Community and Hospital-Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS-CoV-2 During the 2023-2024 Season, Lyon, France.

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 severe symptoms leading to hospitalization, viral circulation in the community remains less extensively monitored. This study compared viral circulation between RELAB, a recently established community-based laboratory surveillance network (n = 22 843 tested patients) and hospital surveillance at the Hospices Civils de Lyon, France (n = 23 046 tested patients), for the season 2023-2024.

A framework to assess the risk of Yellow Fever emergence.

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 the Caribbean, has remained YF-free since 1908.

National burden and optimal vaccine policy for Japanese encephalitis virus in Bangladesh.

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 the underlying burden.

Methods: We conducted a nationally representative serological community study in 70 communities in individuals of all ages (N=2,938, October 2015-January 2016).

Unraveling the role of rat and flea population dynamics on the seasonality of plague epidemics in Madagascar.

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 deterministic compartmental model, calibrated to rat and flea capture data, serological data collected in active rural foci, and human plague surveillance data, we analyzed the effects of seasonal rat and flea population dynamics on plague transmission.

Global burden of chikungunya virus infections and the potential benefit of vaccination campaigns.

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 studies, observed cases and mosquito distributions to quantify the underlying CHIKV burden in 180 countries and territories, and we explored the potential impact of vaccination campaigns. We estimate that 104 countries have experienced CHIKV transmission, covering 2.

Modeling the impact of vaccine campaigns on the epidemic transmission dynamics of chikungunya virus outbreaks.

A licensed chikungunya vaccine now exists; however, it remains unclear whether 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 used models to reconstruct epidemic transmission dynamics, providing a framework to assess the theoretical impact of a vaccine had it been available.

Comparative evaluation of methodologies for estimating the effectiveness of non-pharmaceutical interventions in the context of COVID-19: a simulation study.

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 comparing two frequently used approaches in terms of parameter bias and confidence interval coverage of NPI effectiveness parameters. We compared two-step approaches, where NPI effects are regressed on by-products of a first analysis, such as the effective reproduction number ${\mathcal{R}}_t$, with more integrated models that jointly estimate NPI effects and transmission rates in a single-step approach.

Why the growth of arboviral diseases necessitates a new generation of global risk maps and future projections.

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, identify gaps in surveillance, estimate disease burden, and target and evaluate the impact of interventions. Here, we describe how current approaches to mapping arboviral diseases have become unnecessarily siloed, ignoring the strengths and weaknesses of different data types and methods.

Artificial intelligence for modelling infectious disease epidemics.

Infectious disease threats to individual and public health are numerous, varied and frequently unexpected. Artificial intelligence (AI) and related technologies, which are already supporting human decision making in economics, medicine and social science, have the potential to transform the scope and power of infectious disease epidemiology. Here we consider the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science.

Evolution of social contacts patterns in France over the SARS-CoV-2 pandemic: results from the SocialCov survey.

Background: Non-pharmaceutical measures such as lockdowns, curfews and place closures were implemented in France during 2020-2022 to reduce contacts in the population, to limit the spread of SARS-CoV-2 and reduce COVID-19 healthcare burden. Individuals also changed their behaviours as a response to the pandemic. Here, we present the results of the SocialCov survey that characterise the evolution of contacts in France between December 2020 and May 2022 to better understand the short and long term impact of these interventions on social mixing.

Factors Associated With the Transmission of the Delta Severe Acute Respiratory Syndrome Coronavirus 2 Variant in Households: The Israeli COVID-19 Family Study (ICoFS).

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 transmission model to evaluate the effects of isolation, parental care, and vaccine-induced immunity on Delta variant transmission from the follow-up of 1093 Israeli households (July-August 2021). Among the 2883 household contacts, 1096 (38%) were infected.

RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies.

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 force of infection (FOI) (i.e.

Revealing trends in measles immunity during periods of varying measles circulation in Madagascar.

Estimating the durability of immunity from vaccination is complicated by unreported re-vaccination, and unobserved natural infection or reexposure, which could result in overestimation of protection longevity. We tested serial cross-sectional serum samples from 2005 to 2015 (N=2,530) for IgG to examine measles seroprevalence, spatiotemporal patterns of titers across regions and antibody dynamics among children aged 1-9 years who grew up during varying measles circulation in Madagascar under a one-dose vaccination schedule. We found that measles seroprevalence has generally decreased over this time period.

Monitoring SARS-CoV-2 variants with complementary surveillance systems: risk evaluation of the Omicron JN.1 variant in France, August 2023 to January 2024.

BackgroundEarly 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.

From the 100 Day Mission to 100 lines of software development: how to improve early outbreak analytics.

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 field of outbreak analytics to help ensure reliable, evidence-based decision making. To explore the challenges and key priorities in the field of outbreak analytics, the Epiverse-TRACE initiative brought together a multidisciplinary group of experts, including field epidemiologists, data scientists, academics, and software engineers from public health institutions across multiple countries.

Patterns and drivers of excess mortality during the COVID-19 pandemic in 13 Western European countries.

Background: Important differences in excess mortality between European countries during the COVID-19 pandemic have been reported. Understanding the drivers of these differences is essential to pandemic preparedness.

Methods: We examined patterns in age- and sex-standardized cumulative excess mortality in 13 Western European countries during the first 30 months of the COVID-19 pandemic and the correlation of country-level characteristics of interest with excess mortality.

Integrating information from historical data into mechanistic models for influenza forecasting.

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 models used for epidemic forecasting can either include parameters capturing the infection process (mechanistic or compartmental models) or rely on time series analysis approaches that do not make mechanistic assumptions (statistical or phenomenological models).

Addressing current limitations of household transmission studies by collecting contact data.

Modeling studies of household transmission data have helped characterize the role of children in influenza and coronavirus disease 2019 (COVID-19) epidemics. However, estimates from these studies may be biased since they do not account for the heterogeneous nature of household contacts. Here, we quantified the impact of contact heterogeneity between household members on the estimation of child relative susceptibility and infectivity.

Indian Ocean temperature anomalies predict long-term global dengue trends.

Despite identifying El Niño events as a factor in dengue dynamics, predicting the oscillation of global dengue epidemics remains challenging. Here, we investigate climate indicators and worldwide dengue incidence from 1990 to 2019 using climate-driven mechanistic models. We identify a distinct indicator, the Indian Ocean basin-wide (IOBW) index, as representing the regional average of sea surface temperature anomalies in the tropical Indian Ocean.