@article{rivarez_faure_svanella-dumas_pecman_tusek-znidaric_schonegger_de jonghe_blouin_rasmussen_massart_et al._2023, title={Diversity and Pathobiology of an Ilarvirus Unexpectedly Detected in Diverse Plants and Global Sequencing Data}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO-12-22-0465-V}, abstractNote={ High-throughput sequencing (HTS) and sequence mining tools revolutionized virus detection and discovery in recent years, and implementing them with classical plant virology techniques results in a powerful approach to characterize viruses. An example of a virus discovered through HTS is Solanum nigrum ilarvirus 1 (SnIV1) ( Bromoviridae), which was recently reported in various solanaceous plants from France, Slovenia, Greece, and South Africa. It was likewise detected in grapevines ( Vitaceae) and several Fabaceae and Rosaceae plant species. Such a diverse set of source organisms is atypical for ilarviruses, thus warranting further investigation. In this study, modern and classical virological tools were combined to accelerate the characterization of SnIV1. Through HTS-based virome surveys, mining of sequence read archive datasets, and a literature search, SnIV1 was further identified from diverse plant and non-plant sources globally. SnIV1 isolates showed relatively low variability compared with other phylogenetically related ilarviruses. Phylogenetic analyses showed a distinct basal clade of isolates from Europe, whereas the rest formed clades of mixed geographic origin. Furthermore, systemic infection of SnIV1 in Solanum villosum and its mechanical and graft transmissibility to solanaceous species were demonstrated. Near-identical SnIV1 genomes from the inoculum ( S. villosum) and inoculated Nicotiana benthamiana were sequenced, thus partially fulfilling Koch's postulates. SnIV1 was shown to be seed-transmitted and potentially pollen-borne, has spherical virions, and possibly induces histopathological changes in infected N. benthamiana leaf tissues. Overall, this study provides information to better understand the diversity, global presence, and pathobiology of SnIV1; however, its possible emergence as a destructive pathogen remains uncertain. }, journal={PHYTOPATHOLOGY}, author={Rivarez, Mark Paul Selda and Faure, Chantal and Svanella-Dumas, Laurence and Pecman, Anja and Tusek-Znidaric, Magda and Schonegger, Deborah and De Jonghe, Kris and Blouin, Arnaud and Rasmussen, David A. and Massart, Sebastien and et al.}, year={2023}, month={Jul} }
 @article{rasmussen_guo_2023, title={Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests}, volume={72}, ISSN={["1076-836X"]}, DOI={10.1093/sysbio/syad040}, abstractNote={Abstract}, number={5}, journal={SYSTEMATIC BIOLOGY}, author={Rasmussen, David A. and Guo, Fangfang}, year={2023}, month={Nov}, pages={1154–1170} }
 @article{hasegawa_techer_adjlane_al-hissnawi_antunez_beaurepaire_christmon_delatte_dukku_eliash_et al._2023, title={Evolutionarily diverse origins of deformed wing viruses in western honey bees}, volume={120}, ISSN={["1091-6490"]}, DOI={10.1073/pnas.2301258120}, abstractNote={Novel transmission routes can allow infectious diseases to spread, often with devastating consequences. Ectoparasitic varroa mites vector a diversity of RNA viruses, having switched hosts from the eastern to western honey bees (Apis ceranatoApis mellifera). They provide an opportunity to explore how novel transmission routes shape disease epidemiology. As the principal driver of the spread of deformed wing viruses (mainly DWV-A and DWV-B), varroa infestation has also driven global honey bee health declines. The more virulent DWV-B strain has been replacing the original DWV-A strain in many regions over the past two decades. Yet, how these viruses originated and spread remains poorly understood. Here, we use a phylogeographic analysis based on whole-genome data to reconstruct the origins and demography of DWV spread. We found that, rather than reemerging in western honey bees after varroa switched hosts, as suggested by previous work, DWV-A most likely originated in East Asia and spread in the mid-20th century. It also showed a massive population size expansion following the varroa host switch. By contrast, DWV-B was most likely acquired more recently from a source outside East Asia and appears absent from the original varroa host. These results highlight the dynamic nature of viral adaptation, whereby a vector’s host switch can give rise to competing and increasingly virulent disease pandemics. The evolutionary novelty and rapid global spread of these host–virus interactions, together with observed spillover into other species, illustrate how increasing globalization poses urgent threats to biodiversity and food security.}, number={26}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Hasegawa, Nonno and Techer, Maeva A. and Adjlane, Noureddine and al-Hissnawi, Muntasser Sabah and Antunez, Karina and Beaurepaire, Alexis and Christmon, Krisztina and Delatte, Helene and Dukku, Usman H. and Eliash, Nurit and et al.}, year={2023}, month={Jun} }
 @article{mahmud_wallace_reske_alvarado_muenks_rasmussen_burnham_lanzas_dubberke_dantas_2022, title={Epidemiology of Plasmid Lineages Mediating the Spread of Extended-Spectrum Beta-Lactamases among Clinical Escherichia coli}, volume={8}, ISSN={["2379-5077"]}, url={https://doi.org/10.1128/msystems.00519-22}, DOI={10.1128/msystems.00519-22}, abstractNote={
            The increasing incidence of nosocomial infections with extended-spectrum beta-lactamase (ESBL)-producing
            Escherichia coli
            represents a significant threat to public health, given the limited treatment options available for such infections. The rapid ESBL spread is suggested to be driven by localization of the resistance genes on conjugative plasmids.
