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Objectives: To investigate the relationship between the severity of proteinuria and adverse maternal and neonatal outcomes in patients with preeclampsia (PE)., Design: Prospective cohort study conducted in Gauteng, South Africaover 12 months. Patientswith PE 18 years or olderwith singleton pregnancieswere recruited. Weincluded248in the final analysis., Methods: Proteinuria was quantified using urine protein: creatinine ratio (UPCR). Preeclamptic patients' outcomeswere compared according to the UPCR values using regression models and by generating receiver operator characteristic (ROC) curves. Primary maternal outcomes were gestational age (GA) at diagnosis, GA at delivery, development of eclampsia, development of severe features and the need for more than one antihypertensiveagent. Neonatal outcomes were admission to neonatal unit, 5-min APGAR score, need for ventilatory support and early neonatal death., Results: There was a weak but significant negative correlation between GA at delivery and UPCR (Spearman's correlation coefficient (SCC) -0.191, p = 0.002). Most patients (77 %) required >1 agent to control their blood pressure, however there was no correlation between UPCR and the need for additional agents (SCC -0.014, p = 0.828). There was a statistically significant correlation between UPCR and severe features, especially the development of haemolysis, elevated liver enzymes and low platelet (HELLP) syndrome (p = 0.005). There was no significant correlation between neonatal outcomes and UPCR., Conclusion: Severity of proteinuria correlated with earlier delivery and development of severe features, specifically HELLP syndrome and pulmonary oedema. There was no correlation between UPCR and requiring additional antihypertensiveagentsor neonatal outcomes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Since the discovery of the breast cancer susceptibility genes, BRCA1 and BRCA2, various other genes conferring an increased risk for breast cancer have been identified. Studies to evaluate sequence variants in cancer predisposition genes among women of African ancestry are limited and mostly focused on BRCA1 and BRCA2. To characterize germline sequence variants in cancer susceptibility genes, we analysed a cohort of 165 South African women of self-identified African ancestry diagnosed with breast cancer, who were unselected for family history of cancer. With the exception of four cases, all others were previously investigated for BRCA1 and BRCA2 deleterious variants, and were negative for pathogenic variants. We utilized the Illumina TruSight cancer panel for targeted sequencing of 94 cancer susceptibility genes. A total of 3.6% of patients carried a pathogenic/likely pathogenic variant in a known breast cancer susceptibility gene: 1.2% in BRCA1, 0.6% in each of BRCA2, ATM, CHEK2 and PALB, none of whom had any family history of breast cancer. The mean age of patients who carried deleterious variant in BRCA1/BRCA2 was 39 years and 8 months compared to 47 years and 3 months among women who carried a deleterious variant in other breast cancer susceptibility genes., (© 2022. The Author(s).)

Objective: To describe risk factors and outcomes of pregnant women infected with SARS-CoV-2 admitted to South African healthcare facilities., Methods: A population-based cohort study was conducted utilizing an amended International Obstetric Surveillance System protocol. Data on pregnant women with SARS-CoV-2 infection, hospitalized between April 14, 2020, and November 24, 2020, were analyzed., Results: A total of 36 hospitals submitted data on 673 infected hospitalized pregnant women; 217 (32.2%) were admitted for COVID-19 illness and 456 for other indications. There were 39 deaths with a case fatality rate of 6.3%: 32 (14.7%) deaths occurred in women admitted for COVID-19 illness compared to 7 (1.8%) in women admitted for other indications. Of the women, 106 (15.9%) required critical care. Maternal tuberculosis, but not HIV co-infection or other co-morbidities, was associated with admission for COVID-19 illness. Rates of cesarean delivery did not differ significantly between women admitted for COVID-19 and those admitted for other indications. There were 179 (35.4%) preterm births, 25 (4.7%) stillbirths, 12 (2.3%) neonatal deaths, and 162 (30.8%) neonatal admissions. Neonatal outcomes did not differ significantly from those of infected women admitted for other indications., Conclusion: The maternal mortality rate was high among women admitted with SARS-CoV-2 infection and higher in women admitted primarily for COVID-19 illness with tuberculosis being the only co-morbidity associated with admission., (© 2021 International Federation of Gynecology and Obstetrics.)

By the end of 2012, more than 6.1 million people were infected with HIV-1 in South Africa. Subtype C was responsible for the majority of these infections and more than 300 near full-length genomes (NFLGs) have been published. Currently very few non-subtype C isolates have been identified and characterized within the country, particularly full genome non-C isolates. Seven patients from the Tygerberg Virology (TV) cohort were previously identified as possible non-C subtypes and were selected for further analyses. RNA was isolated from five individuals (TV047, TV096, TV101, TV218, and TV546) and DNA from TV016 and TV1057. The NFLGs of these samples were amplified in overlapping fragments and sequenced. Online subtyping tools REGA version 3 and jpHMM were used to screen for subtypes and recombinants. Maximum likelihood (ML) phylogenetic analysis (phyML) was used to infer subtypes and SimPlot was used to confirm possible intersubtype recombinants. We identified three subtype B (TV016, TV047, and TV1057) isolates, one subtype A1 (TV096), one subtype G (TV546), one unique AD (TV101), and one unique AC (TV218) recombinant form. This is the first NFLG of subtype G that has been described in South Africa. The subtype B sequences described also increased the NFLG subtype B sequences in Africa from three to six. There is a need for more NFLG sequences, as partial HIV-1 sequences may underrepresent viral recombinant forms. It is also necessary to continue monitoring the evolution and spread of HIV-1 in South Africa, because understanding viral diversity may play an important role in HIV-1 prevention strategies.

