UC Irvine

As of the year 2023, there has yet to be developed an effective prophylactic vaccine against HIV-1 infection. One likely reason for prior failures in vaccine trials is that vaccines have been designed against epitopes from non-transmitting variants of the virus. HIV-1 transmission results in a restrictive genetic bottleneck wherein a single viral strain, termed the transmitted/founder (T/F) virus, out of a diverse viral swarm leads to productive infection in recipients, and it is precisely these strains against which a successful vaccine could be developed. While the genetic bottleneck has been studied extensively, the rate of T/F discovery is severely limited by the availability of genetic records from clinical and animal studies, leading to scientific uncertainties regarding T/F selection. In order to accelerate such discoveries, an experimental model was developed to recapitulate the genetic bottleneck in vitro, garner insight into the mechanisms of T/F selection, and identify selected polymorphisms under particular physiological and immunological conditions that favor (or disfavor) them. Healthy donor cells (derived from peripheral blood mononuclear cells) were infected in vitro with various clinical isolates of HIV-1 in order to test the hypotheses that (1) transcytosis results in T/F selection, (2) trans-infection results in T/F selection, and (3) selection pressures can be modulated in favor of different T/Fs using antibodies, complement, or type-1 interferons. gp120 variable loops from output viruses in these experiments were PCR-amplified, sequenced, and phylogenetically analyzed. Animal studies revealed that antibody may propagate positive selection in favor of SIV variants transmitted through the penile route with a more positively charged V4 loop, while in vitro studies showed that antibody did not result in selection during trans-infection. Furthermore, complement opsonization of virus led to differential selection patterns favoring viral variants from two different lineages. Finally, priming of unstimulated T-lymphocytes prior to direct infection resulted in profound, replicate-specific genetic bottlenecks of single viral strains that share some polymorphisms with known T/F viruses. The data here demonstrate that a clinical-like genetic bottleneck can be modeled in vitro, and such an approach may be an invaluable tool in order to understand the genetic bottleneck and provide useful insight toward the development of an effective vaccine.