Search Results - "Alizon, Samuel"

Predicting the virulence of future emerging zoonotic viruses by Alizon, Samuel

“…Would you rather kiss a platypus, a hedgehog, or a llama? According to a new study in this issue of PLOS Biology, the virulence of a zoonotic virus in humans…”
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Multiple infections and the evolution of virulence by Alizon, Samuel, de Roode, Jacobus C, Michalakis, Yannis, Drake, John

“…Infections that consist of multiple parasite strains or species are common in the wild and are a major public health concern. Theory suggests that these…”
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Reconstructing contact network structure and cross-immunity patterns from multiple infection histories by Selinger, Christian, Alizon, Samuel

“…Interactions within a population shape the spread of infectious diseases but contact patterns between individuals are difficult to access. We hypothesised that…”
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Within-host and between-host evolutionary rates across the HIV-1 genome by Alizon, Samuel, Fraser, Christophe

“…HIV evolves rapidly at the epidemiological level but also at the within-host level. The virus' within-host evolutionary rates have been argued to be much…”
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Introducing the outbreak threshold in epidemiology by Hartfield, Matthew, Alizon, Samuel

“…When a pathogen is rare in a host population, there is a chance that it will die out because of stochastic effects instead of causing a major epidemic. Yet no…”
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Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study by Saulnier, Emma, Gascuel, Olivier, Alizon, Samuel

“…Inferring epidemiological parameters such as the R0 from time-scaled phylogenies is a timely challenge. Most current approaches rely on likelihood functions,…”
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Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021 by Alizon, Samuel, Haim-Boukobza, Stéphanie, Foulongne, Vincent, Verdurme, Laura, Trombert-Paolantoni, Sabine, Lecorche, Emmanuel, Roquebert, Bénédicte, Sofonea, Mircea T

“…We analysed 9,030 variant-specific RT-PCR tests performed on SARS-CoV-2-positive samples collected in France between 31 May and 21 June 2021. This analysis…”
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Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic by Richard, Quentin, Alizon, Samuel, Choisy, Marc, Sofonea, Mircea T, Djidjou-Demasse, Ramsès

“…In an epidemic, individuals can widely differ in the way they spread the infection depending on their age or on the number of days they have been infected for…”
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Predicting COVID-19 incidence in French hospitals using human contact network analytics by Selinger, Christian, Choisy, Marc, Alizon, Samuel

“…•We produce novel human contact network analytics for the COVID-19 pandemic.•We use these analytics for time series models of French hospital…”
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Virulence and Pathogenesis of HIV-1 Infection: An Evolutionary Perspective by Fraser, Christophe, Lythgoe, Katrina, Leventhal, Gabriel E., Shirreff, George, Hollingsworth, T. Déirdre, Alizon, Samuel, Bonhoeffer, Sebastian

“…Why some individuals develop AIDS rapidly whereas others remain healthy without treatment for many years remains a central question of HIV research. An…”
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Epidemic spread on weighted networks by Kamp, Christel, Moslonka-Lefebvre, Mathieu, Alizon, Samuel

“…The contact structure between hosts shapes disease spread. Most network-based models used in epidemiology tend to ignore heterogeneity in the weighting of…”
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COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences by Bourret, Jérôme, Alizon, Samuel, Bravo, Ignacio G

“…Codon Usage Preferences (CUPrefs) describe the unequal usage of synonymous codons at the gene, chromosome, or genome levels. Numerous indices have been…”
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Reconciling Pasteur and Darwin to control infectious diseases by Alizon, Samuel, Méthot, Pierre-Olivier

“…The continual emergence of new pathogens and the increased spread of antibiotic resistance in bacterial populations remind us that microbes are living entities…”
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Emerging dynamics from high-resolution spatial numerical epidemics by Thomine, Olivier, Alizon, Samuel, Boennec, Corentin, Barthelemy, Marc, Sofonea, Mircea

“…Simulating nationwide realistic individual movements with a detailed geographical structure can help optimise public health policies. However, existing tools…”
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Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model by Massey, Alexander, Boennec, Corentin, Restrepo-Ortiz, Claudia Ximena, Blanchet, Christophe, Alizon, Samuel, Sofonea, Mircea T

“…Projects such as the European Covid-19 Forecast Hub publish forecasts on the national level for new deaths, new cases, and hospital admissions, but not direct…”
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Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data by Danesh, Gonché, Virlogeux, Victor, Ramière, Christophe, Charre, Caroline, Cotte, Laurent, Alizon, Samuel

“…Opioid substitution and syringes exchange programs have drastically reduced hepatitis C virus (HCV) spread in France but HCV sexual transmission in men having…”
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Correction: Introducing the Outbreak Threshold in Epidemiology by Hartfield, Matthew, Alizon, Samuel

“…[This corrects the article DOI: 10.1371/journal.ppat.1003277.]…”
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Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26-February 16, 2021 by Haim-Boukobza, Stéphanie, Roquebert, Bénédicte, Trombert-Paolantoni, Sabine, Lecorche, Emmanuel, Verdurme, Laura, Foulongne, Vincent, Selinger, Christian, Michalakis, Yannis, Sofonea, Mircea T, Alizon, Samuel

“…Variants of severe acute respiratory syndrome coronavirus 2 raise concerns regarding the control of coronavirus disease epidemics. We analyzed 40,000 specific…”
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Within-host bacterial growth dynamics with both mutation and horizontal gene transfer by Djidjou-Demasse, Ramsès, Alizon, Samuel, Sofonea, Mircea T.

“…The evolution and emergence of antibiotic resistance is a major public health concern. The understanding of the within-host microbial dynamics combining…”
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Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021-February 2022 by Sofonea, Mircea T, Roquebert, Bénédicte, Foulongne, Vincent, Morquin, David, Verdurme, Laura, Trombert-Paolantoni, Sabine, Roussel, Mathilde, Bonetti, Jean-Christophe, Zerah, Judith, Haim-Boukobza, Stéphanie, Alizon, Samuel

“…We analyzed 324,734 SARS-CoV-2 variant screening tests from France enriched with 16,973 whole-genome sequences sampled during September 1, 2021-February 28,…”
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