Germline mutations in BRCA1 and BRCA2 increase the risk for developing breast and ovarian cancer. Previously, the techniques available allowed only for the identification of small genomic alterations, but the dawn of new technology now allows for the rapid detection of large genomic rearrangements (LGRs). LGRs in BRCA1 are responsible for between 0 and 27% of all BRCA1 disease-causing mutations identified in numerous populations. Such alterations are far less common in the BRCA2 gene. To determine the impact of BRCA1 and BRCA2 LGRs in South Africa, 52 hereditary breast and/or ovarian South African families (36 were Afrikaners) were screened for BRCA1 and BRCA2 LGRs using multiplex ligation-dependent probe amplification. These patients were previously shown to be BRCA1 and BRCA2 small mutation negative. One LGR was detected in BRCA1 in a South African family with Greek ancestry. This is a novel deletion of both exons 23 and 24 (NG_005905.2:g.169527_180579del). This first study of BRCA rearrangements in South Africa reveals that LGRs comprise ~3% of identified BRCA1 mutations, a low rate in comparison to other populations. In addition, we have reviewed all 98 previously characterized BRCA1/2 LGRs and re-named them according to the recommended HGVS nomenclature, using the recently released RefSeqGene records, NG_005905.2 and NG_012772.1 for BRCA1 and BRCA2. A standardized resource is now provided which will assist researchers in determining whether their LGRs are novel. Furthermore, we have clarified some of the previously misunderstood rules of nomenclature, which will make uniform reporting of BRCA1/2 easier in the future.

HIV-1 is a major health problem in South Africa with an average prevalence rate of 29.1% in pregnant women and between 4.9 and 6.1 million people infected. Using env gp120 V3 serotyping and genotyping techniques 410 patient samples were investigated. Most of the samples were obtained from different clinics in the greater Cape Town area of the Western Cape Province in South Africa. These included an academic hospital, state and private clinics, an informal settlement, sex worker cohorts, and the blood transfusion services. RNA was extracted from plasma samples followed by RT-PCR and sequencing of the env gp120 V3 region. Sequence fragments were assembled using Sequencher V4.7 and subsequently codon aligned. Distance calculation, tree construction methods, and bootstrap analysis were implemented using MEGA version 4.0. Viral load measurements indicated that HIV-1 RNA levels from 74 samples were below the assay detection limit. Three hundred thirty-six samples were used for env PCR and sequencing and 320 were assigned to subtypes. The majority of the sequences were subtyped as C (n = 285, 89.0%). Other subtypes detected were subtype A (n = 10, 3.1%); subtype B (n = 22, 6.8%); one each of subtypes F1, G, U, and a CH recombinant. Whether this diversity will have major implications for HIV-1 evolution and vaccine development in this region remains undetermined.

To elucidate the genetic architecture of familial schizophrenia we combine linkage analysis with studies of fine-level chromosomal variation in families recruited from the Afrikaner population in South Africa. We demonstrate that individually rare inherited copy number variants (CNVs) are more frequent in cases with familial schizophrenia as compared to unaffected controls and affect almost exclusively genic regions. Interestingly, we find that while the prevalence of rare structural variants is similar in familial and sporadic cases, the type of variants is markedly different. In addition, using a high-density linkage scan with a panel of nearly 2,000 markers, we identify a region on chromosome 13q34 that shows genome-wide significant linkage to schizophrenia and show that in the families not linked to this locus, there is evidence for linkage to chromosome 1p36. No causative CNVs were identified in either locus. Overall, our results from approaches designed to detect risk variants with relatively low frequency and high penetrance in a well-defined and relatively homogeneous population, provide strong empirical evidence supporting the notion that multiple genetic variants, including individually rare ones, that affect many different genes contribute to the genetic risk of familial schizophrenia. They also highlight differences in the genetic architecture of the familial and sporadic forms of the disease.

