8 research outputs found
On the use of phylogeographic inference to infer the dispersal history of rabies virus: A review study
No full textRabies is a neglected zoonotic disease which is caused by negative strand RNA-viruses belonging to the genus Lyssavirus. Within this genus, rabies viruses circulate in a diverse set of mammalian reservoir hosts, is present worldwide, and is almost always fatal in non-vaccinated humans. Approximately 59,000 people are still estimated to die from rabies each year, leading to a global initiative to work towards the goal of zero human deaths from dog-mediated rabies by 2030, requiring scientific efforts from different research fields. The past decade has seen a much increased use of phylogeographic and phylodynamic analyses to study the evolution and spread of rabies virus. We here review published studies in these research areas, making a distinction between the geographic resolution associated with the available sequence data. We pay special attention to environmental factors that these studies found to be relevant to the spread of rabies virus. Importantly, we highlight a knowledge gap in terms of applying these methods when all required data were available but not fully exploited. We conclude with an overview of recent methodological developments that have yet to be applied in phylogeographic and phylodynamic analyses of rabies virus.SCOPUS: re.jinfo:eu-repo/semantics/publishe
Untangling introductions and persistence in COVID-19 resurgence in Europe
No full textAfter the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting in late summer 2020 that was deadlier and more difficult to contain
1. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave
2. Here we build a phylogeographical model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the resurgence of COVID-19 in Europe. We inform this model using genomic, mobility and epidemiological data from 10 European countries and estimate that in many countries more than half of the lineages circulating in late summer resulted from new introductions since 15 June 2020. The success in onward transmission of newly introduced lineages was negatively associated with the local incidence of COVID-19 during this period. The pervasive spread of variants in summer 2020 highlights the threat of viral dissemination when restrictions are lifted, and this needs to be carefully considered in strategies to control the current spread of variants that are more transmissible and/or evade immunity. Our findings indicate that more effective and coordinated measures are required to contain the spread through cross-border travel even as vaccination is reducing disease burden.
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Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley
No full textInternational audienceTo 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
Un workflow phylodynamique pour obtenir rapidement un aperçu de l'historique de la dispersion et de la dynamique des lignées SARS-CoV-2
No full textpeer reviewedSince the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (SARS-CoV-2) have been publicly released. The resulting volume of available genetic data presents a unique opportunity to gain real-time insights into the pandemic, but also a daunting computational hurdle if analysed with gold-standard phylogeographic methods. We
here describe and apply an analytical pipeline that is a compromise between fast and rigorous analytical steps. As a proof of concept, we focus on Belgium, one of the countries with the highest
spatial density of sequenced SARS-CoV-2 genomes. At the global scale, our analyses confirm the importance of external introduction events in establishing transmission chains in the country. At
the country scale, our spatially-explicit phylogeographic analyses highlight an impact of the national lockdown of mid-March on the dispersal velocity of viral lineages. Our pipeline has the
potential to be quickly applied to other countries or regions, with key benefits in complementing epidemiological analyses in assessing the impact of intervention measures or their progressive easement
Relax, Keep Walking - A Practical Guide to Continuous Phylogeographic Inference with BEAST
