Co-divergence and host-switching in the evolution of tobamoviruses

Research Progress on Viruses of Passiflora edulis

Passiflora edulis, also known as passion fruit, is celebrated for its rich nutritional content, distinctive flavour, and significant medicinal benefits. At present, viral diseases pose a major challenge to the passion fruit industry, affecting both the production and quality of the fruit. These diseases impede the sustainable and healthy growth of the passion fruit sector. In recent years, with the expansion of P. edulis cultivation areas, virus mutations, and advances in virus detection technology, an increasing number of virus species infecting P. edulis have been discovered. To date, more than 40 different virus species have been identified; however, there are different strains within the same virus. This poses a challenge for the control and prevention of P. edulis virus disease. Therefore, this review discusses the different types of viruses and their characteristics, modes of transmission, and effects on the growth of the passion fruit plant, as well as the mechanisms of virus generation and preventive measures, with the hope that these discussions will provide a comprehensive understanding of and countermeasures for viruses in passion fruit.

One-Step Reverse-Transcription Recombinase-Aided Amplification CRISPR/Cas12a-Based Lateral Flow Assay for Fast Field Screening and Accurate Differentiation of Four Major Tobamoviruses Infecting Tomato and Pepper

Several tobamoviruses cause substantial economic losses to tomato and pepper crops globally, especially the pepper mild mosaic virus (PMMoV), tomato brown rugose fruit virus (ToBRFV), tomato mosaic virus (ToMV), and tomato mottle mosaic virus (ToMMV). A fast and accurate detection method is essential for virus identification. An all-in-one reaction method combining a one-step reverse-transcription recombinase-aided amplification (RT-RAA) and CRISPR/Cas12a-based lateral flow assay in one mixture was developed to rapidly screen and accurately differentiate among these four tobamoviruses for field detection in tomato and pepper plants. With a generic RT-RAA primer set and a mix of four specific crRNAs, along with a portable metal incubator and the use of a crude extraction method, this method screened for PMMoV, ToBRFV, ToMV, and ToMMV concurrently in less than 1 h, enabling field workers to take action immediately. The accurate differentiation of these four viruses could be achieved by later adding a single specific crRNA.

TOM1 family conservation within the plant kingdom for tobacco mosaic virus accumulation

The susceptibility factor TOBAMOVIRUS MULTIPLICATION 1 (TOM1) is required for efficient multiplication of tobacco mosaic virus (TMV). Although some phylogenetic and functional analyses of the TOM1 family members have been conducted, a comprehensive analysis of the TOM1 homologues based on phylogeny from the most ancient to the youngest representatives within the plant kingdom, analysis of support for tobamovirus accumulation and interaction with other host and viral proteins has not been reported. In this study, using Nicotiana benthamiana and TMV as a model system, we functionally characterized the TOM1 homologues from N. benthamiana and other plant species from different plant lineages. We modified a multiplex genome editing tool and generated a sextuple mutant in which TMV multiplication was dramatically inhibited. We showed that TOM1 homologues from N. benthamiana exhibited variable capacities to support TMV multiplication. Evolutionary analysis revealed that the TOM1 family is restricted to the plant kingdom and probably originated in the Chlorophyta division, suggesting an ancient origin of the TOM1 family. We found that the TOM1 family acquired the ability to promote TMV multiplication after the divergence of moss and spikemoss. Moreover, the capacity of TOM1 orthologues from different plant species to promote TMV multiplication and the interactions between TOM1 and TOM2A and between TOM1 and TMV-encoded replication proteins are highly conserved, suggesting a conserved nature of the TOM2A-TOM1-TMV Hel module in promoting TMV multiplication. Our study not only revealed a conserved nature of a gene module to promote tobamovirus multiplication, but also provides a valuable strategy for TMV-resistant crop development.

Evolution of cucurbit-infecting tobamoviruses: Recombination and codon usage bias

Currently, there are seven cucurbit-infecting tobamoviruses comprising cucumber green mottle mosaic virus (CGMMV), Kyuri green mottle mosaic virus (KGMMV), cucumber fruit mottle mosaic virus (CFMMV), zucchini green mottle mosaic virus (ZGMMV), cucumber mottle virus (CMoV), watermelon green mottle mosaic virus (WGMMV), and Trichosanthes mottle mosaic virus (TrMMV). To gain more insights into their evolution, recombination analyses were conducted. Four CGMMV isolates and one KGMMV isolate were suggested to be recombinants. And there was an interspecies recombination event between CGMMV and ZGMMV. Phylogenetic incongruence was also observed for CGMMV and KGMMV. A probable ancestral pattern was inferred for the gene junction region between RdRp and MP. Codon usage bias analysis revealed that the viral genes had additional influence independent of compositional constraint. In codon preference, the seven viruses were both similar to and different from the host cucumber (Cucumis sativus). Moreover, the viruses were not deficient in CpG and UpA dinucleotides.