Background: To evaluate the prevalence of human papilloma virus (HPV) infection and types in the oral and cervix mucosa of treatment-naïve HIV-1-positive women with CD4 counts less than 300 cells per ml with no HPV-associated oral lesions., Methods: Oral epithelium was harvested from the buccal mucosa and lateral borders of the tongue and cervical samples were collected from the endocervical area of 30 women, 22-64 years old. Cytobrush Plus cell collectors were used for sampling both anatomical areas. Genital pathology, obstetric and gynaecological history, co-morbid disease, hormone therapy, sexual behavior and smoking history were assessed via physical examination and clinical interviews. Special investigations included cervical Papanicolau smears, CD4 counts and HIV-1 viral loads. The linear array HPV test was used to determine HPV genotypes present in the specimens., Results: Oral HPV were identified in 20% (n = 6) of the patients, of which two had infection with two HPV types. Genital HPV was found in 96.7% (n = 29) of the women, of which only 14 had cytological abnormalities on Papanicolau smear. Infection with multiple HPV types were present in 93.1% (n = 27) of the patients, with an average of four HPV types per individual., Conclusions: South African HIV-positive women with CD4 counts less than 300 cells per ml have a significant risk of cervical HPV strains and multiple strain infection of the cervix. The prevalence of HPV in normal oral mucosa was low but high-risk types were present. Limited correlation between oral HPV types and those identified in the cervical mucosa was found.

We analyzed the HIV-1 pol gene from patients in Cape Town to determine the genetic diversity of HIV-1 in the region and to assess the baseline HIV-1 resistance level of treatment-naive patients. Plasma was collected prior to the national antiretroviral therapy (ART) program. RNA was extracted, followed by RT-PCR and automated DNA sequencing of the viral protease (PR) and reverse transcriptase (RT) coding region. Genotyping was done through phylogenetic analysis. The sequences were inspected for resistance-associated mutations against PR and RT inhibitors. A total of 140 pol sequences were analyzed, of which 133 (95%) belong to HIV-1 subtype C, five (3.6%) were subtype B, and one each was subtype G and CRF02_AG. Five sequences (3.6%) had resistance-associated mutations. These include three (2.1%) NNRTI mutations. With the progression of the national ART program, it is important to monitor the resistance profile of naive and treatment-experienced patients.

South Africa has the highest number of HIV-1-infected individuals in the world, with HIV-1 subtype C prevailing. However, HIV-1 subtype C accessory genes are rarely characterized in the country. These genes are important for establishing viral pathogenesis. The Vif protein has been shown to counteract the antiretroviral activity of APOBEC3G/F cytidine deaminases. In this study an additional 50 HIV-1 vif sequences are characterized. These include 48 HIV-1 subtype C and 2 HIV-1 subtype B sequences. Highly conserved HIV-1 subtype C motifs are outlined. The previously identified RLRR (90-93) motif does not seem to be conserved among our newly analyzed sequences. Conserved motifs can be useful for developing new vaccine strategies or antiretroviral drugs.

It is estimated that between 5.5 and 6.1 million people are infected with HIV/acquired immunodeficiency syndrome (AIDS) in South Africa, with subtype C responsible for the majority of these infections. The Khayelitsha suburb of Cape Town has one of the highest HIV prevalence rates in South Africa. Overcrowding combined with unemployment and crime in parts of the area perpetuates high-risk sexual behavior, which increases exposure to infection by HIV. Against this background, the objective of this study was to characterize HIV-1 in residents confirmed to be seropositive. Serotyping was performed through a competitive enzyme-linked immunosorbent assay (cPEIA). Genotyping methods included RNA isolation followed by RT-PCR and sequencing of the gag p24, env gp41 immunodominant region (IDR), and env gp120 V3 genome regions of HIV-1. With the exception of a possible C/D recombinant strain, all HIV-1 strains were characterized as HIV-1 group M subtype C. One individual was shown to harbor multiple strains of HIV-1 subtype C. In Southern Africa, the focus has been to develop a subtype C candidate vaccine, as this is the major subtype found in this geographical area. Therefore, the spread of HIV-1 and its recombinant strains needs to be monitored closely., ((c) 2006 Wiley-Liss, Inc.)

CXC chemokine ligand 12 (CXCL12), or stromal cell-derived factor 1 (SDF1), is the only known natural ligand for the HIV-1 coreceptor, CXC chemokine receptor 4 (CXCR4). A single nucleotide polymorphism (SNP) in the CXCL12 gene (SDF1-3'A) has been associated with disease progression to AIDS in some studies, but not others. Mutations in the CXCR4 gene are generally rare and have not been implicated in HIV-1/AIDS pathogenesis. This study analyzed the SDF1-3'A SNP and performed mutation screening for polymorphic markers in the CXCR4 gene to determine the presence or absence of significant associations with susceptibility to HIV-1 infection. The study consisted of 257 HIV-1-seropositive patients and 113 HIV-1-seronegative controls representing a sub-Saharan African population belonging to the Xhosa ethnic group of South Africa. The SDF1-3'A SNP was associated with an increased risk for HIV-1 infection (P = 0.0319) whereas no significant association was observed between the occurrence of the SDF1-3'A SNP and increased or decreased plasma levels of CXCL12. Comprehensive mutation analysis of the CXCR4 gene confirmed a high degree of genetic conservation within the coding region of this ancient population.

