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Bastide P, Rocu P, Wirtz J, Hassler GW, Chevenet F, Fargette D, Suchard MA, Dellicour S, Lemey P, Guindon S. Modeling the velocity of evolving lineages and predicting dispersal patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597755. [PMID: 38895258 PMCID: PMC11185746 DOI: 10.1101/2024.06.06.597755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Accurate estimation of the dispersal velocity or speed of evolving organisms is no mean feat. In fact, existing probabilistic models in phylogeography or spatial population genetics generally do not provide an adequate framework to define velocity in a relevant manner. For instance, the very concept of instantaneous speed simply does not exist under one of the most popular approaches that models the evolution of spatial coordinates as Brownian trajectories running along a phylogeny [30]. Here, we introduce a new family of models - the so-called "Phylogenetic Integrated Velocity" (PIV) models - that use Gaussian processes to explicitly model the velocity of evolving lineages instead of focusing on the fluctuation of spatial coordinates over time. We describe the properties of these models and show an increased accuracy of velocity estimates compared to previous approaches. Analyses of West Nile virus data in the U.S.A. indicate that PIV models provide sensible predictions of the dispersal of evolving pathogens at a one-year time horizon. These results demonstrate the feasibility and relevance of predictive phylogeography in monitoring epidemics in time and space.
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Affiliation(s)
- Paul Bastide
- IMAG, Université de Montpellier, CNRS, Montpellier, France
| | - Pauline Rocu
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier. CNRS - UMR 5506. Montpellier, France
| | - Johannes Wirtz
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Gabriel W Hassler
- Department of Economics, Sociology, and Statistics, RAND, Santa Monica, CA, USA
| | | | - Denis Fargette
- PHIM, IRD, INRAE, CIRAD, Université de Montpellier, Montpellier, France
| | - Marc A Suchard
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Stéphane Guindon
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier. CNRS - UMR 5506. Montpellier, France
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2
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Sun YD, Yokomi R. Genotype Sequencing and Phylogenetic Analysis Revealed the Origins of Citrus Yellow Vein Clearing Virus California Isolates. Viruses 2024; 16:188. [PMID: 38399964 PMCID: PMC10891506 DOI: 10.3390/v16020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The Citrus yellow vein clearing virus (CYVCV) causes a viral disease that has been reported in some citrus-growing regions in countries in Eurasia including Pakistan, India, Türkiye, Iran, China, and South Korea. Recently, CYVCV was detected in a localized urban area in a town in the middle of California's citrus-growing region and marks the first occurrence of the virus in North America. CYVCV has been reported to be spread by aphid and whitefly vectors and is graft and mechanically transmitted. Hence, it is an invasive pathogen that presents a significant threat to the California citrus industry, especially lemons, which are highly symptomatic to CYVCV. To elucidate the origin of the CYVCV California strain, we used long-read sequencing technology and obtained the complete genomes of three California CYVCV isolates, CA1, CA2, and CA3. The sequences of these isolates exhibited intergenomic similarities ranging from 95.4% to 97.4% to 54 publicly available CYVCV genome sequences, which indicated a relatively low level of heterogeneity. However, CYVCV CA isolates formed a distinct clade from the other isolates when aligned against other CYVCV genomes and coat protein gene sequences as shown by the neighbor network analysis. Based on the rooted Maximum Likelihood phylogenetic trees, CYVCV CA isolates shared the most recent common ancestor with isolates from India/South Asia. Bayesian evolutionary inferences resulted in a spatiotemporal reconstruction, suggesting that the CYVCV CA lineage diverged from the Indian lineage possibly around 1995. This analysis placed the origin of all CYVCV to around 1990, with South Asia and/or Middle East as the most plausible geographic source, which matches to the first discovery of CYVCV in Pakistan in 1988. Moreover, the spatiotemporal phylogenetic analysis indicated an additional virus diffusion pathway: one from South Asia to China and South Korea. Collectively, our phylogenetic inferences offer insights into the probable dynamics of global CYVCV dissemination, emphasizing the need for citrus industries and regulatory agencies to closely monitor citrus commodities crossing state and international borders.
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Affiliation(s)
- Yong-Duo Sun
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, USA
| | - Raymond Yokomi
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, USA
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3
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Chevenet F, Fargette D, Bastide P, Vitré T, Guindon S. EvoLaps 2: Advanced phylogeographic visualization. Virus Evol 2024; 10:vead078. [PMID: 38188280 PMCID: PMC10771281 DOI: 10.1093/ve/vead078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/08/2023] [Accepted: 12/16/2023] [Indexed: 01/09/2024] Open
Abstract
EvoLaps is a user-friendly web application designed to visualize the spatial and temporal spread of pathogens. It takes an annotated tree as entry, such as a maximum clade credibility tree obtained through continuous phylogeographic inference. By following a 'Top-Down' reading of a tree recursively, transitions (latitude/longitude changes from a node to its children) are represented on a cartographic background using graphical paths. The complete set of paths forms the phylogeographic scenario. EvoLaps offers several features to analyze complex scenarios: (1) enhanced path display using multiple graphical variables with time-dependent gradients, (2) cross-highlighting and selection capabilities between the phylogeographic scenario and the phylogenetic tree, (3) production of specific spatio-temporal scales and synthetic views through dynamic and iterative clustering of localities into spatial clusters, (4) animation of the phylogeographic scenario using tree brushing, which can be done manually or automatically, gradually over time or at specific time intervals, and for the entire tree or a specific clade, and (5) an evolving library of additional tools. EvoLaps is freely available for use at evolaps.org.
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Affiliation(s)
- F Chevenet
- MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - D Fargette
- PHIM, IRD, INRAE, CIRAD, Université de Montpellier, Montpellier, France
| | - P Bastide
- IMAG, CNRS, Université de Montpellier, Montpellier, France
| | - T Vitré
- MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - S Guindon
- LIRMM, CNRS, Université de Montpellier, Montpellier, France
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4
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Kawakubo S, Kim H, Takeshita M, Masuta C. Host-specific adaptation drove the coevolution of leek yellow stripe virus and Allium plants. Microbiol Spectr 2023; 11:e0234023. [PMID: 37706684 PMCID: PMC10581216 DOI: 10.1128/spectrum.02340-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 09/15/2023] Open
Abstract
Host adaptation plays a crucial role in virus evolution and is a consequence of long-term interactions between virus and host in a complex arms race between host RNA silencing and viral RNA silencing suppressor (RSS) as counterdefense. Leek yellow stripe virus (LYSV), a potyvirus causing yield loss of garlic, infects several species of Allium plants. The unexpected discovery of an interspecific hybrid of garlic, leek, and great-headed (GH) garlic motivated us to explore the host-adaptive evolution of LYSV. Here, using Bayesian phylogenetic comparative methods and a functional assay of viral RSS activity, we show that the evolutionary context of LYSV has been shaped by the host adaptation of the virus during its coevolution with Allium plants. Our phylogenetic analysis revealed that LYSV isolates from leek and their taxonomic relatives (Allium ampeloprasum complex; AAC) formed a distinct monophyletic clade separate from garlic isolates and are likely to be uniquely adapted to AAC. Our comparative studies on viral accumulation indicated that LYSV accumulated at a low level in leek, whereas LYSVs were abundant in other Allium species such as garlic and its relatives. When RSS activity of the viral P1 and HC-Pro of leek LYSV isolate was analyzed, significant synergism in RSS activity between the two proteins was observed in leek but not in other species, suggesting that viral RSS activity may be important for the viral host-specific adaptation. We thus consider that LYSV may have undergone host-specific evolution at least in leek, which must be driven by speciation of its Allium hosts. IMPORTANCE Potyviruses are the most abundant plant RNA viruses and are extremely diversified in terms of their wide host range. Due to frequent host switching during their evolution, host-specific adaptation of potyviruses may have been shaped by numerous host factors. However, any critical determinants for viral host range remain largely unknown, possibly because of the repeated gain and loss of virus infectivity of plants. Leek yellow stripe virus (LYSV) is a species of the genus Potyvirus, which has a relatively narrow host range, generally limited to hosts in the genus Allium. Our investigations on leek and leek relatives (Allium ampeloprasum complex), which must have been generated through interspecies hybridization, revealed that LYSV accumulation remained low in leek as a result of viral host adaptation in competition with host resistance such as RNA silencing. This study presents LYSV as an ideal model to study the process of host-adaptive evolution and virus-host coevolution.
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Affiliation(s)
- Shusuke Kawakubo
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hangil Kim
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Minoru Takeshita
- Faculty of Agriculture, Department of Agricultural and Environmental Sciences, University of Miyazaki, Miyazaki, Japan
| | - Chikara Masuta
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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5
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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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6
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Vogels C, Brackney D, Dupuis A, Robich R, Fauver J, Brito A, Williams S, Anderson J, Lubelczyk C, Lange R, Prusinski M, Kramer L, Gangloff-Kaufmann J, Goodman L, Baele G, Smith R, Armstrong P, Ciota A, Dellicour S, Grubaugh N. Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States. Proc Natl Acad Sci U S A 2023; 120:e2218012120. [PMID: 37040418 PMCID: PMC10120011 DOI: 10.1073/pnas.2218012120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/23/2023] [Indexed: 04/12/2023] Open
Abstract
Powassan virus is an emerging tick-borne virus of concern for public health, but very little is known about its transmission patterns and ecology. Here, we expanded the genomic dataset by sequencing 279 Powassan viruses isolated from Ixodes scapularis ticks from the northeastern United States. Our phylogeographic reconstructions revealed that Powassan virus lineage II was likely introduced or emerged from a relict population in the Northeast between 1940 and 1975. Sequences strongly clustered by sampling location, suggesting a highly focal geographical distribution. Our analyses further indicated that Powassan virus lineage II emerged in the northeastern United States mostly following a south-to-north pattern, with a weighted lineage dispersal velocity of ~3 km/y. Since the emergence in the Northeast, we found an overall increase in the effective population size of Powassan virus lineage II, but with growth stagnating during recent years. The cascading effect of population expansion of white-tailed deer and I. scapularis populations likely facilitated the emergence of Powassan virus in the northeastern United States.
