We have reported previously that mutations in regions of HTLV-1 PCR binding probes could be identified using ddPCR [19] and exploited this observation when it was apparent that HAM/TSP patient NIH00261 demonstrated a lower fluorescence amplitude of the HTLV-1 tax sequence in both PBMC and CSF when compared to other HAM/TSP patients. This evidence concerns the gene CNTN2 and tropical spastic paraparesis.