Simon Cauchemez
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View article: Author Correction: Global burden of chikungunya virus infections and the potential benefit of vaccination campaigns
Author Correction: Global burden of chikungunya virus infections and the potential benefit of vaccination campaigns Open
View article: Modeling optimal deployment strategies for Nipah vaccines and monoclonal antibodies
Modeling optimal deployment strategies for Nipah vaccines and monoclonal antibodies Open
Nipah virus (NiV) is endemic in Pteropus bats across South and Southeast Asia. Spillover into human populations results in usually fatal disease with the potential for human-to-human spread, which has led to NiV being classified by WHO as …
View article: Modelling the impact of a quadrivalent ACWY meningococcal vaccination and vaccination targeting serogroup B in France
Modelling the impact of a quadrivalent ACWY meningococcal vaccination and vaccination targeting serogroup B in France Open
Invasive meningococcal disease (IMD) represents a significant global health burden, with high fatality rate and substantial risk of lifelong sequelae. Most cases worldwide are caused by six serogroups (A, B, C, W, X, and Y). Effective vacc…
View article: The Role of Climate Change in the Expansion of Dengue
The Role of Climate Change in the Expansion of Dengue Open
Climate change-related weather and extreme events are increasing in intensity and frequency, affecting infectious disease transmission globally. Dengue, a climate-sensitive vector-borne disease, to which over half the world’s population is…
View article: Global dynamics of antibiotic resistance: a modeling study of the spread of endemic and emerging resistance in <i>E. coli</i>
Global dynamics of antibiotic resistance: a modeling study of the spread of endemic and emerging resistance in <i>E. coli</i> Open
Background Antibiotic resistance (ABR) poses a growing threat at the global level. Emergence and worldwide dissemination of multi-resistant clones are frequently reported. However, associated drivers are still largely unknown and are a cru…
View article: Community and Hospital‐Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS‐CoV‐2 During the 2023–2024 Season, Lyon, France
Community and Hospital‐Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS‐CoV‐2 During the 2023–2024 Season, Lyon, France Open
Influenza, respiratory syncytial virus (RSV) and SARS‐CoV‐2 are among the main respiratory viruses circulating in the population, with a significant burden on public health. While individuals at higher risk are more likely to develop sever…
View article: Now is the time to integrate serology into routine infectious disease surveillance
Now is the time to integrate serology into routine infectious disease surveillance Open
View article: A framework to assess the risk of yellow fever emergence
A framework to assess the risk of yellow fever emergence Open
Background Yellow fever (YF) is a viral hemorrhagic fever transmitted by Aedes aegypti mosquitoes. Symptoms range from mild fever to severe complications such as jaundice and haemorrhages, which can be fatal. Martinique, a French island in…
View article: National burden and optimal vaccine policy for Japanese encephalitis virus in Bangladesh
National burden and optimal vaccine policy for Japanese encephalitis virus in Bangladesh Open
Background Bangladesh first reported Japanese encephalitis virus (JEV) in 1977 and has seen regular cases since, however, no JEV vaccination program currently exists. A barrier to the use of JEV vaccines has been a limited understanding of…
View article: Patterns of Emergence and Circulation of West Nile Virus in Algeria
Patterns of Emergence and Circulation of West Nile Virus in Algeria Open
In recent years, many countries have experienced increased outbreaks of emerging infectious diseases, such as West Nile virus (WNV). WNV is transmitted to humans by Culexmosquitoes and has an enzoonotic transmission cycle involving birds. …
View article: Unraveling the role of rat and flea population dynamics on the seasonality of plague epidemics in Madagascar
Unraveling the role of rat and flea population dynamics on the seasonality of plague epidemics in Madagascar Open
Plague continues to pose a public health problem in multiple regions of the world, including Madagascar, where it is characterized by a pronounced seasonal pattern. The drivers of plague seasonality remain poorly understood. Using a determ…
View article: Global burden of chikungunya virus infections and the potential benefit of vaccination campaigns
Global burden of chikungunya virus infections and the potential benefit of vaccination campaigns Open
The first vaccine against chikungunya virus (CHIKV) has now been licensed; however, due to a limited knowledge of the underlying global burden, its potential to reduce disease burden remains unknown. We used data from seroprevalence studie…
View article: Characterising the benefits and risks of vaccines approved through accelerated pathways
Characterising the benefits and risks of vaccines approved through accelerated pathways Open
Alternative regulatory pathways for vaccine licensure without traditional Phase III efficacy trials are of increasing priority for epidemic pathogens. Using IXCHIQ, a chikungunya virus vaccine licensed through an accelerated pathway, we de…
View article: Modeling the impact of vaccine campaigns on the epidemic transmission dynamics of chikungunya virus outbreaks
Modeling the impact of vaccine campaigns on the epidemic transmission dynamics of chikungunya virus outbreaks Open
View article: Comparative evaluation of methodologies for estimating the effectiveness of non-pharmaceutical interventions in the context of COVID-19: a simulation study
Comparative evaluation of methodologies for estimating the effectiveness of non-pharmaceutical interventions in the context of COVID-19: a simulation study Open
Numerous studies assessing the effectiveness of non-pharmaceutical interventions (NPIs) against COVID-19 have produced conflicting results, partly due to methodological differences. This study aims to clarify these discrepancies by compari…
View article: Why the growth of arboviral diseases necessitates a new generation of global risk maps and future projections
