Determination of HIV-1 coreceptor tropism in clinical practise

Several studies showed that the upcoming drug class of CCR5 coreceptor antagonists have potent virological and immunological activity in treatment experienced patients. In patients failing a CCR5 antagonists-based regimen, the emergence of CXCR4-tropic viral variants has been demonstrated. Clonal analysis of viral isolates from a limited number of patients revealed that these CXCR4-tropic strains did not develop by mutation of a CCR5-tropic virus during therapy, but emerged from a minor population of CXCR4-tropic variants already present in the patients at baseline. Obviously, screening for CXCR4-tropic strains with a functional assay and subsequent exclusion of positive individuals from clinical studies could not completely avoid the selection of CXCR4-tropic strains during failure. But emergence of CXCR4-tropic viruses on therapy may require a critical threshold of CXCR4 viral load at baseline, which may not be the case in patients with a very low proportion of CXCR4-using variants. Therefore, this review addresses to what extent currently available methods are suitable to detect CXCR4-tropic strains in clinical settings. Available functional assays are based on recombinant viruses. These assays are generally restricted to a few laboratories and cannot be easily included in daily clinical settings. Whereas minority detection limits of sequence analyses are generally high with 15 to 30%, functional assays achieve lower detection limits for minorities of 5%. Sequence analyses require an additional interpretation step, and the accuracy of interpretation from clinical samples by current predictions systems has to be improved. In consequence, new methods are arising: genotyping may be improved by hybridisation assays, which quantify CXCR4-tropic viruses by their homology down to 1% minorities, and functional non-infectious cell fusion assays may overcome security restrictions and make phenotypic methods suitable for routine clinical laboratory practise. The highly sensitive detection of CXCR4-tropic viruses may provide the opportunity to clarify the conditions of clinical relevance for CXCR4-tropic minorities.