Case Study: Centers for Disease Control and Prevention achieves automated poliovirus sequencing and faster reporting with MathWorks

Centers for Disease Control and Prevention Automates Poliovirus Sequencing and Tracking

The Centers for Disease Control and Prevention (CDC) Polio Molecular Epidemiology Laboratory faced a labor‑intensive, multi‑platform workflow to process and report poliovirus sequencing and patient data for WHO—assembling and annotating some 3,000 sequences and producing monthly reports and phylogenetic trees could take up to three days and required specialized skills. To automate and simplify this pipeline, the CDC adopted MathWorks tools, including MATLAB, Bioinformatics Toolbox, Mapping Toolbox, MATLAB Compiler, and related products.

Using MathWorks software, CDC built an end‑to‑end system to import databases and FASTA files, perform sequence alignment and neighbor‑joining phylogenies, run automated cluster analysis, generate color‑coded maps, and compile standalone apps for wider lab use. The MathWorks‑based solution reduced monthly report generation from three days to about one hour, cut cluster analysis from roughly three months of manual work to about one week, and produced compiled tools that let partner labs run mapping and annotation without installing MATLAB, improving timeliness and reproducibility.

Centers for Disease Control and Prevention