Human immunodeficiency virus type 1 (HIV-1) subtype C infections are on the rise in Sub-Saharan Africa and Asia. Therefore, there is a need to develop an HIV vaccine capable of eliciting broadly reactive immune responses against members of this subtype. We show here that modified HIV envelope (env) DNA vaccines derived from the South African subtype C TV1 strain are able to prime for humoral responses in rabbits and rhesus macaques. Priming rabbits with DNA plasmids encoding V2-deleted TV1 gp140 (gp140TV1DeltaV2), followed by boosting with oligomeric protein (o-gp140TV1DeltaV2) in MF59 adjuvant, elicited higher titers of env-binding and autologous neutralizing antibodies than priming with DNA vaccines encoding the full-length TV1 env (gp160) or the intact TV1 gp140. Immunization with V2-deleted subtype B SF162 env and V2-deleted TV1 env together using a multivalent vaccine approach induced high titers of oligomeric env-binding antibodies and autologous neutralizing antibodies against both the subtypes B and C vaccine strains, HIV-1 SF162 and TV1, respectively. Low-level neutralizing activity against the heterologous South African subtype C TV2 strain, as well as a small subset of viruses in a panel of 13 heterologous primary isolates, was observed in some rabbits immunized with the V2-deleted vaccines. Immunization of rhesus macaques with the V2-deleted TV1 DNA prime/protein boost also elicited high titers of env-binding antibodies and moderate titers of autologous TV1 neutralizing antibodies. The pilot-scale production of the various TV1 DNA vaccine constructs and env proteins described here should provide an initial platform upon which to improve the immunogenicity of these subtype C HIV envelope vaccines.

South Africa has one of the fastest growing HIV-1 epidemics worldwide, consisting mostly of subtype C. However, HIV-1 subtype B and subtype D viruses were isolated in the beginning of the epidemic in the early 1980s. This study describes the amplification, cloning, and near full-length genome sequencing of four HIV-1 subtype D primary strains, isolated from 1984 to 1986 in Cape Town, in what seems to have been a small restricted subtype D epidemic in the country.

The novel guanidines N-(3,4-dimethoxy-2-chlorobenzylideneamino)-guanidine (ME 10092) and N-(3,4-dimethoxy-2-chlorobenzylideneamino)-N1-hydroxyguanidine (PR5) were recently reported to exhibit promising cardioprotective activities in myocardial ischaemia and reperfusion in rats. The current study investigated for the first time pharmacological effects of ME10092 in the primate, viz. the Cape baboon Papio ursinus. The effects of ME10092 (1 and 2 mg/kg doses) on the cerebral blood flow, heart rates and the systolic and diastolic blood pressure were investigated after intravenous injection to the baboon under anaesthesia. The cerebral perfusion effects of ME10092 were assessed using Single Photon Emission Computed Tomography according to the split-dose approach and 99mTc-hexamethyl-propylene amine oxime as brain perfusion tracer. The observation that the recovery times from the anaesthesia were unacceptably prolonged excluded doses beyond 2 mg/kg. The data indicate that no cerebral perfusion changes were induced at both the 1 and 2 mg/kg doses of ME10092. Both these doses of ME10092 showed blood pressure and heart rate effects, with the latter being more significant. Decreases in heart rate were seen directly after ME10092 administration reaching levels of about 20% for the 2 mg/kg dose and about 15% for the 1 mg/kg dose at around 6 min post drug administration. A transient decrease in both systolic and diastolic blood pressure was observed for the higher dose. The blood pressure data further suggest an attenuation of the anaesthesia induced increase in pressure usually present in non-intervention studies. ME10092 clearly exhibits mycocardial effects in the non-human primate, similar to the effects previously observed in the ischaemia-reperfusion rat model, where ME10092 showed strong protection.

Our multidisciplinary project on TB control in the Free State, South Africa, is targeting two dimensions for intervention: firstly, patients, to facilitate compliance and improve quality of care; secondly, the health care system, to identify weaknesses that require remedying and best practices to promote better TB control. This communication illustrates how social scientists can contribute towards the implementation of interventions related to their research, thus influencing TB policy, programme planning and practice more directly.

Germ-line mutations within BRCA1 are responsible for different proportions of inherited susceptibility to breast/ovarian cancer, and the spectrum of mutations within this gene is often unique to certain populations. At this time, there have been no reports regarding the role of BRCA1 in South African breast and/or ovarian cancer families. We therefore screened 90 South African breast/ovarian cancer families for BRCA1 mutations by means of PCR-based mutation detection assays. Eighteen families (20%) were identified with BRCA1 disease-causing mutations. Four Ashkenazi Jewish families were identified with the 185delAG mutation, whereas 2 Afrikaner and 1 Ashkenazi Jewish family were found to harbor the 5382insC mutation. Five of the families (5.56%), all of whom are Afrikaners, were found to carry the novel E881X mutation. Genotype analyses show that these patients share a common ancestor. Genealogic studies have identified 3 possible founding couples for this mutation, all of whom arrived in the Cape from France in the late 1600s. Of the remaining mutations detected, 3 have not been reported previously and include the S451X, 1493delC (detected twice) and 4957insC mutations., (Copyright 2004 Wiley-Liss, Inc.)

