Interactive SARS-CoV-2 dashboard for real-time geospatial visualisation of sewage and clinical surveillance data from Dhaka, Bangladesh: a tool for public health situational awareness

Throughout the COVID-19 pandemic, many dashboards were created to visualise clinical case incidence. Other dashboards have displayed SARS-CoV-2 sewage data, largely from countries with formal sewage networks. However, very few dashboards from low-income and lower-middle-income countries integrated both clinical and sewage data sets. We created a dashboard to track in real-time both COVID-19 clinical cases and the level of SARS-CoV-2 virus in sewage in Dhaka, Bangladesh. The development of this dashboard was a collaborative iterative process with Bangladesh public health stakeholders to include specific features to address their needs. The final dashboard product provides spatiotemporal visualisations of COVID-19 cases and SARS-CoV-2 viral load at 51 sewage collection sites in 21 wards in Dhaka since 24 March 2020. Our dashboard was updated weekly for the Bangladesh COVID-19 national task force to provide supplemental data for public health stakeholders making public policy decisions on mitigation efforts. Here, we highlight the importance of working closely with public health stakeholders to create a COVID-19 dashboard for public health impact. In the future, the dashboard can be expanded to track trends of other infectious diseases as sewage surveillance is increased for other pathogens

Embedding usage sensors in point-of-use water treatment devices: sensor design and application in Limpopo, South Africa.

Health benefits from point-of-use (POU) water treatment devices come only with consistent use. Embedded sensors can measure the consistency of POU-device use and can provide insights about improving it. We demonstrate both potentials with data from SmartSpouts: accelerometer-based sensors embedded in spigot handles that record the duration and timing of use. In the laboratory, most sensor readings correlated well (>0.98) with manually timed water withdrawals. In the field, SmartSpouts measured >60,000 water withdrawals across 232 households in Limpopo, South Africa. Sensors proved critical to understanding consistent use; surveys overestimated it by 53 percentage points. Sensor data showed when households use POU devices (evening peaks and delayed weekend routines) and user preferences (safe storage over filters). We demonstrate analytically and with data that (i) consistent use (e.g., 7 continuous days) is extremely sensitive to single-day use prevalence and (ii) use prevalence affects the performance of contact-time-based POU devices, exemplified with silver tablets. Deployed SmartSpouts had limitations, including memory overflows and confounding device relocation with water withdrawal. Nevertheless, SmartSpouts provided useful and objective data on the prevalence of single-day and consistent use. Considerably less expensive than alternatives, SmartSpouts enable an order of magnitude increase in how many POU-device sensors can be deployed

Impact of Water Quality, Sanitation, Handwashing, and Nutritional Interventions on Enteric Infections in Rural Zimbabwe: The Sanitation Hygiene Infant Nutrition Efficacy (SHINE) Trial.

BACKGROUND: We assessed the impact of water, sanitation, and hygiene (WASH) and infant and young child feeding (IYCF) interventions on enteric infections in the Sanitation Hygiene Infant Nutrition Efficacy (SHINE) trial in rural Zimbabwe. METHODS: We tested stool samples collected at 1, 3, 6, and 12 months of age and during diarrhea using quantitative molecular diagnostics for 29 pathogens. We estimated the effects of the WASH, IYCF, and combined WASH + IYCF interventions on individual enteropathogen prevalence and quantity, total numbers of pathogens detected, and incidence of pathogen-attributable diarrhea. RESULTS: WASH interventions decreased the number of parasites detected (difference in number compared to non-WASH arms, -0.07 [95% confidence interval, -.14 to -.02]), but had no statistically significant effects on bacteria, viruses, or the prevalence and quantity of individual enteropathogens after accounting for multiple comparisons. IYCF interventions had no significant effects on individual or total enteropathogens. Neither intervention had significant effects on pathogen-attributable diarrhea. CONCLUSIONS: The WASH interventions implemented in SHINE (improved pit latrine, hand-washing stations, liquid soap, point-of-use water chlorination, and clean play space) did not prevent enteric infections. Transformative WASH interventions are needed that are more efficacious in interrupting fecal-oral microbial transmission in children living in highly contaminated environments

Enteropathogens were not associated with rotavirus vaccine immunogenicity in a cluster-randomized trial of improved water, sanitation and hygiene in rural Zimbabwe

This is the accepted manuscript of an article to be published in Pediatric Infectious Disease Journal."This is a non-final version of an article published in final form in The Pediatric Infectious Disease Journal: December 2019 - Volume 38 - Issue 12 - p 1242–1248 doi: 10.1097/INF.0000000000002485.

