Table 1 Use cases for genetic epidemiology in malaria elimination
From: Use cases for genetic epidemiology in malaria elimination
| Â | Description | Pre-conditions | Post-conditions | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Description | Current method or indicator | Population unit for implementation of analysis | Case detection | Prevalencea | Focus type | Sampling frame | Informatics; priors needed | Potential action informed | Presentation of output | Time to information (ideal) | |
1. Detect resistance | Assess the prevalence/frequency of molecular markers associated with antimalarial drug resistance | PCR-based testing (currently research focused) | Individuals | Passive or active | High to very low | Active | Representative | Database of resistance alleles in local population; ability to identify possible new parkers | Intervention selection, treatment guidelines, surveillance | Quantitative, geospatial maps | Rapid (< 1 week)b |
2. Assess drug resistance gene flow | Monitor and predict the spread of genes conferring drug resistance within and among regions and parasite populations | Treatment efficacy surveys at variable frequencies | Multiple foci (e.g. Areas where administration of drugs is a major component of control effort) | Active | High to very low | Active | Representative | Reference distribution of resistance alleles; model for gene flow with genetic data input | Intervention selection, treatment guidelines, surveillance | Quantitative, geospatial maps, phylogenies | Monthlyb |
3. Assess transmission intensity | Stratify regions according to transmission intensity in the area population; monitor interventions and epidemics | Surveillance | Focus | Passive or active | Low to very low | Active | Representativec | Reference distribution of parasite diversity; intensity model using a genetic data input | Intervention selection and evaluation, deployment of resources | Quantitative, qualitative, geospatial maps | Monthly |
4. Identify foci | Identify focal areas of high diversity and clusters of infections | Surveillance, case investigation | Geographic area of interest (e.g. Area with unknown distribution of foci or hotspots) | Passive, active, reactive | Moderate to very low | Active to residual non-active | Representative | Algorithm to integrate case detection with geographic and population characteristics | Intervention selection, surveillance, deployment of resources | Phylogenies, geospatial maps | Fast (< 1 month) |
5. Determine connectivity of parasite populations | Assess degree to which transmission is linked among regions due to parasite population linkages | Migration data (often produced via modeling) | Multiple foci across a region, country, or continent (e.g. Areas where parasite populations may be linked due to human or parasite migration) | Active | High to very low | Active to residual non-active | Representative | Reference distribution of parasite diversity and human migration patterns; model for parasite flow with genetic data input | Intervention selection and evaluation, deployment of resources | Geospatial network maps | Annual |
6. Identify imported cases | Discriminate between indigenous vs. imported cases (sources and sinks) | Travel surveys | Individuals | Passive or reactive | Very low to zero | Active to residual non-active | Dense | Reference distribution of local parasite diversity; high coverage case surveillance | Intervention selection and evaluation, deployment of resources, surveillance, case investigation; certify elimination | Quantitative, phylogenies, network maps | Rapid (< 3 days)d |
7. Characterize local transmission chains | Distinguish contributions factors (e.g. seasonality, migrants, asymptomatics, and highly infectious individuals) to ongoing transmission patterns; certify elimination | Case investigations | Focus with limited transmission | Passive or reactive | Low to very low | Active to residual non-active | Dense | Reference distribution of parasite diversity; models engaging geospatial and/or network analysis to distinguish chain length | Intervention selection and evaluation, deployment of resources, surveillance, case investigation; certify elimination | Quantitative, phylogenies, network maps | Fast (< 1 month) |