Background: To investigate the role of the CYP17 gene promoter polymorphism in the pathobiology of uterine leiomyomas in African and Caucasian women., Methods: During a 6-month period, 145 Caucasian and black South African women undergoing hysterectomy were included prospectively. Blood samples were obtained for DNA analysis. Factors modifying the risk for uterine leiomyoma growth such as age, parity, age at last birth, weight, body mass index, menopausal status, cigarette smoking and oral contraceptive use were determined., Results: The risk for leiomyoma development among black South African homozygous carriers of the CYP17 A2 allele was shown to be significantly increased when compared to women homozygous for the CYP17 A1 allele or to heterozygous women. Logistic regression analysis disclosed age, parity and CYP17 polymorphism to have an impact on the presence of uterine leiomyomas (p-values are, respectively, 0.0006, 0.0001 and 0.03) in black South African women. However, among Caucasian women, logistic regression analysis showed only intake of oral contraceptives to influence the formation of uterine leiomyomas (p = 0.03)., Conclusion: This exploratory trial suggests that among African women, homozygous carriers of the CYP17 A2 allele expose their myometrium to a stronger estrogenic stimulation contributing to the pathobiology of uterine leiomyomas.

Understanding the origin, distribution, and evolving dominance of HIV-1 subtype C strains is an important component in the design and evaluation of a globally effective AIDS vaccine. To better understand subtype C viruses, we constructed complete molecular clones of primary, CCR-5-using isolates from South Africa and analyzed the molecular phylogenies of these clones using best fitting evolutionary substitution models. Analyses were performed on three full-length sequences, and on the individual genes. All clones were nonrecombinant, and although two of three had open reading frames and intact splice sites, they were not infectious. At the genomic level, the models demonstrated the increasing variability of subtype C in South Africa. At the subgenomic level, they revealed marked differences in the evolutionary patterns of individual genes, a finding that suggests that the genes are under different selective pressures and constraints. These data underscore the dynamic nature of the subtype C epidemic and emphasize the need for continuous monitoring of local strains.

Objectives: To evaluate the willingness of medical doctors working at a tertiary hospital to participate in HIV vaccine trials, their perceptions of patients' willingness to participate, and the major reasons underlying these views., Design: A self-administered, anonymous postal survey conducted in two rounds between May and July 2001., Setting: A tertiary care hospital in the Western Cape., Subjects: All medical doctors listed on the hospital's staff directory., Outcome Measures: Willingness to participate in, and to recruit patients into, HIV vaccine trials, and the reasons for this., Results and Conclusions: Of the 289 individuals surveyed, 80% stated either that they would not be willing to participate in HIV vaccine trials or that they were unsure about their participation. Meanwhile, 37% stated that they would be willing to recruit patients into vaccine trials. The most common concerns with trial participation were the possibility of vaccine-induced infection and the possibility of testing positive for antibodies to HIV. The surprisingly low level of willingness to participate in trials in this sample of medical professionals highlights the importance of preparatory work to overcome substantial barriers to HIV vaccine trial participation.

The objective of the study was to assess the genotypic and phenotypic properties of 18 viral strains from human immunodeficiency virus-1 (HIV-1) positive patients and to identify subtype C isolates for vaccine design strategies. All the isolates were non-syncytium-inducing (NSI) in both the primary and MT-2 cell cultures. The amino acid charge of the V3 loop correlated with the NSI phenotype of the strains. The V3 competitive peptide enzyme immunoassay and DNA sequencing of the partial gp120 region gave concordant results on the 15 subtype C strains, whereas the three B genotypes gave a positive to B, a nonreactive to B, and a dual reaction to the B-D peptides, respectively. Sixteen of the isolates used only CCR5 as coreceptor whereas two isolates made use of additional coreceptors including CXCR4. In summary, all our subtype C isolates are NSI phenotypically and almost all of them use CCR5 exclusively as their coreceptor., (Copyright 2002 Wiley-Liss, Inc.)

Human herpesvirus 8 (HHV-8) has been identified as the causative agent for all forms of Kaposi's sarcoma and is also associated with the development of body cavity-based B-cell lymphomas and multicentric Castleman's disease. HHV-8 genomes are now classified into five major subtypes (A-E) that reflect sequence heterogeneity in the highly variable open reading frame (ORF) K1. To identify HHV-8 subtypes associated with different forms of Kaposi's sarcoma, we compared the ORF 26 and ORF-K1 gene sequences from South African patients with the prototype strains of the major subtypes, as well as published sequences from other African strains. DNA prepared from Kaposi's sarcoma biopsies and/or peripheral blood lymphocytes were available from 14 patients with postrenal transplant (iatrogenic) Kaposi's sarcoma, six patients with the African endemic form, and one patient with AIDS-related body cavity-based B-cell lymphoma. We identified a B2 subtype in six patients, four of whom also had a novel B5 type ORF 26 polymorphism. Two patients had B2 type patterns for both the ORF 26 and ORF-K1 genes. The ORF-K1 subtype A5 was identified in samples from three patients with a B3/C2 type polymorphism in the ORF 26 gene. A novel ORF-K1 B variant strain was identified in a patient with African endemic Kaposi's sarcoma, who also had a B3/C2 class ORF 26 pattern. In 58.3% of iatrogenic Kaposi's sarcoma patients, a B5-type ORF 26 gene sequence pattern was identified. No association was found among particular subtypes, geographical origin of patients, or clinical presentation., (Copyright 2002 Wiley-Liss, Inc.)

