Host passage effects with plant viruses

Tobamoviruses as Models for the Study of Virus Evolution

The study of tobacco mosaic virus and other tobamovirus species has greatly contributed to the development of all areas of virology, including virus evolution. Research with tobamoviruses has been pioneer, or particularly significant, in all major areas of research in this field, including: the characterization of the genetic diversity of virus populations, the mechanisms and rates of generation of genetic diversity, the analysis of the genetic structure of virus populations and of the factors that shape it, the adaptation of viruses to hosts and the evolution of host range, and the evolution of virus taxa and of virus-host interactions. Many of these continue to be hot topics in evolutionary biology, or have been identified recently as such, including (i) host-range evolution, (ii) predicting the overcoming of resistance in crops, (iii) trade-offs between virus life-history traits in virus evolution, and (iv) the codivergence of viruses and hosts at different taxonomical and spatial scales. Tobamoviruses may be particularly appropriate to address these topics with plant viruses, as they provide convenient experimental systems, and as the detailed knowledge on their molecular and structural biology allows the analysis of the mechanisms behind evolutionary processes. Also, the extensive information on parameters related to infection dynamics and population structure may facilitate the development of realistic models to predict virus evolution. Certainly, tobamoviruses will continue to be favorite system for the study of virus evolution.

Types and Strains: Their Essential Role in Understanding Protein Aggregation in Neurodegenerative Diseases

Protein misfolding and aggregation is a key event in diseases like Alzheimer’s disease (AD) or Parkinson’s disease (PD) and is associated with neurodegeneration. Factors that initiate protein misfolding and the role of protein aggregation in the pathophysiology of disease pose major challenges to the neuroscientific community. Interestingly, although the accumulation of the same misfolded protein, e.g., α-synuclein is detectable in all idiopathic PD patients, the disease spectrum covers a variety of different clinical presentations and disease courses. In a more recent attempt this clinical variance is being explained in analogy to prion diseases by different protein aggregate conformations. In prion diseases a relationship between protein aggregate conformation properties and the clinical disease course was shown by relating different prion types to a dementia and an ataxic disease course in Creutzfeldt-Jakob patients. This principle is currently transferred to AD, PD and other neurodegenerative diseases with protein aggregation. However, differences in protein aggregate conformation are frequently addressed as disease strains. The term “strain” also derives from prion research and evolved by adopting the virus terminology at a time when transmissible spongiform encephalopathies (TSEs; later called prion diseases) were assumed to be caused by a virus. The problem is that in virus taxonomy the term “type” refers to properties of the disease agent itself and the term “strain” refers to host associated factors that interact with the disease agent and may moderately modify the clinical disease presentation. Strain factors can be discovered only after transmission and passaging of the agent in a host of a different species. The incorrect use of the terminology confuses disease agent and host factors and hampers the understanding of the pathophysiology of protein aggregate-associated neurodegenerative diseases. In this review article the discoveries are reviewed that explain how the terms “type” and “strain” emerged for unconventional disease agents. This may help to avoid confusion in the terminology of protein aggregation diseases and to reflect correctly the impact of protein aggregate conformation as well as host factor contribution on different clinical variations of AD, PD and other neurodegenerative diseases.

Genetic Determinism and Evolutionary Reconstruction of a Host Jump in a Plant Virus

In spite of their widespread occurrence, only few host jumps by plant viruses have been evidenced and the molecular bases of even fewer have been determined. A combination of three independent approaches, 1) experimental evolution followed by reverse genetics analysis, 2) positive selection analysis, and 3) locus-by-locus analysis of molecular variance (AMOVA) allowed reconstructing the Potato virus Y (PVY; genus Potyvirus, family Potyviridae) jump to pepper (Capsicum annuum), probably from other solanaceous plants. Synthetic chimeras between infectious cDNA clones of two PVY isolates with contrasted levels of adaptation to C. annuum showed that the P3 and, to a lower extent, the CI cistron played important roles in infectivity toward C. annuum. The three analytical approaches pinpointed a single nonsynonymous substitution in the P3 and P3N-PIPO cistrons that evolved several times independently and conferred adaptation to C. annuum. In addition to increasing our knowledge of host jumps in plant viruses, this study illustrates also the efficiency of locus-by-locus AMOVA and combined approaches to identify adaptive mutations in the genome of RNA viruses.

