A primary concern of an antibody-based HIV-1 therapy is the virus' ability to rapidly escape antibody responses. Therefore, we investigated the relationships between antibody neutralization sensitivity, viral phenotype, and infectivity in 13 subtype C viruses using a HeLa transfectant-based assay. We observed that the seven tier 3 viruses exhibited higher infectivity than the tier 2 viruses, suggesting that higher neutralization resistance did not have a substantial entry cost. There was no relationship between neutralization resistance and susceptibility to entry inhibitors Maraviroc, PSC RANTES, or the fusion inhibitor T20, indicating that neutralization resistance may not alter these inhibitor target sites. By analyzing glycosylation patterns in 82 subtype C viruses, we found that the presence of an N-linked glycan motif at position N413 and its absence at N332 were the most important predictors of neutralization resistance. In a set of 200 subtype C viruses, tier 3 strains were more resistant than tier 2 or 1B viruses to several broadly neutralizing monoclonal antibodies targeting three different epitopes. This suggests that it is unlikely that resistance to antibodies targeting a single epitope drives overall resistance. In the context of an antibody-based intervention, highly resistant viruses with increased infectivity, circulating in the population, could hinder HIV-1 control since entry of tier 3 viruses is not always selected against. Therefore, for any long-term antibody-based intervention to be globally relevant, it must elicit responses that limit the occurrence of resistance.
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References
1.
SeamanMS, JanesH, HawkinsN, et al.: Tiered categorization of a diverse panel of HIV-1 Env pseudoviruses for assessment of neutralizing antibodies. J Virol, 2010; 84:1439–1452.
2.
MontefioriDC, RoedererM, MorrisL, SeamanMS: Neutralization tiers of HIV-1. Curr Opin HIV AIDS, 2018; 13:128–136.
3.
RademeyerC, KorberB, SeamanMS, et al.: Features of recently transmitted HIV-1 clade C viruses that impact antibody recognition: Implications for active and passive immunization. PLoS Pathog, 2016; 12:e1005742.
4.
BunnikEM, EulerZ, WelkersMR, et al.: Adaptation of HIV-1 envelope gp120 to humoral immunity at a population level. Nat Med, 2010; 16:995–997.
5.
HakeA, PfeiferN: Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time. PLoS Comput Biol, 2017; 13:e1005789.
6.
Bouvin-PleyM, MorgandM, MoreauA, et al.: Evidence for a continuous drift of the HIV-1 species towards higher resistance to neutralizing antibodies over the course of the epidemic. PLoS Pathog, 2013; 9:e1003477.
7.
DingensAS, ArenzD, WeightH, OverbaughJ, BloomJD: An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies distinguishes functional and structural epitopes. Immunity, 2019; 50:520.e3–532.e3.
8.
WeiX, DeckerJM, WangS, et al.: Antibody neutralization and escape by HIV-1. Nature, 2003; 422:307–312.
9.
RongR, Bibollet-RucheF, MulengaJ, AllenS, BlackwellJL, DerdeynCA: Role of V1V2 and other human immunodeficiency virus type 1 envelope domains in resistance to autologous neutralization during clade C infection. J Virol, 2007; 81:1350–1359.
10.
van GilsMJ, BunnikEM, Boeser-NunninkBD, et al.: Longer V1V2 region with increased number of potential N-linked glycosylation sites in the HIV-1 envelope glycoprotein protects against HIV-specific neutralizing antibodies. J Virol, 2011; 85:6986–6995.
11.
MoorePL, GrayES, WibmerCK, et al.: Evolution of an HIV glycan-dependent broadly neutralizing antibody epitope through immune escape. Nat Med, 2012; 18:1688–1692.
12.
MoyoT, FerreiraRC, DavidsR, et al.: Chinks in the armor of the HIV-1 Envelope glycan shield: Implications for immune escape from anti-glycan broadly neutralizing antibodies. Virology, 2017; 501:12–24.
13.
FerreiraRC, GrantOC, MoyoT, et al.: Structural rearrangements maintain the glycan shield of an HIV-1 envelope trimer after the loss of a glycan. Sci Rep, 2018; 8:15031.
