The multiple roles of hla in hiv immunity and treatment

South Africa has a national HIV-1 prevalence of 12.2% and due to the large population size of 52.9 million, this equates to a 6.5 million people living with HIV-1. The high HIV-1 prevalence has warranted the scaling up of the national antiretroviral treatment program with over 2 million people accessing treatment since 2012. The population of South Africa is genetically diverse and consists of South African Black (SAB), South African Mixed ancestry (SAM), South African Caucasian (SAC) and South African Indian (SAI) populations that constitute 79.8%, 9.0%, 8.7% and 2.5% of the total population. The reasons for the disproportionate HIV-1 prevalence rates estimated for the different populations (15.0%, 3.1%, 0.3% and 0.8% for the SAB, SAM, SAC and SAI populations, respectively) are unknown; however, host genetic differences may be a contributory factor. Human leukocyte antigen (HLA) class I genes play a crucial role in the antiviral innate and adaptive immune response, since HLA class I proteins present antigenic peptides to CD8+ Cytotoxic T cells (CTLs) of the adaptive immune system and are also involved in the innate immune response via interaction with killer-cell immunoglobulin-like receptors (KIRs) expressed by Natural Killer cells (NK cells)

Age at antiretroviral therapy initiation and cell-associated HIV-1 DNA levels in HIV-1-infected children

Background The latent viral reservoir is the major obstacle to achieving HIV remission and necessitates life-long antiretroviral therapy (ART) for HIV-infected individuals. Studies in adults and children have found that initiating ART soon after infection is associated with a reduction in the size of the HIV-1 reservoir. Here we quantified cell-associated HIV-1 DNA in early-treated but currently older HIV-infected children suppressed on ART. Methods The study participants comprised of a cohort of 146 early-treated children with HIV-1 RNA <50 copies/ml enrolled as part of a clinical trial in Johannesburg, South Africa. A stored buffy coat sample collected after a median 4.3 years on ART and where HIV-1 RNA was <50 copies/ml was tested for cell-associated HIV-1 DNA levels. An in-house, semi-nested real-time quantitative hydrolysis probe PCR assay to detect total HIV-1 subtype C proviral DNA was used. Children were followed prospectively for up to 3 years after this measurement to investigate subsequent HIV-1 RNA rebound/failure while remaining on ART. Age at ART initiation, HIV-1 RNA decline prior to HIV-1 DNA measurement and other factors were investigated. Results A gradient between age at ART initiation and later HIV-1 DNA levels was observed. When ART was started 50 copies/ml whilst on ART within 3 years after the DNA measurement was 2.07 (95% CI: 1.352–3.167) times greater if the HIV-1 DNA level was above the median of 55 copies/106 cells. Conclusions Cell-associated HIV-1 DNA levels measured after more than 4 years on ART were lower the younger the age of the child when ART was initiated. This marker of the size of the viral reservoir also predicted subsequent viral rebound/treatment failure while ART was sustained. The results provide additional evidence of the benefits of prompt diagnosis and early ART initiation in newborns and infants

Deep sequencing of the HIV‑1 polymerase gene for characterisation of cytotoxic T‑lymphocyte epitopes during early and chronic disease stages