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Affiliation(s)
- Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510
| | - Doug E. Brackney
- Center for Vector Biology and Zoonotic Diseases, Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
| | - Alan P. Dupuis
- The Arbovirus Laboratory, New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY 12222
| | - Rebecca M. Robich
- Vector-borne Disease Laboratory, MaineHealth Institute for Research, Scarborough, ME 04074
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, NE 68198
| | - Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510
- Instituto Todos pela Saúde, São Paulo SP01310-942, Brazil
| | - Scott C. Williams
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
| | - John F. Anderson
- Center for Vector Biology and Zoonotic Diseases, Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
| | - Charles B. Lubelczyk
- Vector-borne Disease Laboratory, MaineHealth Institute for Research, Scarborough, ME 04074
| | - Rachel E. Lange
- The Arbovirus Laboratory, New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY 12222
| | - Melissa A. Prusinski
- New York State Department of Health, Bureau of Communicable Disease Control, Albany, NY 12237
| | - Laura D. Kramer
- The Arbovirus Laboratory, New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY 12222
| | | | - Laura B. Goodman
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY 14853
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven3000, Belgium
| | - Robert P. Smith
- Vector-borne Disease Laboratory, MaineHealth Institute for Research, Scarborough, ME 04074
| | - Philip M. Armstrong
- Center for Vector Biology and Zoonotic Diseases, Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
| | - Alexander T. Ciota
- The Arbovirus Laboratory, New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY 12222
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven3000, Belgium
- Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels1050, Belgium
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511
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7
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Dellicour S, Hong SL, Hill V, Dimartino D, Marier C, Zappile P, Harkins GW, Lemey P, Baele G, Duerr R, Heguy A. Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City - from Alpha to Omicron. PLoS Pathog 2023; 19:e1011348. [PMID: 37071654 PMCID: PMC10180688 DOI: 10.1371/journal.ppat.1011348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 05/12/2023] [Accepted: 04/09/2023] [Indexed: 04/19/2023] Open
Abstract
Since the latter part of 2020, SARS-CoV-2 evolution has been characterised by the emergence of viral variants associated with distinct biological characteristics. While the main research focus has centred on the ability of new variants to increase in frequency and impact the effective reproductive number of the virus, less attention has been placed on their relative ability to establish transmission chains and to spread through a geographic area. Here, we describe a phylogeographic approach to estimate and compare the introduction and dispersal dynamics of the main SARS-CoV-2 variants - Alpha, Iota, Delta, and Omicron - that circulated in the New York City area between 2020 and 2022. Notably, our results indicate that Delta had a lower ability to establish sustained transmission chains in the NYC area and that Omicron (BA.1) was the variant fastest to disseminate across the study area. The analytical approach presented here complements non-spatially-explicit analytical approaches that seek a better understanding of the epidemiological differences that exist among successive SARS-CoV-2 variants of concern.
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Affiliation(s)
- Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Dacia Dimartino
- Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America
| | - Christian Marier
- Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America
| | - Paul Zappile
- Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America
| | - Gordon W. Harkins
- South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, United States of America
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, United States of America
- Vaccine Center, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Adriana Heguy
- Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America
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8
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Avila-Rios S, García-Morales C, Reyes-Terán G, González-Rodríguez A, Matías-Florentino M, Mehta SR, Chaillon A. Phylodynamics of HIV in the Mexico City Metropolitan Region. J Virol 2022; 96:e0070822. [PMID: 35762759 PMCID: PMC9327710 DOI: 10.1128/jvi.00708-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/06/2022] [Indexed: 12/30/2022] Open
Abstract
Evolutionary analyses of viral sequences can provide insights into transmission dynamics, which in turn can optimize prevention interventions. Here, we characterized the dynamics of HIV transmission within the Mexico City metropolitan area. HIV pol sequences from persons recently diagnosed at the largest HIV clinic in Mexico City (between 2016 and 2021) were annotated with demographic/geographic metadata. A multistep phylogenetic approach was applied to identify putative transmission clades. A data set of publicly available sequences was used to assess international introductions. Clades were analyzed with a discrete phylogeographic model to evaluate the timing and intensity of HIV introductions and transmission dynamics among municipalities in the region. A total of 6,802 sequences across 96 municipalities (5,192 from Mexico City and 1,610 from the neighboring State of Mexico) were included (93.6% cisgender men, 5.0% cisgender women, and 1.3% transgender women); 3,971 of these sequences formed 1,206 clusters, involving 78 municipalities, including 89 clusters of ≥10 sequences. Discrete phylogeographic analysis revealed (i) 1,032 viral introductions into the region, over one-half of which were from the United States, and (ii) 354 migration events between municipalities with high support (adjusted Bayes factor of ≥3). The most frequent viral migrations occurred between northern municipalities within Mexico City, i.e., Cuauhtémoc to Iztapalapa (5.2% of events), Iztapalapa to Gustavo A. Madero (5.4%), and Gustavo A. Madero to Cuauhtémoc (6.5%). Our analysis illustrates the complexity of HIV transmission within the Mexico City metropolitan area but also identifies a spatially active transmission area involving a few municipalities in the north of the city, where targeted interventions could have a more pronounced effect on the entire regional epidemic. IMPORTANCE Phylogeographic investigation of the Mexico City HIV epidemic illustrates the complexity of HIV transmission in the region. An active transmission area involving a few municipalities in the north of the city, with transmission links throughout the region, is identified and could be a location where targeted interventions could have a more pronounced effect on the entire regional epidemic, compared with those dispersed in other manners.
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Affiliation(s)
- Santiago Avila-Rios
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Claudia García-Morales
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Coordinating Commission of the National Institutes of Health and High Specialty Hospitals, Ministry of Health, Mexico City, Mexico
| | | | | | - Sanjay R. Mehta
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, California, USA
- Veterans Affairs Health System, San Diego, California, USA
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, California, USA
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9
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Dellicour S, Lemey P, Suchard MA, Gilbert M, Baele G. Accommodating sampling location uncertainty in continuous phylogeography. Virus Evol 2022; 8:veac041. [PMID: 35795297 PMCID: PMC9248920 DOI: 10.1093/ve/veac041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/22/2022] [Accepted: 05/18/2022] [Indexed: 02/01/2023] Open
Abstract
Phylogeographic inference of the dispersal history of viral lineages offers key opportunities to tackle epidemiological questions about the spread of fast-evolving pathogens across human, animal and plant populations. In continuous space, i.e. when locations are specified by longitude and latitude, these reconstructions are however often limited by the availability or accessibility of precise sampling locations required for such spatially explicit analyses. We here review the different approaches that can be considered when genomic sequences are associated with a geographic area of sampling instead of precise coordinates. In particular, we describe and compare the approaches to define homogeneous and heterogeneous prior ranges of sampling coordinates.
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Affiliation(s)
| | | | | | - Marius Gilbert
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, Bruxelles 1050, Belgium
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Trovão NS, Thijssen M, Vrancken B, Pineda-Peña AC, Mina T, Amini-Bavil-Olyaee S, Lemey P, Baele G, Pourkarim MR. Reconstruction of the Origin and Dispersal of the Worldwide Dominant Hepatitis B Virus Subgenotype D1. Virus Evol 2022; 8:veac028. [PMID: 35712523 PMCID: PMC9194798 DOI: 10.1093/ve/veac028] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/18/2022] [Accepted: 04/07/2022] [Indexed: 12/01/2022] Open
Abstract
Hepatitis B is a potentially life-threatening liver infection caused by the hepatitis B virus (HBV). HBV-D1 is the dominant subgenotype in the Mediterranean basin, Eastern Europe, and Asia. However, little is currently known about its evolutionary history and spatio-temporal dynamics. We use Bayesian phylodynamic inference to investigate the temporal history of HBV-D1, for which we calibrate the molecular clock using ancient sequences, and reconstruct the viral global spatial dynamics based, for the first time, on full-length publicly available HBV-D1 genomes from a wide range of sampling dates. We pinpoint the origin of HBV subgenotype D1 before the current era (BCE) in Turkey/Anatolia. The spatial reconstructions reveal global viral transmission with a high degree of mixing. By combining modern-day and ancient sequences, we ensure sufficient temporal signal in HBV-D1 data to enable Bayesian phylodynamic inference using a molecular clock for time calibration. Our results shed light on the worldwide HBV-D1 epidemics and suggest that this originally Middle Eastern virus significantly affects more distant countries, such as those in mainland Europe.
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Affiliation(s)
- Nídia Sequeira Trovão
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium, Herestraat 49, BE-3000 Leuven, Belgium
| | - Marijn Thijssen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium, Herestraat 49, BE-3000 Leuven, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium, Herestraat 49, BE-3000 Leuven, Belgium
| | - Andrea-Clemencia Pineda-Peña
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT; Universidade Nova de Lisboa, UNL, Lisbon, Portugal Rua da Junqueira No 100, 1349-008, Lisbon, Portugal
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC); Faculty of Animal Science, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Avenida 50 No. 26-20 Bogotá, Colombia
| | - Thomas Mina
- Mina Clinical Laboratory, Gregori Afxentiou, Iocasti Court Block A, Flat 22 Mesa Yitonia, 4003 Lemesos, Cyprus
| | - Samad Amini-Bavil-Olyaee
- Biosafety Development Group, Cellular Sciences Department, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium, Herestraat 49, BE-3000 Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium, Herestraat 49, BE-3000 Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium, Herestraat 49, BE-3000 Leuven, Belgium
- Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Hemmat Exp. Way, 14665-1157, Tehran, Iran
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11
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Morais P, Trovão N, Abecasis A, Parreira R. Insect-specific viruses in the Parvoviridae family: genetic lineage characterization and spatiotemporal dynamics of the recently established Brevihamaparvovirus genus. Virus Res 2022; 313:198728. [DOI: 10.1016/j.virusres.2022.198728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
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12
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Barro M, Kassankogno AI, Wonni I, Sérémé D, Somda I, Kaboré HK, Béna G, Brugidou C, Tharreau D, Tollenaere C. Spatiotemporal Survey of Multiple Rice Diseases in Irrigated Areas Compared to Rainfed Lowlands in the Western Burkina Faso. PLANT DISEASE 2021; 105:3889-3899. [PMID: 34142847 DOI: 10.1094/pdis-03-21-0579-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Multiple constraints affect rice yields in West Africa. Among these constraints are viral, bacterial, and fungal pathogens. We aimed to describe the spatiotemporal patterns of occurrence and incidence of multiple rice diseases in farmers' fields in contrasting rice growing systems in the western Burkina Faso. For this purpose, we selected a set of three pairs of sites, each comprising an irrigated area and a neighboring rainfed lowland, and studied them over four consecutive years. We first performed interviews with the rice farmers to better characterize the management practices at the different sites. This study revealed that the transplanting of rice and the possibility of growing rice twice a year are restricted to irrigated areas, while other practices, such as the use of registered rice cultivars, fertilization, and pesticides, are not specific but differ between the two rice growing systems. Then, we performed symptom observations at these study sites to monitor the following four diseases: yellow mottle disease, Bacterial Leaf Streak (BLS), rice leaf blast, and brown spot. The infection rates were found to be higher in irrigated areas than in rainfed lowlands, both when analyzing all observed symptoms together (any of the four diseases) and when specifically considering each of the two diseases: BLS and rice leaf blast. Brown spot was particularly prevalent in all six study sites, while yellow mottle disease was particularly structured geographically. Various diseases were frequently found together in the same field (co-occurrence) or even on the same plant (coinfection), especially in irrigated areas.
