Broadly Neutralizing Antibodies (bNAbs) can bind and neutralize multiple strains of HIV-1 at evolutionarily and structurally conserved sites of the Env surface protein. bNAbs develop in some HIV-infected individuals during infection, and they have been shown to prevent infection upon SHIV challenge in the Macaque model. This makes bNAb elicitation a primary objective in the effort to create a vaccine for HIV-1.

The origin of bNAbs during natural infection is a result of co-evolution between the HIV-1 Env population and the broad antibody lineage, and studies of longitudinal donor samples can help us understand how these bNAbs arise. These studies are typically quite time consuming, and, in this thesis, I will explore preliminary investigations into high-throughput strategies for characterizing the co-evolution of HIV env and antibody lineages.

By creating libraries of diverse env sequences, a range of high-throughput experiments become available. This thesis describes the efforts to create libraries of diverse env for different projects: we would aim to conduct one project that uses the libraries for transduction of HEK293T cells for cell sorting to determine sequence similarities among envs that bind the bNAb, as well as enriched features. The other project uses libraries to grow virus and observe the ability of the virus to escape certain bNAbs. Both projects require cloning Env libraries from primary samples into large plasmid vectors, and this cloning is the focus of my thesis.