Oved detection of minor variants. The genotypic rule used to predict CXCR4-usage can be changed according to the virus subtype, particularly for subtypes D and CRF01-AE for which we have developed specific algorithms25,26. We used the combined 11/25 and net charge rules to infer the tropism of each virus clone from the V3 amino acid sequence. It requires one of the following criteria for predictin