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. 2022 Dec 21;96(24):e0127022.
doi: 10.1128/jvi.01270-22. Epub 2022 Dec 1.

Subtle Longitudinal Alterations in Env Sequence Potentiate Differences in Sensitivity to Broadly Neutralizing Antibodies following Acute HIV-1 Subtype C Infection

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Subtle Longitudinal Alterations in Env Sequence Potentiate Differences in Sensitivity to Broadly Neutralizing Antibodies following Acute HIV-1 Subtype C Infection

Tawanda Mandizvo et al. J Virol. .

Abstract

Broadly neutralizing antibodies (bNAbs) for HIV-1 prevention or cure strategies must inhibit transmitted/founder and reservoir viruses. Establishing sensitivity of circulating viruses to bNAbs and genetic patterns affecting neutralization variability may guide rational bNAbs selection for clinical development. We analyzed 326 single env genomes from nine individuals followed longitudinally following acute HIV-1 infection, with samples collected at ~1 week after the first detection of plasma viremia; 300 to 1,709 days postinfection but prior to initiating antiretroviral therapy (ART) (median = 724 days); and ~1 year post ART initiation. Sequences were assessed for phylogenetic relatedness, potential N- and O-linked glycosylation, and variable loop lengths (V1 to V5). A total of 43 env amplicons (median = 3 per patient per time point) were cloned into an expression vector and the TZM-bl assay was used to assess the neutralization profiles of 15 bNAbs targeting the CD4 binding site, V1/V2 region, V3 supersite, MPER, gp120/gp41 interface, and fusion peptide. At 1 μg/mL, the neutralization breadths were as follows: VRC07-LS and N6.LS (100%), VRC01 (86%), PGT151 (81%), 10-1074 and PGT121 (80%), and less than 70% for 10E8, 3BNC117, CAP256.VRC26, 4E10, PGDM1400, and N123-VRC34.01. Features associated with low sensitivity to V1/V2 and V3 bNAbs were higher potential glycosylation sites and/or relatively longer V1 and V4 domains, including known "signature" mutations. The study shows significant variability in the breadth and potency of bNAbs against circulating HIV-1 subtype C envelopes. VRC07-LS, N6.LS, VRC01, PGT151, 10-1074, and PGT121 display broad activity against subtype C variants, and major determinants of sensitivity to most bNAbs were within the V1/V4 domains. IMPORTANCE Broadly neutralizing antibodies (bNAbs) have potential clinical utility in HIV-1 prevention and cure strategies. However, bNAbs target diverse epitopes on the HIV-1 envelope and the virus may evolve to evade immune responses. It is therefore important to identify antibodies with broad activity in high prevalence settings, as well as the genetic patterns that may lead to neutralization escape. We investigated 15 bNAbs with diverse biophysical properties that target six epitopes of the HIV-1 Env glycoprotein for their ability to inhibit viruses that initiated infection, viruses circulating in plasma at chronic infection before antiretroviral treatment (ART), or viruses that were archived in the reservoir during ART in subtype C infected individuals in South Africa, a high burden country. We identify the antibodies most likely to be effective for clinical use in this setting and describe mutational patterns associated with neutralization escape from these antibodies.

