Adaptive strategies for the deployment of rapid diagnostic tests for COVID-19: a modelling study.

Background: Lateral flow assays (LFAs) for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provide an affordable, rapid and decentralised mean for diagnosing coronavirus disease 2019 (COVID-19). Concentrating on urban areas in low- and middle-income countries, the aim of this analysis was to estimate the degree to which 'dynamic' screening algorithms, that adjust the use of confirmatory polymerase chain reaction (PCR) testing based on epidemiological conditions, could reduce cost without substantially reducing the impact of testing.

Methods: Concentrating on a hypothetical 'second wave' of COVID-19 in India, we modelled the potential impact of testing 0.

The : a tool for projecting the epidemiological impact of TB policy options.

Background: Tuberculosis (TB) remains one of the deadliest infectious diseases globally. Despite the World Health Organization's (WHO) End TB Strategy targets for 2035, progress has been hindered by structural, financial, and implementation barriers, including recent cuts in global funding. Strategic use of mathematical modelling is useful for prioritizing high-impact interventions and optimizing limited resources.

Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA).

The study of genomic variants is increasingly important for public health surveillance of pathogens. Traditional variant-calling methods from whole-genome sequencing data rely on reference-based alignment, which can introduce biases and require significant computational resources. Alignment- and reference-free approaches offer an alternative by leveraging k-mer-based methods, but existing implementations often suffer from sensitivity limitations, particularly in high mutation density genomic regions.

The potential impact on tuberculosis of interventions to reduce undernutrition in the WHO South-East Asian Region: a modelling analysis.

Background: Undernutrition is a major risk factor for TB incidence in the WHO South-East (SE) Asia Region. We examined the potential impact of addressing undernutrition as a preventive measure, for reducing TB burden in region.

Methods: We developed a deterministic, compartmental mathematical model, capturing undernutrition and its associated excess risk of TB, amongst countries in the Region.

Estimates of resource use in the public-sector health-care system and the effect of strengthening health-care services in Malawi during 2015-19: a modelling study (Thanzi La Onse).

Background: In all health-care systems, decisions need to be made regarding allocation of available resources. Evidence is needed for these decisions, especially in low-income countries. We aimed to estimate how health-care resources provided by the public sector were used in Malawi during 2015-19 and to estimate the effects of strengthening health-care services.

Estimating community-wide indirect effects of influenza vaccination: triangulation using mathematical models and bias analysis.

Understanding whether influenza vaccine promotion strategies produce community-wide indirect effects is important for establishing vaccine coverage targets and optimizing vaccine delivery. Empirical epidemiologic studies and mathematical models have been used to estimate indirect effects of vaccines but rarely for the same estimand in the same data set. Using these approaches together could be a powerful tool for triangulation in infectious disease epidemiology because each approach is subject to distinct sources of bias.

Improving the contribution of mathematical modelling evidence to guidelines and policy: Experiences from tuberculosis.

We read with great interest the recent paper by Lo et al., who argue that there is an urgent need to ensure the quality of modelling evidence used to support international and national guideline development. Here we outline efforts by the Tuberculosis Modelling and Analysis Consortium, together with the World Health Organization Global Task Force on Tuberculosis Impact Measurement, to develop material to improve the quality and transparency of country-level tuberculosis modelling to inform decision-making.

Assessing population-level target product profiles of universal human influenza A vaccines.

Influenza A has two hemagglutinin groups, with stronger cross-immunity to reinfection within than between groups. Here, we explore the implications of this heterogeneity for proposed cross-protective influenza vaccines that may offer broad, but not universal, protection. While the development goal for the breadth of human influenza A vaccine is to provide cross-group protection, vaccines in current development stages may provide better protection against target groups than non-target groups.

Operational priorities for engaging with India's private healthcare sector for the control of tuberculosis: a modelling study.

Objectives: To estimate the potential impact of expanding services offered by the Joint Effort for Elimination of Tuberculosis (JEET), the largest private sector engagement initiative for tuberculosis (TB) in India.

Design: We developed a mathematical model of TB transmission dynamics, coupled with a cost model.

Setting: Ahmedabad and New Delhi, two cities with contrasting levels of JEET coverage.

fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing.

Summary: Fastlin is a bioinformatics tool designed for rapid Mycobacterium tuberculosis complex (MTBC) lineage typing. It utilizes an ultra-fast alignment-free approach to detect previously identified barcode single nucleotide polymorphisms associated with specific MTBC lineages. In a comprehensive benchmarking against existing tools, fastlin demonstrated high accuracy and significantly faster running times.

