Patterns and rates of viral evolution in HIV-1 subtype B infected females and males.

Biological sex differences affect the course of HIV infection, with untreated women having lower viral loads compared to their male counterparts but, for a given viral load, women have a higher rate of progression to AIDS. However, the vast majority of data on viral evolution, a process that is clearly impacted by host immunity and could be impacted by sex differences, has been derived from men. We conducted an intensive analysis of HIV-1 gag and env-gp120 evolution taken over the first 6-11 years of infection from 8 Women's Interagency HIV Study (WIHS) participants who had not received combination antiretroviral therapy (ART). This was compared to similar data previously collected from men, with both groups infected with HIV-1 subtype B. Early virus populations in men and women were generally homogenous with no differences in diversity between sexes. No differences in ensuing nucleotide substitution rates were found between the female and male cohorts studied herein. As previously reported for men, time to peak diversity in env-gp120 in women was positively associated with time to CD4+ cell count below 200 (P = 0.017), and the number of predicted N-linked glycosylation sites generally increased over time, followed by a plateau or decline, with the majority of changes localized to the V1-V2 region. These findings strongly suggest that the sex differences in HIV-1 disease progression attributed to immune system composition and sensitivities are not revealed by, nor do they impact, global patterns of viral evolution, the latter of which proceeds similarly in women and men

Neutralization profiles of HIV-1 viruses from the VRC01 Antibody Mediated Prevention (AMP) trials

The VRC01 Antibody Mediated Prevention (AMP) efficacy trials conducted between 2016 and 2020 showed for the first time that passively administered broadly neutralizing antibodies (bnAbs) could prevent HIV-1 acquisition against bnAb-sensitive viruses. HIV-1 viruses isolated from AMP participants who acquired infection during the study in the sub-Saharan African (HVTN 703/HPTN 081) and the Americas/European (HVTN 704/HPTN 085) trials represent a panel of currently circulating strains of HIV-1 and offer a unique opportunity to investigate the sensitivity of the virus to broadly neutralizing antibodies (bnAbs) being considered for clinical development. Pseudoviruses were constructed using envelope sequences from 218 individuals. The majority of viruses identified were clade B and C; with clades A, D, F and G and recombinants AC and BF detected at lower frequencies. We tested eight bnAbs in clinical development (VRC01, VRC07-523LS, 3BNC117, CAP256.25, PGDM1400, PGT121, 10–1074 and 10E8v4) for neutralization against all AMP placebo viruses (n = 76). Compared to older clade C viruses (1998–2010), the HVTN703/HPTN081 clade C viruses showed increased resistance to VRC07-523LS and CAP256.25. At a concentration of 1μg/ml (IC80), predictive modeling identified the triple combination of V3/V2-glycan/CD4bs-targeting bnAbs (10-1074/PGDM1400/VRC07-523LS) as the best against clade C viruses and a combination of MPER/V3/CD4bs-targeting bnAbs (10E8v4/10-1074/VRC07-523LS) as the best against clade B viruses, due to low coverage of V2-glycan directed bnAbs against clade B viruses. Overall, the AMP placebo viruses represent a valuable resource for defining the sensitivity of contemporaneous circulating viral strains to bnAbs and highlight the need to update reference panels regularly. Our data also suggests that combining bnAbs in passive immunization trials would improve coverage of global viruses

Patterns and rates of viral evolution in HIV-1 subtype B infected females and males.

Biological sex differences affect the course of HIV infection, with untreated women having lower viral loads compared to their male counterparts but, for a given viral load, women have a higher rate of progression to AIDS. However, the vast majority of data on viral evolution, a process that is clearly impacted by host immunity and could be impacted by sex differences, has been derived from men. We conducted an intensive analysis of HIV-1 gag and env-gp120 evolution taken over the first 6-11 years of infection from 8 Women's Interagency HIV Study (WIHS) participants who had not received combination antiretroviral therapy (ART). This was compared to similar data previously collected from men, with both groups infected with HIV-1 subtype B. Early virus populations in men and women were generally homogenous with no differences in diversity between sexes. No differences in ensuing nucleotide substitution rates were found between the female and male cohorts studied herein. As previously reported for men, time to peak diversity in env-gp120 in women was positively associated with time to CD4+ cell count below 200 (P = 0.017), and the number of predicted N-linked glycosylation sites generally increased over time, followed by a plateau or decline, with the majority of changes localized to the V1-V2 region. These findings strongly suggest that the sex differences in HIV-1 disease progression attributed to immune system composition and sensitivities are not revealed by, nor do they impact, global patterns of viral evolution, the latter of which proceeds similarly in women and men

Inter-participant <i>env-gp120</i> phylograms.