Keywords: HIV-1 envelope; HIV-1 intraparticipant diversity; HIV-1 subtype C; acute HIV-1 infection; bNAbs; longitudinal HIV-1 diversity; sensitivity to bNAbs.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIG 1
FIG 1
Maximum likelihood phylogenetic tree of 317 full-length subtype C HIV Env amino acid sequences. Transmitter/founder (TF) sequences are shown with black labels, chronic sequences (BT, before treatment) are denoted by red labels, while PBMC reservoir sequences (AT, ~1 year after treatment) are denoted by green labels. Lymph node (LN)-derived sequences for participants 079, 093, and 651 are denoted by orange labels, whereas their matching time point PBMC-derived sequences are denoted by blue labels. The branch length is drawn to scale to assess the relatedness between different sequences, with branch lengths measured in the number of substitutions per site. Model/method, Jones-Taylor-Thornton (JTT) model; Test of phylogeny, bootstrap method; No. of bootstrap replications, 200 (86–88). Reference sequences (denoted in pink) included: (Ref. A1.RW accession number BAF31340.1); (Ref. A1.UG accession number BAF31412.1); (Ref. A2.CM accession number ADA83368.1); (Ref. A2.CY accession number AAK65976.1); (Ref. D.TZ accession number AAQ98188.1); (Ref. D.UG accession number AAC97570.1); and (Ref. B.FR accession number NP057856.1); (Ref. C.ZA accession number AAV41353.1) and (Ref. C.IN accession number AAD12085.1).
FIG 2
FIG 2
Line graphs showing distribution of the V1 to V5 loop characteristics over time. (A) V1 to V5 length; (B) V1 to V5 PNGSs; and (C) V1 to V5 S/T counts. Each color-coded line represents a different participant. The geometric mean distribution of each parameter is represented as a dot for each time point. y axis, subregion variable loop parameter; x axis, sampled compartment and the relative days post observed plasma viremia increase from left to right (TF, transmitted/founder; BT, before treatment; AT, after treatment; LN, lymph node; and PBMC, sequences from PMBC at time point matching lymph node excision). The asterisk (*) denotes sequences obtained from participant 079 only, who remained ART naive throughout the study. Time points TF, BT, AT, LN, and PBMC differ from participant to participant, please see the exact time points in Table 2. Logo plots showing longitudinal intraparticipant V1 and V4 sequence variation are shown in Fig.S3 and S4.
FIG 3
FIG 3
Epitope-targeted neutralizing antibody-phenotyping of acute and chronic phase HIV-1 subtype C envelopes. (A) Neutralization data are presented as scatterplots of IC50 titers (μg/mL) in which each virus is represented by an individual circle. Antibodies targeting each epitope are color-coded. The highest concentration tested for each bNAb, and the percentage of viruses (n = 43) neutralized are indicated. Solid black bars represent median titers and their interquartile ranges. The asterisks (*) adjacent to each bNAb indicate the corresponding number of viruses (n = 13) tested against that antibody; The rest of the bNAbs were tested against 43 viruses, apart from PGT151, which was tested against 30 viruses. (B) Neutralization breadth (% of viruses with IC50 ≤1 μg/mL) and potency of each tested bNAb (median IC50 of the subtype C virus panel [n = 13 to 43] against each bNAb). The neutralization was assessed by a TZM-bl pseudovirus assay. Each circle represents the neutralization breadth at a given median IC50 (μg/mL) of the virus panel. Each color-coded circle represents neutralization by a respective bNAb.
FIG 4
FIG 4
Longitudinal epitope-targeted neutralization IC50 titers for each tested bNAb. (A to E) V3-targeting antibodies: 10-1074, PGT121, PGT128, 2G12, and PGT135. (F to I) CD4bs-targeting antibodies: VRC01, VRC07-LS, 3BNC117, and N6.LS. (J and K) MPER-targeting antibodies: 10E8 and 4E10. (L and M) V1/V2-targeting antibodies: CAP256.VRC26.25 and PGDM1400. (N) gp120/gp41 interface-targeting antibody: PGT151. (O) Fusion peptide-targeting antibody: N123-VRC34.01. Each dot represents each tested pseudovirus and each group represents the sampled time point/compartment. TF, transmitted founder viruses within 1 week of positive plasma viremia detection (black dots). BT, viruses circulating in plasma at chronic prior ART initiation (red dots). AT, viruses circulating in PBMC after ~1 year of ART (green dots). LN, viruses sampled from the lymph node (orange dots). PBMC, viruses sampled from the PBMC at a time point matching the lymph node (blue dots). Significant differences among groups of variants using the Mann-Whitney unpaired t test are indicated by asterisks. Nonsignificant, P > 0.05; *, P = 0.05 to 0.01; **, P = 0.01 to 0.001.
FIG 5
FIG 5
Signature mutations, V1/V4 sequence characteristics, and neutralization activity of antibodies against each epitope. (A) V3 antibodies; (B) V1/V2 antibodies; (C) CD4bs antibodies; (D) MPER antibody; and (E) gp120/gp41 interface antibody. In each panel, the first column shows the name of each tested representative clones, the second column shows their respective escape mutations from literature, denoted in vertical labels above the heatmap of each bNAb category (89) and in magenta, is the corresponding HXB2 AA numbering. The red and orange heatmaps (drawn per participant) show the neutralization activity (IC50 in μg/mL) of each antibody, where red is the most neutralizing and white least neutralizing. The blue heatmaps (drawn per participant) show the V1 loop characteristics (V1 length, total PNGs in V1 and total S/T counts in V1), where dark shade represents higher values and lighter shade represents the least values. The green heatmaps (drawn per participant) show the V4 loop characteristics (V4 length, total PNGs in V4 and total S/T counts in V4), where dark shade represents higher values and lighter shade represents the (lower values). TF, transmitted founder viruses within 1 week of positive plasma viremia detection. BT, viruses circulating in plasma at chronic prior ART initiation. AT, viruses circulating in PBMC after ~1 year of ART. LN, viruses sampled from the lymph node. PBMC, viruses sampled from the PBMC at a time point matching the lymph node.

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