Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks.

The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.

EuCARE-hospitalised study protocol: a cohort study of patients hospitalised with COVID-19 in the EuCARE project.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), can lead to hospitalisation, particularly in elderly, immunocompromised, and non-vaccinated or partially vaccinated individuals. Although vaccination provides protection, the duration of this protection wanes over time. Additional doses can restore immunity, but the influence of viral variants, specific sequences, and vaccine-induced immune responses on disease severity remains unclear. Moreover, the efficacy of therapeutic interventions during hospitalisation requires further investigation. The study aims to analyse the clinical course of COVID-19 in hospitalised patients, taking into account SARS-CoV-2 variants, viral sequences, and the impact of different vaccines. The primary outcome is all-cause in-hospital mortality, while secondary outcomes include admission to intensive care unit and length of stay, duration of hospitalisation, and the level of respiratory support required. METHODS: This ongoing multicentre study observes hospitalised adult patients with confirmed SARS-CoV-2 infection, utilising a combination of retrospective and prospective data collection. It aims to gather clinical and laboratory variables from around 35,000 patients, with potential for a larger sample size. Data analysis will involve biostatistical and machine-learning techniques. Selected patients will provide biological material. The study started on October 14, 2021 and is scheduled to end on October 13, 2026. DISCUSSION: The analysis of a large sample of retrospective and prospective data about the acute phase of SARS CoV-2 infection in hospitalised patients, viral variants and vaccination in several European and non-European countries will help us to better understand risk factors for disease severity and the interplay between SARS CoV-2 variants, immune responses and vaccine efficacy. The main strengths of this study are the large sample size, the long study duration covering different waves of COVID-19 and the collection of biological samples that allows future research. TRIAL REGISTRATION: The trial has been registered on ClinicalTrials.gov. The unique identifier assigned to this trial is NCT05463380.

Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya.

Genomic surveillance and identification of COVID-19 outbreaks are important in understanding the genetic diversity, phylogeny, and lineages of SARS-CoV-2. Genomic surveillance provides insights into circulating infections, and the robustness and design of vaccines and other infection control approaches. We sequenced 57 SARS-CoV-2 isolates from a Kenyan clinical population, of which 55 passed quality checks using the Ultrafast Sample placement on the Existing tRee (UShER) workflow. Phylo-genome-temporal analyses across two regions in Kenya (Nairobi and Kiambu County) revealed that B.1.1.7 (Alpha; n = 32, 56.1%) and B.1 (n = 9, 15.8%) were the predominant lineages, exhibiting low Ct values (5-31) suggesting high infectivity, and variant mutations across the two regions. Lineages B.1.617.2, B.1.1, A.23.1, A.2.5.1, B.1.596, A, and B.1.405 were also detected across sampling sites within target populations. The lineages and genetic isolates were traced back to China (A), Costa Rica (A.2.5.1), Europe (B.1, B.1.1, A.23.1), the USA (B.1.405, B.1.596), South Africa (B.1.617.2), and the United Kingdom (B.1.1.7), indicating multiple introduction events. This study represents one of the genomic SARS-CoV-2 epidemiology studies in the Nairobi metropolitan area, and describes the importance of continued surveillance for pandemic control.

Comparison of enzyme-linked immunosorbent assay systems using rift valley fever virus nucleocapsid protein and inactivated virus as antigens.

BACKGROUND: Rift Valley Fever (RVF) is a mosquito-borne viral zoonosis. To detect RVF virus (RVFV) infection, indirect immunoglobulin G (IgG) and immunoglobulin M (IgM) enzyme linked immunosorbent assays (ELISAs) which utilize recombinant RVFV nucleocapsid (RVFV-N) protein as assay antigen, have reportedly been used, however, there is still a need to develop more sensitive and specific methods of detection. METHODS: RVFV-N protein was expressed in Escherichia coli (E. coli) and purified by histidine-tag based affinity chromatography. This recombinant RVFV-N (rRVFV-N) protein was then used as antigen to develop an IgG sandwich ELISA and IgM capture ELISAs for human sera. Ninety six serum samples collected from healthy volunteers during the RVF surveillance programme in Kenya in 2013, and 93 serum samples collected from RVF-suspected patients during the 2006-2007 RVF outbreak in Kenya were used respectively, to evaluate the newly established rRVFV-N protein-based IgG sandwich ELISA and IgM capture ELISA systems in comparison with the inactivated virus-based ELISA systems. RESULTS: rRVFV-N protein-based-IgG sandwich ELISA and IgM capture ELISA for human sera were established. Both the new ELISA systems were in 100% concordance with the inactivated virus-based ELISA systems, with a sensitivity and specificity of 100%. CONCLUSIONS: Recombinant RVFV-N is a safe and affordable antigen for RVF diagnosis. Our rRVFV-N-based ELISA systems are safe and reliable tools for diagnosis of RVFV infection in humans and especially useful in large-scale epidemiological investigation and for application in developing countries.

