Modelling Vector Transmission and Epidemiology of Co-Infecting Plant Viruses

The Temporal Order of Mixed Viral Infections Matters: Common Events That Are Neglected in Plant Viral Diseases

Mixed infections of plant viruses are common in crops and represent a critical biotic factor with substantial epidemiological implications for plant viral diseases. Compared to single-virus infections, mixed infections arise from simultaneous or sequential infections, which can inevitably affect the ecology and evolution of the diseases. These infections can either exacerbate or ameliorate symptom severity, including virus-virus interactions within the same host that may influence a range of viral traits associated with disease emergence. This underscores the need for a more comprehensive understanding of how the order of virus arrival to the host can impact plant disease dynamics. From this perspective, we reviewed the current evidence regarding the impact of mixed infections within the framework of simultaneous and sequential infections in plants, considering the mode of viral transmission. We also examined how the temporal order of mixed infections could affect the dynamics of viral populations and present a case study of two aphid-transmitted viruses infecting melon plants, suggesting that the order of virus arrival significantly affects viral load and disease outcomes. Finally, we anticipate future research that reconciles molecular epidemiology and evolutionary ecology, underlining the importance of biotic interactions in shaping viral epidemiology and plant disease dynamics in agroecosystems.

A story of viral co-infection, co-transmission and co-feeding in ticks: how to compute an invasion reproduction number

With a single circulating vector-borne virus, the basic reproduction number incorporates contributions from tick-to-tick (co-feeding), tick-to-host and host-to-tick transmission routes. With two different circulating vector-borne viral strains, resident and invasive, and under the assumption that co-feeding is the only transmission route in a tick population, the invasion reproduction number depends on whether the model system of ordinary differential equations possesses the property of neutrality. We show that a simple model, with two populations of ticks infected with one strain, resident or invasive, and one population of co-infected ticks, does not have Alizon's neutrality property. We present model alternatives that are capable of representing the invasion potential of a novel strain by including populations of ticks dually infected with the same strain. The invasion reproduction number is analysed with the next-generation method and via numerical simulations.

Report of Citrus tristeza virus in Diaphorina citri (Hemiotera: Liviidae) insects of different sexes, color morphs, and developmental stages

Diaphorina citri, also known as the Asian citrus psyllid, is the main vector of 'Candidatus Liberibacter asiaticus' (CLas) associated with citrus Huanglongbing. It has been reported that D. citri could also be infected by Citrus tristeza virus (CTV), a virus that has been previously reported to be vectored by certain aphid species. In this study, the CTV and CLas profiles in different organs, color variants, developmental stages, or sexes of D. citri insects were analyzed. Although no significant differences were found between nymphs and adults in CTV titers, we found that the third instar nymph of D. citri was more efficient in CTV and CLas acquisition compared to the fourth and fifth instars and adults. With the instars of D. citri development, the relationship between the acquiring of CTV and CLas by D. citri seemed to follow an inverse trend, with the titer of CLas increased and the titer of CTV decreased. No significant differences were observed between the 2 sexes of D. citri in acquiring either CTV or CLas titers in the field. However, no differences were drawn among the 3 color morph variants for CTV titers. CTV titers in the midguts of adult D. citri were significantly higher than those in the salivary glands. Both CTV-positive incidence and CTV titers in the midguts of adult D. citri increased with increasing exposure periods. This study provides new data to deepen our understanding of the CTV-involved interaction between D. citri and CLas.

