, which seemed to have been maintained predominantly in mixed infections.

TABLE 1.
Collection of tomato samples analyzed, grouped by year and locality

Phylogenetic analysis supports the cocirculation of isolates of the CH2 and EU types.

To analyze the phylogenetic relationships among PepMV isolates, we sequenced a 2,223-nt genomic fragment of 50 random isolates. This fragment included the triple gene block (TGBp1, TGBp2, and TGBp3) and the CP gene (Fig. (Fig.1)1) and covered ca. 34% of the complete virus genome. After the sequences were aligned, a matrix of genetic distances among isolates was computed as synonymous substitutions per synonymous site. This distance matrix was used to build up a minimum evolution tree for each ORF independently and for all concatenated coding sequences. The different trees were indistinguishable and the tree derived for the concatenated coding sequence is shown as an example in Fig. Fig.2.2. A similar tree structure was obtained by maximum parsimony (data not shown). Two well-defined groups were identified, one containing PepMV-EU isolates and the other containing the PepMV-CH2 isolates. There was no differentiation between isolates collected in different seasons or at different locations (Fig. (Fig.2).2). In addition, comparisons of the trees for each ORF revealed no indication of recombination among PepMV types (data not shown), unlike similar analyses performed with other populations of the same virus (27, 51).

FIG. 2.
Phylogenetic relationships of PepMV isolates sampled during 2005 to 2008. Minimum evolution phylogenetic tree for the TGB and CP genes. Bootstrap values (1,000 pseudoreplicates) above 70% are shown. PepMV isolate sequences available in GenBank ...

Purifying selection restricts diversity in the PepMV population.

To ascertain the direction and strength of selection operating in the PepMV population, we evaluated average dS and dN values among pairs of isolates. We analyzed the resulting data by considering the whole population either divided into subpopulations representing isolates by type (CH2 or EU) (data not shown) or from each year. The amount of genetic diversity significantly differed among synonymous and nonsynonymous sites in yearly subpopulations (F1,40 = 11.424, P = 0.002), with the difference becoming increasingly negative with time (F1,40 = 52.479, P < 0.001) but at a rate that was dependent upon the gene analyzed (F3,40 = 4,384, P = 0.009) (Fig. (Fig.3).3). Indeed, the strongest effect was observed on TGBp3, which could reflect the overlap with TGBp2 (Fig. (Fig.1).1). Similar results have been reported for other viruses with overlapping genes (e.g., Bovine leukemia virus [80]). We therefore evaluated the strength of selection at single codons, estimated as dNdS, with a 95% confidence interval, and plotted these values for each group of isolates (EU and CH2) (see Fig. S2 in the supplemental material). The results showed that none of the 676 codons we analyzed showed significant evidence of positive selection and that only nine codons were subject to negative selection (see Fig. S2 in the supplemental material). In EU isolates, the codons under purifying selection were R109, T160, and S183 in TGBp1; H122 in TGBp2; and Q90, S91, E186, and K196 in the CP. In CH2 isolates, the only codon under purifying selection was G51 (TGBp3). Several population neutrality tests were also performed, all supporting the notion that purifying selection is the main force explaining the divergence between CH2 and EU isolates; accordingly, the number of nonsynonymous substitutions was significantly higher within isolates of the same type than between isolates of different types (data not shown).

FIG. 3.
Genetic diversity of PepMV isolates for yearly subpopulations. Diversity values (± the standard error) in synonymous (dS) and nonsynonymous (dN) positions are represented in the left vertical axis, and the difference between these in the right ...

Mixed infections expand the PepMV host range.

Plants from a panel of 19 potential host species were mechanically inoculated with PepMV-Sp13 (EU type) and PepMV-PS5 (CH2 type) either independently or in mixed inoculations. To avoid potential cross-contamination with field isolates, we prepared the inocula using virions purified from N. benthamiana plants previously inoculated using agroinfectious PepMV clones. All infected plants showed symptoms, except for N. glauca and N. rustica, in which PepMV infected asymptomatically only the inoculated leaves. Single isolates showed essentially the same host range regardless of the isolate, although N. occidentalis and Solanum melongena plants showed more severe stunting when inoculated with PepMV-Sp13 rather than when inoculated with PepMV-PS5 (Table (Table2).2). Surprisingly, mixed inoculations extended the PepMV host range (Table (Table2):2): N. glutinosa and N. tabacum plants could be infected after simultaneous inoculation with both isolates, resulting in occasional mild chlorotic symptoms in uninoculated leaves (Table (Table2).2). Since recombinant viruses could have arisen and be responsible of these infections, a RT-PCR/RFLP-based assay was performed on extracts of systemically infected N. glutinosa and N. tabacum plants. If a recombinant virus was responsible of these infections, a single RT-PCR/RFLP pattern would have been observed; however, samples from systemically infected N. glutinosa and N. tabacum plants consistently gave rise to a superposition of the patterns expected for PepMV-Sp13 and PepMV-PS5.