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Affiliation(s)
- Mariam Barro
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
- Université Nazi Boni, Institut du Développement Rural, Laboratoire des Systèmes Naturels, Agrosystèmes et Ingénierie de l'Environnement (SyNAIE), Bobo-Dioulasso, Burkina Faso
| | - Abalo Itolou Kassankogno
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Issa Wonni
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Drissa Sérémé
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Irénée Somda
- Université Nazi Boni, Institut du Développement Rural, Laboratoire des Systèmes Naturels, Agrosystèmes et Ingénierie de l'Environnement (SyNAIE), Bobo-Dioulasso, Burkina Faso
| | - Hilaire Kouka Kaboré
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR PHIM, 34390 Montpellier, France
| | - Gilles Béna
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Christophe Brugidou
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Didier Tharreau
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR PHIM, 34390 Montpellier, France
| | - Charlotte Tollenaere
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
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13
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Iannella M, De Simone W, D'Alessandro P, Biondi M. Climate change favours connectivity between virus-bearing pest and rice cultivations in sub-Saharan Africa, depressing local economies. PeerJ 2021; 9:e12387. [PMID: 34820174 PMCID: PMC8607929 DOI: 10.7717/peerj.12387] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/04/2021] [Indexed: 12/18/2022] Open
Abstract
Aims Rice is a staple food for many countries, being fundamental for a large part of the worlds’ population. In sub-Saharan Africa, its importance is currently high and is likely to become even more relevant, considering that the number of people and the per-capita consumption are both predicted to increase. The flea beetles belonging to the Chaetocnema pulla species group (pulla group), a harmful rice pest, are an important vector of the Rice Yellow Mottle Virus, a disease which leads even to 80–100% yield losses in rice production. We present a continental-scale study aiming at: (1) locating current and future suitable territories for both pulla group and rice; (2) identifying areas where rice cultivations may occur without suffering the presence of pulla group using an Ecological Niche Modelling (ENM) approach; (3) estimating current and future connectivity among pulla group populations and areas predicted to host rice cultivations, based on the most recent land-use estimates for future agricultural trends; (4) proposing a new connectivity index called “Pest Aggression Index” (PAI) to measure the agricultural susceptibility to the potential future invasions of pests and disease; (5) quantifying losses in terms of production when rice cultivations co‐occur with the pulla group and identifying the SSA countries which, in the future inferred scenarios, will potentially suffer the greatest losses. Location Sub-Saharan Africa. Methods Since the ongoing climate and land-use changes affect species’ distributions, we first assess the impact of these changes through a spatially-jackknifed Maxent-based Ecological Niche Modelling in GIS environment, for both the pulla group and rice, in two climatic/socioeconomic future scenarios (SSP_2.45 and 3.70). We then assess the connectivity potential of the pulla group populations towards rice cultivations, for both current and future predictions, through a circuit theory-based approach (Circuitscape implemented in Julia language). We finally measure the rice production and GPD loss per country through the spatial index named “Pest Aggression Index”, based on the inferred connectivity magnitude. Results The most considerable losses in rice production are observed for Liberia, Sierra Leone and Madagascar in all future scenarios (2030, 2050, 2070). The future economic cost, calculated as USD lost from rice losses/country’s GDP results are high for Central African Republic (−0.6% in SSP_2.45 and −3.0% in SSP_3.70) and Guinea–Bissau (−0.4% in SSP_2.45 and −0.68% in SSP_3.70), with relevant losses also obtained for other countries. Main conclusions Since our results are spatially explicit and focused on each country, we encourage careful land-use planning. Our findings could support best practices to avoid the future settlement of new cultivations in territories where rice would be attacked by pulla group and the virus, bringing economic and biodiversity losses.
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Affiliation(s)
- Mattia Iannella
- Department of Life, Health & Environmental Sciences, University of L'Aquila, L'Aquila, Abruzzo, Italy
| | - Walter De Simone
- Department of Life, Health & Environmental Sciences, University of L'Aquila, L'Aquila, Abruzzo, Italy
| | - Paola D'Alessandro
- Department of Life, Health & Environmental Sciences, University of L'Aquila, L'Aquila, Abruzzo, Italy
| | - Maurizio Biondi
- Department of Life, Health & Environmental Sciences, University of L'Aquila, L'Aquila, Abruzzo, Italy
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Rieux A, Campos P, Duvermy A, Scussel S, Martin D, Gaudeul M, Lefeuvre P, Becker N, Lett JM. Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history. Sci Rep 2021; 11:21280. [PMID: 34711837 PMCID: PMC8553777 DOI: 10.1038/s41598-021-00518-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022] Open
Abstract
Emerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient genomics, it is now possible to sequence historical genomes to provide a better understanding of viral plant disease emergence and pathogen evolutionary history. In this context, herbarium specimens represent a valuable source of dated and preserved material. We report here the first historical genome of a crop pathogen DNA virus, a 90-year-old African cassava mosaic virus (ACMV), reconstructed from small RNA sequences bearing hallmarks of small interfering RNAs. Relative to tip-calibrated dating inferences using only modern data, those performed with the historical genome yielded both molecular evolution rate estimates that were significantly lower, and lineage divergence times that were significantly older. Crucially, divergence times estimated without the historical genome appeared in discordance with both historical disease reports and the existence of the historical genome itself. In conclusion, our study reports an updated time-frame for the history and evolution of ACMV and illustrates how the study of crop viral diseases could benefit from natural history collections.
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Affiliation(s)
- Adrien Rieux
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France.
| | - Paola Campos
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
| | | | - Sarah Scussel
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
| | - Darren Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
- Herbier national (P), Muséum national d'Histoire Naturelle, CP39, 57 Rue Cuvier, 75005, Paris, France
| | | | - Nathalie Becker
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
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15
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Chevenet F, Fargette D, Guindon S, Bañuls AL. EvoLaps: a web interface to visualize continuous phylogeographic reconstructions. BMC Bioinformatics 2021; 22:463. [PMID: 34579644 PMCID: PMC8474961 DOI: 10.1186/s12859-021-04386-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/20/2021] [Indexed: 10/25/2022] Open
Abstract
BACKGROUND Phylogeographic reconstructions serve as a basis to understand the spread and evolution of pathogens. Visualization of these reconstructions often lead to complex graphical representations which are difficult to interpret. RESULT We present EvoLaps, a user-friendly web interface to visualize phylogeographic reconstructions based on the analysis of latitude/longitude coordinates with various clustering levels. EvoLaps also produces transition diagrams that provide concise and easy to interpret summaries of phylogeographic reconstructions. CONCLUSION The main contribution of EvoLaps is to assemble known numerical and graphical methods/tools into a user-friendly interface dedicated to the visualization and edition of evolutionary scenarios based on continuous phylogeographic reconstructions. EvoLaps is freely usable at www.evolaps.org .
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Affiliation(s)
- François Chevenet
- MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France. .,LIRMM, CNRS, Université de Montpellier, Montpellier, France.
| | - Denis Fargette
- IPME, IRD, CIRAD, Université de Montpellier, Montpellier, France
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16
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Issaka S, Traoré O, Longué RDS, Pinel-Galzi A, Gill MS, Dellicour S, Bastide P, Guindon S, Hébrard E, Dugué MJ, Séré Y, Semballa S, Aké S, Lemey P, Fargette D. Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley. Virus Evol 2021; 7:veab072. [PMID: 36819970 PMCID: PMC9927878 DOI: 10.1093/ve/veab072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/08/2021] [Accepted: 08/16/2021] [Indexed: 11/14/2022] Open
Abstract
To investigate the spread of Rice yellow mottle virus (RYMV) along the Niger River, regular sampling of virus isolates was conducted along 500 km of the Niger Valley in the Republic of Niger and was complemented by additional sampling in neighbouring countries in West Africa and Central Africa. The spread of RYMV into and within the Republic of Niger was inferred as a continuous process using a Bayesian statistical framework applied previously to reconstruct its dispersal history in West Africa, East Africa, and Madagascar. The spatial resolution along this section of the Niger River was the highest implemented for RYMV and possibly for any plant virus. We benefited from the results of early field surveys of the disease for the validation of the phylogeographic reconstruction and from the well-documented history of rice cultivation changes along the Niger River for their interpretation. As a prerequisite, the temporal signal of the RYMV data sets was revisited in the light of recent methodological advances. The role of the hydrographic network of the Niger Basin in RYMV spread was examined, and the link between virus population dynamics and the extent of irrigated rice was assessed. RYMV was introduced along the Niger River in the Republic of Niger in the early 1980s from areas to the southwest of the country where rice was increasingly grown. Viral spread was triggered by a major irrigation scheme made of a set of rice perimeters along the river valley. The subsequent spatial and temporal host continuity and the inoculum build-up allowed for a rapid spread of RYMV along the Niger River, upstream and downstream, over hundreds of kilometres, and led to the development of severe epidemics. There was no evidence of long-distance dissemination of the virus through natural water. Floating rice in the main meanders of the Middle Niger did not contribute to virus dispersal from West Africa to Central Africa. RYMV along the Niger River is an insightful example of how agricultural intensification favours pathogen emergence and spread.
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Affiliation(s)
| | - Oumar Traoré
- Laboratoire de Virologie et de Biotechnologie Végétale (LVBV), Laboratoire National de Biosécurité, Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou 01 BP 476, Burkina Faso
| | - Régis Dimitri Skopé Longué
- Laboratoire des Sciences Biologiques et Agronomiques pour le Développement (LaSBAD), Département des Sciences de la Vie, Université de Bangui, Bangui BP 908, République Centrafricaine
| | - Agnès Pinel-Galzi
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro., Montpellier cedex 5 BP 64501 34394, France
| | - Mandev S Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, Leuven 3000, Belgium,Spatial Epidemiology Lab. (SpELL), Université Libre de Bruxelles, CP160/12, 50, av. FD Roosevelt, Bruxelles 1050, Belgium
| | - Paul Bastide
- IMAG – UMR 5149, Université de Montpellier, Case courrier 051, Place Eugène Bataillon, Montpellier 34090, France
| | - Stéphane Guindon
- Department of Computer Science, LIRMM, CNRS and Université de Montpellier, Montpellier, France
| | - Eugénie Hébrard
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro., Montpellier cedex 5 BP 64501 34394, France
| | - Marie-Jo Dugué
- Agronomy and Farming Systems, 3 avenue des Cistes, Saint Mathieu de Tréviers 34270, France
| | - Yacouba Séré
- Agricultural Research and Development, Bobo-Dioulasso BP 1324, Burkina Faso
| | - Silla Semballa
- Laboratoire des Sciences Biologiques et Agronomiques pour le Développement (LaSBAD), Département des Sciences de la Vie, Université de Bangui, Bangui BP 908, République Centrafricaine
| | - Séverin Aké
- UFR Biosciences, Laboratoire de Physiologie Végétale, Université Félix Houphouët-Boigny, Abidjan 22 BP 582, Côte d’Ivoire
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Kinship networks of seed exchange shape spatial patterns of plant virus diversity. Nat Commun 2021; 12:4505. [PMID: 34301941 PMCID: PMC8302746 DOI: 10.1038/s41467-021-24720-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 06/28/2021] [Indexed: 12/02/2022] Open
Abstract
By structuring farmers’ informal networks of seed exchange, kinship systems play a key role in the dynamics of crop genetic diversity in smallholder farming systems. However, because many crop diseases are propagated through infected germplasm, local seed systems can also facilitate the dissemination of seedborne pathogens. Here, we investigate how the interplay of kinship systems and local networks of germplasm exchange influences the metapopulation dynamics of viruses responsible for the cassava mosaic disease (CMD), a major threat to food security in Africa. Combining anthropological, genetic and plant epidemiological data, we analyzed the genetic structure of local populations of the African cassava mosaic virus (ACMV), one of the main causal agents of CMD. Results reveal contrasted patterns of viral diversity in patrilineal and matrilineal communities, consistent with local modes of seed exchange. Our results demonstrate that plant virus ecosystems have also a cultural component and that social factors that shape regional seed exchange networks influence the genetic structure of plant virus populations. This study combines ethnobotanical and epidemiological data to understand how social networks of seed exchange influence the genetic structure of the African cassava mosaic virus in Gabon. Results reveal contrasted patterns of viral diversity in patrilineal and matrilineal communities, consistent with cultural differences in modes of seed exchange.
