ArticleProceedings of the National Academy of Sciences of the United States of America2018
Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
What it found
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Who cites it
67 citing papers in PubMed, 133 citations in OpenAlex.
- Relationship between latent and rebound viruses in a clinical trial of anti-HIV-1 antibody 3BNC117.The Journal of experimental medicine · 2018Trial
- Optimal control and the dynamics of ancestral lineages.Genetics · 2026Article
- Design of an immunogen containing multidimensionally conserved and immunogenic parts of the HIV proteome.PLoS computational biology · 2026Article
- Modeling quantifies in vivo neutralization, Fc-mediated killing, and resistance in human clinical trials of five anti-HIV broadly neutralizing antibodies.bioRxiv : the preprint server for biology · 2026Article
- Dual role of glycosylation in resistance to CD4-binding site broadly neutralizing antibodies.Journal of virology · 2026Article
- Mechanism for evolution of diverse autologous antibodies upon broadly neutralizing antibody therapy of people with HIV.Cell reports · 2025Article
- Article
- A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Rapamycin enhances CAR-T control of HIV replication and reservoir elimination in vivo.The Journal of clinical investigation · 2025Article
- Article
- A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses.bioRxiv : the preprint server for biology · 2024Article
- Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors.Cell systems · 2024Article
- Computational Design of Peptides for Biomaterials Applications.ACS applied bio materials · 2024Review
- In vivo functional phenotypes from a computational epistatic model of evolution.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes.Virus evolution · 2024Article
- Direct-acting antiviral resistance of Hepatitis C virus is promoted by epistasis.Nature communications · 2023Article
- GENERALIST: A latent space based generative model for protein sequence families.PLoS computational biology · 2023Article
- Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants.Science advances · 2023Article
- A classification algorithm based on dynamic ensemble selection to predict mutational patterns of the envelope protein in HIV-infected patients.Algorithms for molecular biology : AMB · 2023Article
- Inferring Cultural Landscapes with the Inverse Ising Model.Entropy (Basel, Switzerland) · 2023Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
HIV is a highly mutable virus, and over 30 years after its discovery, a vaccine or cure is still not available. The isolation of broadly neutralizing antibodies (bnAbs) from HIV-infected patients has led to renewed hope for a prophylactic vaccine capable of combating the scourge of HIV. A major challenge is the design of immunogens and vaccination protocols that can elicit bnAbs that target regions of the virus's spike proteins where the likelihood of mutational escape is low due to the high fitness cost of mutations. Related challenges include the choice of combinations of bnAbs for therapy. An accurate representation of viral fitness as a function of its protein sequences (a fitness landscape), with explicit accounting of the effects of coupling between mutations, could help address these challenges. We describe a computational approach that has allowed us to infer a fitness landscape for gp160, the HIV polyprotein that comprises the viral spike that is targeted by antibodies. We validate the inferred landscape through comparisons with experimental fitness measurements, and various other metrics. We show that an effective antibody that prevents immune escape must selectively bind to high escape cost residues that are surrounded by those where mutations incur a low fitness cost, motivating future applications of our landscape for immunogen design.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.