TABLE 2.
Symptoms of PepMV-EU (isolate Sp13) and PepMV-CH2 (isolate PS5) in single and mixed infections of herbaceous test plants

Mixed infections appear to affect PepMV fitness under experimental conditions.

The accumulation of PepMV-Sp13 and PepMV-PS5 in tomato plants was measured to obtain a fitness estimate for each isolate in single and mixed infections. Viral RNA accumulation was measured by qPCR in sets of inoculated tomato plants harvested after 8, 16, 24, and 32 dpi. Prior to harvest, we determined also the average heights and fresh weights of each set of plants at the different time points after inoculation.

Virus accumulation differed significantly depending on the isolate and type of infection (F2,93 = 21.856, P ≤ 0.001). In single infections, PepMV-PS5 accumulated, on average, 75.35% more than PepMV-Sp13 (F2,44 = 4.632, P = 0.015) (Fig. (Fig.4).4). However, asymmetrical antagonism was observed during mixed infections. The accumulation of PepMV-PS5 was suppressed (84.59% averaging across time samples) in the presence of PePMV-Sp13 relative to the viral loads reached in single infections (F2,44 = 8.954, P = 0.001), mixed infections did not appear to affect PepMV-Sp13 accumulation (F2,44 = 1.272, P = 0.290). This asymmetry may explain why PepMV-EU isolates are maintained in the population predominantly in mixed infections.

FIG. 4.
Virus accumulation of different PepMV types in single and mixed infections. The fitness of PepMV-EU (isolate Sp13) and PepMV-CH2 (isolate PS5) was estimated as the accumulation of viral RNA in inoculated tomato plants, which was measured by qPCR at 8, ...

Figure Figure55 shows the growth dynamics for mock-inoculated plants, plants infected with either PepMV-PS5 or PepMV-Sp13 isolates, and plants coinoculated with both isolates. Single infections significantly reduced the average fresh weight (Sp13, F2,43 = 13.164, P < 0.001; PS5, F2,44 = 9.343, P < 0.001) but not the average plant height (Sp13, F2,16 = 3.257, P = 0.065; PS5, F2,16 = 2.383, P = 0.124) compared to mock-inoculated plants. Moreover, there was a 6.75% greater reduction in weight when plants were infected with PepMV-Sp13 compared to PepMV-PS5 (F2,67 = 20.619, P < 0.001). These data also allowed the effect of infection on the rate (i.e., slope) of plant development to be tested. This second type of analysis produced congruent results for both morphological traits, with PepMV-Sp13 having a more significant impact (F1,16 = 27.002, P < 0.001) on fresh weight than PepMV-PS5 (F1,16 = 7.511, P = 0.015). Interestingly, these results showed that the EU isolate is more virulent despite accumulating to a lower extent than the CH2 isolate. In all four cases, differences in growth rate were not evident up to 24 dpi but became so afterward. Coinfected plants were as tall (F2,24 = 1.540, P = 0.226) and weighed as much (F2,16 = 0.325, P = 0.727) as the mock-inoculated ones. Furthermore, the rates of plant development for coinfected plants were undistinguishable from the mock-inoculated plants (height, F1,44 = 0.511, P = 0.479; fresh weight, F1,16 = 1.865, P = 0.191), suggesting an alleviation of PepMV-induced symptoms in tomato associated with mixed infections. Hence, mixed-infected plants in the fields may look, at least initially, like healthy plants.

FIG. 5.
Effect of single and mixed PepMV infections on growth dynamics of tomato plants. The growth of plants infected with PepMV-EU (isolate Sp13) and PepMV-CH2 (isolate PS5) in single and mixed infections is shown by the height (A) and fresh weight (B) of plants, ...

The potential correlation between virus load and the height and fresh weight of infected plants was also analyzed at 32 dpi; no significant differences were found between virus accumulation levels and height or fresh weight in single (r = 0.091, 4 df, P = 0.779; and r = −0.780, 10 df, P = 0.068, respectively) or in mixed infections (r = −0.366, 1 df, P = 0.373; and r = 0.653, 10 df, P = 0.547, respectively).