BACKGROUND : Despite multiple attempts, there is still no effective HIV-1 vaccine available. The HIV-1 polymerase (pol) gene is highly conserved and encodes cytotoxic T-lymphocyte (CTL) epitopes. The aim of the study was to characterise HIV-1 Pol CTL epitopes in mostly sample pairs obtained during early and chronic stages of infection. METHODS : Illumina deep sequencing was performed for all samples while Sanger sequencing was only performed on baseline samples. Codons under immune selection pressure were assessed by computing nonsynonymous to synonymous mutation ratios using MEGA. Minority CTL epitope variants occurring at 5% were detected using lowfrequency variant tool in CLC Genomics. Los Alamos HIV database was used for mapping mutations to known HIV-1 CTL epitopes. RESULTS : Fifty-two participants were enrolled in the study. Their median age was 28 years (interquartile range: 24–32 years) and majority of participants (92.3%) were female. Illumina minority variant analysis identified a significantly higher number of CTL epitopes (n = 65) compared to epitopes (n = 8) identified through Sanger sequencing. Most of the identified epitopes mapped to reverse transcriptase (RT) and integrase (IN) regardless of sequencing method. There was a significantly higher proportion of minority variant epitopes in RT (n = 39, 60.0%) compared to IN (n = 17, 26.2%) and PR (n = 9, 13.8%), p = 0.002 and < 0.0001, respectively. However, no significant difference was observed between the proportion of minority variant epitopes in IN versus PR, p = 0.06. Some epitopes were detected in either early or chronic HIV-1 infection whereas others were detected in both stages. Different distribution patterns of minority variant epitopes were observed in sample pairs; with some increasing or decreasing over time, while others remained constant. Some of the identified epitopes have not been previously reported for HIV-1 subtype C. There were also variants that could not be mapped to reported CTL epitopes in the Los Alamos HIV database. CONCLUSION : Deep sequencing revealed many Pol CTL epitopes, including some not previously reported for HIV-1 subtype C. The findings of this study support the inclusion of RT and IN epitopes in HIV-1 vaccine candidates as these proteins harbour many CTL epitopes.Additional file 1. Supplementary Table 1: The in-house complete HIV pol nested PCR conditions and Sanger sequencing primers.Additional file 2. Supplementary Table 2: Pol CTL epitopes identified through Sanger sequencing and comparison by stage of infectionAdditional file 3. Supplementary Table 3: Minority variant proportions within Pol CTL epitopes by stage of infection.Additional file 4. Supplementary Figure 1: Neighbour-joining phylogenetic analysis of Illumina consensus and Sanger consensus sequences for baseline samples. Sanger and Illumina consensus of the same sample significantly clustered together. Majority of the sequences clustered with HIV-1 subtype C references. HIV group O was used for rooting the tree and a bootstrap value of 1000 was used for analysis. S = Sanger sequencing; D = Deep sequencing.The National Research Foundation of South Africa; Poliomyelitis Research Foundation (PRF); Discovery Foundation; National Health Laboratory Service Research Trust (NHLS-RT); South African Medical Research Council Self-Initiated Research (MRC-SIR); University of Pretoria Faculty of Health Sciences Research Committee; the South African Research Chairs Initiative of the Department of Science and Innovation and ADR—The Division of Intramural Research, NIAID, NIH.http://www.virologyj.comam2023Medical Virolog

Evaluation of the HIV-1 polymerase gene sequence diversity for prediction of recent HIV-1 infections using Shannon entropy analysis

SUPPLEMENTARY MATERIALS : TABLE S1: List of articles from which HIV-1 subtype C reference sequences were obtained; Supplementary TABLE S2: Nucleotide differences within amino acid mutations found to have a different distribution between recent and chronic infection sequences; FIGURE S1: Amino acid sequence alignment to show the difference in sequences between recent and chronic HIV-1 infection; FIGURE S2: Comparison of differences in amino acids E628 and R629 in study sequences and non-subtype C reference sequences, for recent and chronic sequences.DATA AVAILABILITY STATEMENT : All data generated or analysed during this study are included in this manuscript and its supplementary information files.HIV-1 incidence is an important parameter for assessing the impact of HIV-1 interventions. The aim of this study was to evaluate HIV-1 polymerase (pol) gene sequence diversity for the prediction of recent HIV-1 infections. Complete pol Sanger sequences obtained from 45 participants confirmed to have recent or chronic HIV-1 infection were used. Shannon entropy was calculated for amino acid (aa) sequences for the entire pol and for sliding windows consisting of 50 aa each. Entropy scores for the complete HIV-1 pol were significantly higher in chronic compared to recent HIV-1 infections (p < 0.0001) and the same pattern was observed for some sliding windows (p-values ranging from 0.011 to <0.001), leading to the identification of some aa mutations that could discriminate between recent and chronic infection. Different aa mutation groups were assessed for predicting recent infection and their performance ranged from 64.3% to 100% but had a high false recency rate (FRR), which was decreased to 19.4% when another amino acid mutation (M456) was included in the analysis. The pol-based molecular method identified in this study would not be ideal for use on its own due to high FRR; however, this method could be considered for complementing existing serological assays to further reduce FRR.The National Research Foundation (NRF), Poliomyelitis Research Foundation, Discovery Foundation, National Health Laboratory Service Research Trust (NHLS-RT), South African Medical Research Council Self-Initiated Research (MRC-SIR), University of Pretoria Faculty of Health Sciences Research Committee, the South African Research Chairs Initiative of the Department of Science and Innovation and National Research Foundation of South Africa and the Division of Intramural Research.https://www.mdpi.com/journal/virusesam2023Medical Virolog