Meeting the 2030 END TB goals in the wake of COVID-19: A modelling study of countries in the USAID TB portfolio.

Progress towards the 2030 End TB goals has seen severe setbacks due to disruptions arising from the COVID-19 pandemic. For governments and international partner organizations supporting the global TB response, there is a need to assess what level of effort is now needed to reach these goals. Using mathematical modelling, we addressed this question for the countries being supported by the United States Agency for International Development (USAID).

Multimodeling approach to evaluating the efficacy of layering pharmaceutical and nonpharmaceutical interventions for influenza pandemics.

When an influenza pandemic emerges, temporary school closures and antiviral treatment may slow virus spread, reduce the overall disease burden, and provide time for vaccine development, distribution, and administration while keeping a larger portion of the general population infection free. The impact of such measures will depend on the transmissibility and severity of the virus and the timing and extent of their implementation. To provide robust assessments of layered pandemic intervention strategies, the Centers for Disease Control and Prevention (CDC) funded a network of academic groups to build a framework for the development and comparison of multiple pandemic influenza models.

Exploring the Impact of the COVID-19 Pandemic on Tuberculosis Care and Prevention.

The COVID-19 pandemic has set back the global tuberculosis (TB) response by several years. In 2020, access to TB prevention and care declined sharply, with TB notifications dropping by 18% compared to 2019. Declines were more pronounced in children, with a 24% drop in 0-14 year-olds and a 28% drop in 0-4 year-olds.

Symptom-based vs asymptomatic testing for controlling SARS-CoV-2 transmission in low- and middle-income countries: A modelling analysis.

Background: Diagnostic testing plays a critical role in the global COVID-19 response. Polymerase chain reaction (PCR) tests are highly accurate, but in resource-limited settings, limited capacity has led to testing delays; whereas lateral flow assays (LFAs) offer opportunities for rapid and affordable testing. We examined the potential epidemiological impact of different strategies for LFA deployment.

Scaling up target regimens for tuberculosis preventive treatment in Brazil and South Africa: An analysis of costs and cost-effectiveness.

Background: Shorter, safer, and cheaper tuberculosis (TB) preventive treatment (TPT) regimens will enhance uptake and effectiveness. WHO developed target product profiles describing minimum requirements and optimal targets for key attributes of novel TPT regimens. We performed a cost-effectiveness analysis addressing the scale-up of regimens meeting these criteria in Brazil, a setting with relatively low transmission and low HIV and rifampicin-resistant TB (RR-TB) prevalence, and South Africa, a setting with higher transmission and higher HIV and RR-TB prevalence.

Prioritising attributes for tuberculosis preventive treatment regimens: a modelling analysis.

Background: Recent years have seen important improvements in available preventive treatment regimens for tuberculosis (TB), and research is ongoing to develop these further. To assist with the formulation of target product profiles for future regimens, we examined which regimen properties would be most influential in the epidemiological impact of preventive treatment.

Methods: Following expert consultation, we identified 5 regimen properties relevant to the incidence-reducing impact of a future preventive treatment regimen: regimen duration, efficacy, ease-of-adherence (treatment completion rates in programmatic conditions), forgiveness to non-completion and the barrier to developing rifampicin resistance during treatment.

'Imperfect but useful': pandemic response in the Global South can benefit from greater use of mathematical modelling.

Mathematical modelling has been a helpful resource for planning public health responses to COVID-19. However, there is a need to improve the accessibility of models built within country contexts in the Global South. Immediately following the overwhelming 'second wave' of COVID-19 in India, we developed a user-friendly, web-based modelling simulator in partnership with the public health experts and health administrators for subnational planning.

A global system for the next generation of vaccines.

COVID-19 has shown that hurdles can be overcome.

Achieving a "step change" in the tuberculosis epidemic through comprehensive community-wide intervention: a model-based analysis.

Background: Global progress towards reducing tuberculosis (TB) incidence and mortality has consistently lagged behind the World Health Organization targets leading to a perception that large reductions in TB burden cannot be achieved. However, several recent and historical trials suggest that intervention efforts that are comprehensive and intensive can have a substantial epidemiological impact. We aimed to quantify the potential epidemiological impact of an intensive but realistic, community-wide campaign utilizing existing tools and designed to achieve a "step change" in the TB burden.