DISCUSSION

We have analyzed a PepMV population sampled between 2005 and 2008 in tomato crops from two nearby localities in southeastern Spain. Our results showed that the population mainly comprised PepMV-CH2 isolates, which appeared to have spread in an epidemic fashion after recent introduction into a niche previously occupied by PepMV-EU isolates. Similar results have been recently observed for a Watermelon mosaic virus population sampled from zucchini squash, showing that emergent isolates have replaced the preexisting isolates and that emergent isolates have reached dominance in all locations where both groups occurred (13). The PepMV-CH2 presence in tomato crops has been reported in other European countries (27, 54, 55) and from North America (27, 35). It is currently unclear how PepMV-CH2 was introduced in Europe, although its genetic homogeneity (27, 35, 55) and its presence in a commercial tomato seed lot imported to the United States from Chile (36) suggest a common demographic origin. Perhaps, the movements of infected planting material together with the ease of plant-to-plant PepMV transmission may have resulted in PepMV-CH2 infections within areas where PepMV-EU was already endemic or across new areas.

A remarkable observation was the significant frequency of PepMV mixed infections and the fact that PepMV isolates of the EU type appeared in mixed but not in single infections; a coincident observation has been published recently (4). This led us to hypothesize that mixed infections could have a role in the maintenance of diversity in the virus population. In this regard, an interesting question was whether PepMV-EU and PepMV-CH2 cocirculating in the same host might influence each other's evolution. To try and answer this question, we studied the genetic variability and evolution of the PepMV population over a 4-year period and examined the in planta influence of one isolate on another in mixed infections.

Phylogenetic analysis revealed no differentiation within isolates from different seasons or locations and supported the cocirculation of both strains. On the other hand, most nucleotide positions within the analyzed segment of the PepMV genome were invariant, with very few nonsynonymous substitutions occurring within this region, reflecting strong purifying selection. Thus, most mutations had an impact on evolutionary rate but not on the functional properties of the virus proteins. A number of plant virus populations have been shown to be genetically stable, reflecting the need to maintain functional integrity within small viral genomes (40, 45, 61). The invariance of most codons and the presence of strong purifying selection operating on polymorphic codons is consistent with recent reports showing that the genome of RNA viruses is very fragile and that most mutations are either lethal or strongly deleterious (7, 63) as a consequence of the lack of functional redundancy and the existence of overlapping coding regions. Therefore, the observed polymorphisms may simply reflect deleterious or slightly deleterious mutations segregating in the population. We found few codons under significant purifying selection, and most of them were in the TGBp1 and CP genes. The TGP1 codons under purifying selection in the PepMV-EU subpopulation (R109, T160, and S183) appear to be located in the NTPase/helicase domain, which contains a conserved motif necessary for CP-TGBp1 interaction in Potato virus X (46, 79). Most of the sites in TGBp2 and TGBp3 were selectively neutral and likely being transiently present in the populations. TGBp2 and TGBp3 are predicted to reside in the endoplasmic reticulum and contain conserved hydrophobic sequences (46, 66). Possibly, the only codons under purifying selection, H122 in TGBp2 (EU type) and G51 in TGBp3 (CH2 type), are essential for endoplasmic reticulum membrane localization and virus movement (34, 43). Moreover, positions under purifying selection in the PepMV-EU CP (Q90, S91, E186, and K196) are localized between amino acids 91 and 198, corresponding to a domain involved in the interaction between CP and genomic RNA in Papaya mosaic virus (genus Potexvirus), and can play an important role in assembly and packaging of the viral genome (73). Different amino acid positions appeared to be under purifying selection in the two subpopulations of each PepMV type. This can simply be a spurious consequence of the small sample size but, more interestingly, it can also reflect different functional constraints for the two PepMV types, opening the possibility for future functional analysis of PepMV proteins.

The presence of different viral types in populations can alter the population structure and influence its evolution. For instance, the coexistence of different viral types within a population is a prerequisite for recombination, which is a very important source of variation for certain plant viruses. Notably, a significant case is the tomato yellow leaf curl disease complex, which shares an agroecological niche with the PepMV population studied here (21, 44, 61, 62). The cocirculation of PepMV-EU and PepMV-CH2 types could favor recombination, and other researchers have identified recombinant PepMV isolates that have exchanged portions of the TGB and CP genes (51) and portions of the RdRp gene (27). However, we found no evidence of recombination among the PepMV types studied. Genetic exchange may still have occurred but may have involved sequences such as RdRp, which is upstream of the fragment we studied, or new recombinant strains may have been less fit than the parental strains, thus being eliminated from the population by strong purifying selection (see, for example, references 14, 16, and 45). Because recombinant isolates may have quite different biological properties compared to their parental strains (1, 6, 22), genetic studies of the PepMV populations during future seasons should be undertaken to anticipate efficient control strategies.