Emerging Themes and Approaches in Plant Virus Epidemiology

Plant diseases caused by viruses share many common features with those caused by other pathogen taxa in terms of the host-pathogen interaction, but there are also distinctive features in epidemiology, most apparent where transmission is by vectors. Consequently, the host-virus-vector-environment interaction presents a continuing challenge in attempts to understand and predict the course of plant virus epidemics. Theoretical concepts, based on the underlying biology, can be expressed in mathematical models and tested through quantitative assessments of epidemics in the field; this remains a goal in understanding why plant virus epidemics occur and how they can be controlled. To this end, this review identifies recent emerging themes and approaches to fill in knowledge gaps in plant virus epidemiology. We review quantitative work on the impact of climatic fluctuations and change on plants, viruses, and vectors under different scenarios where impacts on the individual components of the plant-virus-vector interaction may vary disproportionately; there is a continuing, sometimes discordant, debate on host resistance and tolerance as plant defense mechanisms, including aspects of farmer behavior and attitudes toward disease management that may affect deployment in crops; disentangling host-virus-vector-environment interactions, as these contribute to temporal and spatial disease progress in field populations; computational techniques for estimating epidemiological parameters from field observations; and the use of optimal control analysis to assess disease control options. We end by proposing new challenges and questions in plant virus epidemiology.

Analysis of Virus-Derived siRNAs in Strawberry Plants Co-Infected with Multiple Viruses and Their Genotypes

Plants can be infected with multiple viruses. High-throughput sequencing tools have enabled numerous discoveries of multi-strain infections, when more than one viral strain or divergent genomic variant infects a single plant. Here, we investigated small interfering RNAs (siRNAs) in a single strawberry plant co-infected with several strains of strawberry mottle virus (SMoV), strawberry crinkle virus (SCV) and strawberry virus 1 (StrV-1). A range of plants infected with subsets of the initial viral species and strains that were obtained by aphid-mediated transmission were also evaluated. Using high-throughput sequencing, we characterized the small RNA fractions associated with different genotypes of these three viruses and determined small RNA hotspot regions in viral genomes. A comparison of virus-specific siRNA (vsiRNA) abundance with relative viral concentrations did not reveal any consistent agreement. Strawberry mottle virus strains exhibiting considerable variations in concentrations were found to be associated with comparable quantities of vsiRNAs. Additionally, by estimating the specificity of siRNAs to different viral strains, we observed that a substantial pool of vsiRNAs could target all SMoV strains, while strain-specific vsiRNAs predominantly targeted rhabdoviruses, SCV and StrV-1. This highlights the intricate nature and potential interference of the antiviral response within a single infected plant when multiple viruses are present.

Interactions between insect vectors and plant pathogens span the parasitism-mutualism continuum

Agricultural crops infected with vector-borne pathogens can suffer severe negative consequences, but the extent to which phytopathogens affect the fitness of their vector hosts remains unclear. Evolutionary theory predicts that selection on vector-borne pathogens will favour low virulence or mutualistic phenotypes in the vector, traits facilitating effective transmission between plant hosts. Here, we use a multivariate meta-analytic approach on 115 effect sizes across 34 unique plant-vector-pathogen systems to quantify the overall effect of phytopathogens on vector host fitness. In support of theoretical models, we report that phytopathogens overall have a neutral fitness effect on vector hosts. However, the range of fitness outcomes is diverse and span the parasitism-mutualism continuum. We found no evidence that various transmission strategies, or direct effects and indirect (plant-mediated) effects, of phytopathogens have divergent fitness outcomes for the vector. Our finding emphasizes diversity in tripartite interactions and the necessity for pathosystem-specific approaches to vector control.

Decoding the double trouble: A mathematical modelling of co-infection dynamics of SARS-CoV-2 and influenza-like illness

After the detection of coronavirus disease 2019 (Covid-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, Hubei Province, China in late December, the cases of Covid-19 have spiralled out around the globe. Due to the clinical similarity of Covid-19 with other flulike syndromes, patients are assayed for other pathogens of influenza like illness. There have been reported cases of co-infection amongst patients with Covid-19. Bacteria for example Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Mycoplasma pneumoniae, Chlamydia pneumonia, Legionella pneumophila etc and viruses such as influenza, coronavirus, rhinovirus/enterovirus, parainfluenza, metapneumovirus, influenza B virus etc are identified as co-pathogens. In our current effort, we develop and analysed a compartmental based Ordinary Differential Equation (ODE) type mathematical model to understand the co-infection dynamics of Covid-19 and other influenza type illness. In this work we have incorporated the saturated treatment rate to take account of the impact of limited treatment resources to control the possible Covid-19 cases. As results, we formulate the basic reproduction number of the model system. Finally, we have performed numerical simulations of the co-infection model to examine the solutions in different zones of parameter space.

