4.6 Article

Epidemic Spread on Weighted Networks

期刊

PLOS COMPUTATIONAL BIOLOGY
卷 9, 期 12, 页码 -

出版社

PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pcbi.1003352

关键词

-

资金

  1. French Ministries in charge of Agriculture and Environment
  2. CNRS
  3. INSERM
  4. IRD

向作者/读者索取更多资源

The contact structure between hosts shapes disease spread. Most network-based models used in epidemiology tend to ignore heterogeneity in the weighting of contacts between two individuals. However, this assumption is known to be at odds with the data for many networks (e.g. sexual contact networks) and to have a critical influence on epidemics' behavior. One of the reasons why models usually ignore heterogeneity in transmission is that we currently lack tools to analyze weighted networks, such that most studies rely on numerical simulations. Here, we present a novel framework to estimate key epidemiological variables, such as the rate of early epidemic expansion (r(0)) and the basic reproductive ratio (R-0), from joint probability distributions of number of partners (contacts) and number of interaction events through which contacts are weighted. These distributions are much easier to infer than the exact shape of the network, which makes the approach widely applicable. The framework also allows for a derivation of the full time course of epidemic prevalence and contact behaviour, which we validate with numerical simulations on networks. Overall, incorporating more realistic contact networks into epidemiological models can improve our understanding of the emergence and spread of infectious diseases.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.6
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Biology

Within-host bacterial growth dynamics with both mutation and horizontal gene transfer

Ramses Djidjou-Demasse, Samuel Alizon, Mircea T. Sofonea

Summary: The evolution and emergence of antibiotic resistance is a major public health concern. Understanding the within-host microbial dynamics, including mutational processes, horizontal gene transfer, and resource consumption, is key to solving this problem. By analyzing a generic model describing interactions dynamics of four bacterial strains with different resistance profiles, researchers have been able to define conditions for the existence of non-trivial stationary states and identify factors influencing the strains' thresholds for survival and coexistence. The model's qualitative dynamics range from strain extinction to coexistence of all strains at equilibrium, depending on the strains' interaction and the presence of drug action.

JOURNAL OF MATHEMATICAL BIOLOGY (2021)

Editorial Material Multidisciplinary Sciences

Superspreading genomes

Samuel Alizon

SCIENCE (2021)

Article Infectious Diseases

Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020

Samuel Alizon, Christian Selinger, Mircea T. Sofonea, Stephanie Haim-Boukobza, Jean-Marc Giannoli, Laetitia Ninove, Sylvie Pillet, Vincent Thibault, Alexis de Rougemont, Camille Tumiotto, Morgane Solis, Robin Stephan, Celine Bressollette-Bodin, Maud Salmona, Anne-Sophie L'honneur, Sylvie Behillil, Caroline Lefeuvre, Julia Dina, Sebastien Hantz, Cedric Hartard, David Veyer, Heloise M. Delagreverie, Slim Fourati, Benoit Visseaux, Cecile Henquell, Bruno Lina, Vincent Foulongne, Sonia Burrel

Summary: This study explores the use of Cq values from SARS-CoV-2 screening tests to better understand the spread of an epidemic and the biology of the infection. The results show significant associations between Cq values and patient age, number of days after symptom onset, and the state of the epidemic. The study suggests that Cq values can improve short-term predictions for epidemic surveillance.

EUROSURVEILLANCE (2022)

Article Infectious Diseases

Predicting COVID-19 incidence in French hospitals using human contact network analytics

Christian Selinger, Marc Choisy, Samuel Alizon

Summary: Researchers developed predictive models of hospital incidence between July 2020 and April 2021 by incorporating human contact network analytics, which significantly improved predictions at both the national and subnational levels by more than 50%. This innovative use of network analytics from colocalization data opens new possibilities for epidemic forecasting and public health.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2021)

Article Infectious Diseases

SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France

Benedicte Roquebert, Stephanie Haim-Boukobza, Sabine Trombert-Paolantoni, Emmanuel Lecorche, Laura Verdurme, Vincent Foulongne, Sonia Burrel, Samuel Alizon, Mircea T. Sofonea

Summary: The analysis of 88,375 cycle amplification (Ct) values revealed that the Alpha variant of SARS-CoV-2 had a transmission advantage over wild type strains, causing a rapid increase in infections. Additionally, tests positive for Alpha and Beta/Gamma variants showed significantly lower Ct values, indicating higher viral loads.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2021)

Editorial Material Ecology

Can we eradicate viral pathogens?

Samuel Alizon, Paul E. Turner

JOURNAL OF EVOLUTIONARY BIOLOGY (2021)

Article Virology

Variant-specific SARS-CoV-2 within-host kinetics

Baptiste Elie, Benedicte Roquebert, Mircea T. Sofonea, Sabine Trombert-Paolantoni, Vincent Foulongne, Jeremie Guedj, Stpehanie Haim-Boukobza, Samuel Alizon

Summary: This study analyzed a longitudinal cohort in France and found that infections caused by the Alpha variant have a higher number of viral genome copies and a slower decay rate, leading to significantly higher transmission potentials, especially in older populations. There was no significant difference in peak viral copy number between infections caused by the Alpha and Delta variants.

