Stefic K, Bouvin-Pley M, Braibant M, Barin F. Impact of HIV-1 diversity on its sensitivity to neutralization. Vaccines (Basel). 2019;7:3.
Google Scholar
Sok D, Burton DR. Recent progress in broadly neutralizing antibodies to HIV. Nat Immunol. 2018;19(11):1179–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sok D, Le KM, Vadnais M, Saye-Francisco KL, Jardine JG, Torres JL, Berndsen ZT, Kong L, Stanfield R, Ruiz J, et al. Rapid elicitation of broadly neutralizing antibodies to HIV by immunization in cows. Nature. 2017;548(7665):108–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Walker LM, Huber M, Doores KJ, Falkowska E, Pejchal R, Julien JP, Wang SK, Ramos A, Chan-Hui PY, Moyle M, et al. Broad neutralization coverage of HIV by multiple highly potent antibodies. Nature. 2011;477(7365):466–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Walker LM, Phogat SK, Chan-Hui PY, Wagner D, Phung P, Goss JL, Wrin T, Simek MD, Fling S, Mitcham JL, et al. Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target. Science. 2009;326(5950):285–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Doria-Rose NA, Bhiman JN, Roark RS, Schramm CA, Gorman J, Chuang GY, Pancera M, Cale EM, Ernandes MJ, Louder MK, et al. New Member of the V1V2-Directed CAP256-VRC26 lineage that shows increased breadth and exceptional potency. J Virol. 2016;90(1):76–91.
Article
CAS
PubMed
Google Scholar
Wu X, Yang ZY, Li Y, Hogerkorp CM, Schief WR, Seaman MS, Zhou T, Schmidt SD, Wu L, Xu L, et al. Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1. Science. 2010;329(5993):856–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kumar R, Qureshi H, Deshpande S, Bhattacharya J. Broadly neutralizing antibodies in HIV-1 treatment and prevention. Ther Adv Vacc Imunother. 2018;6(4):61–8.
Article
CAS
Google Scholar
Sok D, van Gils MJ, Pauthner M, Julien JP, Saye-Francisco KL, Hsueh J, Briney B, Lee JH, Le KM, Lee PS, et al. Recombinant HIV envelope trimer selects for quaternary-dependent antibodies targeting the trimer apex. Proc Natl Acad Sci USA. 2014;111(49):17624–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu Y, Cao W, Sun M, Li T. Broadly neutralizing antibodies for HIV-1: efficacies, challenges and opportunities. Emerg Microb Infect. 2020;9(1):194–206.
Article
CAS
Google Scholar
Caskey M, Klein F, Lorenzi JC, Seaman MS, West AP, Jr., Buckley N, Kremer G, Nogueira L, Braunschweig M, Scheid JF et al: Viraemia suppressed in HIV-1-infected humans by broadly neutralizing antibody 3BNC117. Nature 2015.
Caskey M, Klein F, Nussenzweig MC. Broadly neutralizing anti-HIV-1 monoclonal antibodies in the clinic. Nat Med. 2019;25(4):547–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Caskey M, Schoofs T, Gruell H, Settler A, Karagounis T, Kreider EF, Murrell B, Pfeifer N, Nogueira L, Oliveira TY, et al. Antibody 10–1074 suppresses viremia in HIV-1-infected individuals. Nat Med. 2017;23(2):185–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mendoza P, Gruell H, Nogueira L, Pai JA, Butler AL, Millard K, Lehmann C, Suarez I, Oliveira TY, Lorenzi JCC, et al. Combination therapy with anti-HIV-1 antibodies maintains viral suppression. Nature. 2018;561(7724):479–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bar-On Y, Gruell H, Schoofs T, Pai JA, Nogueira L, Butler AL, Millard K, Lehmann C, Suarez I, Oliveira TY, et al. Safety and antiviral activity of combination HIV-1 broadly neutralizing antibodies in viremic individuals. Nat Med. 2018;24(11):1701–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Scheid JF, Horwitz JA, Bar-On Y, Kreider EF, Lu CL, Lorenzi JC, Feldmann A, Braunschweig M, Nogueira L, Oliveira T, et al. HIV-1 antibody 3BNC117 suppresses viral rebound in humans during treatment interruption. Nature. 2016;535(7613):556–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Binley JM, Wrin T, Korber B, et al. Comprehensive cross-clade neutralization analysis of a panel of anti-human immunodeficiency virus type 1 monoclonal antibodies. J Virol. 2004;78:13232–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bures R, Morris L, Williamson C, Ramjee G, Deers M, Fiscus SA, Abdool-Karim S, Montefiori DC. Regional clustering of shared neutralization determinants on primary isolates of clade C human immunodeficiency virus type 1 from South Africa. J Virol. 2002;76(5):2233–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hraber P, Korber BT, Lapedes AS, Bailer RT, Seaman MS, Gao H, Greene KM, McCutchan F, Williamson C, Kim JH, et al. Impact of clade, geography, and age of the epidemic on HIV-1 neutralization by antibodies. J Virol. 2014;88(21):12623–43.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kulkarni SS, Lapedes A, Tang H, Gnanakaran S, Daniels MG, Zhang M, Bhattacharya T, Li M, Polonis VR, McCutchan FE, et al. Highly complex neutralization determinants on a monophyletic lineage of newly transmitted subtype C HIV-1 Env clones from India. Virology. 2009;385(2):505–20.
