The Effect of Treatment-Associated Mutations on HIV Replication and Transmission Cycles

Abstract

HIV/AIDS mortality has been decreasing over the last decade. While promising, this decrease correlated directly with increased use of antiretroviral drugs. As a natural consequence of its high mutation rate, treatments provide selection pressure that promotes the natural selection of escape mutants. Individuals may acquire drug-naive strains, or those that have already mutated due to treatment. Even within a host, mutation affects HIV tropism, where initial infection begins with R5-tropic virus, but the clinical transition to AIDS correlates with mutations that lead to an X4-tropic switch. Furthermore, the high mutation rate of HIV has spelled failure for all attempts at an effective vaccine. Pre-exposure drugs are currently the most effective drug-based preventatives, but their effectiveness is also threatened by viral mutation. From attachment and entry to assembly and release, the steps in the replication cycle are also discussed to describe the drug mechanisms and mutations that arise due to those drugs. Revealing the patterns of HIV-1 mutations, their effects, and the coordinated attempt to understand and control them will lead to effective use of current preventative measures and treatment options, as well as the development of new ones.

Keywords: HIV-1; drug resistance; mutation; vaccines.

Figure 1

Expected resistance types due to treatment effectiveness and the characteristics of the initiating virus strain. Acquired (yellow) and transmitted (blue) resistance are shown. Viruses that infect as a wild-type are unmutated and highly susceptible to antiretroviral therapy. Ideally, when therapy is effective, this strain would not develop escape mutations and any spread to new hosts would remain susceptible to treatment (lower right). After therapy however, these strains could acquire drug-resistance mutations (ADR, lower left). Viruses that infect after acquiring drug resistance are less susceptible to treatment, potentially acquiring additional mutations if less effective drug combinations are used or adherence is inconsistent (upper left) or spreading with existing mutations to new hosts, referred to as transmitted drug resistance (TDR, upper right). Pre-exposure prophylaxis would also be most effective against wild-type viruses.

Figure 2

The outcome of tropic switching over time due to HIV mutation. (A). The normal pattern of HIV infection starts with becoming infected with the R5 variant which attacks the CCR5 receptor. The virus then mutates and becomes X4-tropic, gaining entry via the CXCR4 receptor, also correlating with the progression to AIDS. (B). The Berlin patient received a bone marrow transplant from a donor with the CCR5^Δ32/Δ32 mutation, however the patient was cleared of both R5-tropic and X4-tropic HIV, a rare and unusual cure. (C). Treatment with CCR5 inhibitors like Maraviroc quickly induces a tropic switch to X4 variants. Viral load remains low due to other components that would be used in combination.

Figure 3

bNAb binding sites. Individual monomers are shown in orange, green, and purple and form the trimeric gp120. Yellow, pink, and neon green depict monomers within the trimeric gp41. The bNAb binding sites are indicated with arrows: the CD4 binding site, gp120/gp41 interface, V1/V2, V3, and MPER. Drawn from PDB ID: 6VRW [43,44,45,46,47].

Figure 4

HIV-1 vaccine trial history. Arrows indicate spans of time and are color coded based on their progress. The number of participants and vaccine descriptions are noted. Starting at the left, the RV144 trial (2003–2006, monitoring until 2009) showed a modest 31% efficacy result [51]. The STEP study (2004–2007, monitoring until 2009) found that vaccinated participants were at a higher probability of HIV-1 infection if they had prior high levels of antibodies against the vector, adenovirus serotype 5 [52]. HVTN503, also known as the Phambili trial (2007, monitoring until 2012), used a MRKad5 gag/pol/nef HIV-1 subtype B vaccine, similar to the STEP trial. It was stopped within a few months, due to the STEP results. Although similar to the STEP trial, it did not result in an increased risk of HIV infection [53,54]. The HVTN505 trial (2009–2013, monitoring until 2017) was stopped due to a lack of efficacy. This trial looked at the efficacy of a DNA vaccine with clade B Gag, Pol, and Nef proteins and clade A, B, and C’s Env proteins. There was also a booster administered using a rAd5 vector that expressed clade B Gag-Pol fusion protein and clades A, B, and C’s Env glycoproteins [55]. The HVTN100 study (2015–2018) was the smallest clinical vaccine trial [56]. HVTN702, the Uhambo trial (2016–2021), utilized two priming immunizations of subtype C envelope ALVAC-HIV and four boosters of a subtype C bivalent gp120 protein adjuvanted by MF59 [57]. The HVTN703, or AMP trial (2016–2021), tested an intravenous antibody (VRC01). There were ten different infusions over the course of 72 total weeks [54]. In HVTN704 (2016–2020), AMP participants received the same treatment as the HVTN703 trial [50]. For the HVTN705, or Imbokodo trial (2017–2022), a priming vaccination of Ad26.Mos4.HIV was administered at four different time periods with boosting adjuvanted vaccinations of Clade C gp140 protein administered twice [58]. The HVTN706 or Mosaico trial (2019–2024, expected) has a similar experimental design to HVTN705. This study administered the priming vaccinations of Ad26.Mos4.HIV at four different time periods with boosting vaccinations of Clade C and Mosaic gp140 protein administered twice [58].