14.
GuttmanM, CupoA, JulienJP, et al.: Antibody potency relates to the ability to recognize the closed, pre-fusion form of HIV Env. Nat Commun, 2015; 6:6144.
15.
MunroJB, MothesW: Structure and dynamics of the native HIV-1 Env trimer. J Virol, 2015; 89:5752–5755.
16.
MunroJB, GormanJ, MaX, et al.: Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions. Science, 2014; 346:759–763.
17.
CaiY, Karaca-GriffinS, ChenJ, et al.: Antigenicity-defined conformations of an extremely neutralization-resistant HIV-1 envelope spike. Proc Natl Acad Sci U S A, 2017; 114:4477–4482.
18.
SandersRW, DerkingR, CupoA, et al.: A next-generation cleaved, soluble HIV-1 Env trimer, BG505 SOSIP.664 gp140, expresses multiple epitopes for broadly neutralizing but not non-neutralizing antibodies. PLoS Pathog, 2013; 9:e1003618.
19.
LuM, MaX, Castillo-MenendezLR, et al.: Associating HIV-1 envelope glycoprotein structures with states on the virus observed by smFRET. Nature, 2019; 568:415–419.
20.
ReitterJN, MeansRE, DesrosiersRC: A role for carbohydrates in immune evasion in AIDS. Nat Med, 1998; 4:679–684.
21.
KarstenCB, AlterG: The HIV-1 glycan shield: Strategically placed kinks in the armor improve antigen design. Cell Rep, 2017; 19:669–670.
22.
DooresKJ: The HIV glycan shield as a target for broadly neutralizing antibodies. FEBS J, 2015; 282:4679–4691.
23.
RingeRP, PugachP, CottrellCA, et al.: Closing and opening holes in the glycan shield of HIV-1 envelope glycoprotein SOSIP trimers can redirect the neutralizing antibody response to the newly unmasked epitopes. J Virol, 2019; 93:e01656-18.
24.
TraversSA: Conservation, compensation, and evolution of N-linked glycans in the HIV-1 group M subtypes and circulating recombinant forms. ISRN AIDS, 2012; 2012:823605.
25.
Zolla-PaznerS, CohenSS, BoydD, et al.: Structure/function studies involving the V3 region of the HIV-1 envelope delineate multiple factors that affect neutralization sensitivity. J Virol, 2015; 90:636–649.
26.
TownsleyS, LiY, KozyrevY, ClevelandB, HuSL: Conserved role of an N-linked glycan on the surface antigen of human immunodeficiency virus type 1 modulating virus sensitivity to broadly neutralizing antibodies against the receptor and coreceptor binding sites. J Virol, 2016; 90:829–841.
27.
McCoyLE, van GilsMJ, OzorowskiG, et al.: Holes in the glycan shield of the native HIV envelope are a target of trimer-elicited neutralizing antibodies. Cell Rep, 2016; 16:2327–2338.
28.
CrooksET, TongT, ChakrabartiB, et al.: Vaccine-elicited tier 2 HIV-1 neutralizing antibodies bind to quaternary epitopes involving glycan-deficient patches proximal to the CD4 binding site. PLoS Pathog, 2015; 11:e1004932.
29.
KlassePJ, LaBrancheCC, KetasTJ, et al.: Sequential and simultaneous immunization of rabbits with HIV-1 envelope glycoprotein SOSIP.664 trimers from clades A, B and C. PLoS Pathog, 2016; 12:e1005864.
30.
WaghK, KreiderEF, LiY, et al.: Completeness of HIV-1 envelope glycan shield at transmission determines neutralization breadth. Cell Rep, 2018; 25:893.e7–908.e7.
31.
SimekMD, RidaW, PriddyFH, et al.: Human immunodeficiency virus type 1 elite neutralizers: Individuals with broad and potent neutralizing activity identified by using a high-throughput neutralization assay together with an analytical selection algorithm. J Virol, 2009; 83:7337–7348.
32.
MontefioriDC: Evaluating neutralizing antibodies against HIV, SIV, and SHIV in luciferase reporter gene assays. Curr Protoc Immunol, 2005;Chapter 12:Unit 12.11.
