Methods for the detection of non-pathogenic HIV-1 strains containing deletions in the Nef coding region and U3 region of the LTR

The present invention is directed toward immunologic- and nucleic acid-based methodologies for the detection of non-pathogenic human immunodeficiency virus type 1 (HIV-1) strains in the body fluids of HIV-infected individuals. A blood donor infected with HIV-1 and a cohort of six blood or blood product recipients infected from this donor were studied. These patients, who remained free of HIV-1-related disease and displayed stable and normal CD4 lymphocyte counts 10 to 14 years after infection, were termed long-term nonprogressors (LTNPs). The molecular characterization of HIV-1 sequences obtained from either virus isolates or patient peripheral blood mononuclear cells (PBMCs) of LTNPs identified similar deletions in the nef gene and in the region of overlap of nef and the U3 region of the long terminal repeat (LTR). These deletions corresponded to amino acids 166-206, or nucleotides 9281 to 9437, of the HIV-1NL43 nef/LTR region. Methods were developed to detect the presence of nonpathogenic HIV-1 strains carrying these deletions in HIV-infected patients.