To understand the dynamics of PepMV populations in Southeastern Spain, we have studied the host range and fitness in its principal host using two infectious full-length cDNA clones derived from isolates Sp13 (EU type) and PS5 (CH2 type). The PepMV host range appears to be limited to certain solanaceous hosts, but mixed inoculations extended the host range beyond that available to any single isolate. The plant species studied here included potential alternative hosts that grow in the same geographical area than infected tomatoes. PepMV did not infect pepper plants after 28 dpi, but eggplants were infected and displayed severe symptoms, showing more severe stunting when inoculated with PepMV-Sp13 than PepMV-PS5 (Table (Table2).2). Therefore, eggplants could serve as an alternative host and/or reservoir in the fields, particularly since the eggplant cropping season in southeastern Spain is long enough to bridge between tomato cropping seasons (M. Juarez and A. Lacasa, unpublished data). An epidemiological study of the more frequent weed species around tomato fields in Murcia and Almería with PepMV-infected tomato plants revealed 19 weed hosts that tested positive for PepMV (10), pointing to potential sources of PepMV-EU isolates. Unfortunately, data of this kind are not available for PepMV-CH2 isolates.

The analysis of the accumulation of PepMV-Sp13 and PepMV-PS5 in single and mixed infections in tomato provided empirical data demonstrating the action of intrahost competition among coinfecting strains of a plant virus. The outcome of plant virus coinfections has been shown to be variable. Whereas in some cases the replication and accumulation of coinfecting strains can diminish in coinfected plants relative to single infections (see, for example, references 4, 8, and 53), in other cases less-virulent strains may experience enhanced multiplication and virulence in mixed infections relative to single infections (see, for example, references 9 and 64). Here, the analysis of virus accumulation in single infections revealed that PS5 was significantly fitter than Sp13, and therefore this competitive advantage may explain the rapid spread and prevalence of the PepMV-CH2 type after its introduction. To detect potential cross-influences between PepMV types and the effect on the dynamics of viral populations, we studied viral fitness in mixed infections. The accumulation of the PS5 isolate in coinfected plants was very much depressed compared to single infections, suggesting that Sp13 antagonizes PS5 in mixed infections. However, from 16 dpi onward, the growth rate of isolate PS5 was similar to or even higher than that of Sp13; therefore, after long periods postinoculation, it may be that both isolates accumulate to comparable levels in mixed infections. These findings suggest that the competition among PepMV isolates from different types do not affect the final viral load of PepMV-Sp13, having this contributed to the persistence of PepMV-EU in mixed infections. In this regard, it remains unknown how different PepMV types occur in tissues and cells within tomato plants, an information that would help elucidate how PS5 is suppressed.

No correlation was observed between virus load and the severity of symptoms in single and mixed infected plants. Furthermore, the analysis of symptom severity in singly or doubly infected plants showed that plants with mixed infections were indistinguishable from mock-inoculated plants. Such symptomless, mixed-infected plants can represent a problem for the disease prevention and management by farmers, who are not able to distinguish mixed-infected plants from healthy plants at least at early stages after infection; mixed-infected plants would be retained in otherwise healthy crops, acting as unnoticed sources of infection. A recent study reporting the biological characterization of several different PepMV isolates has recorded a differential symptom expression upon single or mixed inoculations in plants maintained under greenhouse conditions in a long-term trial (26). In any case, all of these results suggest that mixed infections can be significantly contributing to shaping the genetic structure and dynamics of PepMV populations.

Supplementary Material

[Supplemental material]

Acknowledgments

M. C. Montesinos and J. Tudela provided excellent technical assistance. R. Twyman checked the English.

Financial support was provided by grant AGL2006-08069 (Ministerio de Ciencia e Innovación [MICINN], Madrid, Spain). Work in Valencia was supported by grant BFU2006-14819-C02-01/BMC (MICINN) and by the Santa Fe Institute. P.G. was supported by a Juan de la Cierva postdoctoral contract from MICINN. R.N.S. is the recipient of a graduate fellowship from the Fundación Seneca (Murcia, Spain).

Footnotes

[down-pointing small open triangle]Published ahead of print on 16 September 2009.

Supplemental material for this article may be found at http://jvi.asm.org/.

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