Vector acquisition and co-inoculation of two plant viruses influences transmission, infection, and replication in new hosts

This study investigated the role of vector acquisition and transmission on the propagation of single and co-infections of tomato yellow leaf curl virus (TYLCV,) and tomato mottle virus (ToMoV) (Family: Geminiviridae, Genus: Begomovirus) by the whitefly vector Bemisia tabaci MEAM1 (Gennadius) in tomato. The aim of this research was to determine if the manner in which viruses are co-acquired and co-transmitted changes the probability of acquisition, transmission and new host infections. Whiteflies acquired virus by feeding on singly infected plants, co-infected plants, or by sequential feeding on singly infected plants. Viral titers were also quantified by qPCR in vector cohorts, in artificial diet, and plants after exposure to viruliferous vectors. Differences in transmission, infection status of plants, and titers of TYLCV and ToMoV were observed among treatments. All vector cohorts acquired both viruses, but co-acquisition/co-inoculation generally reduced transmission of both viruses as single and mixed infections. Co-inoculation of viruses by the vector also altered virus accumulation in plants regardless of whether one or both viruses were propagated in new hosts. These findings highlight the complex nature of vector-virus-plant interactions that influence the spread and replication of viruses as single and co-infections.

Transmission of Diverse Variants of Strawberry Viruses Is Governed by a Vector Species

Advances in high-throughput sequencing methods have boosted the discovery of multistrain viral infections in diverse plant systems. This phenomenon appears to be pervasive for certain viral species. However, our knowledge of the transmission aspects leading to the establishment of such mixed infections is limited. Recently, we reported a mixed infection of a single strawberry plant with strawberry mottle virus (SMoV), strawberry crinkle virus (SCV) and strawberry virus 1 (StrV-1). While SCV and StrV-1 are represented by two and three molecular variants, respectively, SmoV has three different RNA1 and RNA2 segments. In this study, we focus on virus acquisition by individual adult aphids of the Aphis gossypii, Aphis forbesi and Chaetosiphon fragaefolii species. Single-aphid transmission trials are performed under experimental conditions. Both different viruses and individual virus strains show varying performances in single aphid acquisition. The obtained data suggests that numerous individual transmission events lead to the establishment of multistrain infections. These data will be important for the development of epidemiological models in plant virology.

Mathematical Modeling Suggests Cooperation of Plant-Infecting Viruses

Viruses are major pathogens of agricultural crops. Viral infections often start after the virus enters the outer layer of a tissue, and many successful viruses, after local replication in the infected tissue, are able to spread systemically. Quantitative details of virus dynamics in plants, however, are poorly understood, in part, because of the lack of experimental methods which allow the accurate measurement of the degree of infection in individual plant tissues. Recently, a group of researchers followed the kinetics of infection of individual cells in leaves of Nicotiana tabacum plants using Tobacco etch virus (TEV) expressing either Venus or blue fluorescent protein (BFP). Assuming that viral spread occurs from lower to upper leaves, the authors fitted a simple mathematical model to the frequency of cellular infection by the two viral variants found using flow cytometry. While the original model could accurately describe the kinetics of viral spread locally and systemically, we found that many alternative versions of the model, for example, if viral spread starts at upper leaves and progresses to lower leaves or when virus dissemination is stopped due to an immune response, fit the data with reasonable quality, and yet with different parameter estimates. These results strongly suggest that experimental measurements of the virus infection in individual leaves may not be sufficient to identify the pathways of viral dissemination between different leaves and reasons for viral control. We propose experiments that may allow discrimination between the alternatives. By analyzing the kinetics of coinfection of individual cells by Venus and BFP strains of TEV we found a strong deviation from the random infection model, suggesting cooperation between the two strains when infecting plant cells. Importantly, we showed that many mathematical models on the kinetics of coinfection of cells with two strains could not adequately describe the data, and the best fit model needed to assume (i) different susceptibility of uninfected cells to infection by two viruses locally in the leaf vs. systemically from other leaves, and (ii) decrease in the infection rate depending on the fraction of uninfected cells which could be due to a systemic immune response. Our results thus demonstrate the difficulty in reaching definite conclusions from extensive and yet limited experimental data and provide evidence of potential cooperation between different viral variants infecting individual cells in plants.