JOURNAL OF MEDICAL VIROLOGY (2022)

Article Biology

The source of individual heterogeneity shapes infectious disease outbreaks

Baptiste Elie, Christian Selinger, Samuel Alizon

Summary: There is heterogeneity in infectious disease transmission patterns between individuals, which can affect epidemiological dynamics. Studies have found that heterogeneity in the number of secondary cases decreases the probability of outbreak emergence, and more realistic infection duration distributions lead to faster outbreaks and higher epidemic peaks. The impact of heterogeneity depends on the underlying evolutionary model when parasites require adaptive mutations for large epidemics. These findings emphasize the importance of accounting for realistic distributions of transmission rates in epidemiological dynamics.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2022)

Editorial Material Anesthesiology

Challenges for mathematical epidemiological modelling

Pascal Crepey, Harold Noel, Samuel Alizon

ANAESTHESIA CRITICAL CARE & PAIN MEDICINE (2022)

Article Biochemistry & Molecular Biology

Does exposure to different menstrual products affect the vaginal environment?

Nicolas Tessandier, Ilkay Basak Uysal, Baptiste Elie, Christian Selinger, Claire Bernat, Vanina Boue, Sophie Grasset, Soraya Groc, Massilva Rahmoun, Bastien Reyne, Noemi Bender, Marine Bonneau, Christelle Graf, Vincent Tribout, Vincent Foulongne, Jacques Ravel, Tim Waterboer, Christophe Hirtz, Ignacio G. Bravo, Jacques Reynes, Michel Segondy, Carmen Lia Murall, Nathalie Boulle, Tsukushi Kamiya, Samuel Alizon

Summary: The study examines the association between the use of different types of menstrual products and microbial, immunological, demographic, and behavioral indicators. The results suggest a potential link between the use of menstrual cups and fungal genital infection, highlighting the possible influence of menstrual products on menstrual health.

MOLECULAR ECOLOGY (2023)

Article Ecology

TiPS: Rapidly simulating trajectories and phylogenies from compartmental models

Gonche Danesh, Emma Saulnier, Olivier Gascuel, Marc Choisy, Samuel Alizon

Summary: Stochastic population dynamics simulations play a crucial role in ecological and epidemiological studies as they can generate time series and genealogies that capture the relatedness between individuals. However, current software packages for simulating phylogenetic trees often have simplified population dynamics models and are not suitable for simulating a large number of trees. To address these limitations, this study introduces TiPS, an R package that can generate trajectories and phylogenetic trees associated with a compartmental model. TiPS uses different simulation algorithms and a backwards-in-time approach to simulate trajectories and trees, respectively. It combines the flexibility of R for model definition and the speed of C++ for simulations execution. Benchmarking analyses show that TiPS is faster than existing packages and it is particularly useful for population genetics and phylodynamics studies that require a large number of phylogenies for population dynamics analysis.

METHODS IN ECOLOGY AND EVOLUTION (2023)

Editorial Material Biochemistry & Molecular Biology

Predicting the virulence of future emerging zoonotic viruses

Samuel Alizon

Summary: According to a new study in PLOS Biology, the virulence of a zoonotic virus in humans depends on its reservoir host. Physiology could be the key to anticipating viral threats lethality.

PLOS BIOLOGY (2023)

Article Infectious Diseases

Concomitant and productive genital infections by HSV-2 and HPV in two young women: A case report

Ilkay Basak Uysal, Vanina Boue, Carmen Lia Murall, Christelle Graf, Christian Selinger, Christophe Hirtz, Claire Bernat, Jacques Ravel, Jacques Reynes, Marine Bonneau, Massilva Rahmoun, Michel Segondy, Nathalie Boulle, Sophie Grasset, Soraya Groc, Tim Waterboer, Vincent Tribout, Ignacio G. Bravo, Sonia Burrel, Vincent Foulongne, Samuel Alizon, Nicolas Tessandier

Summary: This study reports two cases of concomitant HSV-2 and HPV infections in young women. By analyzing their viral loads, immune responses, and vaginal microbiota, we gain a better understanding of the coinfection between these two viruses, highlighting the need for further research to confirm these interactions.

IDCASES (2022)

Article Immunology

Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021-February 2022

Mircea T. Sofonea, Benedicte Roquebert, Vincent Foulongne, David Morquin, Laura Verdurme, Sabine Trombert-Paolantoni, Mathilde Roussel, Jean-Christophe Bonetti, Judith Zerah, Stephanie Haim-Boukobza, Samuel Alizon

Summary: The study found that the Omicron variant has a greater growth advantage compared to the Delta variant and can generate significant COVID-19 activity in hospitals in France. Additionally, the magnitude of the BA.2 wave depends on the relaxation of control measures, but remains lower than that of BA.1 in median scenarios.

EMERGING INFECTIOUS DISEASES (2022)

Article Mathematical & Computational Biology

Non-Markovian modelling highlights the importance of age structure on Covid-19 epidemiological dynamics

Bastien Reyne, Quentin Richard, Christian Selinger, Mircea T. Sofonea, Ramses Djidjou-Demasse, Samuel Alizon

Summary: This study proposes a non-Markovian alternative formalism based on partial differential equations for modeling the COVID-19 pandemic. It applies and analyzes the major factors contributing to hospital admissions in the 2021 epidemic in France, taking into account vaccine-induced and natural immunity. The findings suggest that vaccination rate alone is insufficient to control the epidemic, and there is significant uncertainty associated with the age-structured contact matrix.

MATHEMATICAL MODELLING OF NATURAL PHENOMENA (2022)

暂无数据