Project 1
Project 1 focuses on how viral genomic variation; adoption of public health mitigation measures and mobility patterns contribute to spatially and temporally explicit pathways of SARS-CoV-2 transmission at local and regional scales.
PRINCIPAL INVESTIGATOR
Kristen Stafford, PhD, MPH
Dr. Stafford is an infectious disease epidemiologist with 28 years of experience, 20 in Africa, in the design, implementation, and evaluation of domestic and international HIV care and treatment programs as well as infrastructure development for clinical and epidemiological research. Domestically she directly implemented Ryan White funded programs as well as served as the Deputy Program Manager and Manager of the Continuous Quality Improvement Program for the Ryan White Part A Program for the Baltimore EMA.
TEAM MEMBERS
COLLABORATORS
University of Minnesota & University of Port Harcourt
ACTIVITIES
To start assessing the potential effectiveness of COVID-19 public health measures in sub-Saharan Africa, we conducted an ecological study using publicly-available data from Nigeria and South Africa from April 23rd, 2020 to May 1st, 2022 to describe patterns between population-level adoption of public health measures with the number of reported new COVID-19 cases across the different COVID-19 waves in these two countries. Our preliminary results demonstrated how Nigeria’s consistent self-reported mask use never reached levels of 70% and its use declined with each wave. While in South Africa, mask use levels reached the upper nineties. The least adopted measures in both countries were avoiding grocery markets/pharmacies, avoiding spending time with individuals outside their households, and working at home. Consistent mask use and vaccination at high levels and preferably with the addition of at least one booster were shown to have an indirect relationship with new COVID-19 cases in these settings. As we face new COVID-19 variants and limited vaccine supply in Africa, it is essential to identify which public health measures are implementable with high adoption and fidelity for this unique context.
Dr. Thomas Kono, a bioinformatics analyst at the University of Minnesota Supercomputing Institute, has led the effort to assess SARS-CoV-2 phylogenetic changes and transmission potential over time within Nigeria. This Project 1 project involves the genetic analysis of SARS-CoV-2 genomes collected from patients in Nigeria and submitted to GISAID. Working with other researchers on the INFORM project, we were able to identify which viral sequences were collected during various “waves” of viral spread through Nigeria and which geographic region they were collected from. Comparisons among the samples revealed a pattern of increasing viral diversity over time, especially in the spike protein region, consistent with global patterns of SARS-CoV-2 evolution. Future efforts will involve identification of potential recombinant viral lineages and characterization of variation in mutation rate, both across Nigeria and across the viral genome.
Additionally, Project 1 continues to collaborate with Akros, our industry partner to strengthen the Reveal geospatial platform. Reveal is an open-source platform that uses spatial intelligence to drive the delivery of life-saving interventions. Akros has developed several additions to the tool including, the creation of the visualization module that supports dataset import and geospatial data tagging, data attribute selection and visualization, basic data aggregation, heat mapping, import and visualization of GPS-point type data, and download of multiple overlaid datasets and geospatial features as one dataset. We are currently developing functionality for multiple attribute overlays that will inform the creation of risk layers and additional geospatial analysis and modeling. Under project 1, we will be conducting deeper geospatial analysis on the overlaid project datasets; the INFORM consortium will utilize Reveal moving forward to visualize and geospatially analyze datasets across all projects. The eventual goal is to take these data and create targeted public health plans through the Reveal platform in order to guide and track in-field delivery of health interventions at a granular level with each area of interest.
AKROS
Akros is a cutting-edge organization based in Lusaka, Zambia that establishes data-driven systems to improve the health and well-being of disadvantaged communities. We pride ourselves in our ground-level knowledge of the service delivery systems where we work, and our ability to provide novel, lasting solutions implemented in developing regions. Akros’s role within the INFORM Research Hub is to serve as the industry partner to support the translation of Research Hub findings into real-world operationalization through the utilization of the Reveal geospatial platform. Reveal is an open-source platform that uses spatial intelligence to drive the delivery of life-saving interventions.
TEAM MEMBERS
Dr. Anna Winters, Co-Investigator
Dr. Anna Winters trained as a spatial epidemiologist during her masters and PhD programs and at the US Centers for Disease Control and Prevention (CDC) Division of Vector Borne Infectious Disease (DVBID). Anna has lived and worked globally focusing her efforts on vector-borne disease, non communicable disease and health systems strengthening over the past 20 years. She co-founded Akros, which provides technical support for disease surveillance and response systems to Ministries of Health across the Global South. Anna’s interest is to apply the power of spatial intelligence to optimize health interventions bringing impact and equitable health service delivery to the very last mile.
Christina Riley, Portfolio Lead
Christina Riley is a Director and Portfolio Lead at Akros. She leads the design, management, research, and technical implementation of programs that utilize geospatial data for targeted public health intervention deployment and monitoring. She has trained as an infectious disease epidemiologist and has conducted a wide range of malaria-related operational, behavioral, and implementation research across the African continent and southeast Asia for more than ten years.
AKROS ACTIVITIES
INFORM Research Hub
As part of our work under INFORM we have developed several additions to the Reveal tool including the creation of the visualization module that supports dataset import and geospatial data tagging; complex data attribute creation; and data visualization, aggregation, and heat mapping of multiple data overlays for further exploration, download, and analysis. Under Project 1, we will be conducting deeper geospatial analysis that will inform the creation of risk layers and additional geospatial analysis and modeling. The INFORM consortium will utilize Reveal moving forward to visualize and geospatially analyze datasets across all projects, and use Reveal as a tool to engage with in-country stakeholders for easy data visualization, exploration, and operationalization of findings. The eventual goal is to take these data and create targeted public health plans through the Reveal platform to guide and track in-field delivery of health interventions at a granular level with each area of interest.
Geo-enabled detect and respond system for antimalarial resistance in Ghana (GDRS)
Under a new U01 grant that expands the DS-I Africa Consortium’s reach and impact, Akros and IHVN are collaborating with the West African Centre for Cell Biology of Infectious Pathogens (WACCBIP) to strengthen Ghana’s malaria genomic surveillance network to include capture of community-level, geo-enabled dried blood spot (DBS) samples and expand this network to include additional epidemiologic and genomic data streams across geographies in Africa. This work will utilize the Reveal platform to conduct geospatially targeted malaria genomic surveillance at the community level by geoenabling WACCBIP’s existing malaria genomic surveillance network and further expanding the platform to link DBS data at the household level to advanced next generation sequencing (NGS) labs. The team will then use geospatial and temporal genomics surveillance data to inform timely, responsive programmatic action via visualization and monitoring of molecular markers of antimalarial resistance captured from the DBS samples, and geospatially align these genomic data to other data streams including epidemiologic, programmatic, and sociodemographic data.