Article
CAS
PubMed
Google Scholar
Seaman MS, Janes H, Hawkins N, Grandpre LE, Devoy C, Giri A, Coffey RT, Harris L, Wood B, Daniels MG, et al. Tiered categorization of a diverse panel of HIV-1 Env pseudoviruses for assessment of neutralizing antibodies. J Virol. 2010;84(3):1439–52.
Article
CAS
PubMed
Google Scholar
Burnie J, Guzzo C. The Incorporation of Host Proteins into the External HIV-1 Envelope. Viruses. 2019;11:1.
Article
CAS
Google Scholar
Rusert P, Kouyos RD, Kadelka C, Ebner H, Schanz M, Huber M, Braun DL, Hoze N, Scherrer A, Magnus C, et al. Determinants of HIV-1 broadly neutralizing antibody induction. Nat Med. 2016;22(11):1260–7.
Article
CAS
PubMed
Google Scholar
Novitsky V, Smith UR, Gilbert P, McLane MF, Chigwedere P, Williamson C, Ndung’u T, Klein I, Chang SY, Peter T, et al. Human immunodeficiency virus type 1 subtype C molecular phylogeny: consensus sequence for an AIDS vaccine design? J Virol. 2002;76(11):5435–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wagh K, Bhattacharya T, Williamson C, Robles A, Bayne M, Garrity J, Rist M, Rademeyer C, Yoon H, Lapedes A, et al. Optimal Combinations of Broadly Neutralizing Antibodies for Prevention and Treatment of HIV-1 Clade C Infection. PLoS Pathog. 2016;12(3):e1005520.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lorenzi JCC, Mendoza P, Cohen YZ, Nogueira L, Lavine C, Sapiente J, Wiatr M, Mugo NR, Mujugira A, Delany S et al: Neutralizing Activity of Broadly Neutralizing anti-HIV-1 Antibodies against Primary African Isolates. J Virol 2020.
Bai H, Li Y, Michael NL, Robb ML, Rolland M. The breadth of HIV-1 neutralizing antibodies depends on the conservation of key sites in their epitopes. PLoS Comput Biol. 2019;15(6):e1007056.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rademeyer C, Korber B, Seaman MS, Giorgi EE, Thebus R, Robles A, Sheward DJ, Wagh K, Garrity J, Carey BR, 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(7):e1005742.
Article
PubMed
PubMed Central
CAS
Google Scholar
Crowell TA, Colby DJ, Pinyakorn S, Sacdalan C, Pagliuzza A, Intasan J, Benjapornpong K, Tangnaree K, Chomchey N, Kroon E, et al. Safety and efficacy of VRC01 broadly neutralising antibodies in adults with acutely treated HIV (RV397): a phase 2, randomised, double-blind, placebo-controlled trial. The lancet HIV. 2019;6(5):e297–306.
Article
PubMed
PubMed Central
Google Scholar
Reeves DB, Huang Y, Duke ER, Mayer BT, Cardozo-Ojeda EF, Boshier FA, Swan DA, Rolland M, Robb ML, Mascola JR, et al. Mathematical modeling to reveal breakthrough mechanisms in the HIV Antibody Mediated Prevention (AMP) trials. PLoS Comput Biol. 2020;16(2):e1007626.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mahomed S, Garrett N, Karim QA, Zuma NY, Capparelli E, Baxter C, Gengiah T, Archary D, Samsunder N, Rose ND, et al. Assessing the safety and pharmacokinetics of the anti-HIV monoclonal antibody CAP256V2LS alone and in combination with VRC07-523LS and PGT121 in South African women: study protocol for the first-in-human CAPRISA 012B phase I clinical trial. BMJ Open. 2020;10(11):e042247.
