About the Authors

Matthew R. Henn

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Christian L. Boutwell

Contributed equally to this work with: Christian L. Boutwell, Patrick Charlebois

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Patrick Charlebois

Contributed equally to this work with: Christian L. Boutwell, Patrick Charlebois

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Niall J. Lennon

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Karen A. Power

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Alexander R. Macalalad

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Aaron M. Berlin

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Christine M. Malboeuf

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Elizabeth M. Ryan

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Sante Gnerre

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Michael C. Zody

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Rachel L. Erlich

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Lisa M. Green

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Andrew Berical

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Yaoyu Wang

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Monica Casali

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Hendrik Streeck

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Allyson K. Bloom

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Tim Dudek

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Damien Tully

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Ruchi Newman

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Karen L. Axten

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Adrianne D. Gladden

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Laura Battis

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Michael Kemper

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Qiandong Zeng

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Terrance P. Shea

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Sharvari Gujja

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Carmen Zedlack

Affiliation HIV Clinic Praxis. Jessen, Berlin, Germany

Olivier Gasser

Affiliation Immunobiology Lab, Department of Biomedicine, University Hospital Basel, Basel, Switzerland

Christian Brander

Affiliations Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain, Irsicaixa AIDS Research Institute-HIVACAT, Hospital University Germans Trias I Pujol, Badalona, Spain

Christoph Hess

Affiliation Immunobiology Lab, Department of Biomedicine, University Hospital Basel, Basel, Switzerland

Huldrych F. Günthard

Affiliation Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland

Zabrina L. Brumme

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Chanson J. Brumme

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Suzane Bazner

Affiliation Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America

Jenna Rychert

Affiliation Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America

Jake P. Tinsley

Affiliation The Fenway Institute, Fenway Health, Boston, Massachusetts, United States of America

Ken H. Mayer

Affiliation The Fenway Institute, Fenway Health, Boston, Massachusetts, United States of America

Eric Rosenberg

Affiliation Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America

Florencia Pereyra

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Joshua Z. Levin

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Sarah K. Young

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Heiko Jessen

Affiliation HIV Clinic Praxis. Jessen, Berlin, Germany

Marcus Altfeld

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Bruce W. Birren

Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Bruce D. Walker

Affiliations Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America, Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America

Todd M. Allen

tallen2@partners.org

Affiliation Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: TMA MRH CLB PC NJL KAP ARM MCZ. Performed the experiments: CMM EMR RLE LMG AB YW MC HS AKB TD RN ADG LB MK. Analyzed the data: TMA MRH CLB PC NJL KAP ARM AMB CMM EMR SG MCZ RLE YW HS DT RN QZ TPS SG JZL SKY MA. Contributed reagents/materials/analysis tools: KLA CZ OG CB CH HFG ZLB CJB SB JR JPT KHM ER FP HJ BWB BDW. Wrote the paper: TMA MRH CLB PC NJL KAP ARM MCZ BWB BDW.