Ecological and genetic determinants of Pepino Mosaic Virus emergence

Virus emergence is a complex phenomenon, which generally involves spread to a new host from a wild host, followed by adaptation to the new host. Although viruses account for the largest fraction of emerging crop pathogens, knowledge about their emergence is incomplete. We address here the question of whether Pepino Mosaic Virus (PepMV) emergence as a major tomato pathogen worldwide could have involved spread from wild to cultivated plant species and host adaptation. For this, we surveyed natural populations of wild tomatoes in southern Peru for PepMV infection. PepMV incidence, genetic variation, population structure, and accumulation in various hosts were analyzed. PepMV incidence in wild tomatoes was high, and a strain not yet reported in domestic tomato was characterized. This strain had a wide host range within the Solanaceae, multiplying efficiently in most assayed Solanum species and being adapted to wild tomato hosts. Conversely, PepMV isolates from tomato crops showed evidence of adaptation to domestic tomato, possibly traded against adaptation to wild tomatoes. Phylogenetic reconstructions indicated that the most probable ancestral sequence came from a wild Solanum species. A high incidence of PepMV in wild tomato relatives would favor virus spread to crops and its efficient multiplication in different Solanum species, including tomato, allowing its establishment as an epidemic pathogen. Later, adaptation to tomato, traded off against adaptation to other Solanum species, would isolate tomato populations from those in other hosts.

IMPORTANCE

Virus emergence is a complex phenomenon involving multiple ecological and genetic factors and is considered to involve three phases: virus encounter with the new host, virus adaptation to the new host, and changes in the epidemiological dynamics. We analyze here if this was the case in the recent emergence of Pepino Mosaic Virus (PepMV) in tomato crops worldwide. We characterized a new strain of PepMV infecting wild tomato populations in Peru. Comparison of this strain with PepMV isolates from tomato crops, plus phylogenetic reconstructions, supports a scenario in which PepMV would have spread to crops from wild tomato relatives, followed by adaptation to the new host and eventually leading to population isolation. Our data, which derive from the analysis of field isolates rather than from experimental evolution approaches, significantly contribute to understanding of plant virus emergence, which is necessary for its anticipation and prevention.

Host effect on the genetic diversification of beet necrotic yellow vein virus single-plant populations

Theoretical models predict that, under restrictive host conditions, virus populations will exhibit greater genetic variability. This virus response has been experimentally demonstrated in a few cases but its relation with a virus's capability to overcome plant resistance is unknown. To explore the genetic host effects on Beet necrotic yellow vein virus (BNYVV) populations that might be related to resistance durability, a wild-type virus isolate was vector inoculated into partially resistant Rz1, Rz2, and susceptible sugar beet cultivars during a serial planting experiment. Cloning and sequencing a region of the viral RNA-3, involving the pathogenic determinant p25, revealed that virus diversity significantly increased in direct proportion to the strength of host resistance. Thus, whereas virus titers were highest, intermediate, and lowest in susceptible, Rz1, and Rz2 plants, respectively; the average number of nucleotide differences among single-plant populations was 0.8 (±0.1) in susceptible, 1.4 (±0.1) in Rz1, and 2.4 (±0.2) in Rz2 genotypes. A similar relationship between host restriction to BNYVV root accumulation and virus genetic variability was detected in fields of sugar beet where these specific Rz1- and Rz2-mediated resistances have been defeated.

