1
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Richard H, Martinetti D, Lercier D, Fouillat Y, Hadi B, Elkahky M, Ding J, Michel L, Morris CE, Berthier K, Maupas F, Soubeyrand S. Computing Geographical Networks Generated by Air-Mass Movement. GEOHEALTH 2023; 7:e2023GH000885. [PMID: 37859755 PMCID: PMC10584379 DOI: 10.1029/2023gh000885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/21/2023]
Abstract
As air masses move within the troposphere, they transport a multitude of components including gases and particles such as pollen and microorganisms. These movements generate atmospheric highways that connect geographic areas at distant, local, and global scales that particles can ride depending on their aerodynamic properties and their reaction to environmental conditions. In this article we present an approach and an accompanying web application called tropolink for measuring the extent to which distant locations are potentially connected by air-mass movement. This approach is based on the computation of trajectories of air masses with the HYSPLIT atmospheric transport and dispersion model, and on the computation of connection frequencies, called connectivities, in the purpose of building trajectory-based geographical networks. It is illustrated for different spatial and temporal scales with three case studies related to plant epidemiology. The web application that we designed allows the user to easily perform intensive computation and mobilize massive archived gridded meteorological data to build weighted directed networks. The analysis of such networks allowed us for example, to describe the potential of invasion of a migratory pest beyond its actual distribution. Our approach could also be used to compute geographical networks generated by air-mass movement for diverse application domains, for example, to assess long-term risk of spread from persistent or recurrent sources of pollutants, including wildfire smoke.
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Affiliation(s)
| | | | | | | | - B. Hadi
- Plant Production and Protection Division (NSP)Food and Agriculture Organization of the United Nations (FAO)RomeItaly
| | - M. Elkahky
- Plant Production and Protection Division (NSP)Food and Agriculture Organization of the United Nations (FAO)RomeItaly
| | - J. Ding
- Plant Production and Protection Division (NSP)Food and Agriculture Organization of the United Nations (FAO)RomeItaly
| | - L. Michel
- Plateforme ESVINRAEBioSPAvignonFrance
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2
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Ribaud M, Gabriel E, Hughes J, Soubeyrand S. Identifying potential significant factors impacting zero-inflated proportion data. Stat Med 2023; 42:3467-3486. [PMID: 37290435 DOI: 10.1002/sim.9814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 04/03/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
Classical supervised methods like linear regression and decision trees are not completely adapted for identifying impacting factors on a response variable corresponding to zero-inflated proportion data (ZIPD) that are dependent, continuous and bounded. In this article we propose a within-block permutation-based methodology to identify factors (discrete or continuous) that are significantly correlated with ZIPD, we propose a performance indicator quantifying the percentage of correlation explained by the subset of significant factors, and we show how to predict the ranks of the response variables conditionally on the observation of these factors. The methodology is illustrated on simulated data and on two real data sets dealing with epidemiology. In the first data set, ZIPD correspond to probabilities of transmission of Influenza between horses. In the second data set, ZIPD correspond to probabilities that geographic entities (eg, states and countries) have the same COVID-19 mortality dynamics.
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Affiliation(s)
| | | | - Joseph Hughes
- Centre for Virus Research, MRC-University of Glasgow, Glasgow, UK
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3
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Billard E, Barro M, Sérémé D, Bangratz M, Wonni I, Koala M, Kassankogno AI, Hébrard E, Thébaud G, Brugidou C, Poulicard N, Tollenaere C. Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot. Virus Evol 2023; 9:vead049. [PMID: 37649958 PMCID: PMC10465090 DOI: 10.1093/ve/vead049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023] Open
Abstract
The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at a local scale remains scarce, in spite of potential implications for crop protection. Here, we describe a 5-year (2015-9) monitoring of RYMV prevalence in six sites from western Burkina Faso (geographic areas of Bama, Banzon, and Karfiguela). It confirmed one irrigated site as a disease hotspot and also found one rainfed lowland (RL) site with occasional high prevalence levels. Within the studied fields, a pattern of disease aggregation was evidenced at a 5-m distance, as expected for a mechanically transmitted virus. Next, we monitored RYMV genetic diversity in the irrigated disease hotspot site, revealing a high viral diversity, with the current coexistence of various distinct genetic groups at the site scale (ca. 520 ha) and also within various specific fields (25 m side). One genetic lineage, named S1bzn, is the most recently emerged group and increased in frequency over the studied period (from 20 per cent or less in 2015-6 to more than 65 per cent in 2019). Its genome results from a recombination between two other lineages (S1wa and S1ca). Finally, experimental work revealed that three rice varieties commonly cultivated in Burkina Faso were not different in terms of resistance level, and we also found no significant effect of RYMV genetic groups on symptom expression and viral load. We found, however, that infection outcome depended on the specific RYMV isolate, with two isolates from the lineage S1bzn accumulating at the highest level at early infections. Overall, this study documents a case of high viral prevalence, high viral diversity, and co-occurrence of divergent genetic lineages at a small geographic scale. A recently emerged lineage, which comprises viral isolates inducing severe symptoms and high accumulation under controlled conditions, could be recently rising through natural selection. Following up the monitoring of RYMV diversity is required to confirm this trend and further understand the factors driving the local maintenance of viral diversity.