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18
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Morais P, Trovão NS, Abecasis AB, Parreira R. Genetic lineage characterization and spatiotemporal dynamics of classical insect-specific flaviviruses: outcomes and limitations. Virus Res 2021; 303:198507. [PMID: 34271039 DOI: 10.1016/j.virusres.2021.198507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022]
Abstract
The genus Flavivirus incorporates bona fide arboviruses, as well as others viruses with restricted replication in insect cells. Among the latter, a large monophyletic cluster of viruses, known as cISF (classical insect-specific flaviviruses), has been sampled in many species of mosquitoes collected over a large geographic range. In this study, we investigated nucleotide and protein sequences with a suite of molecular characterization approaches including genetic distance, Shannon entropy, selective pressure analysis, polymorphism identification, principal coordinate analysis, likelihood mapping, phylodynamic reconstruction, and spatiotemporal dispersal, to further characterize this diverse group of insect-viruses. The different lineages and sub-lineages of viral sequences presented low sequence diversity and entropy (though some displayed lineage-specific polymorphisms), did not show evidence of frequent recombination and evolved under strong purifying selection. Moreover, the reconstruction of the evolutionary history and spatiotemporal dispersal was highly impacted by overall low signals of sequence divergence throughout time but suggested that cISF distribution in space and time is dynamic and may be dependent on human activities, including commercial trading and traveling.
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Affiliation(s)
- Paulo Morais
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (NOVA), Lisboa, Portugal/Global Health and Tropical Medicine (GHTM), Lisboa, Portugal
| | - Nídia S Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Ana B Abecasis
- Unidade de Saúde Pública Internacional e Bioestatística, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (NOVA), Lisboa, Portugal/Global Health and Tropical Medicine (GHTM), Lisboa, Portugal
| | - Ricardo Parreira
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (NOVA), Lisboa, Portugal/Global Health and Tropical Medicine (GHTM), Lisboa, Portugal.
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19
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Odongo PJ, Onaga G, Ricardo O, Natsuaki KT, Alicai T, Geuten K. Insights Into Natural Genetic Resistance to Rice Yellow Mottle Virus and Implications on Breeding for Durable Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:671355. [PMID: 34267770 PMCID: PMC8276079 DOI: 10.3389/fpls.2021.671355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Abstract
Rice is the main food crop for people in low- and lower-middle-income countries in Asia and sub-Saharan Africa (SSA). Since 1982, there has been a significant increase in the demand for rice in SSA, and its growing importance is reflected in the national strategic food security plans of several countries in the region. However, several abiotic and biotic factors undermine efforts to meet this demand. Rice yellow mottle virus (RYMV) caused by Solemoviridae is a major biotic factor affecting rice production and continues to be an important pathogen in SSA. To date, six pathogenic strains have been reported. RYMV infects rice plants through wounds and rice feeding vectors. Once inside the plant cells, viral genome-linked protein is required to bind to the rice translation initiation factor [eIF(iso)4G1] for a compatible interaction. The development of resistant cultivars that can interrupt this interaction is the most effective method to manage this disease. Three resistance genes are recognized to limit RYMV virulence in rice, some of which have nonsynonymous single mutations or short deletions in the core domain of eIF(iso)4G1 that impair viral host interaction. However, deployment of these resistance genes using conventional methods has proved slow and tedious. Molecular approaches are expected to be an alternative to facilitate gene introgression and/or pyramiding and rapid deployment of these resistance genes into elite cultivars. In this review, we summarize the knowledge on molecular genetics of RYMV-rice interaction, with emphasis on host plant resistance. In addition, we provide strategies for sustainable utilization of the novel resistant sources. This knowledge is expected to guide breeding programs in the development and deployment of RYMV resistant rice varieties.
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Affiliation(s)
- Patrick J. Odongo
- Molecular Biotechnology of Plants and Micro-Organisms, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
| | - Geoffrey Onaga
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
- M’bé Research Station, Africa Rice Center (AfricaRice), Bouaké, Côte d’Ivoire
| | - Oliver Ricardo
- Breeding Innovations Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Keiko T. Natsuaki
- Graduate School of Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| | - Titus Alicai
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
| | - Koen Geuten
- Molecular Biotechnology of Plants and Micro-Organisms, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
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20
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Munsey A, Mwiine FN, Ochwo S, Velazquez-Salinas L, Ahmed Z, Maree F, Rodriguez LL, Rieder E, Perez A, Dellicour S, VanderWaal K. Phylogeographic analysis of foot-and-mouth disease virus serotype O dispersal and associated drivers in East Africa. Mol Ecol 2021; 30:3815-3825. [PMID: 34008868 DOI: 10.1111/mec.15991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023]
Abstract
The continued endemicity of foot and mouth disease virus (FMDV) in East Africa has significant implications for livestock production and poverty reduction, yet its complex epidemiology in endemic settings remains poorly understood. Identifying FMDV dispersal routes and drivers of transmission is key to improved control strategies. Environmental heterogeneity and anthropogenic drivers (e.g., demand for animal products) can impact viral spread by influencing host movements. Here, we utilized FMDV serotype O VP1 genetic sequences and corresponding spatiotemporal data in order to (i) infer the recent dispersal history, and (II) investigate the impact of external factors (cattle density, human population density, proximity to livestock markets, and drought) on dispersal velocity, location, and direction of FMDV serotype O in East Africa. We identified statistical evidence of long-distance transmission events, and we found that FMDV serotype O tends to remain circulating in areas of high cattle density, high human population density, and in close proximity to livestock markets. The latter two findings highlight the influence of anthropogenic factors on FMDV serotype O spread in this region. These findings contribute to the understanding of FMDV epidemiology in East Africa and can help guide improved control measures.
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Affiliation(s)
- Anna Munsey
- Veterinary Population Medicine Department, University of Minnesota College of Veterinary Medicine, St. Paul, MN, USA
| | - Frank Norbert Mwiine
- Makerere University College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Kampala, Uganda
| | - Sylvester Ochwo
- Makerere University College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Kampala, Uganda
| | - Lauro Velazquez-Salinas
- Veterinary Population Medicine Department, University of Minnesota College of Veterinary Medicine, St. Paul, MN, USA.,Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture, Greenport, NY, USA
| | - Zaheer Ahmed
- Animal and Plant Health Inspection Services (APHIS), National Veterinary Services Laboratories, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, United States Department of Agriculture, Greenport, NY, USA
| | - Francois Maree
- Onderstepoort Veterinary Institute, Pretoria, South Africa
| | - Luis L Rodriguez
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture, Greenport, NY, USA
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture, Greenport, NY, USA
| | - Andres Perez
- Veterinary Population Medicine Department, University of Minnesota College of Veterinary Medicine, St. Paul, MN, USA
| | - Simon Dellicour
- Spatial Epidemiology Laboratory (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium.,Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Kimberly VanderWaal
- Veterinary Population Medicine Department, University of Minnesota College of Veterinary Medicine, St. Paul, MN, USA
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21
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Dellicour S, Hong SL, Vrancken B, Chaillon A, Gill MS, Maurano MT, Ramaswami S, Zappile P, Marier C, Harkins GW, Baele G, Duerr R, Heguy A. Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City. PLoS Pathog 2021; 17:e1009571. [PMID: 34015049 PMCID: PMC8136714 DOI: 10.1371/journal.ppat.1009571] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
During the first phase of the COVID-19 epidemic, New York City rapidly became the epicenter of the pandemic in the United States. While molecular phylogenetic analyses have previously highlighted multiple introductions and a period of cryptic community transmission within New York City, little is known about the circulation of SARS-CoV-2 within and among its boroughs. We here perform phylogeographic investigations to gain insights into the circulation of viral lineages during the first months of the New York City outbreak. Our analyses describe the dispersal dynamics of viral lineages at the state and city levels, illustrating that peripheral samples likely correspond to distinct dispersal events originating from the main metropolitan city areas. In line with the high prevalence recorded in this area, our results highlight the relatively important role of the borough of Queens as a transmission hub associated with higher local circulation and dispersal of viral lineages toward the surrounding boroughs.
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Affiliation(s)
- Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California San Diego, California, United States of America
| | - Mandev S. Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Matthew T. Maurano
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Sitharam Ramaswami
- Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America
| | - Paul Zappile
- Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America
| | - Christian Marier
- Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America
| | - Gordon W. Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Ralf Duerr
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Adriana Heguy
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America
- Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America
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22
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Duchene S, Lemey P, Stadler T, Ho SYW, Duchene DA, Dhanasekaran V, Baele G. Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations. Mol Biol Evol 2021; 37:3363-3379. [PMID: 32895707 PMCID: PMC7454806 DOI: 10.1093/molbev/msaa163] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimation of evolutionary rates and timescales for rapidly evolving pathogens and data sets containing ancient DNA samples. A key aspect of such calibrations is whether a sufficient amount of molecular evolution has occurred over the sampling time window, that is, whether the data can be treated as having come from a measurably evolving population. Here, we investigate the performance of a fully Bayesian evaluation of temporal signal (BETS) in sequence data. The method involves comparing the fit to the data of two models: a model in which the data are accompanied by the actual (heterochronous) sampling times, and a model in which the samples are constrained to be contemporaneous (isochronous). We conducted simulations under a wide range of conditions to demonstrate that BETS accurately classifies data sets according to whether they contain temporal signal or not, even when there is substantial among-lineage rate variation. We explore the behavior of this classification in analyses of five empirical data sets: modern samples of A/H1N1 influenza virus, the bacterium Bordetella pertussis, coronaviruses from mammalian hosts, ancient DNA from Hepatitis B virus, and mitochondrial genomes of dog species. Our results indicate that BETS is an effective alternative to other tests of temporal signal. In particular, this method has the key advantage of allowing a coherent assessment of the entire model, including the molecular clock and tree prior which are essential aspects of Bayesian phylodynamic analyses.
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Affiliation(s)
- Sebastian Duchene
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland
| | - Simon Y W Ho
- Swiss Institute of Bioinformatics, Basel, Switzerland.,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - David A Duchene
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Vijaykrishna Dhanasekaran
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
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23
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Abstract
The conservation field is experiencing a rapid increase in the amount, variety, and quality of spatial data that can help us understand species movement and landscape connectivity patterns. As interest grows in more dynamic representations of movement potential, modelers are often limited by the capacity of their analytic tools to handle these datasets. Technology developments in software and high-performance computing are rapidly emerging in many fields, but uptake within conservation may lag, as our tools or our choice of computing language can constrain our ability to keep pace. We recently updated Circuitscape, a widely used connectivity analysis tool developed by Brad McRae and Viral Shah, by implementing it in Julia, a high-performance computing language. In this initial re-code (Circuitscape 5.0) and later updates, we improved computational efficiency and parallelism, achieving major speed improvements, and enabling assessments across larger extents or with higher resolution data. Here, we reflect on the benefits to conservation of strengthening collaborations with computer scientists, and extract examples from a collection of 572 Circuitscape applications to illustrate how through a decade of repeated investment in the software, applications have been many, varied, and increasingly dynamic. Beyond empowering continued innovations in dynamic connectivity, we expect that faster run times will play an important role in facilitating co-production of connectivity assessments with stakeholders, increasing the likelihood that connectivity science will be incorporated in land use decisions.
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24
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Rasmussen DA, Grünwald NJ. Phylogeographic Approaches to Characterize the Emergence of Plant Pathogens. PHYTOPATHOLOGY 2021; 111:68-77. [PMID: 33021879 DOI: 10.1094/phyto-07-20-0319-fi] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phylogeography combines geographic information with phylogenetic and population genomic approaches to infer the evolutionary history of a species or population in a geographic context. This approach has been instrumental in understanding the emergence, spread, and evolution of a range of plant pathogens. In particular, phylogeography can address questions about where a pathogen originated, whether it is native or introduced, and when and how often introductions occurred. We review the theory, methods, and approaches underpinning phylogeographic inference and highlight applications providing novel insights into the emergence and spread of select pathogens. We hope that this review will be useful in assessing the power, pitfalls, and opportunities presented by various phylogeographic approaches.
