Virulence: The high frequency of CD8 evasion mutations becomes a new barrier to HIV cure

Background: Combination antiretroviral therapy (CART) has successfully suppressed HIV replication and reduced circulating virus to undetectable levels, improving the quality of life
of people living with HIV by reducing associated mortality and morbidity.
However, CART does not completely clear HIV, and plasma viremia
reappears 2-8 weeks after stopping treatment.
The formation of an HIV reservoir within the first weeks of infection is considered a major obstacle to
HIV eradication.
The expression of viral antigens is silenced
due to the latent state of infected cells that form an HIV host.
As a result, the virus remains hidden from the
immune system.

Among the different strategies aimed at eliminating HIV hosts, the most studied are shock and kill strategies
.
In this strategy, latent HIV can be reactivated by a latency reverser - LRA - and eliminated
by the action of CART or the immune system.
Although this strategy has achieved interesting results, in general, its impact on the elimination of oil and gas reservoirs is far less than optimal
.
First, the HIV reservoir cannot be completely reactivated, and only <1% of replicable-capable proviruses are reactivated
after maximum in vitro stimulation.
Second, evidence suggests that HIV-specific CD8 (CTL) responses in patients who initiate CART during the chronic infection phase are not successful in killing infected cells, mainly due
to poor recognition of antigenic epitopes present in the reservoir due to the accumulation of CTL escape mutations.

In this regard, special patient groups known as elite controllers (ECs) have become a focus of interest because they can induce an efficient CTL-mediated immune response to control viral replication in the absence of CART, thus becoming a potential model
for achieving so-called functional cures.
Given that the position of the elite controller is established from the very beginning of
infection.
Our hypothesis is that since the virus has not had enough time to select for escape mutations, the reservoirs of these patients may be rich in wild-type epitope sequences
recognized by CTL cells.
Thus, the CTL response of EC subjects can efficiently identify their proviral sequences and can employ a "shock and kill" strategy to eliminate their reservoirs
in these patients.

Methods: Ten non-controller (TX) and seven patients (EC)
who received successful CART were included.
Next-generation sequencing of HIV-Gag genes extracted from purified quiescent memory CD4+ T cells
.
Typing of human leukocyte antigen class I alleles to predict optimal HIV-Gag CTL epitopes
.
For each subject, the frequency of mutated epitopes in the HIV-Gag gene, the proportion of them considered CTL escape variants, and their effect
on human leukocyte antigen recognition was assessed.

Results: The proportion of mutated HIV-Gag CTL epitopes (%) was high, and EC and TX were similar (86% [50-100] and 57% [48-82], p=0.
315, respectively).

Many of these are predicted to negatively impact
antigen identification.
In addition, mutant epitopes considered to be CTL escape variants have similar proportions in TX and EC (77% [49-92] vs.
50% [33-75], p=0.
117).

Thus, the most relevant finding in our study is that the proportion of HIV-Gag CTL escape mutations was high and similar
in the pool of HIV non-control patients (TX) and spontaneous HIV controllers (EC) who received CART (TX) and spontaneous HIV control (EC).

Figure 1.
THE WRICKER-BOXPLATE PLOT SHOWS: (A) THE NUMBER OF BEST-DEFINED CTL EPITOPES PREDICTED BASED ON THE PATIENT'S HUMAN LEUKOCYTE ANTIGEN-I HAPLOTYPE; (B) Proportion of mutated CTL epitopes in autologous sequences obtained from the viral library (%); (C) Ratio
of mutated amino acids (mutant amino acids/total amino acids) for each individual CTL epitope.
The P value compared between patients in the EC and TX groups is shown (Mann-Whitney U test).

Figure 2.
Proportion (%)
of automutated CTL epitopes presented by HLA-I alleles shared between groups of EC (white bars) and Tx (gray bars) patients.
There was no statistically significant difference in the proportion of autologous mutation CTL epitopes between the EC and TX groups (chi-square test).

Figure 3: Whisker-Box plot
showing the proportion (%) of escaped mutations in mutated CTL epitopes in (A) EC and TX patients.
(B) Proportion (%)
of mutant CTL epitopes that have a significant effect on reduced human leukocyte antigen recognition in EC and TX patients.
The p-value for the between-group comparison is shown (Mann-Whitney U-test).

Conclusion: Our findings suggest that evasive mutations in the CTL response may be another obstacle to the elimination of the HIV reservoir and pose a challenge to proof
of concept for HIV treatment strategies focused on reactivating the reservoir.
Due to the small sample size, the robustness of the study may be affected, and further studies of larger patient cohorts are needed to confirm these results
.

Navarrete-Muñoz MA, Ramos R, Holguín Á, et al.
High frequency of CD8 escape mutations in elite controllers as new obstacle for HIV cure.
Virulence 2022 Dec; 13(1)