Prevalence of drug-resistant mutations in newly diagnosed drug-naïve HIV-1-infected individuals in a treatment site in the Waterberg District, Limpopo province

Aim. We studied the prevalence of resistance mutations in drug-naïve HIV-infected individuals at the Bela-Bela treatment site to gather information on the presence of antiretroviral (ARV) drug-resistant viruses in drug-naïve populations, so as to improve treatment guidance. Subjects and methods. Drug-naive HIV-1-infected individuals were sequentially recruited between February 2008 and December 2008 from individuals visiting the voluntary counseling and testing (VCT) services of the Bela-Bela HIV/AIDS Wellness Clinic. Viral subtyping was done by phylogenetic analysis; drug-resistant mutations were determined according to the Stanford HIV Drug Resistance Interpretation and the International AIDS society-USA guidelines. Results. A drug-resistant mutation prevalence of 3.5% (95% confidence interval 0.019796 - 0.119077) comprising Y181C and L33F was observed; 98% of the viruses were HIV-1 subtype C on the protease (PR) and reverse transcriptase (RT) gene regions. Conclusion. The prevalence of drug-resistant mutations in drug-naïve persons may be low in Bela-Bela after 8 years of access to antiretroviral treatment (ART), and resistance testing before initiating treatment may not be needed

Prevalence of Antiretroviral Drug Resistance Mutations and HIV-1 Subtypes among Newly-diagnosed Drugna\uefve Persons Visiting a Voluntary Testing and Counselling Centre in Northeastern South Africa

Data on antiretroviral drug resistance among drug-na\uefve persons are important in developing sentinel surveillance policies. This study was conducted to determine the prevalence of antiretroviral drug resistance mutations among drug-na\uefve HIV-infected individuals attending a voluntary testing and counselling centre at the Mankweng Hospital in northeastern South Africa. In total, 79 drug-na\uefve HIV-positive individuals were sequentially recruited during February 2008-December 2008. Drug resistance mutations were determined using the calibrated population resistance tool available on the Stanford HIV drug resistance database. Viral DNA was obtained from 57 (72%) of the 79 individuals. Reliable nucleotide sequences were obtained for 54 reverse transcriptase (RT) and 54 protease (PR) gene regions from 54 individuals. Overall, five sequences (9.3%) harboured drug resistance mutations (95% confidence interval -1.53 to 16.99). Four (7.4%) of these were nucleoside RT inhibitor mutations (D67G, D67E, T69D, and T215Y), and one (1.9%) was a PR inhibitor mutation (M46I). No major non-nucleoside RT resistance mutation was detected. Several minor resistance mutations and polymorphisms common in subtype C viruses were observed in the PR and RT genes. Phylogenetic analysis of the partial pol sequences showed that 52 (96%) of the 54 isolates were HIV-1 subtype C. One isolate (08MB08ZA) was HIV-1 subtype B while another (08MB26ZA) was related to HIV-1 subtype J. HIV-1 subtype recombination analysis with REGA assigned the pol sequence to HIV subtype J (11_cpx) with a bootstrap value of 75%. The prevalence of drug resistance mutations observed in the population studied was relatively higher than previously reported from other parts of South Africa. In addition, this is apparently the first report of an HIV-1 subtype J-like virus from northeastern South Africa

Low seroprevalence of hepatitis E virus in pregnant women in an urban area near Pretoria, South Africa

OBJECTIVES : Hepatitis E virus (HEV) infection is a globally neglected health problem with a high burden in resource-poor communities. Pregnant women are at increased risk of complications. This pilot study sought to assess the seroprevalence of HEV infection in pregnant women at Dr George Mukhari Academic Hospital, South Africa. METHODS : Stored serum samples from 384 HIV-uninfected pregnant women attending the antenatal clinic were initially screened for HEV total antibody. Positive samples were further evaluated for the presence of IgG and IgM antibody isotypes, using commercial ELISA assays. HEV RNA was assessed in antibody-positive samples utilizing qRT-PCR assay. RESULTS : The sample consisted of women with a median age of 31 years (interquartile range: 28–35 years). Total HEV antibody was detected in 12/384 (3.13%, 95% CI: 1.80–5.38) of these pregnant women. All 12 samples were IgG HEV antibody positive, but none tested positive for IgM antibody or for HEV RNA, demonstrating a lack of current or recent exposure. CONCLUSIONS : Our study revealed a low seroprevalence of HEV among pregnant women from an urban area north of Pretoria. This observation warrants further attention to the circulation of HEV in this population, and a greater understanding of the epidemiology of the infection in South Africa.The South African Ministry of Higher Education, Science and Innovation, and the National Research Foundation.http://www.elsevier.com/locate/ijregihj2023Medical Virolog

Impact of lamivudine-based antiretroviral treatment on hepatitis B viremia in HIV-coinfected South Africans