          }, journal={MSYSTEMS}, author={Mahmud, Bejan and Wallace, Meghan A. and Reske, Kimberly A. and Alvarado, Kelly and Muenks, Carol E. and Rasmussen, David A. and Burnham, Carey-Ann D. and Lanzas, Cristina and Dubberke, Erik R. and Dantas, Gautam}, editor={Marshall, Christopher W.Editor}, year={2022}, month={Aug} }
 @article{lapp_obala_abel_rasmussen_sumner_freedman_taylor_prudhomme-o'meara_2022, title={Plasmodium falciparum Genetic Diversity in Coincident Human and Mosquito Hosts}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.02277-22}, abstractNote={
            Plasmodium falciparum
            is the deadliest human malaria parasite, and infections consisting of concurrent, multiple strains are common in regions of high endemicity. During transitions within and between the parasite’s mosquito and human hosts, these strains are subject to population bottlenecks, and distinct parasite strains may have differential fitness in the various environments encountered.
          }, journal={MBIO}, author={Lapp, Zena and Obala, Andrew A. and Abel, Lucy and Rasmussen, David A. and Sumner, Kelsey M. and Freedman, Elizabeth and Taylor, Steve M. and Prudhomme-O'Meara, Wendy}, year={2022}, month={Sep} }
 @article{guo_carbone_rasmussen_2022, title={Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination}, volume={18}, ISSN={["1553-7358"]}, DOI={10.1371/journal.pcbi.1010422}, abstractNote={Movement of individuals between populations or demes is often restricted, especially between geographically isolated populations. The structured coalescent provides an elegant theoretical framework for describing how movement between populations shapes the genealogical history of sampled individuals and thereby structures genetic variation within and between populations. However, in the presence of recombination an individual may inherit different regions of their genome from different parents, resulting in a mosaic of genealogical histories across the genome, which can be represented by an Ancestral Recombination Graph (ARG). In this case, different genomic regions may have different ancestral histories and so different histories of movement between populations. Recombination therefore poses an additional challenge to phylogeographic methods that aim to reconstruct the movement of individuals from genealogies, although also a potential benefit in that different loci may contain additional information about movement. Here, we introduce the Structured Coalescent with Ancestral Recombination (SCAR) model, which builds on recent approximations to the structured coalescent by incorporating recombination into the ancestry of sampled individuals. The SCAR model allows us to infer how the migration history of sampled individuals varies across the genome from ARGs, and improves estimation of key population genetic parameters such as population sizes, recombination rates and migration rates. Using the SCAR model, we explore the potential and limitations of phylogeographic inference using full ARGs. We then apply the SCAR to lineages of the recombining fungusAspergillus flavussampled across the United States to explore patterns of recombination and migration across the genome.}, number={8}, journal={PLOS COMPUTATIONAL BIOLOGY}, author={Guo, Fangfang and Carbone, Ignazio and Rasmussen, David A.}, year={2022}, month={Aug} }
 @article{tegally_san_cotten_moir_tegomoh_mboowa_martin_baxter_lambisia_diallo_et al._2022, title={The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance}, volume={378}, ISSN={["1095-9203"]}, DOI={10.1126/science.abq5358}, abstractNote={Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern—particularly Alpha, Beta, Delta, and Omicron—on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.}, number={6615}, journal={SCIENCE}, author={Tegally, Houriiyah and San, James E. and Cotten, Matthew and Moir, Monika and Tegomoh, Bryan and Mboowa, Gerald and Martin, Darren P. and Baxter, Cheryl and Lambisia, Arnold W. and Diallo, Amadou and et al.}, year={2022}, month={Oct}, pages={42-+} }
 @article{wilkinson_giovanetti_tegally_san_lessells_cuadros_martin_rasmussen_zekri_sangare_et al._2021, title={A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa}, volume={374}, ISSN={["1095-9203"]}, DOI={10.1126/science.abj4336}, abstractNote={SARS-CoV-2 across Africa}, number={6566}, journal={SCIENCE}, author={Wilkinson, Eduan and Giovanetti, Marta and Tegally, Houriiyah and San, James E. and Lessells, Richard and Cuadros, Diego and Martin, Darren P. and Rasmussen, David A. and Zekri, Abdel-Rahman N. and Sangare, Abdoul K. and et al.}, year={2021}, month={Oct}, pages={423-+} }