The evolution of virulence and pathogenicity in plant pathogen populations

The term virulence has a conflicting history among plant pathologists. Here we define virulence as the degree of damage caused to a host by parasite infection, assumed to be negatively correlated with host fitness, and pathogenicity the qualitative capacity of a parasite to infect and cause disease on a host. Selection may act on both virulence and pathogenicity, and their change in parasite populations can drive parasite evolution and host-parasite co-evolution. Extensive theoretical analyses of the factors that shape the evolution of pathogenicity and virulence have been reported in last three decades. Experimental work has not followed the path of theoretical analyses. Plant pathologists have shown greater interest in pathogenicity than in virulence, and our understanding of the molecular basis of pathogenicity has increased enormously. However, little is known regarding the molecular basis of virulence. It has been proposed that the mechanisms of recognition of parasites by hosts will have consequences for the evolution of pathogenicity, but much experimental work is still needed to test these hypotheses. Much theoretical work has been based on evidence from cellular plant pathogens. We review here the current experimental and observational evidence on which to test theoretical hypotheses or conjectures. We compare evidence from viruses and cellular pathogens, mostly fungi and oomycetes, which differ widely in genomic complexity and in parasitism. Data on the evolution of pathogenicity and virulence from viruses and fungi show important differences, and their comparison is necessary to establish the generality of hypotheses on pathogenicity and virulence evolution.

An Analysis of Host Adaptation and Its Relationship with Virulence in Cucumber mosaic virus

ABSTRACT The host range of a pathogen can have special consequences on its evolution and the evolution of its virulence. For generalists, adaptation to different hosts may be conditioned by different trade-offs in the pathogen's life history and be affected by evolutionary processes that shape pathogen populations. We have examined adaptation of Cucumber mosaic virus (CMV) to different hosts, and analyzed the relationship between host adaptation and virulence. For this, six CMV isolates from central Spain from three different hosts were compared for the ability to multiply and to affect host growth. These analyses were done before and after an experimental evolution process consisting of 10 serial passages in the original host of the isolate. The differential capacity to infect different hosts was compatible with host adaptation. However, the capacity to multiply in different hosts did not provide evidence of host adaptation and was not improved after 10 passages, suggesting that fitness of the natural population of CMV was at, or near to, its maximum. No relationship was found between capacity of multiplication and virulence in any of the three different hosts. These results suggest that the "trade-off" model for the evolution of virulence may not apply to CMV.

Evolution and origins of tobamoviruses

More than a dozen tobamoviruses are known. In nature, each species probably survives by moving between several closely related host species. Each infected plant contains a population of variants, but in most host populations the tobamovirus population is stable. The phylogenetic relationships of tobamovirus species broadly correlate with those of their angiosperm hosts. The simplest explanation for this correlation is that they have coevolved with the angiosperms, and hence, like them, are about 120-140 million years old. Gene sequence differences between species also indicate that the tobamoviruses are an ancient genus. Their gene sequences, and the protein motifs they encode, link them to tobraviruses, hordeiviruses and soil-borne wheat mosaic virus, more distantly to the tricornaviruses, and even to hepatitis virus E and other furoviruses, rubiviruses and alphaviruses. Their progenitors may have been associated with charophycean algae, and perhaps also plasmodiophoromycete fungi.

Characterization of a Severe Strain of Cucumber Mosaic Cucumovirus Seedborne in Cowpea

A new seedborne strain of cucumber mosaic cucumovirus (CMV) that induces severe symptoms on many cowpea genotypes was detected in Georgia in 1994. This strain, designated CMV-Csb, is asymptomatic on tobacco, but it produces more severe cowpea stunt symptoms when present in combination with blackeye cowpea mosaic potyvirus than do the more prevalent CMV isolates. The new strain is seedborne in cowpea (1.5 to 37%), has no associated satellite RNA, and is classified as a member of subgroup I of CMV strains based on nucleic acid hybridization assays.

Viral pathogens and the advantage of sex in the perennial grass Anthoxanthum odoratum