South Africa has one of the fastest growing HIV-1 epidemics, with an estimated 4.7 million people infected. To better understand the genetic diversity of this epidemic and its potential impact on vaccine development, we have cloned and sequenced the complete gag and env genes of 13 primary virus isolates. Phylogenetic analysis of our sequences and 69 complete env genes from the Los Alamos and GenBank databases revealed multiple subclusters within subtype C. The V3 loop region was relatively conserved in all our strains when compared with other subtypes, but the region immediately downstream was highly variable. No intersubtype recombinant forms were observed when comparing the gag and env sequences. Characterization of the complete gag and env genes enabled us to select specific strains for further vaccine development.

To acquire new knowledge about the genetic diversity and potential impact on vaccine strategies of HIV-1 subtype C in South Africa, we have characterized the vif, vpr, and vpu genes of 15 isolates. Phylogenetic analysis of the genomic fragment encompassing these genes revealed subtype C subclusters, suggesting close relatedness with subtype C strains from other geographic locations and excluded isolation of South African strains. The putative T155 phosphorylation site in the C terminal of Vif was absent in all subtype C sequences. Variation in the predicted amino acid sequences of the three genes further showed strong correlation with other subtype C sequences.

A well recognized hazard of transfusion with blood or blood products is the acquisition of a viral infection. Parvovirus B19 and transfusion transmitted virus (TTV) are two of several non-enveloped viruses that may on rare occasions be present in coagulation factor concentrates. The prevalence of these viruses in the South African Haemophilia population has not previously been studied. Thirty-nine Haemophiliac children were investigated for evidence of parvovirus and TTV infection. 26 boys with Haemophilia A had been treated with cryoprecipitate or intermediate purity factor VIII, and 13 boys with Haemophilia B had received prothrombin complex concentrates. All the plasma products were prepared from South African donors and were virally inactivated by heat or solvent/detergent since 1992. A control group of 32 children who had not been transfused were also studied. IgG antibodies to B19 were present in 29 of the 39 patients (74%), 18/26 (69%) with Haemophilia A and 12 of the 13 (85%) with Haemophilia B. None of the patients was IgM antibody positive but two children were PCR positive for B19 DNA. Of the control children, 47% had IgG antibodies to B19, but none were IgM antibody or B19 DNA positive. TTV viral DNA was found in 10.2% of patients and in 9% of the control group. The results indicate that our locally produced plasma products are not a significant source of TTV transmitted infection but may contribute to infection by B19 parvovirus.

A new xylanase producing yeast species was isolated from South African soil. A description of the new species, Candida mokoenaii is given.

More than 20.8 million people are living with HIV/AIDS in sub-Saharan Africa, with southern Africa the worst affected area and accounting for one of the fastest growing AIDS epidemics worldwide. Samples from 81 patients, including 25 from KwaZulu-Natal, 26 from Gauteng, 5 from Mpumalanga, and 25 from Western Cape Province, were serotyped using a competitive V3 peptide enzyme immunoassay (cPEIA). Viral RNA was also isolated from serum and the V3 region amplified by reverse transcriptase polymerase chain reaction (RT-PCR) to obtain a 240-bp product for direct sequencing of 29 samples. CLUSTAL W was used to make multiple sequence alignments. Distance calculation, tree construction methods, and bootstrap analysis were done using TREECON. Subtype C-like V3 loop sequences predominate in all provinces tested in South Africa. Discordant sero- and genotype results were observed in one patient only. The correlation between sero- and genotyping was 96% (24 of 25) in KwaZulu-Natal and 100% in Gauteng and Mpumalanga. In Western Cape Province 18% of patients were identified as sero/genotype B and 82% as sero/genotype C. Our data show that results of the second-generation V3 cPEIA correlated well with V3 sequencing and would be a rapid and affordable screening test to monitor the explosive southern African HIV-1 epidemic.