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Affiliation(s)
- David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC
| | - Niklaus J Grünwald
- Horticultural Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR
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25
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Han Z, Song Y, Xiao J, Jiang L, Huang W, Wei H, Li J, Zeng H, Yu Q, Li J, Yu D, Zhang Y, Li C, Zhan Z, Shi Y, Xiong Y, Wang X, Ji T, Yang Q, Zhu S, Yan D, Xu W, Zhang Y. Genomic epidemiology of coxsackievirus A16 in mainland of China, 2000-18. Virus Evol 2020; 6:veaa084. [PMID: 33343924 PMCID: PMC7733612 DOI: 10.1093/ve/veaa084] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hand, foot, and mouth disease (HFMD), which is a frequently reported and concerning disease worldwide, is a severe burden on societies globally, especially in the countries of East and Southeast Asia. Coxsackievirus A16 (CV-A16) is one of the most important causes of HFMD and a severe threat to human health, especially in children under 5 years of age. To investigate the epidemiological characteristics, spread dynamics, recombinant forms (RFs), and other features of CV-A16, we leveraged the continuous surveillance data of CV-A16-related HFMD cases collected over an 18-year period. With the advent of the EV-A71 vaccine since 2016, which targeted the EV-A71-related HFMD cases, EV-A71-related HFMD cases decreased dramatically, whereas the CV-A16-related HFMD cases showed an upward trend from 2017 to October 2019. The CV-A16 strains observed in this study were genetically related and widely distributed in the mainland of China. Our results show that three clusters (B1a-B1c) existed in the mainland of China and that the cluster of B1b dominates the diffusion of CV-A16 in China. We found that eastern China played a decisive role in seeding the diffusion of CV-A16 in China, with a more complex and variant transmission trend. Although EV-A71 vaccine was launched in China in 2016, it did not affect the genetic diversity of CV-A16, and its genetic diversity did not decline, which confirmed the epidemiological surveillance trend of CV-A16. Two discontinuous clusters (2000-13 and 2014-18) were observed in the full-length genome and arranged along the time gradient, which revealed the reason why the relative genetic diversity of CV-A16 increased and experienced more complex fluctuation model after 2014. In addition, the switch from RFs B (RF-B) and RF-C co-circulation to RF-D contributes to the prevalence of B1b cluster in China after 2008. The correlation between genotype and RFs partially explained the current prevalence of B1b. This study provides unprecedented full-length genomic sequences of CV-A16 in China, with a wider geographic distribution and a long-term time scale. The study presents valuable information about CV-A16, aimed at developing effective control strategies, as well as a call for a more robust surveillance system, especially in the Asia-Pacific region.
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Affiliation(s)
- Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Lili Jiang
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Wei Huang
- Chongqing Center for Disease Control and Prevention, Chongqing City, People's Republic of China
| | - Haiyan Wei
- Henan Center for Disease Control and Prevention, Zhengzhou, Henan Province, People's Republic of China
| | - Jie Li
- Beijing Center for Disease Control and Prevention, Beijing City, People's Republic of China
| | - Hanri Zeng
- Guangdong Center for Disease Control and Prevention, Guangzhou, Guangdong Province, People's Republic of China
| | - Qiuli Yu
- Hebei Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, People's Republic of China
| | - Jiameng Li
- Tianjin Center for Disease Control and Prevention, Tianjin City, People's Republic of China
| | - Deshan Yu
- Gansu Center for Disease Control and Prevention, Lanzhou, Gansu Province, People's Republic of China
| | - Yanjun Zhang
- Zhejiang Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, People's Republic of China
| | - Chonghai Li
- Qinghai Center for Disease Control and Prevention, Xining, Qinghai Province, People's Republic of China
| | - Zhifei Zhan
- Hunan Center for Disease Control and Prevention, Changsha, Hunan Province, People's Republic of China
| | - Yonglin Shi
- Anhui Center for Disease Control and Prevention, Hefei, Anhui Province, People's Republic of China
| | - Ying Xiong
- Jiangxi Center for Disease Control and Prevention, Nanchang, Jiangxi Province, People's Republic of China
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, People's Republic of China
| | - Tianjiao Ji
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei Province, People's Republic of China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei Province, People's Republic of China
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26
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Vrancken B, Zhao B, Li X, Han X, Liu H, Zhao J, Zhong P, Lin Y, Zai J, Liu M, Smith DM, Dellicour S, Chaillon A. Comparative Circulation Dynamics of the Five Main HIV Types in China. J Virol 2020; 94:e00683-20. [PMID: 32938762 PMCID: PMC7654276 DOI: 10.1128/jvi.00683-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/02/2020] [Indexed: 01/17/2023] Open
Abstract
The HIV epidemic in China accounts for 3% of the global HIV incidence. We compared the patterns and determinants of interprovincial spread of the five most prevalent circulating types. HIV pol sequences sampled across China were used to identify relevant transmission networks of the five most relevant HIV-1 types (B and circulating recombinant forms [CRFs] CRF01_AE, CRF07_BC, CRF08_BC, and CRF55_01B) in China. From these, the dispersal history across provinces was inferred. A generalized linear model (GLM) was used to test the association between migration rates among provinces and several measures of human mobility. A total of 10,707 sequences were collected between 2004 and 2017 across 26 provinces, among which 1,962 are newly reported here. A mean of 18 (minimum and maximum, 1 and 54) independent transmission networks involving up to 17 provinces were identified. Discrete phylogeographic analysis largely recapitulates the documented spread of the HIV types, which in turn, mirrors within-China population migration flows to a large extent. In line with the different spatiotemporal spread dynamics, the identified drivers thereof were also heterogeneous but are consistent with a central role of human mobility. The comparative analysis of the dispersal dynamics of the five main HIV types circulating in China suggests a key role of large population centers and developed transportation infrastructures as hubs of HIV dispersal. This advocates for coordinated public health efforts in addition to local targeted interventions.IMPORTANCE While traditional epidemiological studies are of great interest in describing the dynamics of epidemics, they struggle to fully capture the geospatial dynamics and factors driving the dispersal of pathogens like HIV as they have difficulties capturing linkages between infections. To overcome this, we used a discrete phylogeographic approach coupled to a generalized linear model extension to characterize the dynamics and drivers of the across-province spread of the five main HIV types circulating in China. Our results indicate that large urbanized areas with dense populations and developed transportation infrastructures are facilitators of HIV dispersal throughout China and highlight the need to consider harmonized country-wide public policies to control local HIV epidemics.
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Affiliation(s)
- Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Leuven, Belgium
| | - Bin Zhao
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xingguang Li
- Department of Hospital Office, The First People's Hospital of Fangchenggang, Fangchenggang, China
| | - Xiaoxu Han
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Haizhou Liu
- Centre for Emerging Infectious Diseases, The State Key Laboratory of Virology, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Yi Lin
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Junjie Zai
- Immunology innovation Team, School of Medicine, Ningbo University, Ningbo, Zhejiang China
| | - Mingchen Liu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Davey M Smith
- Division of Infectious Diseases and Global Public Health, University of California San Diego, California, USA
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California San Diego, California, USA
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27
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Boni MF, Lemey P, Jiang X, Lam TTY, Perry BW, Castoe TA, Rambaut A, Robertson DL. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol 2020; 5:1408-1417. [PMID: 32724171 DOI: 10.1101/2020.03.30.015008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/10/2020] [Indexed: 05/22/2023]
Abstract
There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination and its time of divergence from animal viruses. We find that the sarbecoviruses-the viral subgenus containing SARS-CoV and SARS-CoV-2-undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor-binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses and not one acquired recently via recombination. To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were shown to be consistent for these three approaches and for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% highest posterior density (HPD): 1879-1999), 1969 (95% HPD: 1930-2000) and 1982 (95% HPD: 1948-2009), indicating that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades.
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Affiliation(s)
- Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Leuven, Belgium.
| | - Xiaowei Jiang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Blair W Perry
- Department of Biology, University of Texas Arlington, Arlington, TX, USA
| | - Todd A Castoe
- Department of Biology, University of Texas Arlington, Arlington, TX, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
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28
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Baele G, Gill MS, Lemey P, Suchard MA. Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework. Wellcome Open Res 2020; 5:53. [PMID: 32923688 PMCID: PMC7463299 DOI: 10.12688/wellcomeopenres.15770.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 11/20/2022] Open
Abstract
Nonparametric coalescent-based models are often employed to infer past population dynamics over time. Several of these models, such as the skyride and skygrid models, are equipped with a block-updating Markov chain Monte Carlo sampling scheme to efficiently estimate model parameters. The advent of powerful computational hardware along with the use of high-performance libraries for statistical phylogenetics has, however, made the development of alternative estimation methods feasible. We here present the implementation and performance assessment of a Hamiltonian Monte Carlo gradient-based sampler to infer the parameters of the skygrid model. The skygrid is a popular and flexible coalescent-based model for estimating population dynamics over time and is available in BEAST 1.10.5, a widely-used software package for Bayesian pylogenetic and phylodynamic analysis. Taking into account the increased computational cost of gradient evaluation, we report substantial increases in effective sample size per time unit compared to the established block-updating sampler. We expect gradient-based samplers to assume an increasingly important role for different classes of parameters typically estimated in Bayesian phylogenetic and phylodynamic analyses.
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Affiliation(s)
- Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Mandev S Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Marc A Suchard
- Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, 695 Charles E. Young Drive, Los Angeles, California, 90095-1766, USA
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Boni MF, Lemey P, Jiang X, Lam TTY, Perry BW, Castoe TA, Rambaut A, Robertson DL. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol 2020; 5:1408-1417. [DOI: 10.1038/s41564-020-0771-4] [Citation(s) in RCA: 568] [Impact Index Per Article: 142.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023]
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Pidon H, Chéron S, Ghesquière A, Albar L. Allele mining unlocks the identification of RYMV resistance genes and alleles in African cultivated rice. BMC PLANT BIOLOGY 2020; 20:222. [PMID: 32429875 PMCID: PMC7236528 DOI: 10.1186/s12870-020-02433-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/07/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Rice yellow mottle virus (RYMV) is a major rice pathogen in Africa. Three resistance genes, i.e. RYMV1, RYMV2 and RYMV3, have been previously described. RYMV1 encodes the translation initiation factor eIF(iso)4G1 and the best candidate genes for RYMV2 and RYMV3 encode a homolog of an Arabidopsis nucleoporin (CPR5) and a nucleotide-binding domain and leucine-rich repeat containing domain (NLR) protein, respectively. High resistance is very uncommon in Asian cultivated rice (Oryza sativa), with only two highly resistant accessions identified so far, but it is more frequent in African cultivated rice (Oryza glaberrima). RESULTS Here we report the findings of a resistance survey in a reference collection of 268 O. glaberrima accessions. A total of 40 resistant accessions were found, thus confirming the high frequency of resistance to RYMV in this species. We analysed the variability of resistance genes or candidate genes in this collection based on high-depth Illumina data or Sanger sequencing. Alleles previously shown to be associated with resistance were observed in 31 resistant accessions but not in any susceptible ones. Five original alleles with a frameshift or untimely stop codon in the candidate gene for RYMV2 were also identified in resistant accessions. A genetic analysis revealed that these alleles, as well as T-DNA insertions in the candidate gene, were responsible of RYMV resistance. All 40 resistant accessions were ultimately linked to a validated or candidate resistance allele at one of the three resistance genes to RYMV. CONCLUSION This study demonstrated that the RYMV2 resistance gene is homologous to the Arabidopsis CPR5 gene and revealed five new resistance alleles at this locus. It also confirmed the close association between resistance and an amino-acid substitution in the leucine-rich repeat of the NLR candidate for RYMV3. We also provide an extensive overview of the genetic diversity of resistance to RYMV in the O. glaberrima species, while underlining the contrasted pattern of diversity between O. glaberrima and O. sativa for this trait. The different resistance genes and alleles will be instrumental in breeding varieties with sustainable field resistance to RYMV.
