Distinct populations of human immunodeficiency virus type 1 in blood and cerebrospinal fluid.

The nucleotide sequence of the gp41 transmembrane protein coding region of human immunodeficiency virus type 1 (HIV-1) proviral DNA obtained from blood and cerebrospinal fluid (CSF) from 6 individuals was determined by direct sequencing of polymerase chain reaction (PCR)-amplified DNA. The direct sequencing approach was performed to avoid errors introduced by Taq polymerase during the amplification reaction. In 3 of 6 paired samples distinct sequence differences between proviral DNA from blood and CSF, ranging from 0.64% to 1.73%, were detected. The greatest diversity (4.2% different amino acids) was found between paired samples of a patient suffering from AIDS encephalopathy, with most of the differences clustering near the carboxy-terminal end of gp41. The results demonstrate that genetically different populations of HIV-1 may be present in different biological compartments and specific neurotropic HIV variants may exist.