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HIV-1 sequences from either virus isolates or patient peripheral blood mononuclear cells had similar deletions in the\n            <jats:italic>nef<\/jats:italic>\n            gene and in the region of overlap of\n            <jats:italic>nef<\/jats:italic>\n            and the U3 region of the long terminal repeat (LTR). Full-length sequencing of one isolate genome and amplification of selected HIV-1 genome regions from other cohort members revealed no other abnormalities of obvious functional significance. 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