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Affiliation(s)
- Estelle Billard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Mariam Barro
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Drissa Sérémé
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Martine Bangratz
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Issa Wonni
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Moustapha Koala
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Abalo Itolou Kassankogno
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Eugénie Hébrard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Gaël Thébaud
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Christophe Brugidou
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Nils Poulicard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Charlotte Tollenaere
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
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4
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Alamil M, Thébaud G, Berthier K, Soubeyrand S. Characterizing viral within-host diversity in fast and non-equilibrium demo-genetic dynamics. Front Microbiol 2022; 13:983938. [PMID: 36274731 PMCID: PMC9581327 DOI: 10.3389/fmicb.2022.983938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing has opened the route for a deep assessment of within-host genetic diversity that can be used, e.g., to characterize microbial communities and to infer transmission links in infectious disease outbreaks. The performance of such characterizations and inferences cannot be analytically assessed in general and are often grounded on computer-intensive evaluations. Then, being able to simulate within-host genetic diversity across time under various demo-genetic assumptions is paramount to assess the performance of the approaches of interest. In this context, we built an original model that can be simulated to investigate the temporal evolution of genotypes and their frequencies under various demo-genetic assumptions. The model describes the growth and the mutation of genotypes at the nucleotide resolution conditional on an overall within-host viral kinetics, and can be tuned to generate fast non-equilibrium demo-genetic dynamics. We ran simulations of this model and computed classic diversity indices to characterize the temporal variation of within-host genetic diversity (from high-throughput amplicon sequences) of virus populations under three demographic kinetic models of viral infection. Our results highlight how demographic (viral load) and genetic (mutation, selection, or drift) factors drive variations in within-host diversity during the course of an infection. In particular, we observed a non-monotonic relationship between pathogen population size and genetic diversity, and a reduction of the impact of mutation on diversity when a non-specific host immune response is activated. The large variation in the diversity patterns generated in our simulations suggests that the underlying model provides a flexible basis to produce very diverse demo-genetic scenarios and test, for instance, methods for the inference of transmission links during outbreaks.
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Affiliation(s)
- Maryam Alamil
- INRAE, BioSP, Avignon, France
- Department of Mathematics and Computer Science, Alfaisal University, Riyadh, Saudi Arabia
- *Correspondence: Maryam Alamil ;
| | - Gaël Thébaud
- PHIM Plant Health Institute, INRAE, Univ Montpellier, CIRAD, Institut Agro, IRD, Montpellier, France
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5
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Uhls A, Petersen S, Keith C, Howard S, Bao X, Qiu W. Grapevine vein clearing virus Is Prevalent and Genetically Variable in Grape Aphid ( Aphis illinoisensis Shimer) Populations. PLANT DISEASE 2021; 105:1531-1538. [PMID: 33174799 DOI: 10.1094/pdis-10-20-2176-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Grapevine vein clearing virus (GVCV) causes severe stunting and death of cultivated grapevines and is prevalent in native Vitis spp. and Ampelopsis cordata in the Midwest region of the United States. GVCV can be transmitted from wild A. cordata to Vitis spp. by grape aphid (Aphis illinoisensis) under greenhouse conditions, but its prevalence, genetic composition, and genome number in native grape aphids are unknown. In this study, we collected grape aphids from native Vitaceae across the state of Missouri in 2018 and 2019, and conducted diagnostic, genetic, and quantitative analyses. GVCV was detected in 91 of the 105 randomly sampled communities on 71 Vitaceae plants (87%). It was present in 211 of 525 single grape aphids (40%). Diverse GVCV variants from aphids were present on both GVCV-negative and GVCV-positive plants. Identical GVCV variants were found in grape aphids sampled from wild and cultivated Vitaceae, indicating that viruliferous aphids likely migrate and disperse GVCV variants among wild and cultivated Vitaceae. In addition, we found that the number of GVCV genomes varies largely in the stylet and body of individual aphids. Our study provides a snapshot of GVCV epidemics and genetic structure in its mobile vector and sessile hosts. This presents a good model for studying the epidemiology, ecology, and evolution of a plant virus.