Insight into Population Structure and Evolutionary Analysis of the Emerging Tomato Brown Rugose Fruit Virus

A total of 112 symptomatic tomatoes (Solanum lycopersicum L.) and 83 symptomatic pepper (Capsicum spp.) samples were collected in Ankara, Eskişehir, Bartın, and Zonguldak provinces of Turkey during 2020-2021. Six tomatoes and one pepper sample (3.6%) tested positive for tomato brown rugose fruit virus (ToBRFV, genus Tobamovirus) infection by DAS-ELISA and RT-PCR. ToBRFV-positive tomato and pepper plants were removed from greenhouses as soon as possible, and the greenhouses and tools were disinfected completely. Phylogenetic analysis on the complete CP sequences suggested the clustering of 178 GenBank isolates and 7 novel isolates into three groups. A study using DnaSP software showed very low genetic variation among current global ToBRFV isolates. All four ORFs of the virus genome were under strong negative evolutionary constraints, with a ω value range of 0.0869-0.2066. However, three neutrality tests indicated that most populations of the newly identified ToBRFV are currently expanding by assigning statistically significant negative values to them. The very low F_ST values (0.25 or less) obtained by all comparisons of the isolates from Europe, the Middle East, China, and America concluded that there is no clear genetic separation among currently known isolates from different geographic origins. The divergence time of ToBRFV was estimated to be in the middle of the course of the evolution of 11 tested tobamoviruses. The time to the most recent common ancestors (TMRCAs) of ToBRFV were calculated to be 0.8 and 1.87 with the genetically closest members of Tobamovirus. The results of this study could improve our understanding on the population structure of the emerging ToBRFV.

Knockout of SlTOM1 and SlTOM3 results in differential resistance to tobamovirus in tomato

During tobamovirus-host coevolution, tobamoviruses developed numerous interactions with host susceptibility factors and exploited these interactions for replication and movement. The plant-encoded TOBAMOVIRUS MULTIPLICATION (TOM) susceptibility proteins interact with the tobamovirus replicase proteins and allow the formation of the viral replication complex. Here CRISPR/Cas9-mediated mutagenesis allowed the exploration of the roles of SlTOM1a, SlTOM1b, and SlTOM3 in systemic tobamovirus infection of tomato. Knockouts of both SlTOM1a and SlTOM3 in sltom1a/sltom3 plants resulted in an asymptomatic response to the infection with recently emerged tomato brown rugose fruit virus (ToBRFV). In addition, an accumulation of ToBRFV RNA and coat protein (CP) in sltom1a/sltom3 mutant plants was 516- and 25-fold lower, respectively, than in wild-type (WT) plants at 12 days postinoculation. In marked contrast, sltom1a/sltom3 plants were susceptible to previously known tomato viruses, tobacco mosaic virus (TMV) and tomato mosaic virus (ToMV), indicating that SlTOM1a and SlTOM3 are not essential for systemic infection of TMV and ToMV in tomato plants. Knockout of SlTOM1b alone did not contribute to ToBRFV and ToMV resistance. However, in triple mutants sltom1a/sltom3/sltom1b, ToMV accumulation was three-fold lower than in WT plants, with no reduction in symptoms. These results indicate that SlTOM1a and SlTOM3 are essential for the replication of ToBRFV, but not for ToMV and TMV, which are associated with additional susceptibility proteins. Additionally, we showed that SlTOM1a and SlTOM3 positively regulate the tobamovirus susceptibility gene SlARL8a3. Moreover, we found that the SlTOM family is involved in the regulation of plant development.

The Ups and Downs of an Out-of-the-Box Scientist with a Curious Mind

My early life was challenging, and not conducive to the study of science, but my first introduction to viruses was an epiphany for me. I spent the whole of my career dedicated to understanding viruses, driven largely by curiosity. This led me down many different avenues of study, and to work with many wonderful colleagues, most of whom remain friends. Some highlights of my career include the discovery of a mutualistic three-way symbiosis involving a virus, a fungus, and a plant; genetic mapping of a pathogenicity gene in tomato; uncovering a virus in 1,000-year-old corncobs; exploring virus biodiversity in wild plants; and establishing a system to use a fungal virus to understand the epidemiology of its host. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Evolution and ecology of plant viruses