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Affiliation(s)
- Hélène Pidon
- DIADE, Univ. Montpellier, IRD, Montpellier, France
- Present Address: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
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Chaillon A, Gianella S, Dellicour S, Rawlings SA, Schlub TE, De Oliveira MF, Ignacio C, Porrachia M, Vrancken B, Smith DM. HIV persists throughout deep tissues with repopulation from multiple anatomical sources. J Clin Invest 2020; 130:1699-1712. [PMID: 31910162 PMCID: PMC7108926 DOI: 10.1172/jci134815] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/19/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUNDUnderstanding HIV dynamics across the human body is important for cure efforts. This goal has been hampered by technical difficulties and the challenge of obtaining fresh tissues.METHODSThis observational study evaluated 6 individuals with HIV (n = 4 with viral suppression using antiretroviral [ART] therapy; n = 2 with rebound viremia after stopping ART), who provided serial blood samples before death and their bodies for rapid autopsy. HIV reservoirs were characterized by digital droplet PCR, single-genome amplification, and sequencing of full-length (FL) envelope HIV. Phylogeographic methods were used to reconstruct HIV spread, and generalized linear models were tested for viral factors associated with dispersal.RESULTSAcross participants, HIV DNA levels varied from approximately 0 to 659 copies/106 cells (IQR: 22.9-126.5). A total of 605 intact FL env sequences were recovered in antemortem blood cells and across 28 tissues (IQR: 5-9). Sequence analysis showed (a) the emergence of large, identical, intact HIV RNA populations in blood after cessation of therapy, which repopulated tissues throughout the body; (b) that multiple sites acted as hubs for HIV dissemination but that blood and lymphoid tissues were the main source; (c) that viral exchanges occurred within brain areas and across the blood-brain barrier; and (d) that migration was associated with low HIV divergence between sites and greater diversity at the recipient site.CONCLUSIONHIV reservoirs persisted in all deep tissues, and blood was the main source of dispersal. This may explain why eliminating HIV susceptibility in circulating T cells via bone marrow transplants allowed some individuals with HIV to experience therapy-free remission, even though deeper tissue reservoirs were not targeted.TRIAL REGISTRATIONNot applicable.FUNDINGNIH grants P01 AI31385, P30 AI036214, AI131971-01, AI120009AI036214, HD094646, AI027763, AI134295, and AI68636.
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Affiliation(s)
| | - Sara Gianella
- Department of Medicine, UCSD, La Jolla, California, USA
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Computational and Evolutionary Virology, Leuven, Belgium
| | | | - Timothy E. Schlub
- University of Sydney, Faculty of Medicine and Health, Sydney School of Public Health, Sydney, Australia
| | | | | | | | - Bram Vrancken
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Computational and Evolutionary Virology, Leuven, Belgium
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Vrancken B, Wawina-Bokalanga T, Vanmechelen B, Martí-Carreras J, Carroll MW, Nsio J, Kapetshi J, Makiala-Mandanda S, Muyembe-Tamfum JJ, Baele G, Vermeire K, Vergote V, Ahuka-Mundeke S, Maes P. Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics. PLoS Negl Trop Dis 2020; 14:e0008117. [PMID: 32130210 PMCID: PMC7075637 DOI: 10.1371/journal.pntd.0008117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 03/16/2020] [Accepted: 02/05/2020] [Indexed: 11/18/2022] Open
Abstract
Ebolaviruses pose a substantial threat to wildlife populations and to public health in Africa. Evolutionary analyses of virus genome sequences can contribute significantly to elucidate the origin of new outbreaks, which can help guide surveillance efforts. The reconstructed between-outbreak evolutionary history of Zaire ebolavirus so far has been highly consistent. By removing the confounding impact of population growth bursts during local outbreaks on the free mixing assumption that underlies coalescent-based demographic reconstructions, we find-contrary to what previous results indicated-that the circulation dynamics of Ebola virus in its animal reservoir are highly uncertain. Our findings also accentuate the need for a more fine-grained picture of the Ebola virus diversity in its reservoir to reliably infer the reservoir origin of outbreak lineages. In addition, the recent appearance of slower-evolving variants is in line with latency as a survival mechanism and with bats as the natural reservoir host.
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Affiliation(s)
- Bram Vrancken
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Tony Wawina-Bokalanga
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Bert Vanmechelen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Joan Martí-Carreras
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Miles W. Carroll
- Research and Development Institute, National Infection Service, Public Health England, Porton Down, Wiltshire, United Kingdom
| | - Justus Nsio
- Ministère de la Santé, Kinshasa, Democratic Republic of the Congo
| | - Jimmy Kapetshi
- Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
| | - Sheila Makiala-Mandanda
- Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
| | | | - Guy Baele
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Kurt Vermeire
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Valentijn Vergote
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
| | - Piet Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Leuven, Belgium
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Gibbs AJ, Hajizadeh M, Ohshima K, Jones RA. The Potyviruses: An Evolutionary Synthesis Is Emerging. Viruses 2020; 12:E132. [PMID: 31979056 PMCID: PMC7077269 DOI: 10.3390/v12020132] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/28/2022] Open
Abstract
In this review, encouraged by the dictum of Theodosius Dobzhansky that "Nothing in biology makes sense except in the light of evolution", we outline the likely evolutionary pathways that have resulted in the observed similarities and differences of the extant molecules, biology, distribution, etc. of the potyvirids and, especially, its largest genus, the potyviruses. The potyvirids are a family of plant-infecting RNA-genome viruses. They had a single polyphyletic origin, and all share at least three of their genes (i.e., the helicase region of their CI protein, the RdRp region of their NIb protein and their coat protein) with other viruses which are otherwise unrelated. Potyvirids fall into 11 genera of which the potyviruses, the largest, include more than 150 distinct viruses found worldwide. The first potyvirus probably originated 15,000-30,000 years ago, in a Eurasian grass host, by acquiring crucial changes to its coat protein and HC-Pro protein, which enabled it to be transmitted by migrating host-seeking aphids. All potyviruses are aphid-borne and, in nature, infect discreet sets of monocotyledonous or eudicotyledonous angiosperms. All potyvirus genomes are under negative selection; the HC-Pro, CP, Nia, and NIb genes are most strongly selected, and the PIPO gene least, but there are overriding virus specific differences; for example, all turnip mosaic virus genes are more strongly conserved than those of potato virus Y. Estimates of dN/dS (ω) indicate whether potyvirus populations have been evolving as one or more subpopulations and could be used to help define species boundaries. Recombinants are common in many potyvirus populations (20%-64% in five examined), but recombination seems to be an uncommon speciation mechanism as, of 149 distinct potyviruses, only two were clear recombinants. Human activities, especially trade and farming, have fostered and spread both potyviruses and their aphid vectors throughout the world, especially over the past five centuries. The world distribution of potyviruses, especially those found on islands, indicates that potyviruses may be more frequently or effectively transmitted by seed than experimental tests suggest. Only two meta-genomic potyviruses have been recorded from animal samples, and both are probably contaminants.
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Affiliation(s)
- Adrian J. Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
| | - Mohammad Hajizadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan;
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-2410 Korimoto, Kagoshima 890-0065, Japan
| | - Roger A.C. Jones
- Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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Altinli M, Lequime S, Courcelle M, François S, Justy F, Gosselin-Grenet AS, Ogliastro M, Weill M, Sicard M. Evolution and phylogeography of Culex pipiens densovirus. Virus Evol 2019; 5:vez053. [PMID: 31807318 PMCID: PMC6884738 DOI: 10.1093/ve/vez053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Viruses of the Parvoviridae family infect a wide range of animals including vertebrates and invertebrates. So far, our understanding of parvovirus diversity is biased towards medically or economically important viruses mainly infecting vertebrate hosts, while invertebrate infecting parvoviruses—namely densoviruses—have been largely neglected. Here, we investigated the prevalence and the evolution of the only mosquito-infecting ambidensovirus, Culex pipiens densovirus (CpDV), from laboratory mosquito lines and natural populations collected worldwide. CpDV diversity generally grouped in two clades, here named CpDV-1 and -2. The incongruence of the different gene trees for some samples suggested the possibility of recombination events between strains from different clades. We further investigated the role of selection on the evolution of CpDV genome and detected many individual sites under purifying selection both in non-structural and structural genes. However, some sites in structural genes were under diversifying selection, especially during the divergence of CpDV-1 and -2 clades. These substitutions between CpDV-1 and -2 clades were mostly located in the capsid protein encoding region and might cause changes in host specificity or pathogenicity of CpDV strains from the two clades. However, additional functional and experimental studies are necessary to fully understand the protein conformations and the resulting phenotype of these substitutions between clades of CpDV.
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Affiliation(s)
- Mine Altinli
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sebastian Lequime
- KU Leuven, Department of Microbiology, Immunology, and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Leuven, Belgium
| | - Maxime Courcelle
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sarah François
- DGIMI, INRA, Université de Montpellier, Montpellier, France.,Department of Zoology, University of Oxford, Oxford, UK
| | - Fabienne Justy
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | | | | | - Mylene Weill
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Mathieu Sicard
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
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Duchatel F, Bronsvoort BMDC, Lycett S. Phylogeographic Analysis and Identification of Factors Impacting the Diffusion of Foot-and-Mouth Disease Virus in Africa. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00371] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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36
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Dellicour S, Troupin C, Jahanbakhsh F, Salama A, Massoudi S, Moghaddam MK, Baele G, Lemey P, Gholami A, Bourhy H. Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages - Application to rabies virus spread in Iran. Mol Ecol 2019; 28:4335-4350. [PMID: 31535448 DOI: 10.1111/mec.15222] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 08/04/2019] [Accepted: 08/05/2019] [Indexed: 12/26/2022]
Abstract
Recent years have seen the extensive use of phylogeographic approaches to unveil the dispersal history of virus epidemics. Spatially explicit reconstructions of viral spread represent valuable sources of lineage movement data that can be exploited to investigate the impact of underlying environmental layers on the dispersal of pathogens. Here, we performed phylogeographic inference and applied different post hoc approaches to analyse a new and comprehensive data set of viral genomes to elucidate the dispersal history and dynamics of rabies virus (RABV) in Iran, which have remained largely unknown. We first analysed the association between environmental factors and variations in dispersal velocity among lineages. Second, we present, test and apply a new approach to study the link between environmental conditions and the dispersal direction of lineages. The statistical performance (power of detection, false-positive rate) of this new method was assessed using simulations. We performed phylogeographic analyses of RABV genomes, allowing us to describe the large diversity of RABV in Iran and to confirm the cocirculation of several clades in the country. Overall, we estimate a relatively high lineage dispersal velocity, similar to previous estimates for dog rabies virus spread in northern Africa. Finally, we highlight a tendency for RABV lineages to spread in accessible areas associated with high human population density. Our analytical workflow illustrates how phylogeographic approaches can be used to investigate the impact of environmental factors on several aspects of viral dispersal dynamics.