Simian immunodeficiency viruses (SIVs) have been shown to infect many Old World African primate species. Thus far, no work has been published on southern African primates. In this study we investigated the genetic diversity between SIV strains from Kenyan and South African vervets (Cercopithecus aethiops pygerythrus). We amplified and sequenced a 1113 bp region of the env gene. Phylogenetic analysis of these sequences showed that all strains clustered with members of the vervet subgroup of SIVagm. The SIVs from South African vervets differed by 7% from each other and by 8-14% from the Kenyan SIV strains, while the Kenyan SIV strains differed by 10-21% from SIVagm of other east African vervets. We also isolated and sequenced, for the first time, a SIV strain from a healthy chacma baboon (Papio ursinus), caught in South Africa. Phylogenetic analysis of the env region showed the virus to be closely related to the South African vervet SIV strains, while analysis of its pol region confirmed the virus to be a SIVagm variant.

Study Objective: To assess clinically South African patients with the putative diagnosis of Prader-Willi syndrome (PWS) and confirm this diagnosis by DNA/molecular analysis., Design: Prospective, nationally based, combined clinical and laboratory study., Main Results: Thirty-seven patients with a putative diagnosis of PWS were examined by clinical geneticists. Only 13 (35.1%) of these patients had the diagnosis of PWS confirmed by molecular analysis, and all 13 PWS patients had positive scores using the PWS consensus diagnostic criteria of Holm et al. The clinical features of the remaining 24 (64.9%) non-PWS patients were analysed and 23 did not have the neonatal, infantile and childhood features necessary to warrant consideration of a diagnosis of PWS; neither did they obtain a positive score according to Holm et al.'s criteria., Conclusion: PWS was confirmed in only 35% of South African patients with a putative PWS diagnosis, confirming that this condition is overdiagnosed and that the clinical diagnosis is difficult. Clinically, the diagnostic criteria of Holm et al. are of great assistance in making the diagnosis, but it remains essential to confirm the diagnosis by molecular analysis.

Mutations in the p53 gene have been reported in head and neck carcinomas. We determined the p53 mutation profile in 55 oral squamous cell carcinomas (OSCCs) from a black African population sample. DNA from all the patients were investigated using PCR amplification of the p53 gene (exons 5-9), followed by heteroduplex single-stranded conformational polymorphism (HEX-SSCP) analysis on the PCR products. Direct sequencing was performed on cases where mutations were identified. The results showed mutations in 13 of 55 (23.6%) tumours. Eleven of 13 (85%) were single base pair substitutions (9 transitions and 2 transversions), and 2 were deletions. Two novel mutations were identified: a large 63-base pair deletion, and a single base pair substitution. The mutations in our study occurred outside the head and neck tumour hot spot region (codons 238-248).

The aetiology and detection of human herpes virus type 8 (HHV-8) DNA sequences in Kaposi's sarcoma (KS) is a matter of intense investigation. We report on the detection of HHV-8 DNA and sequence polymorphism in different clinicopathological subtypes of cutaneous KS samples from South Africa. The diagnosis was confirmed by histological examination in all cases. Six patients had classic KS (CKS), 3 epidemic KS (EKS), and 3 iatrogenic KS (IKS). A nested polymerase chain reaction (PCR) assay was used to detect HHV-8 DNA in cell lysates, prepared from formalin fixed, paraffin embedded sections. We investigated polymorphism in the HHV-8 DNA using single-stranded conformational polymorphism (SSCP) analysis on the PCR products, followed by direct sequencing. HHV-8 DNA was detected in all the patients with KS, irrespective of the clinicopathological subtype. Direct sequencing was performed on 5 selected cases and showed single base pair substitutions in all. The spectrum of mutations was similar to those described previously. No correlation was found between the different types of KS and sequence variation. The results support the hypothesis that HHV-8 is strongly associated with different clinicopathological subtypes of KS and confirm the occurrence of HHV-8 in patients with CKS, EKS, and IKS in South Africa.

We report on the subtyping of South African primate T-cell lymphotropic virus type I (PTLV-I) strains by investigating the LTR region using sequence analysis and restriction fragment length polymorphism (RFLP) techniques. DNA from either uncultured peripheral blood mononuclear cells (PBMCs); cultured PBMC or cell lines of eight human T-cell lymphotropic virus type I (HTLV-I); and two simian T-cell lymphotropic virus type I (STLV-I) strains (Cercopithecus aethiops pygerythrus) were amplified by polymerase chain reaction (PCR), cloned, and sequenced. The samples originated from different geographical regions in South Africa. Phylogenetic relationships were estimated using the neighbor-joining method. The South African HTLV-I strains were of Cosmopolitan origin and similar to each other. RFLP analysis confirmed this subtyping. A divergence of 0.3 to 1.6% between the Cosmopolitan strains was observed, while the divergence between the HTLV-I and STLV-I strains ranged from 6.3 to 7%. The STLV-I strains were closely related to that of a chimpanzee, providing evidence of interspecies transmission.

