ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2015
Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- The dengue-specific immune response and antibody identification with machine learning.NPJ vaccines · 2024Article
- Inspecting the interaction between human immunodeficiency virus and the immune system through genetic turnover.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Article
- Understanding repertoire sequencing data through a multiscale computational model of the germinal center.NPJ systems biology and applications · 2023Article
- Characterization of human IgM and IgG repertoires in individuals with chronic HIV-1 infection.Virologica Sinica · 2022Article
- Do Ty3/Gypsy Transposable Elements Play Preferential Roles in Sex Chromosome Differentiation?Life (Basel, Switzerland) · 2022Review
- Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients.Human immunology · 2022Article
- Evaluation of Spike Protein Epitopes by Assessing the Dynamics of Humoral Immune Responses in Moderate COVID-19.Frontiers in immunology · 2022Article
- Review
- Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1.Molecular biology and evolution · 2019Article
- Large-scale network analysis reveals the sequence space architecture of antibody repertoires.Nature communications · 2019Article
- Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires.Frontiers in immunology · 2018Review
- Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections.PLoS genetics · 2016Article
- Statistical inference of a convergent antibody repertoire response to influenza vaccine.Genome medicine · 2016Article
- The Diversity and Molecular Evolution of B-Cell Receptors during Infection.Molecular biology and evolution · 2016Review
- The evolution within us.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Advances in immunoglobulin (Ig) sequencing technology are leading to new perspectives on immune system dynamics. Much research in this nascent field has focused on resolving immune responses to viral infection. However, the dynamics of B-cell diversity in early HIV infection, and in response to anti-retroviral therapy, are still poorly understood. Here, we investigate these dynamics through bulk Ig sequencing of samples collected over 2 years from a group of eight HIV-1 infected patients, five of whom received anti-retroviral therapy during the first half of the study period. We applied previously published methods for visualizing and quantifying B-cell sequence diversity, including the Gini index, and compared their efficacy to alternative measures. While we found significantly greater clonal structure in HIV-infected patients versus healthy controls, within HIV patients, we observed no significant relationships between statistics of B-cell clonal expansion and clinical variables such as viral load and CD4(+) count. Although there are many potential explanations for this, we suggest that important factors include poor sampling resolution and complex B-cell dynamics that are difficult to summarize using simple summary statistics. Importantly, we find a significant association between observed Gini indices and sequencing read depth, and we conclude that more robust analytical methods and a closer integration of experimental and theoretical work is needed to further our understanding of B-cell repertoire diversity during viral infection.
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