{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T19:10:37Z","timestamp":1791227437703,"version":"4.1.0"},"reference-count":58,"publisher":"American Society for Microbiology","issue":"7","license":[{"start":{"date-parts":[[2010,4,1]],"date-time":"2010-04-01T00:00:00Z","timestamp":1270080000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Virol"],"published-print":{"date-parts":[[2010,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Previous relatively small studies have associated particular amino acid replacements and deletions in the HIV-1\n            <jats:italic>nef<\/jats:italic>\n            gene with differences in the rate of HIV disease progression. We tested more rigorously whether particular\n            <jats:italic>nef<\/jats:italic>\n            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\n            <jats:italic>nef<\/jats:italic>\n            s (interrupted by frameshifts or stop codons), but on a per-patient basis there was no excess of LTNP patients with one or more defective\n            <jats:italic>nef<\/jats:italic>\n            sequences compared to the Ps (\n            <jats:italic>P<\/jats:italic>\n            = 0.47). The high frequency of amino acid replacement at residues S\n            <jats:sup>8<\/jats:sup>\n            , V\n            <jats:sup>10<\/jats:sup>\n            , I\n            <jats:sup>11<\/jats:sup>\n            , A\n            <jats:sup>15<\/jats:sup>\n            , V\n            <jats:sup>85<\/jats:sup>\n            , V\n            <jats:sup>133<\/jats:sup>\n            , N\n            <jats:sup>157<\/jats:sup>\n            , S\n            <jats:sup>163<\/jats:sup>\n            , V\n            <jats:sup>168<\/jats:sup>\n            , D\n            <jats:sup>174<\/jats:sup>\n            , R\n            <jats:sup>178<\/jats:sup>\n            , E\n            <jats:sup>182<\/jats:sup>\n            , and R\n            <jats:sup>188<\/jats:sup>\n            in LTNPs was also seen in permuted datasets, implying that these are simply rapidly evolving residues. Permutation testing revealed that residues showing the greatest excess over expectation (A\n            <jats:sup>15<\/jats:sup>\n            , V\n            <jats:sup>85<\/jats:sup>\n            , N\n            <jats:sup>157<\/jats:sup>\n            , S\n            <jats:sup>163<\/jats:sup>\n            , V\n            <jats:sup>168<\/jats:sup>\n            , D\n            <jats:sup>174<\/jats:sup>\n            , R\n            <jats:sup>178<\/jats:sup>\n            , and R\n            <jats:sup>188<\/jats:sup>\n            ) were not significant (\n            <jats:italic>P<\/jats:italic>\n            = 0.77). Exploratory analysis suggested a hypothetical excess of frameshifting in the regions\n            <jats:sup>9<\/jats:sup>\n            SVIG and\n            <jats:sup>118<\/jats:sup>\n            QGYF among LTNPs. The regions V\n            <jats:sup>10<\/jats:sup>\n            and\n            <jats:sup>152<\/jats:sup>\n            KVEEA of\n            <jats:italic>nef<\/jats:italic>\n            were commonly deleted in LTNPs. However, permutation testing indicated that none of the regions displayed significantly excessive deletion in LTNPs. In conclusion, meta-analysis of HIV-1\n            <jats:italic>nef<\/jats:italic>\n            sequences provides no clear evidence of whether defective\n            <jats:italic>nef<\/jats:italic>\n            sequences or particular regions of the protein play a significant role in disease progression.\n          <\/jats:p>","DOI":"10.1128\/jvi.01959-09","type":"journal-article","created":{"date-parts":[[2010,1,14]],"date-time":"2010-01-14T02:59:47Z","timestamp":1263437987000},"page":"3644-3653","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":19,"title":["Meta-Analysis To Test the Association of HIV-1\n            <i>nef<\/i>\n            Amino Acid Differences and Deletions with Disease Progression"],"prefix":"10.1128","volume":"84","author":[{"given":"Ravindra","family":"Pushker","sequence":"first","affiliation":[{"name":"UCD Complex and Adaptive Systems Laboratory"},{"name":"UCD Conway Institute of Biomolecular 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