This study uses ultra-deep single-genome sequencing to show strong purifying selection in early HIV-1 infection, with limited early genetic divergence from founder viruses.

bioRxiv · Aug 26, 2026 · PreprintMicrobiology

Unique CD8+ T Cell Populations Expand during ART and Predict Delayed HIV-1 Rebound

Jie Wang, Gautam Kundu, Philip K. Ehrenberg, Aviva Geretz, Daina Eiser, Timothy Ezebuiro, Ashan Dayananda, Hiroshi Takata, Carlo Sacdalan, Somchai Sriplienchan, Nittaya Phanuphak, Suteeraporn Pinyakorn, Nelson L. Michael, Lydie Trautmann, Fredrick Sawe, , the RV254 study team

The paper identifies a unique CD8+ T cell population that expands during ART and predicts delayed HIV-1 rebound.

bioRxiv · Aug 18, 2026 · PreprintImmunology

Full-length next-generation sequencing of 11 HLA loci of more than 1000 individuals from clinical cohorts in East and West Africa

Yvonne V Rosario, Aviva Geretz, Lakshmi Rani Iyer, Philip K. Ehrenberg, Alya Tyson, Hannah Kibuuka, Fred Wabwire‐Mangen, Lucas Maganga, Abdulwasiu Bolaji Tiamiyu, Jonah K. Maswai, Josphat Kosgei, Frederick K. Sawe, Gary R. Matyas, Merlin Lee Robb, Julie A. Ake, Rasmi Thomas

The paper reports full-length NGS HLA genotyping of 1023 individuals from East and West Africa, identifying 371 unique alleles and 25 novel ones, including those with non-synonymous changes affecting peptide binding.

HLA · Jun 26, 2026Peer-reviewedGenetics

Single-cell analyses reveal that monocyte gene expression profiles influence HIV-1 reservoir size in acutely treated cohorts

Philip K. Ehrenberg, Aviva Geretz, Meta Volčič, Taisuke Izumi, Lauren K. Yum, Adam Tully Waickman, Shida Shangguan, Dominic Paquin‐Proulx, Matthew Creegan, Meera Bose, Kawthar Machmach, Aidan McGraw, Akshara Narahari, Jeffrey R. Currier, Carlo Sacdalan, , Rasmi Thomas

The paper uses scRNA-seq to show that monocyte IL1B expression inversely correlates with HIV-1 reservoir size in ART-treated individuals.

Nature Communications · May 29, 2025Peer-reviewedImmunology

Monocyte-derived transcriptome signature indicates antibody-dependent cellular 1 phagocytosis as the primary mechanism of vaccine-induced protection against HIV-1

Shida Shangguan, Philip K. Ehrenberg, Aviva Geretz, Lauren K. Yum, Gautam Kundu, Kelly May, Slim Fourati, Krystelle Nganou‐Makamdop, LaTonya D. Williams, Sheetal S. Sawant, Éric Lewitus, Punnee Pitisuttithum, Sorachai Nitayaphan, Suwat Chariyalertsak, Supachai Rerks‐Ngarm, , Rasmi Thomas

The paper identifies a monocyte-derived transcriptome signature linked to antibody-dependent cellular phagocytosis as a correlate of vaccine-induced protection against HIV-1 in clinical trials.

eLife · Sep 17, 2021Peer-reviewedSystems Biology