Title: Distinct Biomarker Signatures in HIV Acute Infection Associate with. Viral Dynamics and Reservoir Size. Supplemental Material

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1 1 2 Title: Distinct Biomarker Signatures in HIV Acute Infection Associate with Viral Dynamics and Reservoir Size 3 Supplemental Material Authors: Jeffrey E. Teigler 1,2, Louise Leyre 3, Nicolas Chomont 3, Bonnie Slike 1,2, Ningbo Jian 1,2, Michael A. Eller 1,2, Nittaya Phanuphak, Eugène Kroon, Suteeraporn Pinyakorn 1,2, Leigh Anne Eller 1,2, Merlin L. Robb 1,2, Jintanat Ananworanich 1,2, Nelson L. Michael 1, Hendrik Streeck 1,2,, and Shelly J. Krebs 1,2, on behalf of the RV2/RV21 study groups. 1 U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring MD, USA 2 Henry M. Jackson Foundation, Bethesda, MD, USA 3 CRCHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Canada SEARCH, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand Institute for HIV Research, University Hospital, University of Duisburg-Essen, Germany These authors contributed equally to this work To whom correspondence should be addressed: Shelly J. Krebs 3 Robert Grant Ave; 1N2 Silver Spring, MD skrebs@hivresearch.org 1

2 Figure S1. Clinical parameters of treatment naïve individuals (n=1) assessed for biomarker fluctuations during the course of HIV infection. Longitudinal (A) CD counts and (B) HIV viral load were measured from the first RNA positive sample in acute infection to weeks into chronic infection. CD count (cells/ml) log 1 HIV RNA copies/ml Days Post-Infection 2

3 RV21 RV2 N 1 Age 23 (1-) 2. (1-) Male:Female:TG ::3 3:: Peak (RV21) or Enroll (RV2) LogVL (copies/ml). (.1-.). (3.-.) Nadir (RV21) or Enroll (RV2) CD Abs (cell/ L) 3 (1-) 1. ( ) Ethnicity Thai Thai Table S1. Characteristics of RV21 and RV2 acute infection cohorts. Median values (range) are provided. TG= transgender, VL= viral load, Abs= Absolute Count 3

4 Z Score A 1 1 GRO MCP-1 MCP [Cytokine] (pg/ml) TNF-a stnfr-i stnfr-ii MIG IP-1 I-TAC BCA-1 MIP-3a sil-2ra B MCP-1 MCP-2 GRO TNF-α Days Post-Infection stnfri stnfrii I-TAC IP-1 MIG MIP-3α BCA-1 sil-2rα Figure S2. Representative biomarker pathways are induced in temporally distinct patterns following HIV infection. Selected biomarkers were measured in plasma from HIV infected individuals (n=1) at uninfected ( Day ), Early Acute (Day 1-), Peak Acute (Day1-1), Early Chronic (Day 2-2), and Late Chronic (Day -2) time points by Luminex assays. (A) Longitudinal levels of individual biomarkers representative of different biological pathways Days Post-Infection

5 3 such as inflammation, TNF-α signaling, IFN-γ signaling, and lymphocyte activation (top to bottom, respectively) per individual. (B) Normalized Z score expression of biomarkers from Figure S2A that display differences in expression kinetics. Dashed line at Z=1. included for visual reference to indicate the statistical threshold of significance.

6 rho p-value IP-1.2 <.1 MIP-3β.1 <.1 I-TAC.3 <.1 stnfr-ii.1.1 IL MIG.221. sil-r.1. TNFα..1 MCP GRO.3.21 Table S2. Statistics of the soluble biomarkers present in acute HIV infection that significantly correlate with contemporaneous viral loads prior to treatment initiation.

7 log 2 [IP-1] (pg/ml) log 2 [BCA-1] (pg/ml) log 2 [TNF-a] (pg/ml) log 2 [MIG] (pg/ml) log 2 [MIP-3a] (pg/ml) log 2 [MIP-3b] (pg/ml) Figure S3. Soluble biomarker dynamics following HIV infection with and without ART initiation. Biomarkers were measured in treatment naïve (n=1, RV21) and in individuals who began ART upon enrollment in acute HIV infection (n=, RV2). Levels are shown as median with interquartile ranges. Dashed line indicates the median biomarker level in uninfected individuals (n=1). Significant elevation versus uninfected individuals are shown with black asterisks (RV21) or red asterisks (RV2). Differences between treated and untreated individuals are indicated by blue asterisks. Asterisks indicate p<. by Mann-Whitney U tests. Supplemental Acknowledgments The RV2/SEARCH 1 Study Group includes: from SEARCH/TRCARC/HIV-NAT: Praphan Phanuphak, Nipat Teeratakulpisarn, Carlo Sacdalan, Donn Colby, Mark De Souza, James Fletcher, Nitiya Chomchey, Duanghathai Sutthichom, Peeriya Prueksakaew, Suwanna Puttamaswin, Somporn Tipsuk, Khunthalee Benjapornpong, Nisakorn Ratnaratorn, Kamonkan Tanjnareel, Chutharat Munkong, Tassanee Luekasemsuk, Kultida poltavee, Sasiwimol Ubolyam, Pacharin Eamyoung; from AFRIMS: Robert J O Connell, Siriwat Akapirat, Rapee Trichavaroj, Bessara Nuntapinit; from MHRP: Madelaine Ouellette, Oratai Butterworth. The RV21 Study Group includes: Hannah Kibuuka, Fatima Jallow, Kathleen Rono, Lucas Maganga, Leonard Maboko, Inge Kroidl, Angela Eser, Cornelia Lueer, Arthur Sekiziyivu, Monica Millard, Ali Taylor, Doug Shaffer, Fred Sawe, Kibet Shikuku, Samoel Khamadi, Sorachai Nitayaphan, Samuel Sinei, Somchai Sriplienchan, Matt Johnston, Linda Jagdzinski, Jennifer Malia, Mark Manak, Susan Mason, Alex Schuetz, Mark De Souza, Sodsai Tovanabutra, Eric Sanders-Buell, Morgane Rolland, Vikcy Polonis, Gustavo Kijak, Agnes Chenine, Aimee Bolen, Nan Wang, 2 log 2 [I-TAC] (pg/ml) log 2 [sil-2ra] (pg/ml) Days Post-Infection/Post-Treatment Initiation log 2 [stnfrii] (pg/ml) Untreated Treated

8 3 Julie Dorsey-Spitz, Mark Milazzo, Qun Li, Alan Fix, Libby Adama, Don Stablein, Peter Dawson, Cindy Wu, Phil Renzullo, Edith Swann, Rob O Connell, Sheila Peel, and Jerome Kim.

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