Genetic characterization of human immunodeficiency virus type 1 in elite controllers: lack of gross genetic defects or common amino acid changes

Abstract

Despite reports of viral genetic defects in persons who control human immunodeficiency virus type 1 (HIV-1) in the absence of antiviral therapy, the extent to which such defects contribute to the long-term containment of viremia is not known. Most previous studies examining for such defects have involved small numbers of subjects, primarily focused on subjects expressing HLA-B57, or have examined single viral genes, and they have focused on cellular proviral DNA rather than plasma viral RNA sequences. Here, we attempted viral sequencing from 95 HIV-1 elite controllers (EC) who maintained plasma viral loads of <50 RNA copies/ml in the absence of therapy, the majority of whom did not express HLA-B57. HIV-1 gene fragments were obtained from 94% (89/95) of the EC, and plasma viral sequences were obtained from 78% (61/78), the latter indicating the presence of replicating virus in the majority of EC. Of 63 persons for whom nef was sequenced, only three cases of nef deletions were identified, and gross genetic defects were rarely observed in other HIV-1 coding genes. In a codon-by-codon comparison between EC and persons with progressive infection, correcting for HLA bias and coevolving secondary mutations, a significant difference was observed at only three codons in Gag, all three of which represented the historic population consensus amino acid at the time of infection. These results indicate that the spontaneous control of HIV replication is not attributable to shared viral genetic defects or shared viral polymorphisms.

FIG. 1.

Maximum-likelihood tree of HIV-1 from EC and CP. Trees were computed with DNAml (in PHYLIP) using 1,500 bases of gag nucleotide sequences and were rooted to M ancestral sequences. Two of each subtype reference sequence in LANL were included. Gap was proportionally distributed. Blue lines indicate chronic progressors. Green and red lines indicate EC with protective major histocompatibility complex class I alleles (B*27, B*51, B*57, or B*5801) and the other EC, respectively. Only complete fragments were used for this analysis. § indicates the M ancestral sequence; ¶ indicates the B ancestral sequence.

FIG. 2.

Comparison of length polymorphisms between EC and CP. The lengths of the C terminus of p17 (codons 109 to 133 in HXB2; 24 aa), p6 (codons 1 to 43; 43 aa), V1 (codons 131 to 149; 19 aa), V2 (codons 158 to 197; 39 aa), and V4 (codons 385 to 418; 26 aa) of gp120 and the N terminus of Nef (codons 20 to 32; 13 aa) were compared between EC and CP. Statistical analysis was performed by a Mann-Whitney U test. Black lines indicate median values.

FIG. 3.

Viral replication capacity of S67A and D102E Gag mutant NL4-3. The percentage of GFP expression was normalized to day-2 values and are shown on a log 10 scale. In order to avoid overlay, they were nudged a little bit in the direction of the x axis. The experiment was duplicated, and the representative data are shown.