A change in viral tropism occurs in many HIV positive individuals over
time and may be indicated by a shift in coreceptor use from CCR5 to
CXCR4. The shift in coreceptor use to CXCR4 has been shown to correlate
with increased disease progression. In patients undergoing HAART, the
predominant populations of virus may be shifted back to CCR5-mediated
entry after the CXCR4-specific strains have emerged. The present
invention relates to a diagnostic method to monitor coreceptor use in the
treatment and clinical management of human immunodeficiency virus (HIV)
infection. The present invention further relates to a diagnostic method
applied to HIV-positive individuals undergoing HAART to monitor the
suppression of CCR5- or CXCR4-specific strains. The diagnostic methods
may be used to assist in selecting antiretroviral therapy and to improve
predictions of disease prognosis over time. The methods of the invention
include cell-based methods, including cell fusion assays, and
molecular-based methods, including heteroduplex tracking assay, to both
quantitatively and qualitatively analyze patient-derived HIV for
coreceptor usage.