Health worker knowledge of Integrated Disease Surveillance and Response standard case definitions: a cross-sectional survey at rural health facilities in Kenya.

BACKGROUND: The correct knowledge of standard case definition is necessary for frontline health workers to diagnose suspected diseases across Africa. However, surveillance evaluations commonly assume this prerequisite. This study assessed the knowledge of case definitions for health workers and their supervisors for disease surveillance activities in rural Kenya. METHODS: A cross-sectional survey including 131 health workers and their 11 supervisors was undertaken in two counties in Kenya. Descriptive analysis was conducted to classify the correctness of knowledge into four categories for three tracer diseases (dysentery, measles, and dengue). We conducted a univariate and multivariable logistic regression analyses to explore factors influencing knowledge of the case definition for dysentery. RESULTS: Among supervisors, 81.8% knew the correct definition for dysentery, 27.3% for measles, and no correct responses were provided for dengue. Correct knowledge was observed for 50.4% of the health workers for dysentery, only 12.2% for measles, and none for dengue. Of 10 examined factors, the following were significantly associated with health workers' correct knowledge of the case definition for dysentery: health workers' cadre (aOR 2.71; 95% CI 1.20-6.12; p = 0.017), and display of case definition poster (aOR 2.24; 95% CI 1.01-4.98; p = 0.048). Health workers' exposure to the surveillance refresher training, supportive supervision and guidelines were not significantly associated with the knowledge. CONCLUSION: The correct knowledge of standard case definitions was sub-optimal among health workers and their supervisors, which is likely to impact the reliability of routine surveillance reports generated from health facilities.

"It takes more than a fellowship program": reflections on capacity strengthening for health systems research in sub-Saharan Africa.

Sub-Saharan Africa (SSA) experiences an acute dearth of well-trained and skilled researchers. This dearth constrains the region's capacity to identify and address the root causes of its poor social, health, development, and other outcomes. Building sustainable research capacity in SSA requires, among other things, locally led and run initiatives that draw on existing regional capacities as well as mutually beneficial global collaborations. This paper describes a regional research capacity strengthening initiative-the African Doctoral Dissertation Research Fellowship (ADDRF) program. This Africa-based and African-led initiative has emerged as a practical and tested platform for producing and nurturing research leaders, strengthening university-wide systems for quality research training and productivity, and building a critical mass of highly-trained African scholars and researchers. The program deploys different interventions to ensure the success of fellows. These interventions include research methods and scientific writing workshops, research and reentry support grants, post-doctoral research support and placements, as well as grants for networking and scholarly conferences attendance. Across the region, ADDRF graduates are emerging as research leaders, showing signs of becoming the next generation of world-class researchers, and supporting the transformations of their home-institutions. While the contributions of the ADDRF program to research capacity strengthening in the region are significant, the sustainability of the initiative and other research and training fellowship programs on the continent requires significant investments from local sources and, especially, governments and the private sector in Africa. The ADDRF experience demonstrates that research capacity building in Africa is possible through innovative, multifaceted interventions that support graduate students to develop different critical capacities and transferable skills and build, expand, and maintain networks that can sustain them as scholars and researchers.

Effectiveness of a Mobile Short-Message-Service-Based Disease Outbreak Alert System in Kenya.

We conducted a randomized, controlled trial to test the effectiveness of a text-messaging system used for notification of disease outbreaks in Kenya. Health facilities that used the system had more timely notifications than those that did not (19.2% vs. 2.6%), indicating that technology can enhance disease surveillance in resource-limited settings.

Opportunities and challenges on hospital preparedness to handle motorcycle accidents in Busia County, Kenya: an exploratory qualitative study.

Introduction: motorcycles continue to be a popular mode of transport in Kenya. However, the related injuries cause significant morbidity and mortality and remain to be a major and neglected public health issue. This raised the crucial need for hospital preparedness in managing morbidities and in reducing mortalities. This formed the basis of this paper which aims to document the challenges and opportunities in the healthcare system in handling motorcycle accidents in a Kenyan border town in Busia County. Methods: we drew data from an exploratory qualitative study that was carried out in 2021. All six referral hospitals purposively included in the study. The study targeted a total of 25 top level facility managers as key informants on the facility level opportunities and challenges in handling motorcycle accidents. Descriptive data were analyzed using SPSS version 20. Results: the hospitals were not well prepared to handle motorcycle accidents. The major challenges were understaffing in critical care services; inadequate/lack of equipment to handle motorcycle injuries; inadequate/lack of infrastructure i.e. surgical wards, emergency rooms, inadequate space, functional theatre; lack/inadequate supplies; overstretched referral services arising from the hinge burden of motorcycle accidents in the area; inadequate specialized personnel to provide trauma/care services; mishandling of cases at the site of accident; inability of victims to pay related bills; inappropriate identification of victims at the facility; lack/inadequate on-job training. Some opportunities that currently exist include health system interventions which are not limited to employment of more professionals, improvement of infrastructure, provision of equipment and increase of budgetary allocation. Conclusion: the study reveals vast challenges that are faced by hospitals in managing patients. This calls for the government to step in and capitalize on the proposed opportunities by the health managers to be able to manage morbidities and bring down mortalities due to motorcycle accidents.