33.
SchwarzG: Estimating the dimension of a model. Ann Stat, 1978; 6:461–464.
34.
HoetingJA, MadiganD, RafteryAE, VolinskyCT: Bayesian A model averaging: A tutorial. Stat Sci, 1999; 14:382–417.
35.
R Core Team: R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, 2018.
36.
ReevesJD, GalloSA, AhmadN, et al.: Sensitivity of HIV-1 to entry inhibitors correlates with envelope/coreceptor affinity, receptor density, and fusion kinetics. Proc Natl Acad Sci U S A, 2002; 99:16249–16254.
37.
AlamM, KuwataT, ShimuraK, et al.: Enhanced antibody-mediated neutralization of HIV-1 variants that are resistant to fusion inhibitors. Retrovirology, 2016; 13:70.
38.
Van Der RystE: Maraviroc—A CCR5 antagonist for the treatment of HIV-1 Infection. Front Immunol, 2015; 6:277.
39.
LobritzMA, RatcliffAN, MarozsanAJ, DudleyDM, TiltonJC, ArtsEJ: Multifaceted mechanisms of HIV inhibition and resistance to CCR5 inhibitors PSC-RANTES and Maraviroc. Antimicrob Agents Chemother, 2013; 57:2640–2650.
40.
EgginkD, BerkhoutB, SandersRW: Inhibition of HIV-1 by fusion inhibitors. Curr Pharm Des, 2010; 16:3716–3728.
41.
CrooksET, GrimleySL, CullyM, et al.: Glycoengineering HIV-1 Env creates ‘supercharged’ and ‘hybrid’ glycans to increase neutralizing antibody potency, breadth and saturation. PLoS Pathog, 2018; 14:e1007024.
42.
SokD, DooresKJ, BrineyB, et al.: Promiscuous glycan site recognition by antibodies to the high-mannose patch of gp120 broadens neutralization of HIV. Sci Transl Med, 2014; 6:236ra263.
43.
KrummSA, MohammedH, LeKM, et al.: Mechanisms of escape from the PGT128 family of anti-HIV broadly neutralizing antibodies. Retrovirology, 2016; 13:8.
44.
van SchootenJ, van GilsMJ: HIV-1 immunogens and strategies to drive antibody responses towards neutralization breadth. Retrovirology, 2018; 15:74.
45.
HaynesBF, BurtonDR, MascolaJR: Multiple roles for HIV broadly neutralizing antibodies. Sci Transl Med, 2019; 11:eaaz2686.
46.
WyattR, KwongPD, DesjardinsE, et al.: The antigenic structure of the HIV gp120 envelope glycoprotein. Nature, 1998; 393:705–711.
47.
MouquetH: Antibody B cell responses in HIV-1 infection. Trends Immunol, 2014; 35:549–561.
48.
BurtonDR, AhmedR, BarouchDH, et al.: A blueprint for HIV vaccine discovery. Cell Host Microbe, 2012; 12:396–407.
49.
MoyoT, Ereño-OrbeaJ, JacobRA, et al.: Molecular basis of unusually high neutralization resistance in tier 3 HIV-1 strain 253-11. J Virol, 2018; 92:e02261-17.
50.
TrkolaA, DragicT, ArthosJ, et al.: CD4-dependent, antibody-sensitive interactions between HIV-1 and its co-receptor CCR-5. Nature, 1996; 384:184–187.
51.
IshidaY, YonedaM, OtsukiH, et al.: Generation of a neutralization-resistant CCR5 tropic simian/human immunodeficiency virus (SHIV-MK38) molecular clone, a derivative of SHIV-89.6. J Gen Virol, 2016; 97:1249–1260.
52.
LeamanDP, ZwickMB: Increased functional stability and homogeneity of viral envelope spikes through directed evolution. PLoS Pathog, 2013; 9:e1003184.
53.
DaarES, LiXL, MoudgilT, HoDD: High concentrations of recombinant soluble CD4 are required to neutralize primary human immunodeficiency virus type 1 isolates. Proc Natl Acad Sci U S A, 1990; 87:6574–6578.
