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The genetic interaction between HIV and the antibody repertoire

Nicolas Strauli, Emily Kathleen Fryer, Olivia Pham, Mohamed Abdel-Mohsen, Shelley N. Facente, Christopher Pilcher, Pleuni Pennings, Satish Pillai, View ORCID ProfileRyan D. Hernandez
doi: https://doi.org/10.1101/646968
Nicolas Strauli
1Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
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Emily Kathleen Fryer
2Department of Biology, San Francisco State University, San Francisco, CA, USA
3Carnegie Institution for Science, Plant Biology Department, Stanford, California, USA
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Olivia Pham
2Department of Biology, San Francisco State University, San Francisco, CA, USA
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Mohamed Abdel-Mohsen
4The Wistar Institute, Philadelphia, PA, USA
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Shelley N. Facente
5University of California, San Francisco (UCSF), San Francisco, CA, USA
6Vitalant Research Institute, San Francisco, California, USA
7Facente Consulting, Richmond, CA, USA
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Christopher Pilcher
8Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA
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Pleuni Pennings
2Department of Biology, San Francisco State University, San Francisco, CA, USA
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Satish Pillai
6Vitalant Research Institute, San Francisco, California, USA
9Department of Laboratory Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA
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Ryan D. Hernandez
10Bioengineering & Therapeutic Sciences, University of California, San Francisco (UCSF), San Francisco, CA, USA
11Department of Human Genetics, McGill University, Montreal, QC, Canada
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  • ORCID record for Ryan D. Hernandez
  • For correspondence: ryan.hernandez@me.com
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Abstract

The interaction between human immunodeficiency virus (HIV) and the antibody repertoire (AbR) during chronic infection can provide important information for HIV vaccine research, yet has not been well-characterized on a systems level. We deeply sequenced the HIV population and the AbR of ten HIV-infected, antiretroviral (ART)-naïve individuals, each with 10-20 longitudinal samples spanning 4-14 years. Our unbiased sequencing approach identified partitions of AbRs showing evidence of interaction with autologous HIV populations. We show that these HIV-associated partitions are enriched for the V gene segments of known HIV broadly neutralizing antibodies (bnAbs), indicating that the HIV-responding component of the AbR can be identified via time-series genetic data. Despite this evidence for larger-scale AbR/HIV interactions at the sub-population level, we found little to no evidence for coevolution. This suggests that coevolution is either rare, or hard to detect, which has important vaccine design implications.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 24, 2019.
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The genetic interaction between HIV and the antibody repertoire
Nicolas Strauli, Emily Kathleen Fryer, Olivia Pham, Mohamed Abdel-Mohsen, Shelley N. Facente, Christopher Pilcher, Pleuni Pennings, Satish Pillai, Ryan D. Hernandez
bioRxiv 646968; doi: https://doi.org/10.1101/646968
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The genetic interaction between HIV and the antibody repertoire
Nicolas Strauli, Emily Kathleen Fryer, Olivia Pham, Mohamed Abdel-Mohsen, Shelley N. Facente, Christopher Pilcher, Pleuni Pennings, Satish Pillai, Ryan D. Hernandez
bioRxiv 646968; doi: https://doi.org/10.1101/646968

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