This prospective study investigated the impact of lamivudine-containing antiretroviral therapy (ART) on HIV-positive patients in South Africa with baseline hepatitis B virus (HBV) infection. Follow-up samples from 56 HBV/HIV co-infected patients, 25 with occult HBV infection (OBI) and 31 with chronic HBV infection (CHB), were available for analysis. HBV viral loads were quantified at 6, 12, 18, and 24 months post-ART initiation by the COBAS TaqMan HBV Test 48 assay, and the HBV polymerase gene was amplified with an in-house nested polymerase chain reaction assay. During 24 months of lamivudine-based ART, 6 of 8 (75%) OBI and 4 of 6 (67%) CHB patients achieved undetectable levels of HBV DNA, while 2 patients had persistent HBV DNA levels 2 105 despite lamivudine-based ART for 24 months. HIV viremia was undetectable in all patients at 12 months, suggesting high adherence to ART. Several lamivudine-associated HBV resistance mutations, including L180M, A181T, M204I, and M204V, were observed. Sequence analysis also revealed a rare genotype G infection. While resource-limited settings may use lamivudine-based ART because of availability and low cost, antivirals with dual therapy against HBV and HIV (e.g., lamivudine and tenofovir) should always be recommended with the regular monitoring of HBV viremia levels.The South African National Research Foundation, Poliomyelitis Research Foundation, Stella and Paul Lowenstein Trust, and Canon and Collins scholarship.http://www.mdpi.com/journal/virusesam2021Medical Virolog

High prevalence of and factors associated with human papillomavirus infection among women attending a tertiary hospital in Gauteng Province, South Africa

BACKGROUND: Persistent high-risk (hr) human papillomavirus (HPV) infection is a necessary cause of cervical cancer. Cervical cancer is a major public health problem in Sub-Saharan Africa including South Africa. This study investigated the prevalence of and factors associated with hr-HPV infection among women attending a tertiary hospital in Gauteng Province, South Africa. METHODS: Cervical samples were collected from 526 participants aged ≥ 18 years using a Cervex Brush® Combi and tested for hr-HPV types on the Abbott m2000 analyzer using the Abbott RealTime HR HPV assay. Samples that tested hr-HPV deoxyribonucleic acid (DNA)-positive were further tested for hr-HPV E6/E7 messenger ribonucleic acid (mRNA) using the APTIMA® HPV assay on the Panther system (Hologic, Inc.). Sociodemographic data were collected using a self-administered questionnaire. Binomial regression analysis was used to assess factors associated with hr-HPV infection. RESULTS: Overall hr-HPV DNA prevalence was 48.1% (95%CI: 43.8–52.4%). Of the hr-HPV DNA-positives, 24.5% (95%CI: 19.3–30.1) had HPV-16; 12.3% (95%CI: 8.5–16.9) had HPV-18 and 87.4% (95%CI: 82.6–91.2) had other 12 h-HPVs. Of the samples positive for hr-HPV DNA, 84.2% (95%CI: 79.1–88.5) (213/253) were positive for hr-HPV E6/E7 mRNA. Advanced age was an important factor linked to hr-HPV E6/E7 mRNA positivity. Based on multivariate binomial regression analysis, unemployment (PR: 1.50; 95%CI: 1.23–1.83) and being married (PR: 0.61; 95%CI: 0.47–0.81) were identified as statistically significant (p < 0.0001) predictive and protective factors, respectively, for hr-HPV infection. CONCLUSIONS: The prevalence of hr-HPV infection was high. Furthermore, hr-HPV DNA-positive samples had a high hr-HPV E6/E7 mRNA prevalence. The presence of hr-HPV E6/E7mRNA indicates active infection and thus a greater risk of developing the cervical disease. Therefore, HPV mRNA testing could be a better test to monitor women who are positive with Pap smear before colposcopy is performed to reduce the burden of referrals. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12885-022-09964-9

Prevalence of Antiretroviral Drug Resistance Mutations and HIV-1 Subtypes among Newly-diagnosed Drugnaïve Persons Visiting a Voluntary Testing and Counselling Centre in Northeastern South Africa

Data on antiretroviral drug resistance among drug-naïve persons are important in developing sentinel surveillance policies. This study was conducted to determine the prevalence of antiretroviral drug resistance mutations among drug-naïve HIV-infected individuals attending a voluntary testing and counselling centre at the Mankweng Hospital in northeastern South Africa. In total, 79 drug-naïve HIV-positive individuals were sequentially recruited during February 2008-December 2008. Drug resistance mutations were determined using the calibrated population resistance tool available on the Stanford HIV drug resistance database. Viral DNA was obtained from 57 (72%) of the 79 individuals. Reliable nucleotide sequences were obtained for 54 reverse transcriptase (RT) and 54 protease (PR) gene regions from 54 individuals. Overall, five sequences (9.3%) harboured drug resistance mutations (95% confidence interval -1.53 to 16.99). Four (7.4%) of these were nucleoside RT inhibitor mutations (D67G, D67E, T69D, and T215Y), and one (1.9%) was a PR inhibitor mutation (M46I). No major non-nucleoside RT resistance mutation was detected. Several minor resistance mutations and polymorphisms common in subtype C viruses were observed in the PR and RT genes. Phylogenetic analysis of the partial pol sequences showed that 52 (96%) of the 54 isolates were HIV-1 subtype C. One isolate (08MB08ZA) was HIV-1 subtype B while another (08MB26ZA) was related to HIV-1 subtype J. HIV-1 subtype recombination analysis with REGA assigned the pol sequence to HIV subtype J (11_cpx) with a bootstrap value of 75%. The prevalence of drug resistance mutations observed in the population studied was relatively higher than previously reported from other parts of South Africa. In addition, this is apparently the first report of an HIV-1 subtype J-like virus from northeastern South Africa