Real-time sewage surveillance for SARS-CoV-2 in Dhaka, Bangladesh versus clinical COVID-19 surveillance: a longitudinal environmental surveillance study (Dec 2019 – Dec 2021)

Background: Clinical surveillance for COVID-19 has typically been challenging in low-middle income settings. From December 2019 to December 2021, we implemented environmental surveillance (ES) in a converging informal sewage network in Dhaka, Bangladesh, to investigate SARS-CoV-2 transmission across different income levels of the city compared to clinical surveillance. Methods: All sewage lines were mapped, and sites were selected with estimated catchment population of >1,000 individuals. We analysed 2,073 sewage samples, collected weekly from 37 sites and 648 days of case data from 8 wards with varying socio-economic statuses. We assessed the correlations between the viral load in sewage samples and clinical cases. Findings: SARS-CoV-2 was consistently detected across all wards (low to high income) despite large differences in reported clinical cases and periods of no cases. Most COVID-19 cases (60.3%, n=28,766/47,683) were reported from high-income areas with high levels of clinical testing (261-1603 monthly tests per 100,000 vs. 0-189 in lower-income areas), despite containing 25% (184,117/734,755) of the study population. Conversely, a similar quantity of SARS-CoV-2 was detected in sewage across different income levels (mean difference in high vs. low-income areas: 0.35 log10 viral copies + 1). The correlation between the mean sewage viral load (log10 viral copies + 1) and the log10 clinical cases increased with time (R=0.90 July 2021-December 2021 and R=0.59 July 2020-December 2020). Before major waves of infection, viral load quantity in sewage samples increased one to two weeks before the clinical cases. Interpretation: This study demonstrates the utility and importance of environmental surveillance for SARS-CoV-2 in a low-middle income country. We show ES provides an early warning of increases in transmission and shows evidence of persistent circulation in poorer areas where access to clinical testing is limited. Funding: Bill and Melinda Gates Foundation (INV-022699 and OPP1193124 to M Taniuchi). IM Blake acknowledges funding from the MRC Centre for Global Infectious Disease Analysis (reference MR/R015600/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 programme supported by the European Union

Epidemiology of shigella infections and diarrhea in the first two years of life using culture-independent diagnostics in 8 low-resource settings

Culture-independent diagnostics have revealed a larger burden of Shigella among children in low-resource settings than previously recognized. We further characterized the epidemiology of Shigella in the first two years of life in a multisite birth cohort. We tested 41,405 diarrheal and monthly non-diarrheal stools from 1,715 children for Shigella by quantitative PCR. To assess risk factors, clinical factors related to age and culture positivity, and associations with inflammatory biomarkers, we used log-binomial regression with generalized estimating equations. The prevalence of Shigella varied from 4.9%-17.8% in non-diarrheal stools across sites, and the incidence of Shigella-attributable diarrhea was 31.8 cases (95% CI: 29.6, 34.2) per 100 child-years. The sensitivity of culture compared to qPCR was 6.6% and increased to 27.8% in Shigella-attributable dysentery. Shigella diarrhea episodes were more likely to be severe and less likely to be culture positive in younger children. Older age (RR: 1.75, 95% CI: 1.70, 1.81 per 6-month increase in age), unimproved sanitation (RR: 1.15, 95% CI: 1.03, 1.29), low maternal education (\u3c10 years, RR: 1.14, 95% CI: 1.03, 1.26), initiating complementary foods before 3 months (RR: 1.10, 95% CI: 1.01, 1.20), and malnutrition (RR: 0.91, 95% CI: 0.88, 0.95 per unit increase in weight-for-age z-score) were risk factors for Shigella. There was a linear dose-response between Shigella quantity and myeloperoxidase concentrations. The burden of Shigella varied widely across sites, but uniformly increased through the second year of life and was associated with intestinal inflammation. Culture missed most clinically relevant cases of severe diarrhea and dysentery