No full textSpatially explicit phylogeographic analyses can be performed with an inference framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This core model was first implemented 10 years ago and has opened up new opportunities in the field of phylodynamics, allowing researchers to map and analyze the spatial dissemination of rapidly evolving pathogens. We here provide a detailed and step-by-step guide on how to set up, run, and interpret continuous phylogeographic analyses using the programs BEAUti, BEAST, Tracer, and TreeAnnotator.sponsorship: S.D. is supported by the Fonds National de la Recherche Scientifique (FNRS, Belgium). S.D. and P.L. acknowledge funding from the European Union's Horizon 2020 Project MOOD (Grant Agreement No. 874850). N.R.F. is supported by a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (204311/Z/16/Z) and by a Medical Research Council-S~ao Paulo Research Foundation CADDE partnership award (MR/S0195/1 and FAPESP 18/14389-0). A.R., M.A.S., and P.L. acknowledge funding from the European Research Council under the European Union's Horizon 2020 Research and Innovation Program (Grant Agreement No. 725422-ReservoirDOCS) and from the Wellcome Trust through project 206298/Z/17/Z (The Artic Network). M.A.S. acknowledges support from National Institutes of Health (Grant Nos. U19 AI135995 and R65 AI149004). P.L. acknowledges support by the Research Foundation-Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen, G066215N, G0D5117N, and G0B9317N). This work is published with the support of the Fondation Universitaire de Belgique. (Fonds National de la Recherche Scientifique (FNRS, Belgium), European Union's Horizon 2020 Project MOOD|874850, Wellcome Trust|204311/Z/16/Z, Wellcome Trust|206298/Z/17/Z, Royal Society|204311/Z/16/Z, Medical Research Council-Sao Paulo Research Foundation CADDE partnership award|MR/S0195/1, Medical Research Council-Sao Paulo Research Foundation CADDE partnership award|FAPESP 18/14389-0, European Research Council under the European Union's Horizon 2020 Research and Innovation Program|725422-ReservoirDOCS, National Institutes of Health|U19 AI135995, National Institutes of Health|R65 AI149004, Research Foundation-Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen)|G066215N, Research Foundation-Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen)|G0D5117N, Research Foundation-Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen)|G0B9317N, Fondation Universitaire de Belgique, Wellcome Trust|204311/Z/16/Z, MRC|MR/S019510/1, Medical Research Council|MR/R015600/1, National Institute of Allergy and Infectious Diseases|U19AI135995, Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)|18/14389-0)status: Publishe
Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City
No full textDuring 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.sponsorship: SD is supported by the Fonds National de la Recherche Scientifique (FNRS, Belgium). SLH acknowledges support from the Research Foundation -Flanders (Fonds voor Wetenschappelijk Onderzoek -Vlaanderen, G0D5117N). BV is supported by a post-doctoral research fellowship (grant nr. 12U7121N) of the Research Foundation -Flanders (Fonds voor Wetenschappelijk Onderzoek). AC was supported by grants from the NIH (San Diego Center for AIDS Research, CFAR, AI306214 and AI100665), and the James B. Pendleton Charitable Trust. MTM is supported by a NIH Grant (R35GM119703). GWH is jointly funded by the South African Medical Research Council and the National Institutes of Health, USA grant 1U01Al152151-01. GB acknowledges support from the Research Foundation -Flanders (Fonds voor Wetenschappelijk Onderzoek -Vlaanderen, G0E1420N, G098321N) and from the Interne Fondsen KU Leuven/Internal Funds KU Leuven under grant agreement C14/18/094. RD was partially supported by the NIH grant 1R01AI122953. AH, SR, CM, and PZ are supported by the Genome Technology Center, which is in part by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (Fonds National de la Recherche Scientifique (FNRS, Belgium), Research Foundation -Flanders (Fonds voor Wetenschappelijk Onderzoek -Vlaanderen)|G0D5117N, Research Foundation -Flanders (Fonds voor Wetenschappelijk Onderzoek -Vlaanderen)|12U7121N, Research Foundation -Flanders (Fonds voor Wetenschappelijk Onderzoek -Vlaanderen)|G0E1420N, Research Foundation -Flanders (Fonds voor Wetenschappelijk Onderzoek -Vlaanderen)|G098321N, NIH (San Diego Center for AIDS Research, CFAR)|AI306214, NIH (San Diego Center for AIDS Research, CFAR)|AI100665, James B. Pendleton Charitable Trust, NIH|R35GM119703, NIH|1R01AI122953, South African Medical Research Council, National Institutes of Health, USA|1U01Al152151-01, Genome Technology Center, Cancer Center Support Grant at the Laura and Isaac Perlmutter Cancer Center|P30CA016087, Interne Fondsen KU Leuven/Internal Funds KU Leuven|C14/18/094, National Institute of Allergy and Infectious Diseases|K24AI100665)status: Publishe
Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework
No full textComputational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We illustrate our approach by focusing on the West Nile virus (WNV) spread in North America that has substantially impacted public, veterinary, and wildlife health. We apply an analytical workflow to a comprehensive WNV genome collection to test the impact of environmental factors on the dispersal of viral lineages and on viral population genetic diversity through time. We find that WNV lineages tend to disperse faster in areas with higher temperatures and we identify temporal variation in temperature as a main predictor of viral genetic diversity through time. By contrasting inference with simulation, we find no evidence for viral lineages to preferentially circulate within the same migratory bird flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient.sponsorship: We are grateful to Frank La Sorte for sharing their estimated flyway grids. The research leading to these results has received funding from the European Research Council under the European Union's Horizon 2020 research and innovation programme (grant agreement no. 725422-ReservoirDOCS), from the Welcome Trust (Artic Network, project 206298/Z/17/Z), and from the European Union's Horizon 2020 project MOOD (grant agreement no. 874850). S.D. is supported by the Fonds National de la Recherche Scientifique (FNRS, Belgium) and was previously funded by the Fonds Wetenschappelijk Onderzoek (FWO, Belgium). S.L. and P.B. were funded by the Fonds Wetenschappelijk Onderzoek (FWO, Belgium). B.V. was supported by a postdoctoral grant (12U7118N) of the Research Foundation - Flanders (Fonds voor Wetenschappelijk Onderzoek). L.d.P. and O.G.P. are supported by the European Research Council under the European Commission Seventh Framework Programme (grant agreement no. 614725-PATHPHYLODYN) and by the Oxford Martin School. M.A.S. is partially supported by NSF grant DMS 1264153 and NIH grants R01 AI107034, U19 AI135995, and R56 AI149004. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. P.L. acknowledges support by the Research Foundation-Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen, G066215N, G0D5117N, and G0B9317N). (European Research Council under the European Union|725422-ReservoirDOCS, Welcome Trust (Artic Network)|206298/Z/17/Z, European Union|874850, Fonds National de la Recherche Scientifique (FNRS, Belgium), Fonds Wetenschappelijk Onderzoek (FWO, Belgium), Research Foundation - Flanders (Fonds voor Wetenschappelijk Onderzoek)|12U7118N, European Research Council under the European Commission|614725-PATHPHYLODYN, Oxford Martin School, NSF|DMS 1264153, NIH|R01 AI107034, NIH|U19 AI135995, NIH|R56 AI149004, Research Foundation-Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen)|G066215N, Research Foundation-Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen)|G0D5117N, Research Foundation-Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen)|G0B9317N)status: Publishe
Transmission dynamics of re-emerging rabies in domestic dogs of rural China
No full textInternational audienceDespite ongoing efforts to control transmission, rabies prevention remains a challenge in many developing countries, especially in rural areas of China where re-emerging rabies is under-reported due to a lack of sustained animal surveillance. By taking advantage of detailed genomic and epidemiological data for the re-emerging rabies outbreak in Yunnan Province, China, collected between 1999 and 2015, we reconstruct the demographic and dispersal history of domestic dog rabies virus (RABV) as well as the dynamics of dog-to-dog and dog-to-human transmission. Phylogeographic analyses reveal a lower diffusion coefficient than previously estimated for dog RABV dissemination in northern Africa. Furthermore, epidemiological analyses reveal transmission rates between dogs, as well as between dogs and humans, lower than estimates for Africa. Finally, we show that reconstructed epidemic history of RABV among dogs and the dynamics of rabid dogs are consistent with the recorded human rabies cases. This work illustrates the benefits of combining phylogeographic and epidemic modelling approaches for uncovering the spatiotemporal dynamics of zoonotic diseases, with both approaches providing estimates of key epidemiological parameters
