Performance of an in-house multiplex PCR assay for HIV-1 drug resistance testing - A cheaper alternative.

Background: Currently, most HIV drug resistance PCR assays amplify the protease-reverse transcriptase (PR-RT) fragment separately from the integrase (IN) fragment. The aim of this study was to develop a multiplex PCR assay that simultaneously amplifies PR-RT and IN fragments for HIV-1 drug-resistance testing.

Methods: The in-house multiplex PCR assay was evaluated on extracted total nucleic acids obtained from the National Health Laboratory Service (NHLS) and Lancet laboratories.

Higher CCR5 density on CD4 + T-cells in mothers and infants is associated with increased risk of in-utero HIV-1 transmission.

Objective: CCR5-tropic viruses are preferentially transmitted during perinatal HIV-1 infection. CCR5 density on CD4 + T-cells likely impacts susceptibility to HIV-1 infection.

Design: Fifty-two mother-infant dyads were enrolled.

Evaluation of the HIV-1 Polymerase Gene Sequence Diversity for Prediction of Recent HIV-1 Infections Using Shannon Entropy Analysis.

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.

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.

Predictors of Cell-Associated Human Immunodeficiency Virus (HIV)-1 DNA Over 1 Year in Very Early Treated Infants.

Background: Younger age of antiretroviral therapy (ART) initiation is associated with smaller viral reservoirs in perinatally acquired HIV-1 infection, but there is wide variability among early-treated infants. Predictors of this variability are not fully described.

Methods: Sixty-three neonates diagnosed with HIV-1 <48 hours after birth in Johannesburg, South Africa, were started on ART as soon as possible.

Normalization of B Cell Subsets but Not T Follicular Helper Phenotypes in Infants With Very Early Antiretroviral Treatment.

Infant HIV-1-infection is associated with high morbidity and mortality if antiretroviral treatment (ART) is not initiated promptly. We characterized development of circulating T follicular helper cells (cTfh) and their relationship to naïve/memory B cell subsets in a cohort of neonates initiating ART within the first week of life. Infants were diagnosed within 48 hours of birth and started ART as soon as possible.

Lack of association of KIR2DL1-R and KIR2DL1-C with HIV-1 control in black South Africans with HLA-C2.

Activating/inhibitory Killer-cell Immunoglobulin-like Receptors (KIRs) partly regulate Natural Killer (NK) cells. KIR2DL1 allotypes with cysteine at position-245 (KIR2DL1-C) express at lower levels and demonstrate weaker inhibitory signaling compared to allotypes with arginine at position-245 (KIR2DL1-R). The functional consequence of either allotype in infectious diseases is unknown.

Human leukocyte antigen associations with protection against tuberculosis infection and disease in human immunodeficiency virus-1 infected individuals, despite household tuberculosis exposure and immune suppression.

Background: To determine the association of human leukocyte antigen (HLA) alleles as correlates of risk for and protection against tuberculin skin test (TST) positivity and active TB disease amongst HIV-infected adults.

Methods: Genomic DNA was extracted from 754 HIV-infected adults whole-blood. HLA-A, -B, -C and -DRB1 loci were genotyped by next generation sequencing methods.

Human leukocyte antigen class I (A, B, C) and class II (DPB1, DQB1, DRB1) allele and haplotype variation in Black South African individuals.

South Africa has a population of 58.78 million, of which 80.7% are Black African individuals, representing 9 predominant ethnic/linguistic groups (Zulu, Xhosa, Pedi, Tswana, South Sotho, Tsonga, Swati, Venda and Ndebele).

Identification of a novel recombinant allele, HLA-DPB1*835:01:01:02, in Black South African individuals.

Genetic characterisation of a novel intra-locus recombinant allele, HLA-DPB1*835:01:01:02, in Black South African individuals.

Identification of a novel allele, HLA-DPB1*34:01:01:03, in Black South African individuals.

Genetic characterisation of a non-coding region allelic variant, HLA-DPB1*34:01:01:03, in Black South African individuals.

Cis-regulatory genetic variants in the CCR5 gene and natural HIV-1 control in black South Africans.

Studies have investigated CCR5 haplotypes (HHA, HHB, HHC, HHD, HHE, HHF*1, HHF*2, HHG*1, HHG*2), defined by seven 5'UTR single nucleotide polymorphisms (SNPs), CCR2-V64I and CCR5Δ32, in HIV-1 disease. CCR5 cis-regulatory regions were sequenced, CCR2-V64I and CCR5Δ32 genotyped, and compared in HIV-1-infected black South Africans: 71 HIV-1 controllers (23 elite controllers, 37 viraemic controllers (VCs), 11 high viral load long-term non-progressors) and 74 progressors. The HHE haplotype and 3'UTR +2919 T > G SNP heterozygosity were underrepresented in total controllers and VCs vs.

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

Understanding HIV remission in rare individuals who initiated antiretroviral therapy (ART) soon after infection and then discontinued, may inform HIV cure interventions. Here we describe features of virus and host of a perinatally HIV-1 infected child with long-term sustained virological control. The child received early limited ART in the Children with HIV Early antiRetroviral therapy (CHER) trial.

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.

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 "hotspot" 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.

Killer-cell immunoglobulin-like receptor (KIR) and human leukocyte antigen (HLA) class I genetic diversity in four South African populations.

Killer-cell Immunoglobulin-like Receptor (KIR) and Human Leukocyte Antigen (HLA) genotypes vary considerably between individuals and populations due to KIR/HLA allelic variation and variable haplotype configurations of KIR. HLA mediate natural killer cell activity by serving as KIR ligands. KIR/HLA polymorphisms associate with both disease susceptibility and severity.

Human leukocyte antigen class I (A, B and C) allele and haplotype variation in a South African Indian population.

In 2013, ∼1,329,300 individuals made up the South African Indian population, which constituted ∼2.5% of the total population of ∼53 million. Historically, from 1860 to 1911, indentured labourers were imported from India, to work in the sugar-cane plantations in the KwaZulu-Natal Province.

Human leukocyte antigen class I (A, B and C) allele and haplotype variation in a South African Mixed ancestry population.

South Africa has a large (∼53million), ethnically diverse population (black African, Caucasian, Indian/Asian and Mixed ancestry) and a high disease burden (particularly HIV-1 and Mycobacterium tuberculosis). The Mixed ancestry population constitutes ∼9% of the total population and was established ∼365years ago in the Western Cape region through interracial mixing of black Africans, Europeans and Asians. Admixed populations present unique opportunities to identify genetic factors involved in disease susceptibility.

Decay of K103N mutants in cellular DNA and plasma RNA after single-dose nevirapine to reduce mother-to-child HIV transmission.

Objectives: Single-dose nevirapine (sd-NVP) for prevention of mother-to-child HIV-1 transmission is associated with selection of resistant viral variants, particularly the Lysine (K) to Asparagine (N) mutation at codon 103 (K103N) of reverse transcriptase. As this may influence subsequent treatment responses, a better understanding of the dynamics of decay and persistence of this variant is needed.

Design And Methods: We measured the frequency of K103N mutants among a cohort of HIV-1-infected pregnant women recruited at an out-patient clinic in Johannesburg, South Africa.