Temporal contact patterns and the implications for predicting superspreaders and planning of targeted outbreak control.

Directly transmitted infectious diseases spread through social contacts that change over time, but outbreak models typically make simplifying assumptions about network structure and dynamics. To assess how common assumptions relate to real-world interactions, we analysed 11 networks from five settings and developed metrics, capturing crucial epidemiological features of these networks. We developed a novel metric, the 'retention index', to characterize the distribution of retained contacts over consecutive time steps relative to fully static and dynamic networks.

Inferring the proportion of undetected cholera infections from serological and clinical surveillance in an immunologically naive population.

Most infections with pandemic are thought to result in subclinical disease and are not captured by surveillance. Previous estimates of the ratio of infections to clinical cases have varied widely (2 to 100 infections per case). Understanding cholera epidemiology and immunity relies on the ability to translate between numbers of clinical cases and the underlying number of infections in the population.

Building in-house capabilities in health agencies and outsourcing to academia or industry: Considerations for effective infectious disease modelling.

Infectious disease models provide a systematic way to estimate crucial features of epidemic dynamics and explore different transmission and control scenarios. Given the importance of model-based analysis in managing public health crises, there has been an increase in post-pandemic creation of both academia-driven modelling centres, hubs and consortiums and government-driven public health agencies with in-house modelling units or teams. However, in the past, the delineation of roles and responsibilities between government- and academia-led modelling groups has often been unclear.

The potential impact of new TB vaccines on the burden of TB in people living with HIV in South Africa.

Background: People living with HIV (PLHIV) are at increased risk of tuberculosis (TB). New TB vaccines may help reduce this burden. New TB vaccine candidates are safe and immunogenic in PLHIV.

Human movement and environmental barriers shape the emergence of dengue.

Understanding how emerging infectious diseases spread within and between countries is essential to contain future pandemics. Spread to new areas requires connectivity between one or more sources and a suitable local environment, but how these two factors interact at different stages of disease emergence remains largely unknown. Further, no analytical framework exists to examine their roles.

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.

Accelerating Progress Towards the 2030 Neglected Tropical Diseases Targets: How Can Quantitative Modeling Support Programmatic Decisions?

Over the past decade, considerable progress has been made in the control, elimination, and eradication of neglected tropical diseases (NTDs). Despite these advances, most NTD programs have recently experienced important setbacks; for example, NTD interventions were some of the most frequently and severely impacted by service disruptions due to the coronavirus disease 2019 (COVID-19) pandemic. Mathematical modeling can help inform selection of interventions to meet the targets set out in the NTD road map 2021-2030, and such studies should prioritize questions that are relevant for decision-makers, especially those designing, implementing, and evaluating national and subnational programs.

Determinants of animal disease and nontherapeutic antibiotic use on smallholder livestock farms.

Introduction: Reducing nontherapeutic antibiotic use (ABU) in livestock animals has been identified as an important way of curbing the growth of antimicrobial resistance (AMR). However, nontherapeutic ABU may be important for managing animal disease. In order to reduce nontherapeutic ABU, farmers may need to implement other complementary interventions to safeguard animal health and minimize risk.

Detecting changes in generation and serial intervals under varying pathogen biology, contact patterns and outbreak response.

The epidemiological characteristics of SARS-CoV-2 transmission have changed over the pandemic due to emergence of new variants. A decrease in the generation or serial intervals would imply a shortened transmission timescale and, hence, outbreak response measures would need to expand at a faster rate. However, there are challenges in measuring these intervals.

A global dataset of publicly available dengue case count data.

OpenDengue is a global database of dengue case data collated from public sources and standardised and formatted to facilitate easy reanalysis. Dataset version 1.2 of this database contains information on over 56 million dengue cases from 102 countries between 1924 and 2023, making it the largest and most comprehensive dengue case database currently available.

Modelling the health and economic impacts ofM72/AS01 vaccination and BCG-revaccination: Estimates for South Africa.

Background: Tuberculosis remains a major public health problem in South Africa, with an estimated 300,000 cases and 55,000 deaths in 2021. New tuberculosis vaccines could play an important role in reducing this burden. Phase IIb trials have suggested efficacy of the M72/AS01 vaccine candidate and BCG-revaccination.

Reconstructing the phylodynamic history and geographic spread of the CRF01_AE-predominant HIV-1 epidemic in the Philippines from PR/RT sequences sampled from 2008 to 2018.

The Philippines has had a rapidly growing human immunodeficiency virus (HIV) epidemic with a shift in the prevalent subtype from B to CRF01_AE. However, the phylodynamic history of CRF01_AE in the Philippines has yet to be reconstructed. We conducted a descriptive retrospective study reconstructing the history of HIV-1 CRF01_AE transmissions in the Philippines through molecular epidemiology.