Narcissus Plants: A Melting Pot of Potyviruses

Our paper presents detailed evolutionary analyses of narcissus viruses from wild and domesticated Narcissus plants in Japan. Narcissus late season yellows virus (NLSYV) and narcissus degeneration virus (NDV) are major viruses of Narcissus plants, causing serious disease outbreaks in Japan. In this study, we collected Narcissus plants showing mosaic or striped leaves along with asymptomatic plants in Japan for evolutionary analyses. Our findings show that (1) NLSYV is widely distributed, whereas the distribution of NDV is limited to the southwest parts of Japan; (2) the genomes of NLSYV isolates share nucleotide identities of around 82%, whereas those of NDV isolates are around 94%; (3) three novel recombination type patterns were found in NLSYV; (4) NLSYV comprises at least five distinct phylogenetic groups whereas NDV has two; and (5) infection with narcissus viruses often occur as co-infection with different viruses, different isolates of the same virus, and in the presence of quasispecies (mutant clouds) of the same virus in nature. Therefore, the wild and domesticated Narcissus plants in Japan are somewhat like a melting pot of potyviruses and other viruses.

Modeling the transmission dynamics of plant viral disease using two routes of infection, nonlinear terms and incubation delay

Plant viral diseases have devastating effects on agricultural products worldwide. In this research, a delay differential equation model has been proposed for the transmission dynamics of plant viral disease using the vector-to-plant (primary) transmission and plant-to-plant (i.e. secondary) transmissions modeled via nonlinear (saturated) terms. Also, a time delay is considered in the model due to the incubation period of the plant. Feasibility and stability analyses of the equilibria of the model have been provided based on the basic reproduction numbers. Stability changes occur through Hopf bifurcation in both the delayed and non-delayed systems. Sensitivity analysis shows the impact of a parameter on the infection. The mathematical analysis of the model and numerical examples suggested that the disease will occur if the incubation period of the plant is small. Viral disease of a plant can be controlled by maintaining the distance between plants, removing the infected plants, and increasing crop resistance towards the disease.

Rice Gall Dwarf Virus Promotes the Propagation and Transmission of Rice Stripe Mosaic Virus by Co-infected Insect Vectors

Rice stripe mosaic virus (RSMV), a newly discovered plant cytorhabdovirus, and rice gall dwarf virus (RGDV), a plant reovirus, are transmitted by leafhopper Recilia dorsalis in a persistent-propagative manner. In this study, field surveys in Luoding city, Guangdong province of southern China, showed that RSMV and RGDV frequently co-infected rice plants. Furthermore, this co-infection had a synergistic effect on viral replication potential and pathogenicity in rice plants. Meanwhile, RSMV and RGDV also co-infected R. dorsalis vectors, and RGDV significantly promoted the propagation of RSMV in co-infected vectors. Accordingly, co-infection significantly promoted the acquisition and transmission efficiencies of RSMV by R. dorsalis. However, such co-infection did not significantly affect the propagation of RGDV in vectors. More importantly, we also observed that non-viruliferous R. dorsalis preferred to feed on co-infected rice plants, and this process further affected the feeding behavior of R. dorsalis to enhance viral release into rice phloem. These results provided the clues as to why RSMV had been a gradually expanding problem, creating an increasing risk of damage to rice production. Our findings revealed that synergism between RSMV and RGDV in their host and vector enhanced the propagation and transmission of RSMV, which will help guide the formulation of viral control strategies.

