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Dellicour, S.

Publications and source records attributed to Dellicour, S..

30 records · Page 2Linked to original sources
bioRxiv2022

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in Mexico. Lineages B.1.1.222 and B.1.1.519 exhibited similar dynamics, constituting clades that likely originated in Mexico and persisted for >12 months. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. For the largest B.1.617.2 clades, we further explored viral lineage movements across Mexico. Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.

evolutionary biology↗
bioRxiv2021

Considerable escape of SARS-CoV-2 variant Omicron to antibody neutralization

The SARS-CoV-2 Omicron variant was first identified in November 2021 in Botswana and South Africa1,2. It has in the meantime spread to many countries and is expected to rapidly become dominant worldwide. The lineage is characterized by the presence of about 32 mutations in the Spike, located mostly in the N-terminal domain (NTD) and the receptor binding domain (RBD), which may enhance viral fitness and allow antibody evasion. Here, we isolated an infectious Omicron virus in Belgium, from a traveller returning from Egypt. We examined its sensitivity to 9 monoclonal antibodies (mAbs) clinically approved or in development3, and to antibodies present in 90 sera from COVID-19 vaccine recipients or convalescent individuals. Omicron was totally or partially resistant to neutralization by all mAbs tested. Sera from Pfizer or AstraZeneca vaccine recipients, sampled 5 months after complete vaccination, barely inhibited Omicron. Sera from COVID-19 convalescent patients collected 6 or 12 months post symptoms displayed low or no neutralizing activity against Omicron. Administration of a booster Pfizer dose as well as vaccination of previously infected individuals generated an anti-Omicron neutralizing response, with titers 5 to 31 fold lower against Omicron than against Delta. Thus, Omicron escapes most therapeutic monoclonal antibodies and to a large extent vaccine-elicited antibodies.

immunology↗
bioRxiv2021

Predicting the evolution of Lassa Virus endemic area and population at risk over the next decades

Lassa fever is listed among the diseases that pose the greatest risks to public health by the World Health Organization. This severe viral hemorrhagic fever is caused by Lassa virus, a zoonotic pathogen that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate change, transformations in land use, and human population growth could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. We project that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in areas suitable for Lassa virus may grow from about 100 million to 700 million by 2070. By analysing geotagged viral genomes, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades. Our results highlight how the endemic area of Lassa virus may expand well beyond West Africa in the next decades due to human impact on the environment, putting hundreds of million more people at risk of infection.

microbiology↗
bioRxiv2021

KoT: an automatic implementation of the K/θ method for species delimitation

AO_SCPLOWBSTRACTC_SCPLOWK/{theta} is a method to delineate species that rests on the calculation of the ratio between the average distance K separating two putative species-level clades and the genetic diversity{theta} of these clades. Although this method is explicitly rooted in population genetic theory, it was never benchmarked due to the absence of a program allowing automated analyses. For the same reason, its application by hand was limited to small datasets of a few tens of sequences. We present an automatic implementation of the K/{theta} method, dubbed KoT (short for "K over Theta"), that takes as input a FASTA file, builds a neighbour-joining tree, and returns putative species boundaries based on a user-specified K/{theta} threshold. This automatic implementation avoids errors and makes it possible to apply the method to datasets comprising many sequences, as well as to test easily the impact of choosing different K/{theta} threshold ratios. KoT is implemented in Haxe, with a javascript webserver interface freely available at https://eeg-ebe.github.io/KoT/

evolutionary biology↗
bioRxiv2020

A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (SARS-CoV-2) have been generated and shared with the scientific community. The unparalleled volume of available genetic data presents a unique opportunity to gain real-time insights into the virus transmission during the pandemic, but also a daunting computational hurdle if analysed with gold-standard phylogeographic approaches. 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 the Belgium epidemic, with one of the highest spatial density of available SARS-CoV-2 genomes. At the global scale, our analyses confirm the importance of external introduction events in establishing multiple transmission chains in the country. At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. 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.