Figure 5

HIV replication cycle and anti-HIV drug targets. ➀. Attachment begins when HIV’s gp120 spike protein binds to the host cell CD4 receptor and a coreceptor. Membrane fusion is induced, and the viral proteins and genetic content is transferred into the cytoplasm. Several drugs are approved that inhibit these early steps. ➁. Upon uncoating, the HIV RNA is released and converted to HIV DNA through reverse transcription. Nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) directly block reverse transcription. ➂. Integration of viral DNA then occurs. The integrase inhibitor drug class functions as a strand transfer inhibitor (INSTI), which blocks the integrase enzyme from inserting viral DNA into the host DNA. During normal viral replication, the integrated DNA becomes the genomic content that provides the template for viral protein synthesis. New HIV proteins are produced as long polyproteins that are later cleaved by protease into functional enzymes and structural proteins. ➃. These proteins will move to the cell surface and surround the genome, assembling into immature HIV particles which are released by budding. There is currently no drug able to target the assembly and release of viral particles. ➄. Inside the released virus, protease acts on the immature HIV particle to create the mature infectious virus. Protease inhibitors (PI) block protease and prevent the formation of mature infectious particles.

Figure 6

HIV receptor interactions. gp120 (green) interacts with both CD4 (orange) and CCR5 (purple). In the top half, the V3 loop is highlighted in magenta. The 11/25 rule, a common guideline to determine tropism, is associated with the locations noted in the V3 loop. The V3 loop’s crown is a crucial location for binding and is highlighted in white. In the lower half, the C4 region of gp120 is shown with its treatment-associated mutations. Based on PDB 6MEO [45,46,47,96].

Figure 7

HIV reverse transcriptase enzyme structure in a two-dimensional map, p66 monomer. Mutational hotspots (yellow) are all found in or near the fingers and palm subdomains. In the center of the palm lies the active site residues that catalyze reverse transcription (red). The RNase H domain contains a DEDD box active site that cleaves template RNA [98]. Nucleotide strand position indicated in green.

Figure 8

HIV RT-inhibitor resistance mutation scores. These resistance scores, when shown in aggregate, can reflect hotspots in the HIV genome which confers resistance to several drugs. Colors represent different drugs, with occurrence rates combined additively. Any negative value represents that HIV had increased susceptibility (instead of resistance) to that drug. NRTI (A) and NNRTI (C) mutations are shown. Combinations of mutations are also shown (B,D) that usually include primary mutations that allow drug escape plus compensatory mutations that reduce fitness costs.

Figure 9

HIV integrase structure, two-dimensional monomer map. Two dimers of this protein bind either end of the HIV genome during integration. The active site is considered to be the essential Asp64, Asp116, and Glu152 (the D,D-35-E motif) [101]. His12, His16, Cys40, and Cys43 bind Zn²⁺ [102]. The sequence of each domain from PDB files 1WJA [103], 1IHV [101], and 1BIS [104]. Multimer structure based on [105]. In the multimer image (lower left), the red DNA (host) and green DNA (virus) represent that these strands will be recombined.

Figure 10

HIV protease structure, two-dimensional monomer map. Protease functions as a dimer and targets various host and viral proteins. HIV polyproteins are cleaved into functional units, most importantly inside maturing capsids. Several drugs interact with the active site and other coordinating amino acids such as I50 in a competitive manner, but mutations may arise that allow for continued function despite drug intervention. Based on sequence from PDB 1AID [134].