CHAVI: Forging New Way Ahead
Center for HIV/AIDS Vaccine Immunology (CHAVI) in its fourth year of funding continues to inform new approaches to HIV vaccine design through discovery of new knowledge about HIV infection.
Tackling the transmitted virus genome
Earlier CHAVI studies described a “bottleneck” effect during HIV transmission: A swarm of HIV variants invade the mucosal surface, but only a few of those viruses initiate infection. The Viral Sequencing Core led by Dr. Beatrice Hahn provided the first detailed look at the envelope gene sequence of the HIV virus that initiates productive infection in the host.
The team sequenced 3451 envelope genes of HIV variants from 102 subjects infected with clade B-HIV for less than 25 days; their immune systems had not yet produced antibodies to HIV circulating in their blood. Using an elegant mathematical model the researchers determined the resemblance between the envelope sequences of the isolated viruses and the initial infecting virus. The model used three simple assumptions:
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the virus’ generation time is two days
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each virus-infected cell then productively infects six new target cells
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the enzyme reverse transcriptase used for reproducing the viral RNA genome introduces a mistake every 50,000 bases.
With a genome of 10,000 nucleotides, the circulating HIV virus swarm amasses few enough mutations such that it still shares 75% identity with the transmitted virus at 10 days after the start of the infection. At day 30 only 40% of the isolated viruses resemble the transmitted virus. After day 30, through the action of antibodies and T cells, the immune system mounts pressure on the virus to change its genome more rapidly. Thus the ability of the model to predict sequence similarity becomes distorted. The researchers discovered that in 80% of the subjects infection resulted from a single virus and in 20% of the subjects from 2-5 variants. Recombination occurred between the viruses in 65% of those infected with 2 or more variants (PNAS 105, 7552, 2008).
The viruses that seed the HIV infection are the ones that a vaccine must intercept. Discovery of sequence similarities between the infecting viruses may yield a new target that may be easier to attack. For 25 years the HIV viruses under study have been the ones isolated long after the initial infection. Now this new knowledge may help us find a vaccine against the infecting virus which may be limited in diversity rather than having to protect against a more diverse population of adapted viruses.
Dissecting properties of neutralizing antibodies
Rare broadly neutralizing antibodies that stop viral entry into cells have been isolated from the sera of a few HIV-infected individuals. Generating a picture of how these neutralizing antibodies recognize and bind to parts of HIV may open new avenues in immunogen design.
Toward that goal, Dr. Barton Haynes’ laboratory is studying the structural properties of two broadly neutralizing antibodies, 2F5 and 4E10 that bind to lipids of the cell membrane as well as HIV surface glycoprotein, gp41. Both 2F5 and 4E10 target a region on gp41, the molecule used by the virus to fuse its viral membrane to the host cell membrane and gain entry into the cell. The two antibodies share another common characteristic –about 20 amino acid long complementarity determining region 3 (CDR3) at tip of their antigen binding site. The CDR loops contain several hydrophobic residues that facilitate lipid binding. Dr. Haynes’ group found that mutating these hydrophobic residues to either disrupt binding of lipid or gp41 results in loss of neutralization activity. Their studies suggested that the antibodies docked on the viral glycoprotein in a 2-step “encounter and docking” process. In this process the antibody first attached to lipids in the viral membrane, and then stably docks on the protein part on gp41 (J. Immunol. 178, 4424, 2007).
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