evolutionary biology↗
bioRxiv2020

nosoi: a stochastic agent-based transmission chain simulation framework in R

The transmission process of an infectious agent creates a connected chain of hosts linked by transmission events, known as a transmission chain. Reconstructing transmission chains remains a challenging endeavor, except in rare cases characterized by intense surveillance and epidemiological inquiry. Inference frameworks attempt to estimate or approximate these transmission chains but the accuracy and validity of such methods generally lack formal assessment on datasets for which the actual transmission chain was observed. We here introduce nosoi, an open-source R package that offers a complete, tunable, and expandable agent-based framework to simulate transmission chains under a wide range of epidemiological scenarios for single-host and dual-host epidemics. nosoi is accessible through GitHub and CRAN, and is accompanied by extensive documentation, providing help and practical examples to assist users in setting up their own simulations. Once infected, each host or agent can undergo a series of events during each time step, such as moving (between locations) or transmitting the infection, all of these being driven by user-specified rules or data, such as travel patterns between locations. nosoi is able to generate a multitude of epidemic scenarios, that can - for example - be used to validate a wide range of reconstruction methods, including epidemic modeling and phylodynamic analyses. nosoi also offers a comprehensive framework to leverage empirically acquired data, allowing the user to explore how variations in parameters can affect epidemic potential. Aside from research questions, nosoi can provide lecturers with a complete teaching tool to offer students a handson exploration of the dynamics of epidemiological processes and the factors that impact it. Because the package does not rely on mathematical formalism but uses a more intuitive algorithmic approach, even extensive changes of the entire model can be easily and quickly implemented.

ecology↗
bioRxiv2019

Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing

Computational 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 been responsible for substantial impacts on public, veterinary, and wildlife health. WNV isolates have been sampled at various times and locations across North America since its introduction to New York twenty years ago. We exploit this genetic data repository to demonstrate that factors hypothesised to affect viral dispersal and demography can be formally tested. Specifically, we detail and apply an analytical workflow consisting of state-of-the art methods that we further improve to test the impact of environmental factors on the dispersal locations, velocity, and frequency of viral lineages, as well as on the genetic diversity of the viral population 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. Using a simulation procedure, we find no evidence that viral lineages preferentially circulate within the same migratory bird flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient. Finally, we also separately apply our testing approaches on the three WNV genotypes that circulated in North America in order to understand and compare their dispersal ability. Our study demonstrates that the development and application of statistical approaches, coupled with comprehensive pathogen genomic data, can address epidemiological questions that might otherwise be difficult or impractically expensive to answer.

evolutionary biology↗
bioRxiv2019

Genomic Surveillance of Yellow Fever Virus Epidemic Waves in Sao Paulo, Brazil, 2017 - 2018

Sao Paulo (SP), a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in SP, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in SP, we generated and analysed virus genomic data and epizootic case data from NHP in SP. We report the occurrence of three spatiotemporally distinct phases of the outbreak in SP prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in SP, mostly sampled from non-human primates between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in Sao Paulo state at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern Sao Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of SP state. Our results shed light on the sylvatic transmission of yellow fever in highly fragmented forested regions in SP state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species. Authors SummarySince July 2016, the southeast region of Brazil has experienced the largest yellow fever virus (YFV) outbreak in decades. Sao Paulo is the most densely populated state in southeast Brazil. The outbreak has caused serious public health concern in the state, as YFV does not normally circulate widely there and most of the 21 million inhabitants were correspondingly unvaccinated against YFV when the outbreak began. In Brazil, YFV typically circulates among non-human primates, and human cases represent isolated spillover events from this predominantly sylvatic cycle. Understanding the epidemiological dynamics and spread of YFV in non-human primates is therefore critical for contextualising human cases, and guiding vaccination strategies that can better protect local human populations. Here, we aim to contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in SP. We analyse the geographic and temporal distribution of observed cases of YFV in non-human primates in Sao Paulo state, and identify three distinct phases of the epizootic. We generate sequence data from 51 YFV-positive cases and perform phylogenetic and phylogeographic analyses aimed at understanding the spatial spread of YFV in Sao Paulo state. Analyses of these data indicate that YFV spread from the north of Sao Paulo state into more densely populated southern regions. Although we observe substantial heterogeneity in the rate at which different sampled YFV lineages spread, the typical rate of spread was low with a mean rate of ~1 km per day. This is consistent with a scenario in which the majority of transmission events occurred between non-human primates and sylvatic vectors across forested patches. Article Summary LineGenomic surveillance of yellow fever in Sao Paulo during the 2016-2018 epizootic