54.
HuangKH, BonsallD, KatzourakisA, et al.: B-cell depletion reveals a role for antibodies in the control of chronic HIV-1 infection. Nat Commun, 2010; 1:102.
55.
InamdarK, FlodererC, FavardC, MuriauxD: Monitoring HIV-1 assembly in living cells: Insights from dynamic and single molecule microscopy. Viruses, 2019; 11:72.
56.
AgrawalN, LeamanDP, RowcliffeE, et al.: Functional stability of unliganded envelope glycoprotein spikes among isolates of human immunodeficiency virus type 1 (HIV-1). PLoS One, 2011; 6:e21339.
DerdeynCA, DeckerJM, Bibollet-RucheF, et al.: Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science, 2004; 303:2019–2022.
59.
JosephSB, SwanstromR, KashubaAD, CohenMS: Bottlenecks in HIV-1 transmission: Insights from the study of founder viruses. Nat Rev Microbiol, 2015; 13:414–425.
60.
FrostSD, LiuY, PondSL, et al.: Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J Virol, 2005; 79:6523–6527.
61.
DeymierMJ, EndeZ, Fenton-MayAE, et al.: Heterosexual transmission of subtype C HIV-1 selects consensus-like variants without increased replicative capacity or interferon-alpha resistance. PLoS Pathog, 2015; 11:e1005154.
62.
BrandenbergOF, MagnusC, RusertP, RegoesRR, TrkolaA: Different infectivity of HIV-1 strains is linked to number of envelope trimers required for entry. PLoS Pathog, 2015; 11:e1004595.
63.
MoyoT, KitchinD, MoorePL: Targeting the N332-supersite of the HIV-1 envelope for vaccine design. Expert Opin Ther Targets, 2020; 24:499–509.
64.
JacobRA, MoyoT, SchomakerM, AbrahamsF, Grau PujolB, DorfmanJR: Anti-V3/glycan and anti-MPER neutralizing antibodies, but not anti-V2/glycan site antibodies, are strongly associated with greater anti-HIV-1 neutralization breadth and potency. J Virol, 2015; 89:5264–5275.
65.
WalkerLM, HuberM, DooresKJ, et al.: Broad neutralization coverage of HIV by multiple highly potent antibodies. Nature, 2011; 477:466–470.
66.
BurtonDR, StanfieldRL, WilsonIA: Antibody vs. HIV in a clash of evolutionary titans. Proc Natl Acad Sci U S A, 2005; 102:14943–14948.
67.
GnanakaranS, BhattacharyaT, DanielsM, et al.: Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog, 2011; 7:e1002209.
68.
van den KerkhofTL, de TaeyeSW, Boeser-NunninkBD, et al.: HIV-1 escapes from N332-directed antibody neutralization in an elite neutralizer by envelope glycoprotein elongation and introduction of unusual disulfide bonds. Retrovirology, 2016; 13:48.
69.
DeshpandeS, PatilS, KumarR, et al.: HIV-1 clade C escapes broadly neutralizing autologous antibodies with N332 glycan specificity by distinct mechanisms. Retrovirology, 2016; 13:60.
70.
CaoL, PauthnerM, AndrabiR, et al.: Differential processing of HIV envelope glycans on the virus and soluble recombinant trimer. Nat Commun, 2018; 9:3693.
71.
ShapiroMB, CheeverT, MalherbeDC, et al.: Single-dose bNAb cocktail or abbreviated ART post-exposure regimens achieve tight SHIV control without adaptive immunity. Nat Commun, 2020; 11:70.
72.
MendozaP, GruellH, NogueiraL, et al.: Combination therapy with anti-HIV-1 antibodies maintains viral suppression. Nature, 2018; 561:479–484.
73.
GilbertPB, JuraskaM, deCampAC, et al.: Basis and statistical design of the passive HIV-1 antibody mediated prevention (AMP) test-of-concept efficacy trials. Stat Commun Infect Dis, 2017; 9:20160001.
74.
FiebigEW, WrightDJ, RawalBD, et al.: Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection. AIDS, 2003; 17:1871–1879.
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