Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals

Hoehn, K. B., Gall, A., Bashford-Rogers, R., Fidler, S.J., Kaye, S., Weber, J.N., McClure, M.O., SPARTAC Trial Investigators, , Kellam, P. and Pybus, O. G. (2015) Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1676), 20140241. (doi: 10.1098/rstb.2014.0241) (PMID:26194755) (PMCID:PMC4528418)

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.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: UNSPECIFIED
• Authors: Hoehn, K. B., Gall, A., Bashford-Rogers, R., Fidler, S.J., Kaye, S., Weber, J.N., McClure, M.O., SPARTAC Trial Investigators, , Kellam, P., and Pybus, O. G.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity
• Journal Name: Philosophical Transactions of the Royal Society B: Biological Sciences
• Publisher: The Royal Society
• ISSN: 0962-8436
• ISSN (Online): 1471-2970
• Copyright Holders: Copyright © 2015 The Authors
• First Published: First published in Philosophical Transactions of the Royal Society B: Biological Sciences 370(1676):20140241
• Publisher Policy: Reproduced under a Creative Commons licence