Defining determinants of broadly neutralizing evolution in viral infection to guide vaccine development

In the frame of this grant our research network aims to unravel which viral and host determinants steer broadly neutralizing antibody (bnAb) evolution in viral infections. We focus on two viral infections in our study: HIV-1 where bnAbs are considered most relevant to prevent infection by vaccines and on LCMV infection of mice as this model system allows to gain insights into basic principles of neutralizing antibody development. In the current funding period we made several exciting discoveries and developed a frame work that will allow us in continuing studies to gain significant insight into the determinants of broadly neutralizing antibody induction both on the host and pathogen level.

In the project parts focusing on HIV bnAb development we analyzed the bnAb response in two Swiss cohorts which amounted with 4484 individuals analyzed to the largest survey thus far worldwide. In total our survey identified 239 bnAb inducers, which is the largest bnAb inducer cohort reported. Using the data we generated on neutralizing antibody in the 4484 participants alongside clinical and demographic data available we had the unique opportunity to investigate which viral, host and disease factors steer bnAb evolution. Our study confirmed three parameters reflecting the exposure to antigen – viral load, length of untreated infection and viral diversity – to independently drive bnAb evolution. Most intriguingly, black ethnicity was associated with significantly higher rates of bnAb induction than white ethnicity, indicating a potential impact of host genetic determinants. Neutralization fingerprint analysis used to delineate plasma specificity identified strong subtype dependencies with higher frequencies of CD4 binding site bnAbs in subtype B (p = 0.02) and V2 glycan bnAbs (p = 1×10-5) in non-B infection. Thus, subtype-specific structural features of the viral envelope trimer exist, which need to be unraveled and harnessed for vaccine design. The follow up studies on these patients for many of whom we have access to longitudinal samples paired with detailed clinical records will allow us to obtain the most comprehensive insight on which factors influence bnAb induction.

While the first study part focuses solely on HIV-1 infection the data we will obtain may also give valuable information for bnAb induction in other settings. This will be directly seen by comparing findings of the HIV / human studies with those conducted in the mouse LCMV model. There we complement the exciting findings in human HIV-1 infection with more mechanistically oriented studies aiming at deciphering the molecular and cellular requirements being instrumental for the diversification and selection of antibody qualities that are capable of physiologically altering the course of a chronic viral infection. Specifically, we have developed and successfully employed novel in vivo systems that allow conditional depletion of follicular helper cells and of LCMV-specific helper cells before or during established chronic infection. Our results have shown that continued presence of LCMV-specific T helper cells is important for the overall maintenance of LCMV-specific antibody titers and that sustained LCMV-specific follicular help is a required for the development of late emerging nAbs which lead to control of chronic LCMV infection in vivo. We believe this being the first direct evidence for a cooperative role of follicular helper cells nAb development (without concomitant alterations in CD8 T cell activity) in permitting resolution of a chronic LCMV infection in vivo. Furthermore, we have stablished an experimental pipeline which will allow us in the near future to track LCMV-specific antibody evolution on a structural and functional level in individual mice using NGS analysis, single plasma cell culture and recombinant expression of identified LCMV-specific antibodies. Using this experimental pipeline we will be in the position to delineate the role of persistent antigen, follicular of virus-specific helper cells for molecular and functional evolution of virus-specific antibody responses. We are convinced that such basic insights will prove instrumental for our current and future understanding of the inter-relation of humoral immunity and persistent viral infections alike the basic insights that have emerged from small animal experimental models in gaining new perspectives into the regulatory mechanisms operating for CD8⁺ T cell immunity in chronic viral infections – some of which have already made their way into clinical application.