COVID-19 Variant Surveillance and Social Determinants in Central Massachusetts: Development Study
Bibliographic record
Abstract
BACKGROUND: Public health scientists have used spatial tools such as web-based Geographical Information System (GIS) applications to monitor and forecast the progression of the COVID-19 pandemic and track the impact of their interventions. The ability to track SARS-CoV-2 variants and incorporate the social determinants of health with street-level granularity can facilitate the identification of local outbreaks, highlight variant-specific geospatial epidemiology, and inform effective interventions. We developed a novel dashboard, the University of Massachusetts' Graphical user interface for Geographic Information (MAGGI) variant tracking system that combines GIS, health-associated sociodemographic data, and viral genomic data to visualize the spatiotemporal incidence of SARS-CoV-2 variants with street-level resolution while safeguarding protected health information. The specificity and richness of the dashboard enhance the local understanding of variant introductions and transmissions so that appropriate public health strategies can be devised and evaluated. OBJECTIVE: We developed a web-based dashboard that simultaneously visualizes the geographic distribution of SARS-CoV-2 variants in Central Massachusetts, the social determinants of health, and vaccination data to support public health efforts to locally mitigate the impact of the COVID-19 pandemic. METHODS: MAGGI uses a server-client model-based system, enabling users to access data and visualizations via an encrypted web browser, thus securing patient health information. We integrated data from electronic medical records, SARS-CoV-2 genomic analysis, and public health resources. We developed the following functionalities into MAGGI: spatial and temporal selection capability by zip codes of interest, the detection of variant clusters, and a tool to display variant distribution by the social determinants of health. MAGGI was built on the Environmental Systems Research Institute ecosystem and is readily adaptable to monitor other infectious diseases and their variants in real-time. RESULTS: We created a geo-referenced database and added sociodemographic and viral genomic data to the ArcGIS dashboard that interactively displays Central Massachusetts' spatiotemporal variants distribution. Genomic epidemiologists and public health officials use MAGGI to show the occurrence of SARS-CoV-2 genomic variants at high geographic resolution and refine the display by selecting a combination of data features such as variant subtype, subject zip codes, or date of COVID-19-positive sample collection. Furthermore, they use it to scale time and space to visualize association patterns between socioeconomics, social vulnerability based on the Centers for Disease Control and Prevention's social vulnerability index, and vaccination rates. We launched the system at the University of Massachusetts Chan Medical School to support internal research projects starting in March 2021. CONCLUSIONS: We developed a COVID-19 variant surveillance dashboard to advance our geospatial technologies to study SARS-CoV-2 variants transmission dynamics. This real-time, GIS-based tool exemplifies how spatial informatics can support public health officials, genomics epidemiologists, infectious disease specialists, and other researchers to track and study the spread patterns of SARS-CoV-2 variants in our communities.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.005 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".