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Affiliation(s)
- Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Cécile Troupin
- Unit Lyssavirus Epidemiology and Neuropathology, WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
| | - Fatemeh Jahanbakhsh
- WHO Collaborating Centre for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran, Iran
| | - Akram Salama
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Siamak Massoudi
- Department of Environment, Wildlife Diseases Group, Wildlife Bureau, Tehran, Iran
| | - Madjid K Moghaddam
- Department of Environment, Wildlife Diseases Group, Wildlife Bureau, Tehran, Iran
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Alireza Gholami
- WHO Collaborating Centre for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran, Iran
| | - Hervé Bourhy
- Unit Lyssavirus Epidemiology and Neuropathology, WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
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Theys K, Lemey P, Vandamme AM, Baele G. Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases. Front Public Health 2019; 7:208. [PMID: 31428595 PMCID: PMC6688121 DOI: 10.3389/fpubh.2019.00208] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 07/12/2019] [Indexed: 01/28/2023] Open
Abstract
Genomic and epidemiological monitoring have become an integral part of our response to emerging and ongoing epidemics of viral infectious diseases. Advances in high-throughput sequencing, including portable genomic sequencing at reduced costs and turnaround time, are paralleled by continuing developments in methodology to infer evolutionary histories (dynamics/patterns) and to identify factors driving viral spread in space and time. The traditionally static nature of visualizing phylogenetic trees that represent these evolutionary relationships/processes has also evolved, albeit perhaps at a slower rate. Advanced visualization tools with increased resolution assist in drawing conclusions from phylogenetic estimates and may even have potential to better inform public health and treatment decisions, but the design (and choice of what analyses are shown) is hindered by the complexity of information embedded within current phylogenetic models and the integration of available meta-data. In this review, we discuss visualization challenges for the interpretation and exploration of reconstructed histories of viral epidemics that arose from increasing volumes of sequence data and the wealth of additional data layers that can be integrated. We focus on solutions that address joint temporal and spatial visualization but also consider what the future may bring in terms of visualization and how this may become of value for the coming era of real-time digital pathogen surveillance, where actionable results and adequate intervention strategies need to be obtained within days.
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Affiliation(s)
- Kristof Theys
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
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38
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Kafetzopoulou LE, Pullan ST, Lemey P, Suchard MA, Ehichioya DU, Pahlmann M, Thielebein A, Hinzmann J, Oestereich L, Wozniak DM, Efthymiadis K, Schachten D, Koenig F, Matjeschk J, Lorenzen S, Lumley S, Ighodalo Y, Adomeh DI, Olokor T, Omomoh E, Omiunu R, Agbukor J, Ebo B, Aiyepada J, Ebhodaghe P, Osiemi B, Ehikhametalor S, Akhilomen P, Airende M, Esumeh R, Muoebonam E, Giwa R, Ekanem A, Igenegbale G, Odigie G, Okonofua G, Enigbe R, Oyakhilome J, Yerumoh EO, Odia I, Aire C, Okonofua M, Atafo R, Tobin E, Asogun D, Akpede N, Okokhere PO, Rafiu MO, Iraoyah KO, Iruolagbe CO, Akhideno P, Erameh C, Akpede G, Isibor E, Naidoo D, Hewson R, Hiscox JA, Vipond R, Carroll MW, Ihekweazu C, Formenty P, Okogbenin S, Ogbaini-Emovon E, Günther S, Duraffour S. Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak. Science 2019; 363:74-77. [PMID: 30606844 DOI: 10.1126/science.aau9343] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022]
Abstract
The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.
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Affiliation(s)
- L E Kafetzopoulou
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S T Pullan
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - P Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - M A Suchard
- Departments of Biomathematics, Biostatistics, and Human Genetics, University of California, Los Angeles, CA, USA
| | - D U Ehichioya
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - M Pahlmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - A Thielebein
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - J Hinzmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - L Oestereich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - D M Wozniak
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - K Efthymiadis
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - D Schachten
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - F Koenig
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - J Matjeschk
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S Lorenzen
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S Lumley
- Public Health England, National Infection Service, Porton Down, UK
| | - Y Ighodalo
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - D I Adomeh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - T Olokor
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E Omomoh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Omiunu
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - J Agbukor
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - B Ebo
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - J Aiyepada
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - P Ebhodaghe
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - B Osiemi
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - P Akhilomen
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - M Airende
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Esumeh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E Muoebonam
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Giwa
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - A Ekanem
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Igenegbale
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Odigie
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Okonofua
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Enigbe
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - J Oyakhilome
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E O Yerumoh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - I Odia
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - C Aire
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - M Okonofua
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Atafo
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E Tobin
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - D Asogun
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - N Akpede
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - P O Okokhere
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - M O Rafiu
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - K O Iraoyah
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - P Akhideno
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - C Erameh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Akpede
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - E Isibor
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - D Naidoo
- World Health Organization, Geneva, Switzerland
| | - R Hewson
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK.,Faculty of Clinical Sciences and International Public Health, Liverpool School of Tropical Medicine, Liverpool, UK
| | - J A Hiscox
- National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - R Vipond
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - M W Carroll
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - C Ihekweazu
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - P Formenty
- World Health Organization, Geneva, Switzerland
| | - S Okogbenin
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | | | - S Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany. .,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - S Duraffour
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
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39
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Rakotomalala M, Vrancken B, Pinel-Galzi A, Ramavovololona P, Hébrard E, Randrianangaly JS, Dellicour S, Lemey P, Fargette D. Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa. Virus Evol 2019; 5:vez023. [PMID: 31384483 PMCID: PMC6671560 DOI: 10.1093/ve/vez023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Rice yellow mottle virus (RYMV) in Madagascar Island provides an opportunity to study the spread of a plant virus disease after a relatively recent introduction in a large and isolated country with a heterogeneous host landscape ecology. Here, we take advantage of field survey data on the occurrence of RYMV disease throughout Madagascar dating back to the 1970s, and of virus genetic data from ninety-four isolates collected since 1989 in most regions of the country to reconstruct the epidemic history. We find that the Malagasy isolates belong to a unique recombinant strain that most likely entered Madagascar through a long-distance introduction from the most eastern part of mainland Africa. We infer the spread of RYMV as a continuous process using a Bayesian statistical framework. In order to calibrate the time scale in calendar time units in this analysis, we pool the information about the RYMV evolutionary rate from several geographical partitions. Whereas the field surveys and the phylogeographic reconstructions both point to a rapid southward invasion across hundreds of kilometers throughout Madagascar within three to four decades, they differ on the inferred origin location and time of the epidemic. The phylogeographic reconstructions suggest a lineage displacement and unveil a re-invasion of the northern regions that may have remained unnoticed otherwise. Despite ecological differences that could affect the transmission potential of RYMV in Madagascar and in mainland Africa, we estimate similar invasion and dispersal rates. We could not identify environmental factors that have a relevant impact on the lineage dispersal velocity of RYMV in Madagascar. This study highlights the value and complementarity of (historical) nongenetic and (more contemporaneous) genetic surveillance data for reconstructing the history of spread of plant viruses.
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Affiliation(s)
- Mbolarinosy Rakotomalala
- Centre Régional de Recherche du Nord-Ouest du FOFIFA, BP 289, Mahavoky Avaratra, Mahajanga 401, Madagascar
| | - Bram Vrancken
- Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Herestraat 49 box 1040, 3000 Leuven, Belgium
| | - Agnès Pinel-Galzi
- IRD, Cirad, Université Montpellier, IPME, 911 avenue Agropolis, BP 64501 34934 Montpellier cedex 5, France
| | - Perle Ramavovololona
- Département de Biologie et d’Ecologie Végétales, Faculté des Sciences, Université d’Antananarivo, BP 906
| | - Eugénie Hébrard
- IRD, Cirad, Université Montpellier, IPME, 911 avenue Agropolis, BP 64501 34934 Montpellier cedex 5, France
| | | | - Simon Dellicour
- Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Herestraat 49 box 1040, 3000 Leuven, Belgium
- Spatial Epidemiology Lab, Université Libre de Bruxelles, CP 264 / 3,50 av FD Roosevelt, B-1050 Brussels, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Herestraat 49 box 1040, 3000 Leuven, Belgium
| | - Denis Fargette
- IRD, Cirad, Université Montpellier, IPME, 911 avenue Agropolis, BP 64501 34934 Montpellier cedex 5, France
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40
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Laenen L, Vergote V, Vanmechelen B, Tersago K, Baele G, Lemey P, Leirs H, Dellicour S, Vrancken B, Maes P. Identifying the patterns and drivers of Puumala hantavirus enzootic dynamics using reservoir sampling. Virus Evol 2019; 5:vez009. [PMID: 31024739 PMCID: PMC6476162 DOI: 10.1093/ve/vez009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hantaviruses are zoonotic hemorrhagic fever viruses for which prevention of human spillover remains the first priority in disease management. Tailored intervention measures require an understanding of the drivers of enzootic dynamics, commonly inferred from distorted human incidence data. Here, we use longitudinal sampling of approximately three decades of Puumala orthohantavirus (PUUV) evolution in isolated reservoir populations to estimate PUUV evolutionary rates, and apply these to study the impact of environmental factors on viral spread. We find that PUUV accumulates genetic changes at a rate of ∼10−4 substitutions per site per year and that land cover type defines the dispersal dynamics of PUUV, with forests facilitating and croplands impeding virus spread. By providing reliable short-term PUUV evolutionary rate estimates, this work facilitates the evaluation of spatial risk heterogeneity starting from timed phylogeographic reconstructions based on virus sampling in its animal reservoir, thereby side-stepping the need for difficult-to-collect human disease incidence data.
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Affiliation(s)
- Lies Laenen
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| | - Valentijn Vergote
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| | - Bert Vanmechelen
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| | - Katrien Tersago
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium.,Epidemiology of Infectious Diseases, Belgian Institute of Health, Sciensano, Brussels, Belgium
| | - Guy Baele
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| | - Philippe Lemey
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Simon Dellicour
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium.,Spatial Epidemiology Lab (spELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Bram Vrancken
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| | - Piet Maes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
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41
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Dellicour S, Vrancken B, Trovão NS, Fargette D, Lemey P. On the importance of negative controls in viral landscape phylogeography. Virus Evol 2018; 4:vey023. [PMID: 30151241 PMCID: PMC6101606 DOI: 10.1093/ve/vey023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phylogeographic reconstructions are becoming an established procedure to evaluate the factors that could impact virus spread. While a discrete phylogeographic approach can be used to test predictors of transition rates among discrete locations, alternative continuous phylogeographic reconstructions can also be exploited to investigate the impact of underlying environmental layers on the dispersal velocity of a virus. The two approaches are complementary tools for studying pathogens' spread, but in both cases, care must be taken to avoid misinterpretations. Here, we analyse rice yellow mottle virus (RYMV) sequence data from West and East Africa to illustrate how both approaches can be used to study the impact of environmental factors on the virus’ dispersal frequency and velocity. While it was previously reported that host connectivity was a major determinant of RYMV spread, we show that this was a false positive result due to the lack of appropriate negative controls. We also discuss and compare the phylodynamic tools currently available for investigating the impact of environmental factors on virus spread.
