Prevalence, incidence and recurrence of sexually transmitted infections in HIV-negative adult women in a rural South African setting.

OBJECTIVE: Sexually transmitted infections (STIs), including syphilis, chlamydia, gonorrhoea and trichomoniasis, are of global public health concern. While STI incidence rates in sub-Saharan Africa are high, longitudinal data on incidence and recurrence of STIs are scarce, particularly in rural areas. We determined the incidence rates of curable STIs in HIV-negative women during 96 weeks in a rural South African setting. METHODS: We prospectively followed participants enrolled in a randomised controlled trial to evaluate the safety and efficacy of a dapivirine-containing vaginal ring for HIV prevention in Limpopo province, South Africa. Participants were included if they were female, aged 18-45, sexually active, not pregnant and HIV-negative. Twelve-weekly laboratory STI testing was performed during 96 weeks of follow-up. Treatment was provided based on vaginal discharge by physical examination or after a laboratory-confirmed STI. RESULTS: A total of 119 women were included in the study. Prevalence of one or more STIs at baseline was 35.3%. Over 182 person-years at risk (PYAR), a total of 149 incident STIs were diagnosed in 75 (65.2%) women with incidence rates of 45.6 events/PYAR for chlamydia, 27.4 events/100 PYAR for gonorrhoea and 8.2 events/100 PYAR for trichomoniasis. Forty-four women developed ≥2 incident STIs. Risk factors for incident STI were in a relationship ≤3 years (adjusted hazard ratio [aHR]: 1.86; 95% confidece interval [CI]: 1.04-2.65) and having an STI at baseline (aHR: 1.66; 95% CI: 1.17-2.96). Sensitivity and specificity of vaginal discharge for laboratory-confirmed STI were 23.6% and 87.7%, respectively. CONCLUSION: This study demonstrates high STI incidence in HIV-negative women in rural South Africa. Sensitivity of vaginal discharge was poor and STI recurrence rates were high, highlighting the shortcomings of syndromic management in the face of asymptomatic STIs in this setting.

Evaluation of the Seegene AllplexTM RV Master Assay for One-Step Simultaneous Detection of Eight Respiratory Viruses in Nasopharyngeal Specimens.

BACKGROUND: The Seegene AllplexTM RV Master (RVM) assay is a one-step multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) system for detecting eight viral respiratory pathogens from nasopharyngeal swab, aspirate, and bronchoalveolar lavage specimens. The eight RVM targets are: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Influenza A (Flu A), Influenza B (Flu B), Human respiratory syncytial virus (RSV), adenovirus (AdV), rhinovirus (HRV), parainfluenza virus (PIV), and metapneumovirus (MPV). The assay is based on Seegene's multiple detection temperature (MuDT) technology and provides cycle threshold (Ct) values for each of its viral targets upon PCR completion. OBJECTIVE: We aimed to evaluate the diagnostic performance of the RVM assay by calculating sensitivity, specificity, accuracy, Positive Predictive Value (PPV), Negative Predictive Value (NPV), Positive Percent Agreement (PPA), Negative Percent Agreement (NPA), and Overall Percent Agreement (OPA) compared to definite diagnosis and analogous reference assays. STUDY DESIGN: Diagnostic sensitivity, specificity, accuracy, PPV, and NPV were calculated by comparing the results of the RVM assay to that of definite diagnosis assays; while PPA, NPA, and OPA were calculated by comparing results of the RVM assay to that of analogous reference products. Definite diagnosis and reference methods comprised whole genome sequencing and PCR genotyping, the AllplexTM SARS-CoV-2/FluA/FluB/RSV and Respiratory Panels 1, 2, and 3 assays (Seegene), and the Xpert® Xpress SARS-CoV-2/FluA/FluB/RSV Plus assay (Cepheid). Reproducibility of the RVM assay using fully-automated and semi-automated nucleic acid (NA) extraction workflows and as performed by independent operators was also assessed. In total, 249 positive respiratory specimens and at least 50 negative specimens for each target tested were used for this evaluation study. RESULTS: Sensitivity, specificity, accuracy, PPV, NPV, PPA, NPA, and OPA ranged from 95.7% to 100% for detecting all eight targets tested on the RVM assay. Reproducibility PPA, NPA, and OPA between automated and semi-automated NA extraction workflows were all >97.9%, while the reproducibility PPA, NPA and OPA between independent operators were all 100%. CONCLUSION: These results demon6strate a high level of sensitivity, specificity, accuracy and diagnostic predictive value of the RVM assay and high agreement with comparable reference assays in identifying all eight of its targets. Taken together, our study underscores the diagnostic utility of the RVM assay in detecting eight viral respiratory pathogens.

Evaluation of a commercial SARS-CoV-2 multiplex PCR genotyping assay for variant identification in resource-scarce settings.

The rapid emergence and spread of numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants across the globe underscores the crucial need for continuous SARS-CoV-2 surveillance to ensure that potentially more pathogenic variants are detected early and contained. Whole genome sequencing (WGS) is currently the gold standard for COVID-19 surveillance; however, it remains cost-prohibitive and requires specialized technical skills. To increase surveillance capacity, especially in resource-scarce settings, supplementary methods that are cost- and time-effective are needed. Real-time multiplex PCR genotyping assays offer an economical and fast solution for screening circulating and emerging variants while simultaneously complementing existing WGS approaches. In this study we evaluated the AllplexTM SARS-CoV-2 Variants II multiplex real-time PCR genotyping assay, Seegene (South Korea), and implemented it in retrospectively characterizing circulating SARS-CoV-2 variants in a rural South African setting between April and October 2021, prior to the emergence of the Omicron variant in South Africa. The AllplexTM SARS-CoV-2 Variants II real-time PCR assay demonstrated perfect concordance with whole-genome sequencing in detecting Beta and Delta variants and exhibited high specificity, sensitivity and reproducibility. Implementation of the assay in characterization of SARS-CoV-2 variants between April and October 2021 in a rural South African setting revealed a rapid shift from the Beta to the Delta variant between April and June. All specimens successfully genotyped in April were Beta variants and the Delta variant was not detected until May. By June, 78% of samples genotyped were Delta variants and in July >95% of all genotyped samples were Delta variants. The Delta variant continued to predominate through to the end of our analysis in October 2021. Taken together, a commercial SARS-CoV-2 variant genotyping assay detected the rapid rate at which the Delta variant displaced the Beta variant in Limpopo, an under-monitored province in South Africa. Such assays provide a quick and cost-effective method of monitoring circulating variants and should be used to complement genomic sequencing for COVID-19 surveillance especially in resource-scarce settings.