Molecular and Genetic Characterization of HIV-1 Tat Exon-1 Gene from Cameroon Shows Conserved Tat HLA-Binding Epitopes: Functional Implications

Abstract

HIV-1 Tat plays a critical role in viral transactivation. Subtype-B Tat has potential use as a therapeutic vaccine. However, viral genetic diversity and population genetics would significantly impact the efficacy of such a vaccine. Over 70% of the 37-million HIV-infected individuals are in sub-Saharan Africa (SSA) and harbor non-subtype-B HIV-1. Using specimens from 100 HIV-infected Cameroonians, we analyzed the sequences of HIV-1 Tat exon-1, its functional domains, post-translational modifications (PTMs), and human leukocyte antigens (HLA)-binding epitopes. Molecular phylogeny revealed a high genetic diversity with nine subtypes, CRF22_01A1/CRF01_AE, and negative selection in all subtypes. Amino acid mutations in Tat functional domains included N24K (44%), N29K (58%), and N40K (30%) in CRF02_AG, and N24K in all G subtypes. Motifs and phosphorylation analyses showed conserved amidation, N-myristoylation, casein kinase-2 (CK2), serine and threonine phosphorylation sites. Analysis of HLA allelic frequencies showed that epitopes for HLAs A*0205, B*5301, Cw*0401, Cw*0602, and Cw*0702 were conserved in 58%–100% of samples, with B*5301 epitopes having binding affinity scores > 100 in all subtypes. This is the first report of N-myristoylation, amidation, and CK2 sites in Tat; these PTMs and mutations could affect Tat function. HLA epitopes identified could be useful for designing Tat-based vaccines for highly diverse HIV-1 populations, as in SSA.

Variability in HIV-1 Integrase Gene and 3′-Polypurine Tract Sequences in Cameroon Clinical Isolates, and Implications for Integrase Inhibitors Efficacy

“…Phylogeny of integrase and nef sequences showed high genetic diversity, with a predominance of AG infections (69-75% of cohort samples). This is similar to previous studies showing that over 60% of HIV+ Cameroonians harbored AG viruses [31][32][33]. The lower proportion of AG infections seen in database samples (28%) is likely due to overrepresentation of other genotypes such as HIV-1 groups O, N, and P from Cameroon in the database, from studies that specifically analyzed sequences from these subtypes [34], rather than sequences from randomly collected patient samples as in our cohort or other studies of Cameroon isolates [31][32][33].…”

Attention/Working Memory, Learning and Memory in Adult Cameroonians: Normative Data, Effects of HIV Infection and Viral Genotype

“…There is also evidence of differential BBB inflammation with clades B and AG viruses, with significantly lower levels of inflammatory cytokines and chemokines in BBB cells exposed to CRF02_AG Tat proteins, compared to cells exposed to subtype-B Tat (Bhargavan & Kanmogne, 2018;Woollard et al, 2014). CRF02_AG is the predominant subtype in West-Central Africa, including in Cameroon (Brennan et al, 2008), and 67-72% of cases in our study harbored CRF02_AG viruses (Teto et al, 2016;Teto et al, 2017). Because of this differential inflammation with CRF02_AG viruses and increased risk of NCI associated with CNS inflammation in PLWH, we investigated whether viral genotype had differential effects on attention/WM, learning, and memory.…”

“…Comparative analyses of T-scores of PLWH who had low (<350 cells/μl) and higher (≥350 cells/μl) CD4 counts showed no significant differences between those with low and higher CD4 count on attention/WM, learning, or memory (Table 6). Analyses of the viral PR, RT, gag, env, tat, and nef sequences showed a high genetic diversity (Acharya, Fonsah, Mbanya, Njamnshi, & Kanmogne et al, 2019;Kanmogne et al, 2018;Teto et al, 2016;Teto et al, 2017). These patients were predominantly infected with HIV-1 CRF02_AG (AG) (59-71.6%), but there were also individuals infected with non-CRF02_AG viruses (non-AG) or viruses that had CRF02_AG genotype in some of the six gene regions analyzed and different genotypes in other gene regions (AG-Plus).…”

Effects of HIV infection, antiretroviral therapy, and immune status on the speed of information processing and complex motor functions in adult Cameroonians

“…Two different commercially available tests (rapid immunochromatographic HIV-1/2 test and the Murex HIV antigen/antibody Combination ELISA, Abbott Diagnostics, Chicago, IL, USA) were used per manufacturer's instructions to determine HIV serology. CD4 T-lymphocyte levels were quantified by flow cytometry, VL by reverse transcription polymerase chain reaction (RT-PCR), and viral genes amplified and sequenced as previously described 37,38 .…”

“…Nucleotide sequences for clinical isolates reported in this study are available in the NCBI database; Genbank accession numbers included in our previous publicationsy 37,38 .…”