Topography and environmental deficiencies are associated with chikungunya virus exposure in urban informal settlements in Salvador, Brazil.

Background: Chikungunya virus (CHIKV) is an arbovirus with a significant global public health burden. Delineating the specific contributions of individual behaviour, household, natural and built environment to CHIKV transmission is important for reducing risk in urban informal settlements but challenging due to their heterogeneous environments. The aim of this study was to quantify variation in CHIKV seroprevalence between and within four urban communities in a large Brazilian city, and identify the respective contributions of individual, household, and environmental factors for seropositivity.

Using Model-Based Geostatistics to Refine Population-Based Estimates of Trachoma Prevalence: Update from a Technical Consultation.

To explore how model-based geostatistics (MBG) could support trachoma elimination efforts, a technical consultation was held on March 4 and 5, 2024 by the Centre for Health Informatics, Computing, and Statistics at Lancaster University, United Kingdom, a WHO Collaborating Centre on Geostatistical Methods for Neglected Tropical Disease Research. The meeting aimed to foster collaboration for sharing insights on using MBG for decision-making; showcase its applications in assessing trachoma elimination status; address challenges, such as setting the probability threshold for elimination and resolving conflicts between survey and MBG evidence; and discuss considerations for integrating MBG into Tropical Data. Participants, including trachoma program managers, experts, academics, donors, and statisticians, reviewed MBG applications, discussed ongoing studies, identified knowledge gaps, and planned future work.

Is multiple sclerosis a length-dependent central axonopathy? Some empirical data from the TONiC study.

There is a long-held hypothesis that multiple sclerosis (MS) affects the central nervous system in a length dependent way reflecting the propensity of longer central axonal projections to accumulate damage, but evidence for this is lacking. To determine the prevalence of body part involvement in MS and relate this to the putative axonal length innervating each body part, we asked people with MS to indicate affected body parts on a somatic diagram. Axonal length for each body part was calculated from neuroanatomical literature.

A systematic review of variables associated with snakebite risk in spatial and temporal analyses.

Background: Snakebite is a priority neglected tropical disease, but incidence data are lacking; current estimates rely upon incomplete health facility reports or ad hoc surveys. Spatial analysis methods harness statistical associations between case incidence and spatially varying factors to improve estimates. This systematic review aimed to identify variables associated with snakebite risk in spatial and temporal analyses for inclusion in geospatial studies to improve risk estimation accuracy.

Community-based snakebite risk mapping for resource prioritisation in Eastern Province, Rwanda.

Background: Snakebite envenoming is a medical emergency that requires rapid access to essential medicines and well-trained personnel. In resource-poor countries, mapping snakebite incidence can help policymakers to make evidence-based decisions for resource prioritisation. This study aimed to characterise the spatial variation in snakebite risk, and in particular to identify areas of relatively high and low risk, in Eastern Province, Rwanda.

Disentangling the influence of reservoir abundance and pathogen shedding on zoonotic spillover of the agent in urban informal settlements.

Rats are major reservoirs for pathogenic , the bacteria causing leptospirosis, particularly in urban informal settlements. However, the impact of variation in rat abundance and pathogen shedding rates on spillover transmission to humans remains unclear. This study aimed to investigate how spatial variation in reservoir abundance and pathogen pressure affect spillover transmission to humans in a Brazilian urban informal settlement.

A Comparison of Markov and Mechanistic Models for Soil-Transmitted Helminth Prevalence Projections in the Context of Survey Design.

Globally, there are over 1 billion people infected with soil-transmitted helminths (STHs), mostly living in marginalized settings with inadequate sanitation in sub-Saharan Africa and Southeast Asia. The World Health Organization recommends an integrated approach to STH morbidity control through improved access to sanitation and hygiene education and the delivery of preventive chemotherapy (PC) to school-age children delivered through schools. Progress of STH control programs is currently estimated using a baseline (pre-PC) school-based prevalence survey and then monitored using periodical school-based prevalence surveys, known as Impact Assessment Surveys (IAS).

Improving the Cost-efficiency of Preventive Chemotherapy: Impact of New Diagnostics on Stopping Decisions for Control of Schistosomiasis.

Background: Control of schistosomiasis (SCH) relies on the regular distribution of preventive chemotherapy (PC) over many years. For the sake of sustainable SCH control, a decision must be made at some stage to scale down or stop PC. These "stopping decisions" are based on population surveys that assess whether infection levels are sufficiently low.

Wastewater-based surveillance models for COVID-19: A focused review on spatio-temporal models.

The evident shedding of the SARS-CoV-2 RNA particles from infected individuals into the wastewater opened up a tantalizing array of possibilities for prediction of COVID-19 prevalence prior to symptomatic case identification through community testing. Many countries have therefore explored the use of wastewater metrics as a surveillance tool, replacing traditional direct measurement of prevalence with cost-effective approaches based on SARS-CoV-2 RNA concentrations in wastewater samples. Two important aspects in building prediction models are: time over which the prediction occurs and space for which the predicted case numbers is shown.

Modernizing the design and analysis of prevalence surveys for neglected tropical diseases.

Current WHO guidelines set prevalence thresholds below which a neglected tropical disease can be considered to have been eliminated as a public health problem, and specify how surveys to assess whether elimination has been achieved should be designed and analysed, based on classical survey sampling methods. In this paper, we describe an alternative approach based on geospatial statistical modelling. We first show the gains in efficiency that can be obtained by exploiting any spatial correlation in the underlying prevalence.

Simplified sewerage to prevent urban leptospirosis transmission: a cluster non-randomised controlled trial protocol in disadvantaged urban communities of Salvador, Brazil.