The ubiquity of sexual reproduction among plants and animals remains one of the major unresolved paradoxes of modern evolutionary biology. In order for sex to be maintained in populations, sex must confer immediate and substantial fitness benefits. Theoreticians have proposed numerous mechanisms to explain how such advantages arise, but experimental data are few. In one well-studied population of the perennial grass Anthoxanthum odoratum in a mown North Carolina field, sexual offspring have been found to have significantly higher fitness than asexual offspring. More recent field experiments show that an aphid-transmitted virus, barley yellow dwarf (BYDV)-strain SGV, specifically transmitted by Schizaphus graminum , frequently infects Anthoxanthum progeny soon after transplantation into the field, BYDV infection is asymptomatic in Anthoxanthum , but BYDV-inoculated clones planted directly in the field had significantly lower fitness than healthy controls. Sexual females have been hypothesized to gain a fitness advantage for their offspring in the presence of pathogens either by providing ‘an escape in time’ from pathogens preadapted to the parental genotype or through the production of rare genotypes, which escape frequency-dependent infection. When parental clones and seed-derived sexual offspring were planted in identical but separate arrays in sites near where the parent was collected, parental clones were twice as frequently infected as sexual offspring. Factors other than genetic variation may have contributed to differences in levels of infection between sexual and asexual progeny: in this experiment, clonally derived asexual offspring tillers were slightly larger than seed-derived sexual tillers; in field experiments, larger plants were more frequently infected than smaller plants. When different families were planted into a common site, there was evidence that genotypes were less frequently infected when locally rare than when common. Taken together, the data suggest that BYDV infection generates advantages for rare or sexually produced genotypes in Anthoxanthum . The pattern of infection is likely to result from a complex interaction between vector, host, and viral genetics and population structure, vector behaviour, and host and vector dispersal patterns. Sexually produced genotypes appear to benefit because they are both novel and rare, but the observed minority advantage was weak. Other viral, bacterial, and fungal pathogens in this Anthoxanthum population may act as frequency-dependent selective forces in different places in the field, collectively generating the substantial and observed overall fitness advantage of rare genotypes. Further study is needed to elucidate their role. Nevertheless, the data do show that viral pathogens, which are often asymptomatic, play a significant evolutionary role in plant populations.

Biological variability of potyviruses, an example: zucchini yellow mosaic virus

Potyviruses present an important variability which may affect biological properties such as host range, symptomatology, virulence towards resistance genes, and transmissibility by vectors. A brief account of this potential is presented and illustrated by some aspects of the biological variability of zucchini yellow mosaic virus (ZYMV).

A potyvirus in nature: indistinct populations

Potyviruses occur in nature as a variable population. A number of strains have been reported for many potyviruses. Two or more viruses have been separated from "one virus" isolate. Experimental isolation and/or transmission often results in atypical viral isolates. A virus may be considered as a fuzzy population. We should properly understand the range of variation in one virus. The range of variation as well as typical characteristics of a virus should be included in future descriptions.

The regions of sequence variation in caulimovirus gene VI

The sequence of gene VI from figwort mosaic virus (FMV) clone x4 was determined and compared with that previously published for FMV clone DxS. Both clones originated from the same virus isolation, but the virus used to clone DxS was propagated extensively in a host of a different family prior to cloning whereas that used to clone x4 was not. Differences in the amino acid sequence inferred from the DNA sequences occurred in two clusters. An N-terminal conserved region preceded two regions of variation separated by a central conserved region. Variation in cauliflower mosaic virus (CaMV) gene VI sequences, all of which were derived from virus isolates from hosts from one host family, was similar to that seen in the FMV comparison, though the extent of variation was less. Alignment of gene VI domains from FMV and CaMV revealed regions of amino acid sequence identical in both viruses within the conserved regions. The similarity in the pattern of conserved and variable domains of these two viruses suggests common host-interactive functions in caulimovirus gene VI homologues, and possibly an analogy between caulimoviruses and certain animal viruses in the influence of the host on sequence variability of viral genes.

Plant-virus-based vectors for gene transfer will be of limited use because of the high error frequency during viral RNA synthesis

The error frequency during the RNA replication of alfalfa mosaic virus (AMV) was calculated to be significantly higher than 10(-5). It may be expected that RNA synthesis in general will have low fidelity compared to DNA synthesis. The low fidelity of RNA replication will severely restrict the usefulness of vectors for genetic engineering which are based on RNA viruses, viroids or DNA viruses which are replicated via an RNA intermediate (e.g. caulimoviruses). Spontaneous mutants selected by host shift were found to be much less stable than UV-induced mutants. This difference points to variations in fidelity during RNA synthesis, probably due to the local sequence of the template.