Electronic Thesis and Dissertation Repository

Thesis Format

Integrated Article


Master of Science


Microbiology and Immunology


Mann, Jamie F.S.

2nd Supervisor

Arts, Eric J.



Currently no vaccine has been developed that can prevent the spread of HIV-1. During sexual transmission, a single viral variant called the Transmitted/Founder (T/F) purportedly with unique physical properties, establishes infection in 70-80% of individuals. Unlike previous studies that have tried to identify T/F viruses based on their structure glycan composition and amino acid sequence, we have analyzed the RNA sequences of HIV-1 to help identify T/F variants. Using a combination of both in silico data analysis and in vitro assays, we have identified that T/F viruses have higher numbers of immunostimulatory motifs than HIV virions that fail to infect. Moreover, we are the first to demonstrate that a higher composition of TNF-a inducing motifs within T/F RNA may enhance transmission success. Using the identified T/F viruses identified previously, we have designed novel vaccine immunogens by engineering the T/F Env glycoproteins to enhance their abilities to elicit neutralizing antibody responses.

Summary for Lay Audience

The human immunodeficiency virus-1 (HIV-1) is the cause of the acquired immunodeficiency syndrome (AIDS) where individuals succumb to alternative infections due to a weakened immune system. The primary route of transmission for this virus is sexual intercourse. During coital acts, the recipient is exposed to millions of viruses from the donor; however, in majority of the cases, only one virus enters the blood stream and causes the infection. This virus is known as the Transmitted/founder (T/F) virus. The virus is able to hide from the immune system by adding sugars on its surface protein, envelope (Env). Unfortunately, there is no vaccine that has been able to encourage the immune system to produce protective broadly neutralizing antibodies (bnAbs). The goal of this study was to create a novel antigen that can be used as a vaccine to produce bnAbs. To start, we created a computer program that is able to read through thousands of viral RNA sequences from transmission pairs and enumerate specific pro-inflammatory motifs. These motifs are sequences that are 4 nucleotides long. Lastly, we removed specific sugars that surround a key region on Env, called the CD4 binding-site (bs). By removing sugars, we create a “glycan hole” on the target protein that can be targeted by the immune system. The presence of a glycan hole on the target protein may encourage bnAbs against the CD4bs to bind. In the end, we demonstrated that the RNA of T/F viruses have more pro-inflammatory sequences and that these viruses are more likely to be present in the semen of the male donor. We proposed that more pro-inflammatory motifs in T/F viruses may explain the enhanced transmission success. Concurrently, we showed that by removing a specific glycan, bnAbs targeting the CD4bs can easily bind and prevent the virus from infecting a cell. Altogether, by removing a specific glycan on potential T/F viruses, we may be able to create a vaccine that can elicit bnAbs. In theory, by targeting the specific virus that causes the infection, we can prevent HIV-1 transmission and stop the AIDS pandemic.