Journal of Virology 2003. 77(24):13376-13388

Improved Coreceptor Usage Prediction and Genotypic Monitoring of R5-to-X4 Transition by Motif Analysis of HIV-1 env V3 Loop Sequences

Jensen, M. A., Li, F.-S., van 't Wout, A. B., Nickle, D. C., Shriner, D., He, H.-X., McLaughlin, S., Shankarappa, R., Margolick, J. B., Mullins, J. I.

Early in infection, HIV-1 generally uses the CCR5 chemokine receptor, along with CD4, for cellular entry. In many HIV-1 infected individuals, viral genotypic changes arise that allow the virus to use CXCR4 as an entry coreceptor, either in addition to CCR5 or alone. This switch has been associated with an acceleration of both CD3⁺ T-cell decline and progression to AIDS. While it is well known that the V3 loop of gp120 largely determines coreceptor usage, and that positively charged residues in V3 play an important role, the process of genetic change in V3 leading to altered coreceptor usage is not well understood. Further, the methods for biological phenotyping of virus for research or clinical purposes are laborious, depend on sample availability, and present biosafety concerns, so that reliable methods for sequence-based "virtual phenotyping" are desirable. We introduce a simple bioinformatic method of scoring V3 amino acid sequences that reliably predicts CXCR4 usage (sensitivity: 84%, specificity: 96%). This score, based on position-specific scoring matrices (PSSM), can be interpreted as the propensity to use CXCR4: known R5 viruses had low scores; R5X4 viruses, intermediate scores; and X4 viruses, high scores. Application of the PSSM scoring method to reconstructed virus phylogenies of 11 longitudinally sampled individuals revealed that the development of X4 virus was generally gradual and involved the accumulation of multiple amino acid changes in V3. We found that X4 virus was lost in two ways: by the die-off of an established X4 lineage, or by mutation back to low-scoring V3 loops.