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Affiliation(s)
- Simon Dellicour
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050 Bruxelles, Belgium
| | - Bram Vrancken
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nídia S Trovão
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Denis Fargette
- Institut de Recherche pour le Développement (IRD), UMR IPME (IRD, CIRAD, Université de Montpellier), BP 64051 34394 Montpellier cedex 5, France
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
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42
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Pagán I. The diversity, evolution and epidemiology of plant viruses: A phylogenetic view. INFECTION GENETICS AND EVOLUTION 2018; 65:187-199. [PMID: 30055330 DOI: 10.1016/j.meegid.2018.07.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
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.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28223, Spain.
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43
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Brunker K, Lemey P, Marston DA, Fooks AR, Lugelo A, Ngeleja C, Hampson K, Biek R. Landscape attributes governing local transmission of an endemic zoonosis: Rabies virus in domestic dogs. Mol Ecol 2018; 27:773-788. [PMID: 29274171 PMCID: PMC5900915 DOI: 10.1111/mec.14470] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 12/24/2022]
Abstract
Landscape heterogeneity plays an important role in disease spread and persistence, but quantifying landscape influences and their scale dependence is challenging. Studies have focused on how environmental features or global transport networks influence pathogen invasion and spread, but their influence on local transmission dynamics that underpin the persistence of endemic diseases remains unexplored. Bayesian phylogeographic frameworks that incorporate spatial heterogeneities are promising tools for analysing linked epidemiological, environmental and genetic data. Here, we extend these methodological approaches to decipher the relative contribution and scale-dependent effects of landscape influences on the transmission of endemic rabies virus in Serengeti district, Tanzania (area ~4,900 km2 ). Utilizing detailed epidemiological data and 152 complete viral genomes collected between 2004 and 2013, we show that the localized presence of dogs but not their density is the most important determinant of diffusion, implying that culling will be ineffective for rabies control. Rivers and roads acted as barriers and facilitators to viral spread, respectively, and vaccination impeded diffusion despite variable annual coverage. Notably, we found that landscape effects were scale-dependent: rivers were barriers and roads facilitators on larger scales, whereas the distribution of dogs was important for rabies dispersal across multiple scales. This nuanced understanding of the spatial processes that underpin rabies transmission can be exploited for targeted control at the scale where it will have the greatest impact. Moreover, this research demonstrates how current phylogeographic frameworks can be adapted to improve our understanding of endemic disease dynamics at different spatial scales.
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Affiliation(s)
- Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
- Animal and Plant Health AgencyAddlestoneUK
| | - Philippe Lemey
- Department of Microbiology and ImmunologyKU Leuven – University of LeuvenLeuvenBelgium
| | | | | | - Ahmed Lugelo
- Department of Veterinary Medicine and Public HealthSokoine University of AgricultureMorogoroUnited Republic of Tanzania
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory AgencyDar es SalaamUnited Republic of Tanzania
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
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44
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Hébrard E, Pinel-Galzi A, Oludare A, Poulicard N, Aribi J, Fabre S, Issaka S, Mariac C, Dereeper A, Albar L, Silué D, Fargette D. Identification of a Hypervirulent Pathotype of Rice yellow mottle virus: A Threat to Genetic Resistance Deployment in West-Central Africa. PHYTOPATHOLOGY 2018; 108:299-307. [PMID: 28990483 DOI: 10.1094/phyto-05-17-0190-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Rice yellow mottle virus (RYMV) causes high losses to rice production in Africa. Several sources of varietal high resistance are available but the emergence of virulent pathotypes that are able to overcome one or two resistance alleles can sometimes occur. Both resistance spectra and viral adaptability have to be taken into account to develop sustainable rice breeding strategies against RYMV. In this study, we extended previous resistance spectrum analyses by testing the rymv1-4 and rymv1-5 alleles that are carried by the rice accessions Tog5438 and Tog5674, respectively, against isolates that are representative of RYMV genetic and pathogenic diversity. Our study revealed a hypervirulent pathotype, named thereafter pathotype T', that is able to overcome all known sources of high resistance. This pathotype, which is spatially localized in West-Central Africa, appears to be more abundant than previously suspected. To better understand the adaptive processes of pathotype T', molecular determinants of resistance breakdown were identified via Sanger sequencing and validated through directed mutagenesis of an infectious clone. These analyses confirmed the key role of convergent nonsynonymous substitutions in the central part of the viral genome-linked protein to overcome RYMV1-mediated resistance. In addition, deep-sequencing analyses revealed that resistance breakdown does not always coincide with fixed mutations. Actually, virulence mutations that are present in a small proportion of the virus population can be sufficient for resistance breakdown. Considering the spatial distribution of RYMV strains in Africa and their ability to overcome the RYMV resistance genes and alleles, we established a resistance-breaking risk map to optimize strategies for the deployment of sustainable and resistant rice lines in Africa.
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Affiliation(s)
- Eugénie Hébrard
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Agnès Pinel-Galzi
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Aderonke Oludare
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Nils Poulicard
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Jamel Aribi
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Sandrine Fabre
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Souley Issaka
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Cédric Mariac
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Alexis Dereeper
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Laurence Albar
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Drissa Silué
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Denis Fargette
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
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45
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Tongo M, Harkins GW, Dorfman JR, Billings E, Tovanabutra S, de Oliveira T, Martin DP. Unravelling the complicated evolutionary and dissemination history of HIV-1M subtype A lineages. Virus Evol 2018; 4:vey003. [PMID: 29484203 PMCID: PMC5819727 DOI: 10.1093/ve/vey003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Subtype A is one of the rare HIV-1 group M (HIV-1M) lineages that is both widely distributed throughout the world and persists at high frequencies in the Congo Basin (CB), the site where HIV-1M likely originated. This, together with its high degree of diversity suggests that subtype A is amongst the fittest HIV-1M lineages. Here we use a comprehensive set of published near full-length subtype A sequences and A-derived genome fragments from both circulating and unique recombinant forms (CRFs/URFs) to obtain some insights into how frequently these lineages have independently seeded HIV-1M sub-epidemics in different parts of the world. We do this by inferring when and where the major subtype A lineages and subtype A-derived CRFs originated. Following its origin in the CB during the 1940s, we track the diversification and recombination history of subtype A sequences before and during its dissemination throughout much of the world between the 1950s and 1970s. Collectively, the timings and numbers of detectable subtype A recombination and dissemination events, the present broad global distribution of the sub-epidemics that were seeded by these events, and the high prevalence of subtype A sequences within the regions where these sub-epidemics occurred, suggest that ancestral subtype A viruses (and particularly sub-subtype A1 ancestral viruses) may have been genetically predisposed to become major components of the present epidemic.
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Affiliation(s)
- Marcel Tongo
- KwaZulu-Natal Research Innovation and Sequencing Platform (Krisp), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa
- Division of Computational Biology, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
| | - Gordon W Harkins
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
| | - Jeffrey R Dorfman
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- Division of Immunology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Erik Billings
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910–7500, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20910–7500, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910–7500, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20910–7500, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (Krisp), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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46
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Vrancken B, Suchard MA, Lemey P. Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling. Virus Evol 2017; 3:vex028. [PMID: 29026650 PMCID: PMC5632516 DOI: 10.1093/ve/vex028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, Journal of Virology, 89/7: 3512–22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the ‘colonization–adaptation–transmission’ model can explain the differential impact of transmission on synonymous and non-synonymous substitution rates. Here, we revisit this dataset using a full probabilistic Bayesian phylogenetic framework that adequately accounts for the non-independence of sequence data when estimating evolutionary parameters. Examination of the transmission chain data under a flexible coalescent prior reveals a general inconsistency between the estimated timings and clustering patterns and the known transmission history, highlighting the need to incorporate host transmission information in the analysis. Using an explicit genealogical transmission chain model, we find strong support for a transmission-associated decrease of the overall evolutionary rate. However, in contrast to the initially reported larger transmission effect on non-synonymous substitution rate, we find a similar decrease in both non-synonymous and synonymous substitution rates that cannot be adequately explained by the colonization-adaptation-transmission model. An alternative explanation may involve a transmission/establishment advantage of hepatitis B virus variants that have accumulated fewer within-host substitutions, perhaps by spending more time in the covalently closed circular DNA state between each round of viral replication. More generally, this study illustrates that ignoring phylogenetic relationships can lead to misleading evolutionary estimates.
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Affiliation(s)
- Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, University of California, Los Angeles, CA 90095, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA.,Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
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Picard C, Dallot S, Brunker K, Berthier K, Roumagnac P, Soubeyrand S, Jacquot E, Thébaud G. Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:139-160. [PMID: 28525307 DOI: 10.1146/annurev-phyto-080516-035616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.
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Affiliation(s)
- Coralie Picard
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Sylvie Dallot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | | | - Philippe Roumagnac
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | | | - Emmanuel Jacquot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Gaël Thébaud
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
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Zhang Y, Vrancken B, Feng Y, Dellicour S, Yang Q, Yang W, Zhang Y, Dong L, Pybus OG, Zhang H, Tian H. Cross-border spread, lineage displacement and evolutionary rate estimation of rabies virus in Yunnan Province, China. Virol J 2017; 14:102. [PMID: 28578663 PMCID: PMC5457581 DOI: 10.1186/s12985-017-0769-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/25/2017] [Indexed: 12/12/2022] Open
Abstract
Background Rabies is an important but underestimated threat to public health, with most cases reported in Asia. Since 2000, a new epidemic wave of rabies has emerged in Yunnan Province, southwestern China, which borders three countries in Southeast Asia. Method We estimated gene-specific evolutionary rates for rabies virus using available data in GenBank, then used this information to calibrate the timescale of rabies virus (RABV) spread in Asia. We used 452 publicly available geo-referenced complete nucleoprotein (N) gene sequences, including 52 RABV sequences that were recently generated from samples collected in Yunnan between 2008 and 2012. Results The RABV N gene evolutionary rate was estimated to be 1.88 × 10−4 (1.37–2.41 × 10−4, 95% Bayesian credible interval, BCI) substitutions per site per year. Phylogenetic reconstructions show that the currently circulating RABV lineages in Yunnan result from at least seven independent introductions (95% BCI: 6–9 introductions) and represent each of the three main Asian RABV lineages, SEA-1, -2 and -3. We find that Yunnan is a sink location for the domestic spread of RABV and connects RABV epidemics in North China, South China, and Southeast Asia. Cross-border spread from southeast Asia (SEA) into South China, and intermixing of the North and South China epidemics is also well supported. The influx of RABV into Yunnan from SEA was not well-supported, likely due to the poor sampling of SEA RABV diversity. We found evidence for a lineage displacement of the Yunnan SEA-2 and -3 lineages by Yunnan SEA-1 strains, and considered whether this could be attributed to fitness differences. Conclusion Overall, our study contributes to a better understanding of the spread of RABV that could facilitate future rabies virus control and prevention efforts. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0769-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuzhen Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Bram Vrancken
- Department of Microbiology and Immunology, Division of Clinical and Epidemiological Virology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Yun Feng
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Simon Dellicour
- Department of Microbiology and Immunology, Division of Clinical and Epidemiological Virology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Qiqi Yang
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Weihong Yang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Yunzhi Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | | | - Hailin Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China.
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China.
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