Performance of the ViroSeq HIV-1 genotyping system v2.0 on HIV-1 strains circulating in Senegal

► We investigated the performance of ViroSeq HIV-1 genotyping system v2.0 on strains identified in Senegalese patients. ► Amplification and sequencing rate were respectively 98% (147/150) and 96.6% (142/147). ► Primer B presented 100% success while the failure rate ranged from 1.4 to 71.4% for the other primers. ► No common polymorphic pattern or mutations between non-B subtypes that could predict the sequencing primer performances. ► Results suggest the need for an alternative technology to genotype non-B strains circulating in Senegal.