Publications by authors named "Debarre F"

Article Synopsis
  • Zoonotic viruses, like SARS-CoV-2, can spill over from animals to humans, often linked to animal trade, with COVID-19 traced back to the Huanan Seafood Wholesale Market.
  • Analysis of environmental samples from the market in early 2020 shows high genetic diversity of SARS-CoV-2, especially near a wildlife stall that had a variety of wildlife DNA, including potential intermediate hosts.
  • The research combines genomic techniques to identify specific animal species and suggest which ones should be prioritized for further research on their role in transmitting the virus.
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Engineered gene-drive techniques for population modification and/or suppression have the potential for tackling complex challenges, including reducing the spread of diseases and invasive species. Gene-drive systems with low threshold frequencies for invasion, such as homing-based gene drive, require initially few transgenic individuals to spread and are therefore easy to introduce. The self-propelled behavior of such drives presents a double-edged sword, however, as the low threshold can allow transgenic elements to expand beyond a target population.

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Article Synopsis
  • Researchers used early case data and a new modeling approach to estimate the timeline of the COVID-19 pandemic's spread, particularly focusing on the Alpha variant.
  • Their findings suggest the first Alpha infection occurred around August 21, 2020, and the initial SARS-CoV-2 infection in Wuhan on November 28, 2019.
  • The model they developed can be adapted for studying the emergence of other infectious outbreaks beyond COVID-19.
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While the exact context of the emergence of SARS-CoV-2 remains uncertain, data accumulated since 2020 have provided an increasingly more precise picture of Wuhan's Huanan Seafood Wholesale Market, to which the earliest clusters of human cases of Covid-19 were linked. After the market closed on January 1st 2020, teams from the Chinese Center for Disease Control and Prevention collected environmental samples, and sequenced them. Metagenomic sequencing data from these samples were shared in early 2023.

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Article Synopsis
  • Zoonotic virus spillovers, including the COVID-19 pandemic, are linked to animal trade, with the Huanan Seafood Market in Wuhan being a focal point of investigation.
  • Analysis of environmental samples from this market showed a specific wildlife stall with high SARS-CoV-2 positivity and identified various animal DNA, including raccoon dogs, which can transmit the virus.
  • The study used genetic data to suggest potential intermediate hosts for SARS-CoV-2, aiming to guide future testing and viral sampling efforts.
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The use of an antibiotic may lead to the emergence and spread of bacterial strains resistant to this antibiotic. Experimental and theoretical studies have investigated the drug dose that minimizes the risk of resistance evolution over the course of treatment of an individual, showing that the optimal dose will either be the highest or the lowest drug concentration possible to administer; however, no analytical results exist that help decide between these two extremes. To address this gap, we develop a stochastic mathematical model of bacterial dynamics under antibiotic treatment.

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Understanding the temporal spread of gene drive alleles-alleles that bias their own transmission-through modeling is essential before any field experiments. In this paper, we present a deterministic reaction-diffusion model describing the interplay between demographic and allelic dynamics, in a one-dimensional spatial context. We focused on the traveling wave solutions, and more specifically, on the speed of gene drive invasion (if successful).

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Objectives: We aimed to quantify how the vaccine efficacy of BNT162b2, messenger RNA-1273, AD26.COV2-S, and ChAdOx1 nCoV-19 against detected infection by the SARS-CoV-2 Delta and Omicron variants varied by time since the last dose, vaccine scheme, age, and geographic areas.

Methods: We analyzed 3,261,749 community polymerase chain reaction tests conducted by private laboratories in France from December 2021 to March 2022 with a test-negative design comparing vaccinated to unvaccinated individuals.

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Background: To encourage Covid-19 vaccination, France introduced during the Summer 2021 a 'Sanitary Pass', which morphed into a 'Vaccine Pass' in early 2022. While the sanitary pass led to an increase in Covid-19 vaccination rates, spatial heterogeneities in vaccination rates remained. To identify potential determinants of these heterogeneities and evaluate the French sanitary and vaccine passes' efficacies in reducing them, we used a data-driven approach on exhaustive nationwide data, gathering 141 socio-economic, political and geographic indicators.