 @article{kepler_hamins-puertolas_rasmussen_2021, title={Decomposing the sources of SARS-CoV-2 fitness variation in the United States}, volume={7}, ISSN={["2057-1577"]}, DOI={10.1093/ve/veab073}, abstractNote={Abstract}, number={2}, journal={VIRUS EVOLUTION}, author={Kepler, Lenora and Hamins-Puertolas, Marco and Rasmussen, David A.}, year={2021}, month={Dec} }
 @article{graf_bello_andrade_arantes_pereira_silva_veiga_mariani_boullosa_arruda_et al._2021, title={HIV-1 molecular diversity in Brazil unveiled by 10 years of sampling by the national genotyping network}, volume={11}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-021-94542-5}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Graf, Tiago and Bello, Gonzalo and Andrade, Paula and Arantes, Ighor and Pereira, Joao Marcos and Silva, Alexandre Bonfim and Veiga, Rafael V. and Mariani, Diana and Boullosa, Lidia Theodoro and Arruda, Monica B. and et al.}, year={2021}, month={Aug} }
 @article{dawson_rasmussen_peng_lanzas_2021, title={Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen}, volume={18}, ISSN={["1742-5662"]}, url={https://doi.org/10.1098/rsif.2021.0041}, DOI={10.1098/rsif.2021.0041}, abstractNote={Indirect (environmental) and direct (host–host) transmission pathways cannot easily be distinguished when they co-occur in epidemics, particularly when they occur on similar time scales. Phylodynamic reconstruction is a potential approach to this problem that combines epidemiological information (temporal, spatial information) with pathogen whole-genome sequencing data to infer transmission trees of epidemics. However, factors such as differences in mutation and transmission rates between host and non-host environments may obscure phylogenetic inference from these methods. In this study, we used a network-based transmission model that explicitly models pathogen evolution to simulate epidemics with both direct and indirect transmission. Epidemics were simulated according to factorial combinations of direct/indirect transmission proportions, host mutation rates and conditions of environmental pathogen growth. Transmission trees were then reconstructed using the phylodynamic approach SCOTTI (structured coalescent transmission tree inference) and evaluated. We found that although insufficient diversity sets a lower bound on when accurate phylodynamic inferences can be made, transmission routes and assumed pathogen lifestyle affected pathogen population structure and subsequently influenced both reconstruction success and the likelihood of direct versus indirect pathways being reconstructed. We conclude that prior knowledge of the likely ecology and population structure of pathogens in host and non-host environments is critical to fully using phylodynamic techniques.}, number={179}, journal={JOURNAL OF THE ROYAL SOCIETY INTERFACE}, author={Dawson, Daniel and Rasmussen, David and Peng, Xinxia and Lanzas, Cristina}, year={2021}, month={Jun} }
 @article{rasmussen_grunwald_2021, title={Phylogeographic Approaches to Characterize the Emergence of Plant Pathogens}, volume={111}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO-07-20-0319-FI}, abstractNote={ 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. }, number={1}, journal={PHYTOPATHOLOGY}, author={Rasmussen, David A. and Grunwald, Niklaus J.}, year={2021}, month={Jan}, pages={68–77} }
 @misc{gadhave_gautam_rasmussen_srinivasan_2020, title={Aphid Transmission ofPotyvirus: The Largest Plant-Infecting RNA Virus Genus}, volume={12}, ISSN={["1999-4915"]}, DOI={10.3390/v12070773}, abstractNote={Potyviruses are the largest group of plant infecting RNA viruses that cause significant losses in a wide range of crops across the globe. The majority of viruses in the genus Potyvirus are transmitted by aphids in a non-persistent, non-circulative manner and have been extensively studied vis-à-vis their structure, taxonomy, evolution, diagnosis, transmission, and molecular interactions with hosts. This comprehensive review exclusively discusses potyviruses and their transmission by aphid vectors, specifically in the light of