epidemiology↗
bioRxiv2019

Global phylogeographical patterns in the spread of foot-and-mouth disease virus

Foot-and-mouth disease virus (FMDV) has proven its potential to propagate across local and international borders on numerous occasions, but yet details about the directionality of the spread along with the role of the different host in transmission remain unexplored. To elucidate FMDV global spread characteristics, we studied the spatiotemporal phylodynamics of serotypes O, A, Asia1, SAT1, SAT2, and SAT3, based on more than 50 years of phylogenetic and epidemiological information. Our results revealed phylogeographic patterns, dispersal rates, and the role of host species in the dispersal and maintenance of virus circulation. Contrary to previous studies, our results showed that three serotypes were monophyletic (O, A, and Asia1), while all SATs serotypes did not evidence a defined common ancestor. Root state posterior probability (RSPP) analysis suggested Belgium as the country of origin for serotype O (RSPP=0.27). India was the ancestral country for serotypes A (RSPP= 0.28), and Asia-1 (RSPP= 0.34), while Uganda appeared as the most likely origin country of all SAT serotypes (RSPP> 0.45). Furthermore, we identified the key centers of dispersal of the virus, being China, India and Uganda the most important ones. Bayes factor analysis revealed cattle as the major source of the virus for most of the serotypes (RSPP> 0.63), where the most important host-species transition route for serotypes O, A, and Asia1 was from cattle Bos taurus to swine Sus scrofa domesticus (BF>500), while, for SAT serotypes was from B. taurus to African buffalo Syncerus caffer. This study provides significant insights into the spatiotemporal dynamics of the global circulation of FMDV serotypes, by characterizing the viral routes of spread at serotype level, especially uncovering the importance of host species for each serotype in the evolution and spread of FMDV which further improve future decisions for more efficient control and eradication.

epidemiology↗
bioRxiv2018

Genomic and epidemiological monitoring of yellow fever virus transmission potential

The yellow fever virus (YFV) epidemic that began in Dec 2016 in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes sp. vectors highlights the urgent need to monitor the risk of re-establishment of domestic YFV transmission in the Americas. We use a suite of epidemiological, spatial and genomic approaches to characterize YFV transmission. We show that the age- and sex-distribution of human cases in Brazil is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally using a new protocol reveals an early phase of sylvatic YFV transmission restricted to Minas Gerais, followed in late 2016 by a rise in viral spillover to humans, and the southwards spatial expansion of the epidemic towards previously YFV-free areas. Our results establish a framework for monitoring YFV transmission in real-time, contributing to the global strategy of eliminating future yellow fever epidemics.

epidemiology↗
bioRxiv2017

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100046). The recent Ebola virus (EBOV) outbreak in West Africa witnessed considerable efforts to obtain viral genomic data as the epidemic was unfolding. If such data can be deployed in real-time, molecular epidemiological investigations could play a role in complementing contact tracing undertaken by public health agencies. Analysing the EBOV genomes accumulated to date can also deliver insights into epidemic dynamics. Such analyses have been shown that metapopulation dynamics were critical for EBOV dispersal between rural and urban areas during the epidemic, but the implications for specific intervention scenarios remain unclear. Here, we address this issue using a collection of phylodynamic approaches. We show that long-distance dispersal events (between administrative areas >250 km apart) were not crucial for epidemic expansion and that preventing viral lineage movement to any given administrative area would, in most cases, have had little impact. However, urban areas - specifically those encompassing the three capital cities and their suburbs - were critical in attracting and further disseminating the virus: preventing viral lineage movement to all three simultaneously would have contained epidemic size by two-thirds. Using continuous phylogeographic reconstructions we estimate a distance kernel for EBOV spread and reveal considerable heterogeneity in dispersal velocity through time. We also show that announcements of border closures were followed by a significant but transient effect on international virus dispersal. By quantifying the hypothetical impact of different intervention strategies as well as the impact of barriers on dispersal frequency, our study illustrates how phylodynamic analyses can help to address specific epidemiological and outbreak control questions.

epidemiology↗