The discovery of the first non-cellular infectious agent, later determined to be tobacco mosaic virus, paved the way for the field of virology. In the ensuing decades, research focused on discovering and eliminating viral threats to plant and animal health. However, recent conceptual and methodological revolutions have made it clear that viruses are not merely agents of destruction but essential components of global ecosystems. As plants make up over 80% of the biomass on Earth, plant viruses likely have a larger impact on ecosystem stability and function than viruses of other kingdoms. Besides preventing overgrowth of genetically homogeneous plant populations such as crop plants, some plant viruses might also promote the adaptation of their hosts to changing environments. However, estimates of the extent and frequencies of such mutualistic interactions remain controversial. In this Review, we focus on the origins of plant viruses and the evolution of interactions between these viruses and both their hosts and transmission vectors. We also identify currently unknown aspects of plant virus ecology and evolution that are of practical importance and that should be resolvable in the near future through viral metagenomics.

Modeling of Mutational Events in the Evolution of Viruses

Diverse studies of viral evolution have led to the recognition that the evolutionary rates of viral taxa observed are dependent on the time scale being investigated—with short-term studies giving fast substitution rates, and orders of magnitude lower rates for deep calibrations. Although each of these factors may contribute to this time dependent rate phenomenon, a more fundamental cause should be considered. We sought to test computationally whether the basic phenomena of virus evolution (mutation, replication, and selection) can explain the relationships between the evolutionary and phylogenetic distances. We tested, by computational inference, the hypothesis that the phylogenetic distances between the pairs of sequences are functions of the evolutionary path lengths between them. A Basic simulation revealed that the relationship between simulated genetic and mutational distances is non-linear, and can be consistent with different rates of nucleotide substitution at different depths of branches in phylogenetic trees.

Protein Structure-Guided Hidden Markov Models (HMMs) as A Powerful Method in the Detection of Ancestral Endogenous Viral Elements

It has been believed for a long time that the transfer and fixation of genetic material from RNA viruses to eukaryote genomes is very unlikely. However, during the last decade, there have been several cases in which “virus-to-host” gene transfer from various viral families into various eukaryotic phyla have been described. These transfers have been identified by sequence similarity, which may disappear very quickly, especially in the case of RNA viruses. However, compared to sequences, protein structure is known to be more conserved. Applying protein structure-guided protein domain-specific Hidden Markov Models, we detected homologues of the Virgaviridae capsid protein in Schizophora flies. Further data analysis supported “virus-to-host” transfer into Schizophora ancestors as a single transfer event. This transfer was not identifiable by BLAST or by other methods we applied. Our data show that structure-guided Hidden Markov Models should be used to detect ancestral virus-to-host transfers.

A Natural Reservoir and Transmission Vector of Grapevine Vein Clearing Virus

Grapevine vein clearing virus (GVCV) is associated with a vein-clearing and vine-decline disease. In this study, we surveyed wild Ampelopsis cordata from the Vitaceae family and found that 31% (35 of 113) of native A. cordata plants are infected with GVCV. The full-length genome sequence of one GVCV isolate from A. cordata shared 99.8% identical nucleotides with an isolate from a nearby cultivated 'Chardonel' grapevine, suggesting the occurrence of an insect vector. To identify a vector, we collected Aphis illinoisensis (common name: grape aphids) from wild A. cordata plants and detected GVCV in the aphid populations. We found that A. illinoisensis is capable of transmitting GVCV from infected A. cordata to Chardonel grapevines in the greenhouse. Upon transmission, GVCV caused severe symptoms on the infected Chardonel 45 days post transmission. We conclude that wild GVCV isolates from A. cordata are capable of inducing a severe disease on cultivated grapevines once they spread from native A. cordata to vineyards via grape aphids. The discovery of a natural reservoir and an insect vector of GVCV provides timely knowledge for disease management in vineyards and critical clues on viral evolution and epidemiology.

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.

The diversity, evolution and epidemiology of plant viruses: A phylogenetic view

During the past four decades, the scientific community has seen an exponential advance in the number, sophistication, and quality of molecular techniques and bioinformatics tools for the genetic characterization of plant virus populations. Predating these advances, the field of Phylogenetics has significantly contributed to understand important aspects of plant virus evolution. This review aims at summarizing the impact of Phylogenetics in the current knowledge on three major aspects of plant virus evolution that have benefited from the development of phylogenetic inference: (1) The identification and classification of plant virus diversity. (2) The mechanisms and forces shaping the evolution of plant virus populations. (3) The understanding of the interaction between plant virus evolution, epidemiology and ecology. The work discussed here highlights the important role of phylogenetic approaches in the study of the dynamics of plant virus populations.