Epidemiological and ecological consequences of virus manipulation of host and vector in plant virus transmission

Many plant viruses are transmitted by insect vectors. Transmission can be described as persistent or non-persistent depending on rates of acquisition, retention, and inoculation of virus. Much experimental evidence has accumulated indicating vectors can prefer to settle and/or feed on infected versus noninfected host plants. For persistent transmission, vector preference can also be conditional, depending on the vector’s own infection status. Since viruses can alter host plant quality as a resource for feeding, infection potentially also affects vector population dynamics. Here we use mathematical modelling to develop a theoretical framework addressing the effects of vector preferences for landing, settling and feeding–as well as potential effects of infection on vector population density–on plant virus epidemics. We explore the consequences of preferences that depend on the host (infected or healthy) and vector (viruliferous or nonviruliferous) phenotypes, and how this is affected by the form of transmission, persistent or non-persistent. We show how different components of vector preference have characteristic effects on both the basic reproduction number and the final incidence of disease. We also show how vector preference can induce bistability, in which the virus is able to persist even when it cannot invade from very low densities. Feedbacks between plant infection status, vector population dynamics and virus transmission potentially lead to very complex dynamics, including sustained oscillations. Our work is supported by an interactive interface https://plantdiseasevectorpreference.herokuapp.com/. Our model reiterates the importance of coupling virus infection to vector behaviour, life history and population dynamics to fully understand plant virus epidemics.

Plant virus diseases–which cause devastating epidemics in plant populations worldwide–are most often transmitted by insect vectors. Recent experimental evidence indicates how vectors do not choose between plants at random, but instead can be affected by whether plants are infected (or not). Virus infection can cause plants to “smell” different, because they produce different combinations of volatile chemicals, or “taste” different, due to chemical changes in infected tissues. Vector reproduction rates can also be affected when colonising infected versus uninfected plants. Potential effects on epidemic spread through a population of plants are not yet entirely understood. There are also interactions with the mode of virus transmission. Some viruses can be transmitted after only a brief probe by a vector, whereas others are only picked up after an extended feed on an infected plant. Furthermore there are differences in how long vectors remain able to transmit the virus. This ranges from a matter of minutes, right up to the entire lifetime of the insect, depending on the plant-virus-vector combination under consideration. Here we use mathematical modelling to synthesise all this complexity into a coherent theoretical framework. We illustrate our model via an online interface https://plantdiseasevectorpreference.herokuapp.com/.

The Epidemiology of Plant Virus Disease: Towards a New Synthesis

Epidemiology is the science of how disease develops in populations, with applications in human, animal and plant diseases. For plant diseases, epidemiology has developed as a quantitative science with the aims of describing, understanding and predicting epidemics, and intervening to mitigate their consequences in plant populations. Although the central focus of epidemiology is at the population level, it is often necessary to recognise the system hierarchies present by scaling down to the individual plant/cellular level and scaling up to the community/landscape level. This is particularly important for diseases caused by plant viruses, which in most cases are transmitted by arthropod vectors. This leads to range of virus-plant, virus-vector and vector-plant interactions giving a distinctive character to plant virus epidemiology (whilst recognising that some fungal, oomycete and bacterial pathogens are also vector-borne). These interactions have epidemiological, ecological and evolutionary consequences with implications for agronomic practices, pest and disease management, host resistance deployment, and the health of wild plant communities. Over the last two decades, there have been attempts to bring together these differing standpoints into a new synthesis, although this is more apparent for evolutionary and ecological approaches, perhaps reflecting the greater emphasis on shorter often annual time scales in epidemiological studies. It is argued here that incorporating an epidemiological perspective, specifically quantitative, into this developing synthesis will lead to new directions in plant virus research and disease management. This synthesis can serve to further consolidate and transform epidemiology as a key element in plant virus research.