Conceived and designed the experiments: NB, RDK, GEL, HFG. Performed the experiments: NB, RDK. Analyzed the data: NB, RDK, TT, CK, AM, MS, HFG. Contributed reagents/materials/analysis tools: JB, VA, TK. Wrote the paper: NB, RDK, HFG. All authors read and approved the final manuscript.
Members of the SHCS include the following: V. Aubert, M. Battegay, E. Bernasconi, J. Böni, H. C. Bucher, C. Burton-Jeangros, A. Calmy, M. Cavassini, G. Dollenmaier, M. Egger, L. Elzi, J. Fehr, J. Fellay, H. Furrer (Chairman, Clinical and Laboratory Committee), C. A. Fux, M. Gorgievski, H. F. Günthard (President, SHCS), D. Haerry (Deputy, “Positive Council”), B. Hasse, H. H. Hirsch, M. Hoffmann, I. Hösli, C. Kahlert, L. Kaiser, O. Keiser, T. Klimkait, R. D. Kouyos, H. Kovari, B. Ledergerber, G. Martinetti, B. Martinez de Tejada, K. Metzner, N. Müller, D. Nadal, D. Nicca, G. Pantaleo, A. Rauch (Chairman, Scientific Board), S. Regenass, M. Rickenbach (Head, Data Center), C. Rudin (Chairman, Mother & Child Substudy), F. Schöni-Affolter, P. Schmid, J. Schüpbach, R. Speck, P. Tarr, A. Trkola, P. L. Vernazza, R. Weber, and S. Yerly.
We thank Sebastian Bonhoeffer for fruitful discussions and Venelin Mitov for fruitful discussions and providing the R-package POUMM. We thank the patients who participate in the Swiss HIV Cohort Study (SHCS); the physicians and study nurses, for excellent patient care; the resistance laboratories, for high-quality genotypic drug resistance testing; SmartGene (Zug, Switzerland), for technical support; Brigitte Remy, RN, Martin Rickenbach, MD, Franziska Schöni-Affolter, MD, and Yannick Vallet, MSc, from the SHCS Data Center (Lausanne, Switzerland), for data management; and Danièle Perraudin and Mirjam Minichiello for administrative assistance.
The institution of H.F. has received unrestricted grant support from ViiV, Gilead, Abbott, Janssen, Roche, Bristol-Myers Squibb (BMS), Merck Sharp & Dohme (MSD), and Boehringer Ingelheim. E.B. has been a consultant for BMS, Gilead, ViiV Healthcare, Pfizer, MSD, and Janssen; has received unrestricted research grants from Gilead, Abbott, Roche, and MSD; and has received travel grants from BMS, Boehringer Ingelheim, Gilead, MSD, and Janssen. H.F.G. has been an adviser and/or consultant for GlaxoSmithKline, Abbott, Gilead, Novartis, Boehringer Ingelheim, Roche, Tibotec, Pfizer, and BMS and has received unrestricted research and educational grants from Roche, Abbott, BMS, Gilead, Astra-Zeneca, GlaxoSmithKline, and MSD (all money to the institution). The authors declare that they have no competing interests.
Ethics approval and consent to participate
The SHCS was approved by the ethics committees of the participating institutions (Kantonale Ethikkommission Bern, Ethikkommission des Kantons St. Gallen, Comite Departemental d’Ethique des Specialites Medicales et de Medicine Communataire et de Premier Recours, Kantonale Ethikkommission Zürich, Repubblica et Cantone Ticino–Comitato Ethico Cantonale, Commission Cantonale d’Étique de la Recherche sur l’Être Humain, Ethikkommission beider Basel for the SHCS and Kantonale Ethikkommission Zürich for the ZPHI), and written informed consent was obtained from all participants.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This study has been financed in the framework of the SHCS, supported by the Swiss National Science Foundation (Grants 33CS30-148522, 324730-112594, and 159868), the SHCS (Projects 470, 528, 569, and 683), the SHCS Research Foundation, the European Community’s Seventh Framework Program (Grant FP7/2007-2013), under the Collaborative HIV and Anti-HIV Drug Resistance Network (Grant 223131 to H.F.G.), the Yvonne-Jacob Foundation, Gilead, Switzerland (unrestricted research Grant to the SHCS Research Foundation), by the HIV-X MRD project 51MRP0_158328 and the University of Zurich’s Clinical Research Priority Program’s ZPHI (to H.F.G.). R.D.K. was supported by the Swiss National Science Foundation (Grant PZ00P3-142411 and BSSGI0_155851).
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.