South African Ebola diagnostic response in Sierra Leone : a modular high biosafety field laboratory

BACKGROUND : In August 2014, the National Institute for Communicable Diseases (NICD) in South Africa established a modular high-biosafety field Ebola diagnostic laboratory (SA FEDL) near Freetown, Sierra Leone in response to the rapidly increasing number of Ebola virus disease (EVD) cases. METHODS AND FINDINGS : The SA FEDL operated in the Western Area of Sierra Leone, which remained a ªhotspotº of the EVD epidemic for months. The FEDL was the only diagnostic capacity available to respond to the overwhelming demand for rapid EVD laboratory diagnosis for several weeks in the initial stages of the EVD crisis in the capital of Sierra Leone. Furthermore, the NICD set out to establish local capacity amongst Sierra Leonean nationals in all aspects of the FEDL functions from the outset. This led to the successful hand-over of the FEDL to the Sierra Leone Ministry of Health and Sanitation in March 2015. Between 25 August 2014 and 22 June 2016, the laboratory tested 11,250 specimens mostly from the Western Urban and Western Rural regions of Sierra Leone, of which 2,379 (21.14%) tested positive for Ebola virus RNA. CONCLUSIONS : he bio-safety standards and the portability of the SA FEDL, offered a cost-effective and practical alternative for the rapid deployment of a field-operated high biocontainment facility. The SA FEDL teams demonstrated that it is highly beneficial to train the national staff in the course of formidable disease outbreak and accomplished their full integration into all operational and diagnostic aspects of the laboratory. This initiative contributed to the international efforts in bringing the EVD outbreak under control in Sierra Leone, as well as capacitating local African scientists and technologists to respond to diagnostic needs that might be required in future outbreaks of highly contagious pathogens.S1 Video. ªHotº processing of Ebola clinical specimens, PPE and decontamination procedures in South African modular, field-operated biocontainment facility in Sierra Leone.Janusz T Paweska was supported by funding from National Research Foundation and the Global Disease Detection Programmehttp://www.plosntds.orgam2017Microbiology and Plant Patholog

A child with perinatal HIV infection and long-term sustained virological control following antiretroviral treatment cessation

Some perinatally HIV infected children who have received early antiretroviral therapy (ART) show long-term sustained virological control after ART cessation. Here the authors describe a case who, at age 9.5 years, shows normal CD4:CD8 T cell ratios and has no detectable levels of replication-competent virus

Characteristics of 146 treated HIV-infected children in Johannesburg, South Africa, at the time of measurement of cell-associated HIV-1 DNA (current time) and at the time of antiretroviral therapy (ART) initiation.

<p>Characteristics of 146 treated HIV-infected children in Johannesburg, South Africa, at the time of measurement of cell-associated HIV-1 DNA (current time) and at the time of antiretroviral therapy (ART) initiation.</p

Associations between age at starting ART and cell-associated HIV-1 DNA levels after a median of 4.3 years of treatment among 146 HIV-infected children.

<p>a: Scatterplot of HIV-1 DNA log₁₀ copies/10⁶ cells (Y-axis) by age at ART start in months (x-axis). LOcally WEighted Scatter-plot Smoother (LOWESS) and linear regression prediction lines are shown in blue and red, respectively; and the grey area shows the 95% prediction elipse. b: Box and whisker plot of HIV-1 DNA log₁₀ copies/10⁶ cells by age at ART start groups; c: Histograms and estimated normal and kernel distributions of HIV-1 DNA log₁₀ copies/10⁶ cells among those who started ART <4.5 and ≥4.5 months of age.</p

Scatterplots showing associations between HIV-1 DNA log₁₀ copies/10⁶ cells and a: Time on ART in years; b: Pre-ART HIV-1 RNA copies/ml and c: Pre-ART CD4 count in cells/mm3.

<p>LOcally WEighted Scatter-plot Smoother (LOWESS) and linear regression prediction lines shown in blue and red, respectively.; grey area shows the 95% prediction elipse.</p