PubMed
PubMed Central
Google Scholar
Gharu L, Ringe R, Bhattacharya J. HIV-1 clade C envelopes obtained from late stage symptomatic Indian patients varied in their ability towards relative CD4 usages and sensitivity to CCR5 antagonist TAK-779. Virus Res. 2011;158:216–24.
Article
CAS
PubMed
Google Scholar
Gharu L, Ringe R, Bhattacharya J. Evidence of extended alternate coreceptor usage by HIV-1 clade C envelope obtained from an Indian patient. Virus Res. 2012;163(1):410–4.
Article
CAS
PubMed
Google Scholar
Gharu L, Ringe R, Pandey S, Paranjape R, Bhattacharya J. HIV-1 clade C env clones obtained from an Indian patient exhibiting expanded coreceptor tropism are presented with naturally occurring unusual amino acid substitutions in V3 loop. Virus Res. 2009;144(1–2):306–14.
Article
CAS
PubMed
Google Scholar
Ringe R, Thakar M, Bhattacharya J. Variations in autologous neutralization and CD4 dependence of b12 resistant HIV-1 clade C env clones obtained at different time points from antiretroviral naive Indian patients with recent infection. Retrovirology. 2010;7(1):76.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mukhopadhyay S, Ringe R, Patil A, Paranjape R, Bhattacharya J. Characterization of Circulating HIV Type 1 env Genes in Plasma of Two Antiretroviral-Naive Slow Progressing Patients with Broad Neutralizing Antibody Response with Evidence of Recombination. AIDS Res Hum Retroviruses. 2012;28(7):739–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Patil S, Kumar R, Deshpande S, Samal S, Shrivastava T, Boliar S, Bansal M, Chaudhary NK, Srikrishnan AK, Murugavel KG, et al. Conformational epitope-specific broadly neutralizing plasma antibodies obtained from an HIV-1 Clade C-infected elite neutralizer mediate autologous virus escape through mutations in the V1 Loop. J Virol. 2016;90(7):3446–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Deshpande S, Patil S, Kumar R, Hermanus T, Murugavel KG, Srikrishnan AK, Solomon S, Morris L, Bhattacharya J. HIV-1 clade C escapes broadly neutralizing autologous antibodies with N332 glycan specificity by distinct mechanisms. Retrovirology. 2016;13(1):60.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sutar J, Deshpande S, Mullick R, Hingankar N, Patel V, Bhattacharya J. Geospatial HIV-1 subtype C gp120 sequence diversity and its predicted impact on broadly neutralizing antibody sensitivity. BioRxiv. 2020. https://doi.org/10.1101/2020.09.09.289132.
Article
Google Scholar
Krumm SA, Mohammed H, Le KM, Crispin M, Wrin T, Poignard P, Burton DR, Doores KJ. Mechanisms of escape from the PGT128 family of anti-HIV broadly neutralizing antibodies. Retrovirology. 2016;13(1):8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ringe R, Phogat S, Bhattacharya J. Subtle alteration of residues including N-linked glycans in V2 loop modulate HIV-1 neutralization by PG9 and PG16 monoclonal antibodies. Virology. 2012;426(1):34–41.
Article
CAS
PubMed
Google Scholar
Kist NC, Lambert B, Campbell S, Katzourakis A, Lunn D, Lemey P, Iversen AKN. HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification. Virus Evol. 2020;6(2):085.
Article
Google Scholar
Hall T: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp 1999().
Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000;16(6):276–7.
Article
CAS
PubMed
Google Scholar
Zhang M, Gaschen B, Blay W, Foley B, Haigwood N, Kuiken C, Korber B. Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin. Glycobiology. 2004;14(12):1229–46.
Article
CAS
PubMed
Google Scholar
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268–74.
Article
CAS
PubMed
Google Scholar
Yu G, Lam TT, Zhu H, Guan Y. Two methods for mapping and visualizing associated data on phylogeny using Ggtree. Mol Biol Evol. 2018;35(12):3041–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu G, Smith D, Zhu H, Guan Y, Lam TT. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8:28–36.
Article
Google Scholar
Team R: RStudio: Integrated Development for R. 2015.
Team RC: R: A language and environment for statistical computing. 2018.