Background: The incidence of oral squamous cell carcinoma (OSCC) is on the increase in developing countries., Materials and Methods: Formalin fixed paraffin embedded blocks of OSCCs from a Black South African population sample of peri-urban and rural origin were selected as follows: Group 1 - 57 OSCCs with a mean age of 59 years; Group 2 - 43 OSCCs all cases younger than 40 years; Group 3 - 46 OSCCs with blocks containing only tumour tissue without any normal epithelium and Group 4, a control group of 38 non-neoplastic epithelial lesions. Type specific primers were used in a standard PCR to amplify a segment of the E6 region of HPV 6, 11, 16 and 18., Results: HPV 11 and 16 DNA were found in one sample each from groups 1 and 2 respectively., Conclusion: HPV is not an etiologic factor in the development of OSCC in the population studied.

The purpose of the study was to develop a specific and sensitive PCR protocol using env, gag and LTR primer pairs to detect HIV-1 subtypes present in the Western Cape, South Africa. Twenty-two virus strains, belonging to HIV-1 subtypes B, C and D, were randomly selected for PCR evaluation. Cell lysates prepared from these virus-infected cultured cells were tested using 5 different primer pairs: gag SK38/SK39; gag 22/SK39; gag a/b, gag c/d (nested); env SK68/SK69 and LTR SK29/SK30. Eight different PCR profiles were evaluated: one profile each for the 3 gag primer pairs, 3 profiles for the env and 2 profiles for the LTR primer pairs. The number of PCR cycles, time per cycle and/or annealing temperature were changed in each profile. The optimum PCR profile for a specific primer pair was defined as that which detected one copy of proviral plasmid DNA after dot-blot hybridisation. Gag primer pairs detected HIV-1 DNA in all 22 samples. With the env primer pair, suboptimal conditions failed to detect most of the HIV-1 subtype C samples. By increasing the number of cycles and time per cycle, a 100% sensitivity was achieved. With the LTR primer pair all samples were detected by decreasing the annealing temperature and increasing the individual cycle times. This confirms that once PCR conditions are optimised, all HIV-1 subtypes in our study could be detected using different PCR primer pairs.

Certain health risks have been associated with recreational exposure to faecally polluted water. Canoeing in certain South African waters is considered to be a high risk activity with regard to schistosomiasis, gastroenteritis and possibly hepatitis. In a cross-sectional study, a serosurvey was conducted amongst canoeists to ascertain whether or not they had a higher seroprevalence to hepatitis A virus, Norwalk virus and Schistosoma spp. than non-canoeists. In comparisons between the two groups, a significant association could not be demonstrated between canoeing and antibody response to hepatitis A and Norwalk viruses (P-values for age-adjusted chi 2 were 0.083 and 0.219 respectively), but a significant association could be demonstrated between canoeing and the antibody response to Schistosoma spp. (P < 0.001; age-adjusted).

Intra-oral carcinoma is the third most common malignancy among men in developing countries, and carries a high mortality rate, particularly in Africa, where patients often present initially with lesions at an advanced stage. The present study was undertaken to determine the prevalence of human papillomavirus (HPV) DNA in oral squamous carcinoma in the west of the Northern Transvaal, an area where a large number of new cases has been diagnosed over the past few years. Paraffin blocks from 66 cases (51 men, 15 women; mean age 58.7 years) of oral squamous carcinoma were randomly selected. Blocks contained samples of both tumour and adjacent normal epithelium. The presence of HPV antigen was established by means of immunocytochemistry and HPV DNA by in situ hybridisation with radiolabelled probes for HPV-6, 11, 16 and 18. Immunocytochemistry for viral antigen was negative in all the specimens. HPV-18 was detected in normal epithelium adjacent to the tumour in one case only. It appears from our study that HPV is of limited importance in oral squamous cell carcinogenesis in the population studied.

Between 1984 and 1990, virus was routinely isolated and serum collected from patients diagnosed at hospitals in the Western Cape as suffering from AIDS or AIDS-related conditions (ARC). From these, 17 virus strains were selected at random for sequencing and molecular characterisation of the env gene. The strains were previously characterised as belonging to HIV-1 subtypes B, C and D. The purpose of the present study was to evaluate retrospectively the serological diagnosis of HIV-1 in these 17 South African patients. Thirteen anti-HIV screening assays, including 7 rapid/simple test devices (RTDs), 4 enzyme-linked immunosorbent assays (EIAs) and 2 Western immunoblot assays were evaluated. Using commercial EIAs, 16 serum samples were HIV antibody-positive and these results were confirmed by Western immunoblot analysis. Serum from one terminal AIDS patient was found negative with all the serological tests. Some RTDs gave false negative antibody reactions on specimens from patients infected with subtype D strains. To investigate the false negative antibody reactions, the polymerase chain reaction (PCR) was used to amplify, clone and sequence proviral DNA from the immunodominant gp41 region from 7 of the HIV-1 strains. Two patients, both subtype D strains (D214 and D482) with false negative results in the RTDs, showed a significant amino acid substitution, i.e., substitution of a histidine residue for leucine at env position 607. It was concluded that although there were false negative RTD reactions on patients with HIV-1 subtype D strains, the commercial EIAs tested are sensitive and are able to detect patients infected with HIV-1 subtypes B, C and D that are present in South Africa.