AHHME: A model for estimating the holistic cost-effectiveness of antimicrobial resistance interventions in food animal production.

Antimicrobial resistance (AMR) is considered a global priority for human health, and reducing antimicrobial use in food animals has been suggested as a key area for interventions aiming to reduce resistant infections in humans. In addition to the effect on human health, such interventions may have effects across food animal productivity, healthcare sector costs, and the broader macroeconomy, but these effects are rarely captured in the AMR health economic literature. Without being able to estimate these effects, it is difficult to understand the true cost-effectiveness of antimicrobial stewardship interventions in food animal production, or to correctly design and prioritise such interventions.

How farm practices and antibiotic use drive disease incidence in smallholder livestock farms: Evidence from a survey in Uganda.

Background: Antimicrobial resistance (AMR) is a growing threat to human and animal health, and the growth in AMR prevalence globally is thought to be partially driven by non-therapeutic antibiotic use in livestock production. However, livestock farms may depend on antibiotics as a prophylactic disease management tool, and reducing antibiotic use in isolation may harm farmers' economic security. In order to help farmers safely reduce their antibiotic use, we must first determine how necessary non-therapeutic antibiotic use is for disease management, and how other farm practices can guard against disease and make antibiotic use reduction safe and feasible.

Inferring the proportion of undetected cholera infections from serological and clinical surveillance in an immunologically naive population.

Most infections with pandemic Vibrio cholerae are thought to result in subclinical disease and are not captured by surveillance. Previous estimates of the ratio of infections to clinical cases have varied widely (2 to 100). Understanding cholera epidemiology and immunity relies on the ability to translate between numbers of clinical cases and the underlying number of infections in the population.

Estimation of waning vaccine effectiveness from population-level surveillance data in multi-variant epidemics.

Monitoring time-varying vaccine effectiveness (e.g., due to waning of immunity and the emergence of novel variants) provides crucial information for outbreak control.

The potential health and economic impacts of new tuberculosis vaccines under varying delivery strategies in Delhi and Gujarat, India: a modelling study.

Background: India has the largest tuberculosis burden globally, but this burden varies nationwide. All-age tuberculosis prevalence in 2021 ranged from 747/100,000 in Delhi to 137/100,000 in Gujarat. Previous modelling has demonstrated the benefits and costs of introducing novel tuberculosis vaccines in India overall.

Epidemiological and genomic investigation of chikungunya virus in Rio de Janeiro state, Brazil, between 2015 and 2018.

Since 2014, Brazil has experienced an unprecedented epidemic caused by chikungunya virus (CHIKV), with several waves of East-Central-South-African (ECSA) lineage transmission reported across the country. In 2018, Rio de Janeiro state, the third most populous state in Brazil, reported 41% of all chikungunya cases in the country. Here we use evolutionary and epidemiological analysis to estimate the timescale of CHIKV-ECSA-American lineage and its epidemiological patterns in Rio de Janeiro.

Scoring epidemiological forecasts on transformed scales.

Forecast evaluation is essential for the development of predictive epidemic models and can inform their use for public health decision-making. Common scores to evaluate epidemiological forecasts are the Continuous Ranked Probability Score (CRPS) and the Weighted Interval Score (WIS), which can be seen as measures of the absolute distance between the forecast distribution and the observation. However, applying these scores directly to predicted and observed incidence counts may not be the most appropriate due to the exponential nature of epidemic processes and the varying magnitudes of observed values across space and time.

Severity of SARS-CoV-2 Omicron XBB subvariants in Singapore.

Several XBB subvariants such as XBB.1.5, XBB.

New tuberculosis vaccines in India: modelling the potential health and economic impacts of adolescent/adult vaccination with M72/AS01 and BCG-revaccination.

Background: India had an estimated 2.9 million tuberculosis cases and 506 thousand deaths in 2021. Novel vaccines effective in adolescents and adults could reduce this burden.

The potential impact of novel tuberculosis vaccines on health equity and financial protection in low-income and middle-income countries.

Introduction: One in two patients developing tuberculosis (TB) in low-income and middle-income countries (LMICs) faces catastrophic household costs. We assessed the potential financial risk protection from introducing novel TB vaccines, and how health and economic benefits would be distributed across income quintiles.

Methods: We modelled the impact of introducing TB vaccines meeting the World Health Organization preferred product characteristics in 105 LMICs.

The potential impact of novel tuberculosis vaccine introduction on economic growth in low- and middle-income countries: A modeling study.

Background: Most individuals developing tuberculosis (TB) are working age adults living in low- and middle-income countries (LMICs). The resulting disability and death impact economic productivity and burden health systems. New TB vaccine products may reduce this burden.