HIV-1 envelope subregion length variation during disease progression

Abstract

The V3 loop of the HIV-1 Env protein is the primary determinant of viral coreceptor usage, whereas the V1V2 loop region is thought to influence coreceptor binding and participate in shielding of neutralization-sensitive regions of the Env glycoprotein gp120 from antibody responses. The functional properties and antigenicity of V1V2 are influenced by changes in amino acid sequence, sequence length and patterns of N-linked glycosylation. However, how these polymorphisms relate to HIV pathogenesis is not fully understood. We examined 5185 HIV-1 gp120 nucleotide sequence fragments and clinical data from 154 individuals (152 were infected with HIV-1 Subtype B). Sequences were aligned, translated, manually edited and separated into V1V2, C2, V3, C3, V4, C4 and V5 subregions. V1-V5 and subregion lengths were calculated, and potential N-linked glycosylation sites (PNLGS) counted. Loop lengths and PNLGS were examined as a function of time since infection, CD4 count, viral load, and calendar year in cross-sectional and longitudinal analyses. V1V2 length and PNLGS increased significantly through chronic infection before declining in late-stage infection. In cross-sectional analyses, V1V2 length also increased by calendar year between 1984 and 2004 in subjects with early and mid-stage illness. Our observations suggest that there is little selection for loop length at the time of transmission; following infection, HIV-1 adapts to host immune responses through increased V1V2 length and/or addition of carbohydrate moieties at N-linked glycosylation sites. V1V2 shortening during early and late-stage infection may reflect ineffective host immunity. Transmission from donors with chronic illness may have caused the modest increase in V1V2 length observed during the course of the pandemic.

Figure 1. Schematic diagram of HIV-1 env subregions (center bar) and distribution of subregion loop lengths (surrounding bar graphs).

The center bar depicts the linear arrangement of subregions V1V2 through V5 within the HIV Env gp120 protein. The amino acid length distribution of each subregion is shown in the linked bar graphs, including sequences in the cross-sectional dataset, the longitudinal dataset and the transmission data described in Text S1. Length distributions in V1V2 and V4 data are shown by isolation site (PBMC  =  blue bars, plasma  =  red bars, cervical cells  =  green bars, CSF  =  light gray bars, dendritic cells  =  orange bars, cell culture  =  dark gray bars, and cells from unknown anatomic compartments represented by open bars), and by subtype (subtype B  =  blue bars, subtype A  =  red bars, subtype C  =  green bars, subtype G  =  orange bars, untyped sequences  =  open bars). V5 sequences were all of subtype B. X-axis: sequence length (amino acids); Y-axis: number of sequences.

Figure 2. V1V2 length vs. time since infection (upper panel) and vs. year of sampling (lower panel).

Lengths are indicated in amino acids. Overlapping data points appear as darker symbols. Sequences from plasma are represented by diamonds and sequences from PBMC are represented by circles. Regression coefficients and coefficients of determination are shown for univariate linear regression, for plasma (red line) and PBMC (blue line).

Figure 3. Correlation between stage of illness and V1V2 length.

Lengths are indicated in amino acids. Sequences from plasma are represented by diamonds and sequences from PBMC are represented by circles. Overlapping data points appear as darker symbols. Quartiles and median values are indicated by horizontal line segments. Stage 1, 2, and 3 subjects were sampled within two months, between two months and three years, and at times >3 years post infection, respectively. Stage 4 subjects were comprised of all individuals meeting 1993 CDC criteria for AIDS when sampling occurred, regardless of time since infection.

Figure 4. V1V2 loop lengths over time in group L1.

Sequences from plasma are represented by diamonds and sequences from PBMC are represented by circles. Significant slopes are indicated in bold. X-axis denotes years elapsed between sampling time points, but do not necessarily indicate the total duration of infection. The first author of the report in which data were originally presented is indicated in the upper left-hand corner of each graph. Group L1 subjects did not meet criteria for AIDS at any time prior to the final sample. Subjects reported by McDonald et al had received AZT monotherapy at one or more times prior to sampling.

Figure 5. V1V2 length vs. time in subjects Q23, CC1 and 1362.

Panel A: Subject Q23, infected with HIV subtype A. Sequences were derived from PBMC (black circles), plasma (black diamonds) and DNA from cervical lymphocytes (green squares) as described by Poss et al . Panel B: Subject CC1, infected with subtype A. Sequences were obtained from plasma (black diamonds) and tissue culture (red squares). Length change of in vitro sequences occurs over ∼ 40 days, and are represented along an expanded X-axis for clarity.

Figure 6. V1V2 loop lengths over time in group L2.

Sequences from plasma are represented by diamonds and sequences from PBMC are represented by circles. Significant slopes are indicated in bold. X-axis denotes years elapsed between sampling time points, but do not necessarily indicate the total duration of infection. The first author of the report in which data were originally presented are indicated in the upper left-hand corner of each graph. Group L2 subjects were reported to have an AIDS-defining illness or peripheral CD4 count <200/mm³ between the first and second samples.

Figure 7. Proposed evolution of V1V2 loop size change during transmission and HIV infection.

At the time of sexual transmission, a significant genetic bottleneck occurs in which one or a small number of donor variants is transmitted to the recipient, without clear selection for loop size (represented on the y-axis). During early infection, prior to an effective host response, viral variants with a compact V1V2 loop have a competitive advantage, and V1V2 loop size remains stable or regresses. During chronic asymptomatic infection, mean V1V2 length increases in response to (humoral) immune selective pressure. As immune function wanes, V1V2 loop length gradually declines.