several virus, aphid and plant factors, and how their interplay influences potyviral binding in aphids, aphid behavior and fitness, host plant biochemistry, virus epidemics, and transmission bottlenecks. We present the heatmap of the global distribution of potyvirus species, variation in the potyviral coat protein gene, and top aphid vectors of potyviruses. Lastly, we examine how the fundamental understanding of these multi-partite interactions through multi-omics approaches is already contributing to, and can have future implications for, devising effective and sustainable management strategies against aphid-transmitted potyviruses to global agriculture.}, number={7}, journal={VIRUSES-BASEL}, author={Gadhave, Kiran R. and Gautam, Saurabh and Rasmussen, David A. and Srinivasan, Rajagopalbabu}, year={2020}, month={Jul} }
 @article{ruark-seward_bonville_kennedy_rasmussen_2020, title={Evolutionary dynamics of Tomato spotted wilt virus within and between alternate plant hosts and thrips}, volume={10}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-020-72691-3}, DOI={10.1038/s41598-020-72691-3}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Ruark-Seward, Casey L. and Bonville, Brian and Kennedy, George and Rasmussen, David A.}, year={2020}, month={Sep} }
 @article{bouckaert_vaughan_barido-sottani_duchene_fourment_gavryushkina_heled_jones_kuehnert_de maio_et al._2019, title={BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis}, volume={15}, ISSN={["1553-7358"]}, DOI={10.1371/journal.pcbi.1006650}, abstractNote={Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release. Author summary Bayesian phylogenetic inference methods have undergone considerable development in recent years, and joint modelling of rich evolutionary data, including genomes, phenotypes and fossil occurrences is increasingly common. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing scientific software is increasingly crucial to advancement in many fields of biology. The challenges range from practical software development and engineering, distributed team coordination, conceptual development and statistical modelling, to validation and testing. BEAST 2 is one such computational software platform for phylogenetics, population genetics and phylodynamics, and was first announced over 4 years ago. Here we describe the full range of new tools and models available on the BEAST 2.5 platform, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics.}, number={4}, journal={PLOS COMPUTATIONAL BIOLOGY}, author={Bouckaert, Remco and Vaughan, Timothy G. and Barido-Sottani, Joelle and Duchene, Sebastian and Fourment, Mathieu and Gavryushkina, Alexandra and Heled, Joseph and Jones, Graham and Kuehnert, Denise and De Maio, Nicola and et al.}, year={2019}, month={Apr} }
 @article{rasmussen_stadler_2019, title={Coupling adaptive molecular evolution to phylodynamics using fittness-dependent birth-death models}, volume={8}, ISSN={["2050-084X"]}, DOI={10.7554/eLife.45562}, abstractNote={Beneficial and deleterious mutations cause the fitness of lineages to vary across a phylogeny and thereby shape its branching structure. While standard phylogenetic models do not allow mutations to feedback and shape trees, birth-death models can account for this feedback by letting the fitness of lineages depend on their type. To date, these multi-type birth-death models have only been applied to cases where a lineage’s fitness is determined by a single character state. We extend these models to track sequence evolution at multiple sites. This approach remains computationally tractable by tracking the genotype and fitness of lineages probabilistically in an approximate manner. Although approximate, we show that we can accurately estimate the fitness of lineages and site-specific mutational fitness effects from phylogenies. We apply this approach to estimate the population-level fitness effects of mutations in Ebola and influenza virus, and compare our estimates with in vitro fitness measurements for these mutations.}, journal={ELIFE}, author={Rasmussen, David A. and Stadler, Tanja}, year={2019}, month={Aug} }
