Research Article: Ancestral sequences from an elite neutralizer proximal to the development of neutralization resistance as a potential source of HIV vaccine immunogens

Date Published: April 10, 2019

Publisher: Public Library of Science

Author(s): Kathryn A. Mesa, Bin Yu, Terri Wrin, Christos J. Petropoulos, Grant H. Pogson, David L. Alexander, Gerardo Perez, Sara M. O’Rourke, Faruk Sinangil, Joseph Robinson, Marcus A. Conant, Phillip W. Berman, Heidi E. Drummer.


A major challenge in HIV vaccine development is the identification of immunogens able to elicit broadly neutralizing antibodies (bNAbs). While remarkable progress has been made in the isolation and characterization of bNAbs, the epitopes they recognize appear to be poorly immunogenic. Thus, none of the candidate vaccines developed to date has induced satisfactory levels of neutralizing antibodies to the HIV envelope protein (Env). One approach to the problem of poor immunogenicity is to build vaccines based on envelope (env) genes retrieved from rare individuals termed elite neutralizers (ENs) who at one time possessed specific sequences that stimulated the formation of bNAbs. Env proteins selected from these individuals could possess uncommon, yet to be defined, structural features that enhance the immunogenicity of epitopes recognized by bNAbs. Here we describe the recovery of envs from an EN that developed unusually broad and potent bNAbs. As longitudinal specimens were not available, we combined plasma and provirus sequences acquired from a single time-point to infer a phylogenetic tree. Combining ancestral reconstruction data with virus neutralization data allowed us to sift through the myriad of virus quasi-species that evolved in this individual to identify envelope sequences from the nodes that appeared to define the transition from neutralization sensitive envs to the neutralization resistant envs that occur in EN plasma. Synthetic genes from these nodes were functional in infectivity assays and sensitive to neutralization by bNAbs, and may provide a novel source of immunogens for HIV vaccine development.

Partial Text

A major goal of HIV-1 vaccine research is to develop HIV envelope glycoprotein immunogens that will induce broadly neutralizing antibodies (bNAbs). The highest levels of bNAbs are found in the sera of rare individuals termed elite neutralizers (ENs). ENs are defined as HIV-1 infected individuals who possess antibodies capable of neutralizing tier 2 and 3 viruses from at least four different clades of virus at serum dilution titers of 1:300 or more [1]. Despite more than 30 years of research, none of the HIV vaccine antigens described to date are able to elicit antibody responses similar to those found in ENs. Moreover, no immunogen has been described that is able to consistently stimulate antibodies to more than one of the five main epitopes recognized by bNAbs thought to be required for protection [2–9]. Historically, a major hypothesis put forward to account for the inability of candidate HIV vaccines to elicit bNAbs was that the immunogens lacked the quaternary epitopes present only on the trimeric structures associated with spikes on the virus surface [10, 11]. Several groups have now developed trimeric forms of the HIV envelope protein that appear to closely resemble the spike proteins [12–16]. These proteins possess the epitopes recognized by all of the major classes of bNAbs, and thus represent a significant advance over the monomeric envelopes tested previously [17, 18]. However, several studies have reported that these trimers are unable to elicit bNAbs when used in immunization studies [14, 19–24]. Thus the epitopes recognized by bNAbs, even in trimeric structures, are poorly immunogenic and the current challenge for HIV vaccine development is to enhance the immunogenicity of epitopes recognized by bNAbs. The outcomes observed so far with the current trimeric vaccine immunogens may parallel the outcomes seen for most individuals infected with HIV whereby only 10–30% of infected individuals produce bNAbs [1, 25–28] despite being continuously exposed to properly-folded trimeric HIV envelope proteins. It is thus likely that only rare envelope proteins possess the specific biophysical features that define the immunogenic structure required to elicit the formation of bNAbs.

The experiments described represent the first steps in the development of an improved HIV vaccine based on envs closely resembling those known to have previously elicited unusually broad and potent bNAbs in humans. The availability of these proteins will allow us to test the hypotheses that Envs from ENs have structural features that enhance the immunogenicity of epitopes recognized by bNAbs. This hypothesis could explain the surprising findings that properly folded trimeric envelope proteins, possessing virtually all of the epitopes recognized by bNAbs have, thus far, failed to consistently elicit bNAbs [15, 19–24]. Since bNAbs are not detected for several years post infection [29–32] and neutralization sensitive viruses appear to be cleared from circulation once bNAbs appear [29], the identification of envelopes that gave rise to bNAbs is challenging. This effort requires searching through the swarm of virus quasi-species that evolve in each individual EN in order to identify viruses with structures closely resembling those that elicited bNAbs. The present studies demonstrate that computational methods of sequence analysis, combined with virus neutralization data, can considerably narrow this search.




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