Why the growth of arboviral diseases necessitates a new generation of global risk maps and future projections Open
Global risk maps are an important tool for assessing the global threat of mosquito and tick-transmitted arboviral diseases. Public health officials increasingly rely on risk maps to understand the drivers of transmission, forecast spread, …
View article: Artificial intelligence for modelling infectious disease epidemics
Artificial intelligence for modelling infectious disease epidemics Open
View article: Evolution of social contacts patterns in France over the SARS-CoV-2 pandemic: results from the SocialCov survey
Evolution of social contacts patterns in France over the SARS-CoV-2 pandemic: results from the SocialCov survey Open
View article: Factors Associated With the Transmission of the Delta Severe Acute Respiratory Syndrome Coronavirus 2 Variant in Households: The Israeli COVID-19 Family Study (ICoFS)
Factors Associated With the Transmission of the Delta Severe Acute Respiratory Syndrome Coronavirus 2 Variant in Households: The Israeli COVID-19 Family Study (ICoFS) Open
Understanding how interpersonal interactions and immunological factors shape severe acute respiratory syndrome coronavirus 2 transmission in households is crucial for designing control measures. We developed a Bayesian data augmentation tr…
View article: RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies
RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies Open
Population-based serological surveys are a key tool in epidemiology to characterize the level of population immunity and reconstruct the past circulation of pathogens. A variety of serocatalytic models have been developed to estimate the f…
View article: Monitoring SARS-CoV-2 variants with complementary surveillance systems: risk evaluation of the Omicron JN.1 variant in France, August 2023 to January 2024
Monitoring SARS-CoV-2 variants with complementary surveillance systems: risk evaluation of the Omicron JN.1 variant in France, August 2023 to January 2024 Open
Background Early detection and characterisation of SARS-CoV-2 variants have been and continue to be essential for assessing their public health impact. In August 2023, Santé publique France implemented enhanced surveillance for BA.2.86 and…
View article: From the 100 Day Mission to 100 lines of software development: how to improve early outbreak analytics
From the 100 Day Mission to 100 lines of software development: how to improve early outbreak analytics Open
Since the COVID-19 pandemic, considerable advances have been made to improve epidemic preparedness by accelerating diagnostics, therapeutics, and vaccine development. However, we argue that it is crucial to make equivalent efforts in the f…
View article: Patterns and drivers of excess mortality during the COVID-19 pandemic in 13 Western European countries
Patterns and drivers of excess mortality during the COVID-19 pandemic in 13 Western European countries Open
These results suggest the benefit of early implementation of NPIs and swift rollout of vaccines to the most vulnerable. Further analyses are required at a more granular level to better understand how these factors impacted excess mortality…
View article: Characterising the 2023 chikungunya outbreak in Paraguay and the potential impact of a vaccine campaign
Characterising the 2023 chikungunya outbreak in Paraguay and the potential impact of a vaccine campaign Open
There now exists a licensed chikungunya vaccine, however, it remains unclear if it could be deployed during outbreaks to reduce the health burden. We used an epidemic in Paraguay as a case study. We conducted a seroprevalence study and use…
View article: Accuracy of Xpert and alternative sampling methods to diagnose childhood pulmonary tuberculosis, a prospective cohort study
Accuracy of Xpert and alternative sampling methods to diagnose childhood pulmonary tuberculosis, a prospective cohort study Open
The Xpert performed on the nasopharyngeal aspirate shows similar accuracy to the culture. It was also similar to that in gastric aspirate. It highlights an interesting CPTB diagnostic combination.
View article: Integrating information from historical data into mechanistic models for influenza forecasting
Integrating information from historical data into mechanistic models for influenza forecasting Open
Seasonal influenza causes significant annual morbidity and mortality worldwide. In France, it is estimated that, on average, 2 million individuals consult their GP for influenza-like-illness (ILI) every year. Traditionally, mathematical mo…
View article: Best practices for estimating and reporting epidemiological delay distributions of infectious diseases
Best practices for estimating and reporting epidemiological delay distributions of infectious diseases Open
Epidemiological delays are key quantities that inform public health policy and clinical practice. They are used as inputs for mathematical and statistical models, which in turn can guide control strategies. In recent work, we found that ce…
View article: The global burden of chikungunya virus and the potential benefit of vaccines
The global burden of chikungunya virus and the potential benefit of vaccines Open
The first chikungunya virus (CHIKV) vaccine has now been licensed, however, its potential to reduce disease burden remains unknown due to a poor knowledge of the underlying global burden. We use data from seroprevalence studies, observed c…
View article: Using pathogen genomics to predict antigenic changes of influenza H3N2 virus
Using pathogen genomics to predict antigenic changes of influenza H3N2 virus Open
Influenza viruses evolve their antigenic phenotype in response to immune-driven selection, necessitating regular updates to the antigens used in influenza vaccines. Characterising antigenic change of influenza virus currently requires inte…
View article: Epidemiological inferences from serological responses to cross-reacting pathogens
Epidemiological inferences from serological responses to cross-reacting pathogens Open
Multiplex immunoassays are facilitating the parallel measurement of antibody responses against multiple antigenically-related pathogens, generating a wealth of high-dimensional data which depict complex antibody-antigen relationships. In t…