<p>(<b>A</b>) A Phylogenetic tree of <i>env-gp120</i> for all 8 WIHS participants was inferred using RAxML [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#pone.0182443.ref051" target="_blank">51</a>] with the GTR substitution model +I +G [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#pone.0182443.ref048" target="_blank">48</a>]. External branches from the first available timepoint after infection are colored black. Branches from participants F1, F2, F3, and F7 are shaded light and dark to indicate taxa from early and late infection, respectively, when sequences from early in infection are found at opposite sides of the root node. The scale at the bottom measures genetic distances in nucleotide substitutions per site. Phylograms from each individual were rooted based on outgroup. Bootstrap values are shown along branches extending to each participant’s clade.</p

Correlates of disease progression and patterns of selection in the WIHS cohort.

<p>(<b>A</b>) Average pairwise diversity in <i>env-gp120</i> was estimated for each timepoint and is shown relative to peak diversity in each participant. (<b>B</b>) CD4⁺ T cell counts were placed relative to the time to peak diversity in <i>env-gp120</i>. The dashed horizontal line indicates the 200 CD4⁺ T cell count per mm³ AIDS-defining threshold. (<b>C</b>) The association between the time CD4+ T cells dropped below 200 per mm³ and the time of peak <i>env-gp120</i> diversity. Participants F4 and F7 were not included as virus had no observable peak in average pairwise diversity during the period of follow up. (<b>D</b>) Average pairwise diversity in <i>gag</i> for each timepoint is shown relative to the time of peak diversity in each participant. No peak was observed except for Subject F3. (<b>E</b>, <b>F</b>) The average pairwise ratio of nonsynonymous (<i>d</i>_<i>N</i>) to synonymous (<i>d</i>_<i>S</i>) substitutions per site at each timepoint compared to the inferred founder strain (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#sec002" target="_blank">Methods</a> section) for <i>gag</i> and <i>env-gp120</i>, respectively, for each participant. Associations were assessed using the Spearman’s correlation test.</p

Phylogenetic analysis of <i>env-gp120</i> nucleotide sequences and predicted co-receptor use.

<p>(<b>A-D</b>) Maximum likelihood <i>env-gp120</i> phylogenetic trees from each participant were reconstructed using PhyML v3.0 (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#sec002" target="_blank">Methods</a>) and rooted to earliest timepoint sequences. Data from 4 participants are shown here and from the remaining four in Fig Sx. Tip symbols indicate years post seroconversion (colored circles). Branch colors represent PSSM-predicted V3 loop co-receptor usage (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#sec002" target="_blank">Methods</a>). The scale at the bottom measures genetic distances in nucleotide substitutions per site.</p

No differences in HIV-1 subtype B <i>env-C2V5</i> evolutionary rates between females and males.

<p>Intra-host <i>env-C2V5</i> (<b>A</b>) diversity at the first time point and (<b>B</b>) substitution rates for both WIHS and MACS cohorts. Substitution rates for both WIHS and MACS participants were estimated using a relaxed molecular clock model using Bayesian inference (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#sec002" target="_blank">Methods</a>). A Mann-Whitney U test was used to test for sex differences. Horizontal bars show the median and interquartile range. 95% HPD is the highest posterior density interval. HPM mean is the evolutionary rate (and 95% HPD) estimated using a hierarchical phylogenetic model applied across the group. Evolutionary rates were defined as nucleotide substitutions/site/year. A non-parametric Mann-Whitney U test was used to test differences between unmatched groups. (<b>C</b> and <b>D</b>) Evolutionary rates from (B) broken out by individual. ESS values were > 200 for meanRate in the analysis of 8/8 <i>env-C2V5</i> WIHS and 10/11 <i>env-C2V5</i> MACS BEAST simulations.</p

HIV-1 genetic distance measures over time.

<p>(<b>A</b>) Average pairwise nucleotide diversity within timepoints (open circles), divergence from the consensus of the initial timepoint sequences (filled squares) was calculated for <i>env-gp120</i> nucleotide sequences. Mean ± standard error is plotted (error bars are not visible as they were not as large as the data points). The proportion of predicted X4-tropic strains (filled magenta circles) computed by the PSSM scoring algorithm from V3 loop sequences is shown at each timepoint. The two distinct variants (1 and 2) within participant F5 were analyzed separately. HIV viral RNA load (copies per mL; red lines), CD4⁺ and CD8⁺ T cell counts (cells per mm³; blue and green lines, respectively), and visits with prescribed ART (black asterisks (*) at the bottom of each panel) are shown. The arrow at the bottom of each panel indicates the first time at which CD4⁺ T cell counts fell below 200. Dashed vertical lines indicate the time of peak viral diversity, when detected, while the solid vertical line indicates the time at which divergence from the initial consensus sequence stabilized (only detected in F6). Time to peak <i>env-gp120</i> diversity is shown associated with time to predicted X4-tropic genotype detection (<b>B</b>) and time to peak X4-tropic genotype representation (<b>C</b>). PSSM scores of ~ -6 or greater were taken as indicative of X4-tropism [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#pone.0182443.ref056" target="_blank">56</a>]). Associations were analyzed using the Spearman’s correlation test; rho and <i>P</i>-values are shown. Lines were fit using a least squares linear regression model.</p

Cohort description^a.

<p>Cohort description<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#t001fn001" target="_blank">^a</a>.</p