Ultradeep sequencing reveals HIV-1 diversity and resistance compartmentalization during HIV-encephalopathy.

Objectives: To examine viral diversity and resistance mutations in different brain areas in cases of HIV-encephalopathy.

Design: Twelve postmortem brain areas from three cases of possible or certain HIV-encephalopathy were analyzed.

Methods: After amplification of the reverse transcriptase and the V3 loop region of the gp120 protein, ultradeep sequencing was performed with Illumina technology.