Identification of viral mutations that confer cross resistance to VRC01 antibody in HIV-1 subtype C viruses

Title

Identification of viral mutations that confer cross resistance to VRC01 antibody in HIV-1 subtype C viruses

Presenter

Asanda Zintle Mbadu

Authors

A.Z. Mbadu * (1), P. Cohen (2), B. Lambson (2), C.A. Magaret (3), P.B. Gilbert (3), C. Williamson (4), L. Morris (2,5), P.L. Moore (2,5), H.T. Mufhandu (1)

Institutions

(1) North West University, Department of Microbiology, Faculty of Natural and Agricultural Sciences, Mmabatho, South Africa, (2) National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service, Centre for HIV and STI, Johannesburg, South Africa, (3) Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Seattle, United States, (4) University of Cape Town, Division of Medical Virology, Faculty of Health Sciences, Observatory, South Africa, (5) University of the Witwatersrand, Faculty of Health Sciences, Parktown, South Africa

BACKGROUND: Human immunodeficiency virus (HIV-1) subtype C remains the cause of most of the new HIV infections worldwide. South Africa being the most burdened region, is one of the participating countries in the Antibody Mediated Prevention (AMP) studies investigating broadly neutralizing antibody (bNAb) VRC01 for HIV prevention. However, the use of this bNAb is hindered by emerging resistant mutations that cause neutralization escape.
METHODS: The study focused on the features that are known by experimental evidence and machine learning predictions to contribute to VRC01 binding. The study included seven HIV-1 subtype C envelope sequences from breakthrough infections during VRC01 therapy, from which seven putative escape mutations were identified (D99, K279, E279, E455, W456, T471, and Q471) by analyzing them using information from HIV LANL database. The role of the identified sites was investigated by reverting them to sensitive residues by site-directed mutagenesis. All wildtypes and their respective mutant pseudoviruses were assessed for neutralization sensitivity towards VRC01 antibody and other related CD4 binding site (CD4bs) bNAbs (VRC07-523LS and 3BNC117) with the use of the TZM-bl neutralization assay.
RESULTS: 'Four envelopes in which we introduced a single mutation (H0902_K279D, V0217_E279D, V1298_E455T, and V1255_D99N) became sensitive to VRC01 and 3BNC117 compared to their respective wildtypes. They were also sensitive towards VRC07-523LS except for H0902_K279D. Interestingly the single mutant, V1298_E455T was completely sensitive to VRC01 although predicted by machine learning (Q455) to cause resistance. However, H1798 envelope with the same mutation (E455T) remained resistant. Similarly, single mutation (V1255_D99N) caused partial sensitivity to VRC01, while mutant V1298_D99N was resistant. Neutralization escape for each mutant may be mediated by a different pathway and dependent upon the gp160 background sequence.
CONCLUSIONS: The V1298_455 mutation warrants further investigation as this is the first report on E455T to show VRC01 sensitivity in HIV-1 subtype C isolates. Overall, our data supports the concept that some HIV-1 subtype C isolates change critical CD4 binding features to escape VRC01, some causing cross-resistance to other CD4 binding antibodies. The data also promote continued efforts of characterizing VRC01 resistant sites in preparation for future passive immunity trials that include CD4bs antibodies.

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