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Article Synopsis
  • Evaluating emerging SARS-CoV-2 variants is crucial for understanding pandemic risks, focusing on their growth advantage determined by the number of secondary infections (R advantage) and their timing (generation time).
  • The study introduces a new analytical framework to assess both R advantage and generation time, revealing that variants with earlier transmission are favored during fast epidemic growth, while those with later transmission thrive in slower conditions.
  • Findings show that the Alpha variant has a 54% R advantage over previous strains, while Delta has a 140% advantage over Alpha, with similar generation times to earlier strains, aiding in predicting future viral dynamics.
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  • The paper analyzes a reaction-diffusion model for gene drive invasion in populations, focusing on how a gene drive that negatively affects individual fitness influences population dynamics.
  • The study emphasizes that the gene drive must counteract demographic forces that could hinder its spread, a factor often overlooked in previous models.
  • Results highlight the importance of understanding the interaction between population dynamics and genetics, suggesting that this interplay can reverse gene drive invasion success and has broader implications for similar biological systems.
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Article Synopsis
  • The study focuses on how randomness affects the early stages of emerging epidemics, particularly how it can influence the initial growth trajectory of local infection clusters.
  • Researchers review existing mathematical results and present new findings that highlight the role of stochasticity in accelerating the early spread of infections that eventually escalate.
  • The work includes practical applications, such as estimating the detection time of infections based on testing efforts, and it suggests optimal testing frequencies to identify outbreaks before they grow too large.
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We compared PCR results from SARS-CoV-2-positive patients tested in the community in France from 14 June to 30 July 2021. In asymptomatic individuals, Cq values were significantly higher in fully vaccinated than non-fully vaccinated individuals (effect size: 1.7; 95% CI: 1-2.

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  • Evolutionary rescue is the process where a population adapts to environmental changes to avoid extinction, and dispersal plays a key role in this process.
  • In a modeled environment with degrading patches, different dispersal rates affect the chances of rescue: low and high dispersal rates can increase survival, while intermediate rates may decrease it.
  • Mutant individuals that can adapt are more successful when they migrate to already degraded areas, and they are more likely to first emerge in non-degraded patches, highlighting the importance of habitat choice in population dynamics.
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Repurposed drugs that are safe and immediately available constitute a first line of defense against new viral infections. Despite limited antiviral activity against SARS-CoV-2, several drugs are being tested as medication or as prophylaxis to prevent infection. Using a stochastic model of early phase infection, we evaluate the success of prophylactic treatment with different drug types to prevent viral infection.

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Multilocus genetic processes in subdivided populations can be complex and difficult to interpret using theoretical population genetics models. Genetic simulators offer a valid alternative to study multilocus genetic processes in arbitrarily complex scenarios. However, the use of forward-in-time simulators in realistic scenarios involving high numbers of individuals distributed in multiple local populations is limited by computation time and memory requirements.

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CRISPR-based homing gene drive is a genetic control technique aiming to modify or eradicate natural populations. This technique is based on the release of individuals carrying an engineered piece of DNA that can be preferentially inherited by the progeny. The development of countermeasures is important to control the spread of gene drives, should they result in unanticipated damages.

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Population management using artificial gene drives (alleles biasing inheritance, increasing their own transmission to offspring) is becoming a realistic possibility with the development of CRISPR-Cas genetic engineering. A gene drive may, however, have to be stopped. "Antidotes" (brakes) have been suggested, but have been so far only studied in well-mixed populations.

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Species interactions lie at the heart of many theories of macroevolution, from adaptive radiation to the Red Queen. Although some theories describe the imprint that interactions will have over long timescales, we are still missing a comprehensive understanding of the effects of interactions on macroevolution. Current research shows strong evidence for the impact of interactions on macroevolutionary patterns of trait evolution and diversification, yet many macroevolutionary studies have only a tenuous relationship to ecological studies of interactions over shorter timescales.

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By consuming and producing environmental resources, organisms inevitably change their habitats. The consequences of such environmental modifications can be detrimental or beneficial not only to the focal organism but also to other organisms sharing the same environment. Social evolution theory has been very influential in studying how social interactions mediated by public 'goods' or 'bads' evolve by emphasizing the role of spatial structure.

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