Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5

Abstract

Although Rhesus macaques are an important animal model for HIV-1 vaccine development research, most transmitted HIV-1 strains replicate poorly in macaque cells. A major genetic determinant of this species-specific restriction is a non-synonymous mutation in macaque CD4 that results in reduced HIV-1 Envelope (Env)-mediated viral entry compared to human CD4. Recent research efforts employing either laboratory evolution or structure-guided design strategies have uncovered several mutations in Env's gp120 subunit that enhance binding of macaque CD4 by transmitted/founder HIV-1 viruses. In order to identify additional Env mutations that promote infection of macaque cells, we utilized deep mutational scanning to screen thousands of Env point mutants for those that enhance HIV-1 entry via macaque receptors. We identified many uncharacterized amino acid mutations in the N-terminal heptad repeat (NHR) and C-terminal heptad repeat (CHR) regions of gp41 that increased entry into cells bearing macaque receptors up to 9-fold. Many of these mutations also modestly increased infection of cells bearing human CD4 and CCR5 (up to 1.5-fold). NHR/CHR mutations identified by deep mutational scanning that enhanced entry also increased sensitivity to neutralizing antibodies targeting the MPER epitope, and to inactivation by cold-incubation, suggesting that they promote sampling of an intermediate trimer conformation between closed and receptor bound states. Identification of this set of mutations can inform future macaque model studies, and also further our understanding of the relationship between Env structure and function.Viruses 2020, 12, 241 2 of 20 in macaque cells [7], most studies employing the SHIV/macaque model have used HIV-1 Envs that were lab adapted to enhance macaque infection, and/or that were derived from HIV-1 variants isolated from the chronic stages of infection [7]. These evolved and chronic-stage Envs are highly pathogenic and transmissible in macaques [8]. While these characteristics enabled robust infection of macaques, evolved and chronic-stage Envs display altered structural conformations and increased susceptibility to neutralizing antibodies compared to Envs from circulating HIV-1 strains [8,9]. Use of these Envs in SHIVs therefore compromises the relevance of the SHIV/macaque model for informing HIV-1 infection in humans [7].In 2012, it was discovered that a single amino acid mutation in macaque CD4 was responsible for the poor ability of HIV-1 to utilize macaque receptors for entry [3]. In vitro evolution experiments also revealed that single amino acid substitutions at sites 204 or 312 in Env's gp120 subunit allow HIV-1 to more effectively use macaque CD4 as an entry receptor [4]. These mutations disrupted quaternary contacts between Env trimer subunits, and similar to Envs encoded by highly pathogenic SHIVs, increased sensitivity to neutralizing antibodies [10].Identification of these mutants prompted further efforts to identify additional Env mutations that would enhance usage of macaque CD4. In 2016, L...

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Association between polymorphisms (rs1800896, rs1800872, rs1800871) in IL-10 gene with human immunodeficiency virus 1-infected patients’ susceptibility

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