biostudies-literatureUnknown84(7)Pushker RPrevious relatively small studies have associated particular amino acid replacements and deletions in the HIV-1 nef gene with differences in the rate of HIV disease progression. We tested more rigorously whether particular nef amino acid differences and deletions are associated with HIV disease progression. Amino acid replacements and deletions in patients' consensus sequences were investigated for 153 progressor (P), 615 long-term nonprogressor (LTNP), and 2,311 unknown progressor sequences from 582 subtype B HIV-infected patients. LTNPs had more defective nefs (interrupted by frameshifts or stop codons), but on a per-patient basis there was no excess of LTNP patients with one or more defective nef sequences compared to the Ps (P = 0.47). The high frequency of amino acid replacement at reJournal of virology3644-53https://www.ebi.ac.uk/biostudies/studies/S-EPMC2838144biostudies-literatureMeta-analysis to test the association of HIV-1 nef amino acid differences and deletions with disease progression.PMC2838144Pushker RJacque JMShields DCfalseMeta-analysis to test the association of HIV-1 nef amino acid differences and deletions with disease progression.Previous relatively small studies have associated particular amino acid replacements and deletions in the HIV-1 nef gene with differences in the rate of HIV disease progression. We tested more rigorously whether particular nef amino acid differences and deletions are associated with HIV disease progression. Amino acid replacements and deletions in patients' consensus sequences were investigated for 153 progressor (P), 615 long-term nonprogressor (LTNP), and 2,311 unknown progressor sequences from 582 subtype B HIV-infected patients. LTNPs had more defective nefs (interrupted by frameshifts or stop codons), but on a per-patient basis there was no excess of LTNP patients with one or more defective nef sequences compared to the Ps (P = 0.47). The high frequency of amino acid replacement at re2010-01-01T00:00:00Z2010 Apr2025-04-29T10:29:31.252Z2019-03-26T23:52:02ZS-EPMC28381442007158310.1128/jvi.01959-0910.1128/JVI.01959-09