In:
Journal of Virology, American Society for Microbiology, Vol. 84, No. 7 ( 2010-04), p. 3644-3653
Abstract:
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 nef 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 nef sequences compared to the Ps ( P = 0.47). The high frequency of amino acid replacement at residues S 8 , V 10 , I 11 , A 15 , V 85 , V 133 , N 157 , S 163 , V 168 , D 174 , R 178 , E 182 , and R 188 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 15 , V 85 , N 157 , S 163 , V 168 , D 174 , R 178 , and R 188 ) were not significant ( P = 0.77). Exploratory analysis suggested a hypothetical excess of frameshifting in the regions 9 SVIG and 118 QGYF among LTNPs. The regions V 10 and 152 KVEEA of nef 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 nef sequences provides no clear evidence of whether defective nef sequences or particular regions of the protein play a significant role in disease progression.
Type of Medium:
Online Resource
ISSN:
0022-538X
,
1098-5514
DOI:
10.1128/JVI.01959-09
Language:
English
Publisher:
American Society for Microbiology
Publication Date:
2010
detail.hit.zdb_id:
1495529-5
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