 @article{chen_dessau_rotenberg_rasmussen_whitfield_2019, title={Entry of bunyaviruses into plants and vectors}, volume={104}, ISBN={["978-0-12-818394-6"]}, ISSN={["1557-8399"]}, DOI={10.1016/bs.aivir.2019.07.001}, abstractNote={The majority of plant-infecting viruses are transmitted by arthropod vectors that deliver them directly into a living plant cell. There are diverse mechanisms of transmission ranging from direct binding to the insect stylet (non-persistent transmission) to persistent-propagative transmission in which the virus replicates in the insect vector. Despite this diversity in interactions, most arthropods that serve as efficient vectors have feeding strategies that enable them to deliver the virus into the plant cell without extensive damage to the plant and thus effectively inoculate the plant. As such, the primary virus entry mechanism for plant viruses is mediated by the biological vector. Remarkably, viruses that are transmitted in a propagative manner (bunyaviruses, rhabdoviruses, and reoviruses) have developed an ability to replicate in hosts from two kingdoms. Viruses in the order Bunyavirales are of emerging importance and with the advent of new sequencing technologies, we are getting unprecedented glimpses into the diversity of these viruses. Plant-infecting bunyaviruses are transmitted in a persistent, propagative manner must enter two unique types of host cells, plant and insect. In the insect phase of the virus life cycle, the propagative viruses likely use typical cellular entry strategies to traverse cell membranes. In this review, we highlight the transmission and entry strategies of three genera of plant-infecting bunyaviruses: orthotospoviruses, tenuiviruses, and emaraviruses.}, journal={VIRUS ENTRY}, author={Chen, Yuting and Dessau, Moshe and Rotenberg, Dorith and Rasmussen, David A. and Whitfield, Anna E.}, year={2019}, pages={65–96} }
 @article{vaughan_leventhal_rasmussen_drummond_welch_stadler_2019, title={Estimating Epidemic Incidence and Prevalence from Genomic Data}, volume={36}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msz106}, abstractNote={Abstract}, number={8}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Vaughan, Timothy G. and Leventhal, Gabriel E. and Rasmussen, David A. and Drummond, Alexei J. and Welch, David and Stadler, Tanja}, year={2019}, month={Aug}, pages={1804–1816} }
 @article{mueller_rasmussen_stadler_2018, title={MASCOT: parameter and state inference under the marginal structured coalescent approximation}, volume={34}, ISSN={["1460-2059"]}, DOI={10.1093/bioinformatics/bty406}, abstractNote={Abstract}, number={22}, journal={BIOINFORMATICS}, author={Mueller, Nicola F. and Rasmussen, David and Stadler, Tanja}, year={2018}, month={Nov}, pages={3843–3848} }
 @article{rasmussen_wilkinson_vandormael_tanser_pillay_stadler_oliveira_2018, title={Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa}, volume={4}, ISSN={["2057-1577"]}, DOI={10.1093/ve/vey037}, abstractNote={Abstract Despite increasing access to antiretrovirals, HIV incidence in rural KwaZulu-Natal remains among the highest ever reported in Africa. While many epidemiological factors have been invoked to explain such high incidence, widespread human mobility and viral movement suggest that transmission between communities may be a major source of new infections. High cross-community transmission rates call into question how effective increasing the coverage of antiretroviral therapy locally will be at preventing new infections, especially if many new cases arise from external introductions. To help address this question, we use a phylodynamic model to reconstruct epidemic dynamics and estimate the relative contribution of local transmission versus external introductions to overall incidence in KwaZulu-Natal from HIV-1 phylogenies. By comparing our results with population-based surveillance data, we show that we can reliably estimate incidence from viral phylogenies once viral movement in and out of the local population is accounted for. Our analysis reveals that early epidemic dynamics were largely driven by external introductions. More recently, we estimate that 35 per cent (95% confidence interval: 20–60%) of new infections arise from external introductions. These results highlight the growing need to consider larger-scale regional transmission dynamics when designing and testing prevention strategies.}, number={2}, journal={VIRUS EVOLUTION}, author={Rasmussen, David A. and Wilkinson, Eduan and Vandormael, Alain and Tanser, Frank and Pillay, Deenan and Stadler, Tanja and Oliveira, Tulio}, year={2018}, month={Jul} }