Using genomic analysis to identify tomato Tm-2 resistance-breaking mutations and their underlying evolutionary path in a new and emerging tobamovirus

In September 2014, a new tobamovirus was discovered in Israel that was able to break Tm-2-mediated resistance in tomato that had lasted 55 years. The virus was isolated, and sequencing of its genome showed it to be tomato brown rugose fruit virus (ToBRFV), a new tobamovirus recently identified in Jordan. Previous studies on mutant viruses that cause resistance breaking, including Tm-2-mediated resistance, demonstrated that this phenotype had resulted from only a few mutations. Identification of important residues in resistance breakers is hindered by significant background variation, with 9-15% variability in the genomic sequences of known isolates. To understand the evolutionary path leading to the emergence of this resistance breaker, we performed a comprehensive phylogenetic analysis and genomic comparison of different tobamoviruses, followed by molecular modeling of the viral helicase. The phylogenetic location of the resistance-breaking genes was found to be among host-shifting clades, and this, together with the observation of a relatively low mutation rate, suggests that a host shift contributed to the emergence of this new virus. Our comparative genomic analysis identified twelve potential resistance-breaking mutations in the viral movement protein (MP), the primary target of the related Tm-2 resistance, and nine in its replicase. Finally, molecular modeling of the helicase enabled the identification of three additional potential resistance-breaking mutations.

Subcellular Localization and Detection of Tobacco mosaic virus ORF6 Protein by Immunoelectron Microscopy

Members of the genus Tobamovirus represent one of the best-characterized groups of plant positive, single stranded RNA viruses. Previous studies have shown that genomes of some tobamoviruses contain not only genes coding for coat protein, movement protein, and the cistron coding for different domains of RNA-polymerase, but also a gene, named ORF6, coding for a poorly conserved small protein. The amino acid sequences of ORF6 proteins encoded by different tobamoviruses are highly divergent. The potential role of ORF6 proteins in replication of tobamoviruses still needs to be elucidated. In this study, using biochemical and immunological methods, we have shown that ORF6 peptide is accumulated after infection in case of two isolates of Tobacco mosaic virus strain U1 (TMV-U1 common and TMV-U1 isolate A15). Unlike virus particles accumulating in the cytoplasm, the product of the ORF6 gene is found mainly in nuclei, which correlates with previously published data about transient expression of ORF6 isolated from TMV-U1. Moreover, we present new data showing the presence of ORF6 genes in genomes of several tobamoviruses. For example, in the genomes of other members of the tobamovirus subgroup 1, including Rehmannia mosaic virus, Paprika mild mottle virus, Tobacco mild green mosaic virus, Tomato mosaic virus, Tomato mottle mosaic virus, and Nigerian tobacco latent virus, sequence comparisons revealed the existence of a similar open reading frame like ORF6 of TMV.

Molecular characterisation of a novel recombinant Ribgrass mosaic virus strain FSHS

Background

The genus Tobamovirus (Virgaviridae) comprises 33 accepted species with the recent addition of eight new viruses and is divided in to three subgroups based on the origin of assembly of the virion and host range. Within the subgroup 1 tobamoviruses the orchid-associated tobamovirus was hypothesized to be a chimeric derivative of recombinations between genome fragments from subgroup 3 and 1. Recombination events involving RdRp, movement and coat protein genes are recorded within subgroup 1 and 2. However natural recombinations have not previously been reported between subgroup 3 tobamoviruses.

Findings

The organization and phylogenetic analyses of the complete genome and the different ORFs placed the new isolate within the Ribgrass mosaic virus clade of subgroup 3 tobamoviruses. Recombination detection analyses indicated that the isolate was a chimeric genome with fragments of high similarity to Ribgrass mosaic virus (RMV) strains NZ-439 (HQ667978) and Actinidia-AC (GQ401365.1) infecting herbaceous Plantago sp. and woody Actinidia spp., respectively. The recombinant differed across the whole genome by 3-8 % from other published RMV genomes.

Conclusion

In this investigation we report an intra-specific recombination between RMV strains NZ-439 (HQ667978) and Actinidia-AC (GQ401365.1), in the replicase component between viral-methyltransferase and viral-helicase regions, resulting in a novel RMV strain FSHS (JQ319720.1) that represents the first described natural recombinant within the RMV cluster of subgroup 3 tobamoviruses.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-016-0487-5) contains supplementary material, which is available to authorized users.