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Affiliation(s)
- Adam Uhls
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Sylvia Petersen
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Cory Keith
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Susanne Howard
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Xiaokai Bao
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Wenping Qiu
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
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Trucco V, Cabrera Mederos D, Lenardon S, Giolitti F. Geographical distribution, genetic studies and vector transmission of alfalfa enamovirus-1 infecting alfalfa crop in Argentina. Virus Genes 2020; 56:662-667. [PMID: 32691201 DOI: 10.1007/s11262-020-01783-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/11/2020] [Indexed: 10/23/2022]
Abstract
Alfalfa (Medicago sativa L.) growing areas of Argentina were surveyed between 2010 and 2018 to determine the geographical distribution and analyse the genetic diversity among alfalfa enamovirus-1 (AEV-1) isolates. The virus was detected in all 17 surveyed alfalfa-producing provinces, with a prevalence of 64%. The plant virus AEV-1 is widely distributed in the country, and its transmission vector has been unknown until now. Here we show that the black aphid Aphis craccivora can transmit AEV-1. The CP sequence identity among 16 AEV-1 isolates from Argentina was from 98 to 100% and from 98.9 to 100% at nucleotide and amino acid levels, respectively, indicating a low level of sequence variation among these isolates. The phylogenetic analysis based on the complete nucleotide sequence of the CP gene indicated that AEV-1 isolates are closely related and clustered in a monophyletic group. These results suggest that AEV-1 has spread very recently in Argentina. In the present study, we report the geographical distribution of AEV-1 in the main alfalfa-growing areas of Argentina and, for the first time, identify an insect vector and describe the CP gene diversity of an enamovirus worldwide.
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Affiliation(s)
- Verónica Trucco
- Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Instituto de Patología Vegetal (INTA-CIAP-IPAVE), Av. 11 de septiembre 4755, X5014MGO, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola (CONICET-UFyMA), Av. 11 de Septiembre 4755, X5014MGO, Córdoba, Argentina
| | - Dariel Cabrera Mederos
- Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Instituto de Patología Vegetal (INTA-CIAP-IPAVE), Av. 11 de septiembre 4755, X5014MGO, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola (CONICET-UFyMA), Av. 11 de Septiembre 4755, X5014MGO, Córdoba, Argentina
| | - Sergio Lenardon
- Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Instituto de Patología Vegetal (INTA-CIAP-IPAVE), Av. 11 de septiembre 4755, X5014MGO, Córdoba, Argentina.,Facultad de Agronomía y Veterinaria (UNRC-FAV), Universidad Nacional de Río Cuarto, Ruta Nacional 36 Km. 601 Río Cuarto, X5804BYA, Córdoba, Argentina
| | - Fabian Giolitti
- Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Instituto de Patología Vegetal (INTA-CIAP-IPAVE), Av. 11 de septiembre 4755, X5014MGO, Córdoba, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola (CONICET-UFyMA), Av. 11 de Septiembre 4755, X5014MGO, Córdoba, Argentina.
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7
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Maejima K, Hashimoto M, Hagiwara‐Komoda Y, Miyazaki A, Nishikawa M, Tokuda R, Kumita K, Maruyama N, Namba S, Yamaji Y. Intra-strain biological and epidemiological characterization of plum pox virus. MOLECULAR PLANT PATHOLOGY 2020; 21:475-488. [PMID: 31978272 PMCID: PMC7060144 DOI: 10.1111/mpp.12908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 05/21/2023]
Abstract
Plum pox virus (PPV) is one of the most important plant viruses causing serious economic losses. Thus far, strain typing based on the definition of 10 monophyletic strains with partially differentiable biological properties has been the sole approach used for epidemiological characterization of PPV. However, elucidating the genetic determinants underlying intra-strain biological variation among populations or isolates remains a relevant but unexamined aspect of the epidemiology of the virus. In this study, based on complete nucleotide sequence information of 210 Japanese and 47 non-Japanese isolates of the PPV-Dideron (D) strain, we identified five positively selected sites in the PPV-D genome. Among them, molecular studies showed that amino acid substitutions at position 2,635 in viral replicase correlate with viral titre and competitiveness at the systemic level, suggesting that amino acid position 2,635 is involved in aphid transmission efficiency and symptom severity. Estimation of ancestral genome sequences indicated that substitutions at amino acid position 2,635 were reversible and peculiar to one of two genetically distinct PPV-D populations in Japan. The reversible amino acid evolution probably contributes to the dissemination of the virus population. This study provides the first genomic insight into the evolutionary epidemiology of PPV based on intra-strain biological variation ascribed to positive selection.
