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Identifying Transmission Clusters with Cluster Picker and HIV-TRACE.
Rebecca Rose1, Susanna L Lamers1, James J Dollar1
11 BioInfoExperts , Thibodaux, Louisiana.
AIDS Research and Human Retroviruses
|November 9, 2016
Summary
Choosing genetic distance thresholds for HIV transmission cluster analysis requires caution. Different methods like Cluster Picker and HIV-TRACE show varying performance, impacting cluster detection accuracy in generalized epidemics.
Area of Science:
- Epidemiology
- Virology
- Computational Biology
Background:
- Identifying HIV transmission clusters is crucial for public health interventions.
- Accurate phylogenetic methods are needed to define transmission links.
Purpose of the Study:
- To compare the performance of Cluster Picker and HIV-TRACE in identifying HIV transmission clusters.
- To evaluate the impact of genetic distance thresholds on cluster detection accuracy.
Main Methods:
- Utilized three HIV gp41 sequence datasets (NGS and Sanger) from the Rakai Community Cohort Study.
- Employed receiver operating curve analysis to determine optimal genetic distance thresholds.
- Assessed cluster detection by Cluster Picker and HIV-TRACE at various genetic distances.
Main Results:
- Optimal gp41 genetic distance thresholds were 5.3% for couples and 4% for individuals.
- HIV-TRACE detected fewer, larger clusters; Cluster Picker identified more, smaller clusters.
- At 5.3% distance, 20% of couples were not clustered, and >1/3 had discordant assignments.
Conclusions:
- Threshold selection significantly impacts HIV transmission cluster identification.
- Caution is advised when applying clustering thresholds in generalized HIV epidemics.
- Methodological choices influence the accuracy of inferred transmission networks.
