LETTER https://doi.org/10.1038/s41586-018-0517-0 Tracing HIV-1 strains that imprint broadly neutralizing antibody responses Roger D. Kouyos 1,2,15,16 *, Peter Rusert 1,15 , Claus Kadelka 1,2,15 , Michael Huber 1 , Alex Marzel 1,2 , Hanna Ebner 1 , Merle Schanz 1 , Thomas Liechti 1,13 , Nikolas Friedrich 1 , Dominique L. Braun 1,2 , Alexandra U. Scherrer 1,2 , Jacqueline Weber 1 , Therese Uhr 1 , Nicolas S. Baumann 1 , Christine Leemann 1,2 , Herbert Kuster 1,2 , Jean-Philippe Chave 3 , Matthias Cavassini 4 , Enos Bernasconi 5 , Matthias Hoffmann 6 , Alexandra Calmy 7 , Manuel Battegay 8 , Andri Rauch 9 , Sabine Yerly 10 , Vincent Aubert 11 , Thomas Klimkait 12 , Jürg Böni 1 , Karin J. Metzner 1,2 , Huldrych F. Günthard 1,2,16 *, Alexandra Trkola 1,16 * & The Swiss HIV Cohort Study 14 Understanding the determinants of broadly neutralizing antibody (bNAb) evolution is crucial for the development of bNAb-based HIV vaccines 1 . Despite emerging information on cofactors that promote bNAb evolution in natural HIV-1 infections, in which the induction of bNAbs is genuinely rare 2 , information on the impact of the infecting virus strain on determining the breadth and specificity of the antibody responses to HIV-1 is lacking. Here we analyse the influence of viral antigens in shaping antibody responses in humans. We call the ability of a virus strain to induce similar antibody responses across different hosts its antibody-imprinting capacity, which from an evolutionary biology perspective corresponds to the viral heritability of the antibody responses. Analysis of 53 measured parameters of HIV-1-binding and neutralizing antibody responses in a cohort of 303 HIV-1 transmission pairs (individuals who harboured highly related HIV-1 strains and were putative direct transmission partners or members of an HIV-1 transmission chain) revealed that the effect of the infecting virus on the outcome of the bNAb response is moderate in magnitude but highly significant. We introduce the concept of bNAb-imprinting viruses and provide evidence for the existence of such viruses in a systematic screening of our cohort. The bNAb-imprinting capacity can be substantial, as indicated by a transmission pair with highly similar HIV-1 antibody responses and strong bNAb activity. Identification of viruses that have bNAb-imprinting capacities and their characterization may thus provide the potential to develop lead immunogens. The capacity to evoke highly similar bNAb responses across vac- cinees is crucial for an effective HIV-1 immunogen. Closely related HIV-1 strains may induce similar neutralization responses, as observa- tions from mother-to-child transmission suggest 3 . To formally evaluate the virus-dictated heritability of antibody responses, we investigated the imprinting capacity of HIV-1 antibody responses within transmis- sion pairs. We designed our study to address two central problems (Extended Data Fig. 1a, b). First, we investigated whether the same virus, when transmitted to two different people, induces similar bind- ing and neutralizing antibody responses (imprints a similar antibody response). Second, we investigated how promising HIV-1 strains with superior bNAb-imprinting capacity can be identified. On the basis of the Swiss 4.5K Screen 4,5 , we established a large, adult transmission-pair cohort (n = 303 putative transmission pairs) with comprehensive information on HIV-1-binding and neutraliz- ing antibody responses (Extended Data Fig. 1a). Extensive data on HIV-binding antibody reactivity encompassing IgG1, IgG2 and IgG3 reactivity with 13 antigens was available for all 606 patients from pre- vious analyses 5 (Supplementary Data 1). Neutralization activity was assessed against a 14 multi-clade virus panel (Extended Data Fig. 2a and Supplementary Data 1, 2) and evaluated by breadth and a cumu- lative neutralization score, reflecting potency and breadth across the analysed virus panel (Extended Data Fig. 2a–d). Overall, the neutraliza- tion activity in the transmission pair cohort showed the typical pattern seen in chronic infection 4 : the majority of patients displayed no or low neutralization activity (73% of patients had below 10% breadth). We hypothesized that if virus-associated factors are important in determining antibody responses, HIV antibody response patterns should be similar in transmission pairs. Using the established 53 HIV-1 antibody parameters (14 neutralization and 39 binding antibody parameters), we conducted a systematic assessment of the HIV-1 anti- body imprinting capacity in transmission pairs (Extended Data Fig. 2e). We detected a significant, positive association of the transmitter and recipient neutralization responses to 7 of the 14 panel viruses (Fig. 1a and Extended Data Fig. 3a). The overall similarity of the neutraliza- tion fingerprint within pairs across the 14 panel viruses was assessed as average Spearman correlation (ρ Spearman-average ) of their neutrali- zation activity (Fig. 1b). To determine the statistical significance of the observed similarity, we used shuffling approaches that randomly reassign recipients to transmitters, thus generating a distribution for the null-expectation of no association. Neutralization fingerprints in observed transmission pairs proved on average positively and signifi- cantly associated (ρ Spearman-average  = 0.11, P shuffling  < 0.001; Fig. 1b). To confirm the influence of the infecting virus, we estimated the herita- bility of antibody responses by two alternative methods adjusting for the influence of various host, viral and disease factors that are known to influence antibody responses 4,5 . First, we restricted the shuffling to pairs with the same infection length, subtype and ethnicity (Fig. 1b). Second, we considered mixed-effect Tobit models adjusted for key drivers of HIV-1 antibody development (infection length, ethnicity, virus load and viral diversity) and bNAb specificity (HIV-1 pol subtype) (Fig. 1c). Both approaches confirmed a significant, within-pair corre- lation of neutralization (Fig. 1b, c). Although other, not yet defined, non-virus-associated factors common to both transmission partners may exist, our data strongly suggest that the infecting virus strain affects the development of neutralization responses. The effects (Fig. 1a, b) remained robust when restricting the analysis to pairs infected with subtype B virus, indicating that the effect is not driven by specific sub- types (Extended Data Fig. 4a, b). 1 Institute of Medical Virology, University of Zurich, Zurich, Switzerland. 2 Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland. 3 Clinique de La Source, Lausanne, Switzerland. 4 Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland. 5 Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland. 6 Division of Infectious Diseases, Cantonal Hospital St. Gallen, St. Gallen, Switzerland. 7 Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland. 8 Division of Infectious Diseases, University Hospital Basel, University of Basel, Basel, Switzerland. 9 Department of Infectious Diseases, University Hospital Bern, University of Bern, Bern, Switzerland. 10 Laboratory of Virology, Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland. 11 Division of Immunology and Allergy, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland. 12 Division of Infection Diagnostics, Department of Biomedicine-Petersplatz, University of Basel, Basel, Switzerland. 13 Present address: ImmunoTechnology Section, Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA. 14 A list of participants and their affiliations appears at the end of the paper. 15 These authors contributed equally: Roger D. Kouyos, Peter Rusert, Claus Kadelka. 16 These authors jointly supervised this work: Roger D. Kouyos, Huldrych F. Günthard, Alexandra Trkola. * email:roger.kouyos@usz.ch; huldrych.guenthard@usz.ch; trkola.alexandra@virology.uzh.ch 406 | NATURE | VOL 561 | 20 SEPTEMBER 2018 © 2018 Springer Nature Limited. All rights reserved.