Determination of coreceptor usage of human immunodeficiency virus type 1 from patient plasma samples by using a recombinant phenotypic assay

We developed a recombinant virus technique to determine the coreceptor usag e of human immunodeficiency virus type 1 (HIV-1) from plasma samples, the s ource expected to represent the most actively replicating virus population in infected subjects. This method is not subject to selective bias associat ed,vith virus isolation in culture, a step required for conventional tropis m determination procedures. The addition of a simple subcloning step allowe d semiquantitative evaluation of virus populations with a different corecep tor (CCR5 or CXCR4) usage specificity present in each plasma sample. This p rocedure detected mixtures of CCR5- and CXCR4-exclusive virus populations a s well as dualtropic viral variants, in variable proportions. Sequence anal ysis of dualtropic clones indicated that changes in the V3 loop are necessa ry for the use of CXCR4 as a coreceptor, but the overall context of the V1- V3 region is important to preserve the capacity to use CCR5. This convenien t technique can greatly assist the study of virus evolution and compartment alization in infected individuals.