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Affiliation(s)
- Kensaku Maejima
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Masayoshi Hashimoto
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Yuka Hagiwara‐Komoda
- Department of Sustainable AgricultureCollege of Agriculture, Food and Environment SciencesRakuno Gakuen UniversityEbetsuHokkaidoJapan
| | - Akio Miyazaki
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Masanobu Nishikawa
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Ryosuke Tokuda
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Kohei Kumita
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Noriko Maruyama
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Shigetou Namba
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
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8
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Marie-Jeanne V, Bonnot F, Thébaud G, Peccoud J, Labonne G, Sauvion N. Multi-scale spatial genetic structure of the vector-borne pathogen 'Candidatus Phytoplasma prunorum' in orchards and in wild habitats. Sci Rep 2020; 10:5002. [PMID: 32193489 PMCID: PMC7081303 DOI: 10.1038/s41598-020-61908-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/31/2020] [Indexed: 11/08/2022] Open
Abstract
Inferring the dispersal processes of vector-borne plant pathogens is a great challenge because the plausible epidemiological scenarios often involve complex spread patterns at multiple scales. The spatial genetic structure of 'Candidatus Phytoplasma prunorum', responsible for European stone fruit yellows disease, was investigated by the application of a combination of statistical approaches to genotype data of the pathogen sampled from cultivated and wild compartments in three French Prunus-growing regions. This work revealed that the prevalence of the different genotypes is highly uneven both between regions and compartments. In addition, we identified a significant clustering of similar genotypes within a radius of 50 km or less, but not between nearby wild and cultivated Prunus. We also provide evidence that infected plants are transferred between production areas, and that both species of the Cacopsylla pruni complex can spread the pathogen. Altogether, this work supports a main epidemiological scenario where 'Ca. P. prunorum' is endemic in - and generally acquired from - wild Prunus by its immature psyllid vectors. The latter then migrate to shelter plants that epidemiologically connect sites less than 50 km apart by later providing infectious mature psyllids to their "migration basins". Such multi-scale studies could be useful for other pathosystems.
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Affiliation(s)
| | - François Bonnot
- BGPI, Univ Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France
| | - Gaël Thébaud
- BGPI, Univ Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France
| | - Jean Peccoud
- BGPI, Univ Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions, (EBI-Joint Research Unit 7267, CNRS), 86000, Poitiers, France
| | - Gérard Labonne
- BGPI, Univ Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France
| | - Nicolas Sauvion
- BGPI, Univ Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France.
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9
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Gilbertson MLJ, Fountain-Jones NM, Craft ME. Incorporating genomic methods into contact networks to reveal new insights into animal behavior and infectious disease dynamics. BEHAVIOUR 2019; 155:759-791. [PMID: 31680698 DOI: 10.1163/1568539x-00003471] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Utilization of contact networks has provided opportunities for assessing the dynamic interplay between pathogen transmission and host behavior. Genomic techniques have, in their own right, provided new insight into complex questions in disease ecology, and the increasing accessibility of genomic approaches means more researchers may seek out these tools. The integration of network and genomic approaches provides opportunities to examine the interaction between behavior and pathogen transmission in new ways and with greater resolution. While a number of studies have begun to incorporate both contact network and genomic approaches, a great deal of work has yet to be done to better integrate these techniques. In this review, we give a broad overview of how network and genomic approaches have each been used to address questions regarding the interaction of social behavior and infectious disease, and then discuss current work and future horizons for the merging of these techniques.
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Affiliation(s)
- Marie L J Gilbertson
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Nicholas M Fountain-Jones
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
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10
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McLeish MJ, Fraile A, García-Arenal F. Ecological Complexity in Plant Virus Host Range Evolution. Adv Virus Res 2018; 101:293-339. [PMID: 29908592 DOI: 10.1016/bs.aivir.2018.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The host range of a plant virus is the number of species in which it can reproduce. Most studies of plant virus host range evolution have focused on the genetics of host-pathogen interactions. However, the distribution and abundance of plant viruses and their hosts do not always overlap, and these spatial and temporal discontinuities in plant virus-host interactions can result in various ecological processes that shape host range evolution. Recent work shows that the distributions of pathogenic and resistant genotypes, vectors, and other resources supporting transmission vary widely in the environment, producing both expected and unanticipated patterns. The distributions of all of these factors are influenced further by competitive effects, natural enemies, anthropogenic disturbance, the abiotic environment, and herbivory to mention some. We suggest the need for further development of approaches that (i) explicitly consider resource use and the abiotic and biotic factors that affect the strategies by which viruses exploit resources; and (ii) are sensitive across scales. Host range and habitat specificity will largely determine which phyla are most likely to be new hosts, but predicting which host and when it is likely to be infected is enormously challenging because it is unclear how environmental heterogeneity affects the interactions of viruses and hosts.
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Affiliation(s)
- Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain.
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