Tobamoviruses have probably co-diverged with their eudicotyledonous hosts for at least 110 million years

A phylogeny has been calculated by maximum likelihood comparisons of the concatenated consensus protein sequences of 29 tobamoviruses shown to be non-recombinant. This phylogeny has statistically significant support throughout, including its basal branches. The viruses form eight lineages that are congruent with the taxonomy of the hosts from which each was first isolated and, with the exception of three of the twenty-nine species, all fall into three clusters that have either asterid or rosid or caryophyllid hosts (i.e. the major subdivisions of eudicotyledonous plants). A modified Mantel permutation test showed that the patristic distances of virus and host phylogenies are significantly correlated, especially when the three anomalously placed viruses are removed. When the internal branches of the virus phylogeny were collapsed the congruence decreased. The simplest explanation of this congruence of the virus and host phylogenies is that most tobamovirus lineages have co-diverged with their primary plant hosts for more than 110 million years, and only the brassica-infecting lineage originated from a major host switch from asterids to rosids. Their co-divergence seems to have been ‘fuzzy’ rather than ‘strict’, permitting viruses to switch hosts within major host clades. Our conclusions support those of a coalesence analysis of tobamovirus sequences, that used proxy node dating, but not a similar analysis of nucleotide sequences from dated samples, which concluded that the tobamoviruses originated only 100 thousand years ago.

The community ecology of pathogens: coinfection, coexistence and community composition

Disease and community ecology share conceptual and theoretical lineages, and there has been a resurgence of interest in strengthening links between these fields. Building on recent syntheses focused on the effects of host community composition on single pathogen systems, we examine pathogen (microparasite) communities using a stochastic metacommunity model as a starting point to bridge community and disease ecology perspectives. Such models incorporate the effects of core community processes, such as ecological drift, selection and dispersal, but have not been extended to incorporate host-pathogen interactions, such as immunosuppression or synergistic mortality, that are central to disease ecology. We use a two-pathogen susceptible-infected (SI) model to fill these gaps in the metacommunity approach; however, SI models can be intractable for examining species-diverse, spatially structured systems. By placing disease into a framework developed for community ecology, our synthesis highlights areas ripe for progress, including a theoretical framework that incorporates host dynamics, spatial structuring and evolutionary processes, as well as the data needed to test the predictions of such a model. Our synthesis points the way for this framework and demonstrates that a deeper understanding of pathogen community dynamics will emerge from approaches working at the interface of disease and community ecology.

Yellow tailflower mild mottle virus: a new tobamovirus described from Anthocercis littorea (Solanaceae) in Western Australia

The complete genome sequence of a tobamovirus was determined from a wild plant of yellow tailflower (Anthocercis littorea, family Solanaceae) that exhibited mild mottling and chlorosis on the leaves. The virus induced severe symptoms including systemic necrosis when inoculated to plants of three other solanaceous species. The viral genome was resequenced after passage in Nicotiana benthamiana. The two genomes were 6379 nucleotides in length, and they differed by three nucleotides. Phylogenetic analysis and the deduced architecture of the genome place the virus, provisionally named yellow tailflower mild mottle virus, with other tobamoviruses that infect solanaceous hosts.

Genomic characterization of Ambrosia asymptomatic virus 1 and evidence of other Tymovirales members in the Oklahoma tallgrass prairie revealed by sequence analysis

The Plant Virus Biodiversity and Ecology project was undertaken to better understand the nature of plant-viral interactions and the occurrence of non-pathogenic viruses. Plants from the Tallgrass Prairie Preserve (TPP), Osage County, Oklahoma, were surveyed from 2005 to 2008 for the presence of viruses, resulting in the detection, using a virus-like particle enrichment method, of the genome a novel virus, Ambrosia asymptomatic virus 1 (AAV1), from Ambrosia psilostachya DC (western ragweed). Here, we present the genomic organization and genetic variability of AAV1. The virus has a single-stranded RNA genome of about 7408 nt, which has six open reading frames (ORFs). Phylogenetic analysis of the replicase and coat protein ORFs of the virus indicates strongly that the virus should be placed in the genus Mandarivirus. No evidence of recombination was detected. We also report the detection in the TPP of two known viruses and seven other putative viruses, members of the order Tymovirales.

Plant virus metagenomics: biodiversity and ecology

Viral metagenomics is the study of viruses in environmental samples, using next generation sequencing that produces very large data sets. For plant viruses, these studies are still relatively new, but are already indicating that our current knowledge grossly underestimates the diversity of these viruses. Some plant virus studies are using thousands of individual plants so that each sequence can be traced back to its precise host. These studies should allow for deeper ecological and evolutionary analyses. The finding of so many new plant viruses that do not cause any obvious symptoms in wild plant hosts certainly changes our perception of viruses and how they interact with their hosts. The major difficulty in these (as in all) metagenomic studies continues to be the need for better bioinformatics tools to decipher the large data sets. The implications of this new information on plant viruses for international agriculture remain to be addressed.