High-risk human papillomavirus detection in self-collected vaginal samples compared with healthcare worker collected cervical samples among women attending gynecology clinics at a tertiary hospital in Pretoria, South Africa

Abstract Background In 2017, the South African National Department of Health (NDoH) Cervical Cancer Prevention and Control Policy was revised. Human papillomavirus (HPV) testing on self-collected samples may offer improved screening uptake. The objectives of the study were to compare the positivity of high-risk (hr)-HPV deoxyribonucleic acid (DNA) and hrHPV viral messenger ribonucleic acid (mRNA) between healthcare worker-collected cervical and self-collected vaginal samples and investigate the accuracy of the applicator-tampon-based self-collected samples in detecting hrHPV DNA and hrHPV mRNA. Methods A total of 527 women aged 18 years and older and seeking gynecology services at a tertiary hospital in Pretoria, South Africa, were enrolled. Vaginal samples were self-collected using SelfCerv applicator tampon, followed by cervical samples collected by a healthcare worker using a Cervex Brush® Combi. Both samples were tested with the Abbott m2000 analyzer for 14-hrHPV types and 285 paired samples were tested for hrHPV E6/E7 mRNA using the Aptima HR-HPV mRNA assay. The prevalence of hrHPV DNA and hrHPV E6/E7 mRNA was estimated and the positivity between the two collection methods was compared for the total group as well as per age group. Results HrHPV prevalence was 48.0% (95% CI 43.7–52.4) among healthcare worker collected samples and 47.6% (95% CI 43.3–52.0) among self-collected samples. There was no difference in positivity between healthcare worker collection (48.0%) and applicator-tampon-based self-collection, 47.6% (p-value = 0.90). The proportions of hrHPV were equal between the age groups as shown by the McNemar test (p = 0.9036) results for correlated proportions. The prevalence of hrHPV mRNA was 78.6% (95% CI 73.4–83.2) and 58.6% (95% CI 52.6–64.4) for healthcare worker- and self-collection, respectively. The McNemar test for correlated proportions was highly significant (p < 0.0001), indicating that the hrHPV mRNA proportions are not comparable, although this differed between age groups. Conclusions Applicator-tampon-based self-collection has a comparable hrHPV DNA positivity rate as healthcare worker collection but different positivity rates for hrHPV mRNA. Self-sampling showed high concordance with healthcare worker-collected sampling for hrHPV DNA detection, especially regarding HPV 16/18 detection. HrHPV DNA was equally detected between the total group as well as per age group. Implementation of self-sampling using an applicator tampon as a primary screening tool may be considered

Evaluation of ILEX SelfCerv for detection of high-risk human papillomavirus infection in gynecology clinic attendees at a tertiary hospital in South Africa

Background: The SelfCerv Self-Collection Cervical Health Screening Kit (Ilex Medical Ltd., Johannesburg, South Africa) is an applicator tampon designed for self-collection of vaginal samples for the detection of human papillomavirus (HPV) deoxyribonucleic acid (DNA) and E6/E7 messenger ribonucleic acid (mRNA). The study aimed to evaluate the performance of the SelfCerv applicator tampon for the detection of hr-HPV for cervical cancer screening, and further to investigate women’s experiences and preferences regarding self-sampling. Methods: Vaginal samples were collected from 527 gynecology clinic attendees aged ≥18 years at a tertiary hospital in Gauteng Province, South Africa. Self-samples were collected using the SelfCerv kit, followed by endocervical samples collected by a healthcare professional using Cervex-Brush® Combi. Participants completed a self-administered questionnaire on self-sampling experiences and preferences. Both samples were tested for 14 high-risk (hr) HPV types and E6/E7 mRNA using the Abbott RealTime HR-HPV and Aptima HR-HPV mRNA assays, respectively. Results: The overall agreement for hr-HPV typing between 527 paired samples was good (87.1%; κ =0.74) with high sensitivity (86.2%) and specificity (88.0%). HPV-16 (96.4%; κ = 0.83) had higher agreement rate than HPV-18 (96.8%; κ = 0.72) and the other 12 hr-HPVs (86.5%; κ = 0.72). Two hundred and eighty-five (285) sample pairs tested for E6/E7 mRNA showed fair agreement (70.2%; κ= 0.34). Furthermore, self-sampling was reported as comfortable (90.5%) and painless (86.7%), with 88.4% of women preferring self-collection. Conclusions: Self-collected samples had good agreement with the healthcare professional-collected samples for the detection of hr-HPV DNA and the procedure was highly preferred by women. Self-sampling using SelfCerv can be used as an alternative to healthcare professional sampling in clinic-based routine cervical cancer screening