Introduction: Leptospirosis is a globally distributed zoonotic and environmentally mediated disease that has emerged as a major health problem in urban slums in developing countries. Its aetiological agent is bacteria of the genus , which are mainly spread in the urine of infected rodents, especially in an environment where adequate sanitation facilities are lacking, and it is known that open sewers are key transmission sources of the disease. Therefore, we aim to evaluate the effectiveness of a simplified sewerage intervention in reducing the risk of exposure to contaminated environments and infection and to characterise the transmission mechanisms involved.

Factors associated with differential seropositivity to and in a high transmission urban setting for leptospirosis in Brazil.

Background: Leptospirosis is a zoonosis caused by pathogenic species of bacteria belonging to the genus . Most studies infer the epidemiological patterns of a single serogroup or aggregate all serogroups to estimate overall seropositivity, thus not exploring the risks of exposure to distinct serogroups. The present study aims to delineate the demographic, socioeconomic and environmental factors associated with seropositivity of serogroup Icterohaemorraghiae and serogroup Cynopteri in an urban high transmission setting for leptospirosis in Brazil.

Linking rattiness, geography and environmental degradation to spillover infections in marginalised urban settings: An eco-epidemiological community-based cohort study in Brazil.

Background: Zoonotic spillover from animal reservoirs is responsible for a significant global public health burden, but the processes that promote spillover events are poorly understood in complex urban settings. Endemic transmission of , the agent of leptospirosis, in marginalised urban communities occurs through human exposure to an environment contaminated by bacteria shed in the urine of the rat reservoir. However, it is unclear to what extent transmission is driven by variation in the distribution of rats or by the dispersal of bacteria in rainwater runoff and overflow from open sewer systems.

Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England.

Rapid transmission of the SARS-CoV-2 Omicron variant has led to record-breaking case incidence rates around the world. Since May 2020, the REal-time Assessment of Community Transmission-1 (REACT-1) study tracked the spread of SARS-CoV-2 infection in England through RT-PCR of self-administered throat and nose swabs from randomly-selected participants aged 5 years and over. In January 2022, we found an overall weighted prevalence of 4.

Omicron SARS-CoV-2 epidemic in England during February 2022: A series of cross-sectional community surveys.

Background: The Omicron wave of COVID-19 in England peaked in January 2022 resulting from the rapid transmission of the Omicron BA.1 variant. We investigate the spread and dynamics of the SARS-CoV-2 epidemic in the population of England during February 2022, by region, age and main SARS-CoV-2 sub-lineage.

Population dynamics of synanthropic rodents after a chemical and infrastructural intervention in an urban low-income community.

Synanthropic rodents are ubiquitous in low-income communities and pose risks for human health, as they are generally resistant to control programs. However, few or no studies have evaluated the long-term effect of chemical and infrastructural interventions on rodent population dynamics, especially in urban low-income communities, or evaluated the potential recovery of their population following interventions. We conducted a longitudinal study in a low-income community in the city of Salvador (BA, Brazil) to characterize the effect of interventions (chemical and infrastructural) on the dynamics of rodent population, and documented the post-intervention recovery of their population.

Interoperability of statistical models in pandemic preparedness: principles and reality.

We present as a guiding framework for statistical modelling to assist policy makers asking multiple questions using diverse datasets in the face of an evolving pandemic response. Interoperability provides an important set of principles for future pandemic preparedness, through the joint design and deployment of adaptable systems of statistical models for disease surveillance using probabilistic reasoning. We illustrate this through case studies for inferring and characterising spatial-temporal prevalence and reproduction numbers of SARS-CoV-2 infections in England.

Twin peaks: The Omicron SARS-CoV-2 BA.1 and BA.2 epidemics in England.

Rapid transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has led to record-breaking incidence rates around the world. The Real-time Assessment of Community Transmission-1 (REACT-1) study has tracked SARS-CoV-2 infection in England using reverse transcription polymerase chain reaction (RT-PCR) results from self-administered throat and nose swabs from randomly selected participants aged 5 years and older approximately monthly from May 2020 to March 2022. Weighted prevalence in March 2022 was the highest recorded in REACT-1 at 6.

Breakthrough SARS-CoV-2 infections in double and triple vaccinated adults and single dose vaccine effectiveness among children in Autumn 2021 in England: REACT-1 study.

Background: Prevalence of SARS-CoV-2 infection with Delta variant was increasing in England in late summer 2021 among children aged 5 to 17 years, and adults who had received two vaccine doses. In September 2021, a third (booster) dose was offered to vaccinated adults aged 50 years and over, vulnerable adults and healthcare/care-home workers, and a single vaccine dose already offered to 16 and 17 year-olds was extended to children aged 12 to 15 years.

Methods: SARS-CoV-2 community prevalence in England was available from self-administered throat and nose swabs using reverse transcriptase polymerase chain reaction (RT-PCR) in round 13 (24 June to 12 July 2021, = 98,233), round 14 (9 to 27 September 2021,  = 100,527) and round 15 (19 October to 5 November 2021,  = 100,112) from the REACT-1 study randomised community surveys.

Rainfall anomalies and typhoid fever in Blantyre, Malawi.

Typhoid fever is a major cause of illness and mortality in low- and middle-income settings. We investigated the association of typhoid fever and rainfall in Blantyre, Malawi, where multi-drug-resistant typhoid has been transmitting since 2011. Peak rainfall preceded the peak in typhoid fever by approximately 15 weeks [95% confidence interval (CI) 13.