Correction: Seroprevalence of SARS-CoV-2 antibodies and retrospective mortality in a refugee camp, Dagahaley, Kenya.

[This corrects the article DOI: 10.1371/journal.pone.0260989.].

Factors associated with viral load non-suppression among treatment-experienced pre-teenage children living with HIV in Kenya: a nationwide population-based cohort study, 2015-2021.

Background: Viral load non-suppression (VLNS) in children is a major public health concern because of attendant HIV disease progression and risk of morbidity and mortality. Based on a nationally representative database we present estimates of the prevalence, trends and factors associated with VLNS in Kenyan pre-teenage children between 2015 and 2021. Methods: Kenya National AIDS & STI Control Program's (NASCOP) maintains an early infant diagnosis and viral load (EID/VL) database for all persons living with HIV who are enrolled in the country's primary care clinics for purposes of monitoring progress towards achievement of the 95% viral suppression goals. Participants were eligible if they were children living with HIV (CLHIV), on combination ART (cART) treatment, and ≤12 years old. The modified Mann-Kendall trend test for serially correlated data was used to identify VLNS trends. Generalized estimating equations (GEE) with a logit link was used to assess the effects of covariates on the odds of VLNS (VL ≥1,000 copies/mL) over repeated points in time, allowing for the correlation among the repeated measures. Findings: Between January 2015 and December 2021, 508,743 viral load tests were performed on samples collected from 109,682 pre-teenage children. The prevalence of VLNS decreased from 22.9% (95% CI 22.4-23.3) to 12.5% (95% CI 12.1-12.9), p < 0.0001, and mean age increased from 3.1 (4.2) to 8.0 (3.2) years in 2015 and 2021 respectively. A modified Mann-Kendall trend test for serially correlated data denotes a statistically significant decreasing trend (τ = -0.300, p < 0.0001) over the study period. In the multivariable GEE analysis adjusted for covariates, the odds of VLNS decreased by 11% per year during the study period, (GEE-aOR 0.89, 95% CI 0.88-0.90; p < 0.0001). Factors positively associated with VLNS were EFV/NVP-based first-line cART regimen (GEE-aOR 1.74, 95% CI 1.65-1.84, p < 0.0001), PI-based cART regimen (GEE-aOR 1.82, 95% CI 1.72-1.92, p < 0.0001), and children aged 1-3 years (toddlers) (GEE-aOR: 1.84, 95% CI 1.79-1.90, p < 0.0001). On the contrary, DTG-based cART regimen, were negatively associated with VLNS (GEE-aOR 0.70, 95% CI 0.65-0.75, p < 0.0001). Interpretation: There is a strong evidence of decreasing viremia between 2015 and 2021. To sustain the decreasing trend, accelerating the switch from the suboptimal EVP/NVP first-line regimen to optimised DTG regimen is warranted. Funding: U.S. President's Emergency Plan for AIDS Relief (PEPFAR) and Clinton Health Access Initiative (CHAI).

In-hospital mortality during the wild-type, alpha, delta, and omicron SARS-CoV-2 waves: a multinational cohort study in the EuCARE project.

Background: Investigating outcomes of hospitalised COVID-19 patients throughout the pandemic is crucial to understand the impact of different SARS-CoV-2 variants. We compared 28-day in-hospital mortality of Wild-type, Alpha, Delta, and Omicron variant infections. Whether the difference in risk by variant varied by age was also evaluated. Methods: We conducted a cohort study including patients ≥18 years, hospitalised between 2020 and 02-01 and 2022-10-15 with a SARS-CoV-2 positive test, from nine countries. Variant was classified based on sequenced viruses or from national public metadata. Mortality was compared using the cumulative incidence function and subdistribution hazard ratios (SHR) adjusted for age, sex, calendar time, and comorbidities. Results were shown age-stratified due to effect measure modification (P < 0.0001 for interaction between age and variant). Findings: We included 38,585 participants: 19,763 Wild-type, 6387 Alpha, 3640 Delta, and 8795 Omicron. The cumulative incidence of mortality decreased throughout the study period. Among participants ≥70 years, the adjusted SHR (95% confidence interval) for Delta vs. Omicron was 1.66 (1.29-2.13). This estimate was 1.66 (1.17-2.36) for Alpha vs. Omicron, and 1.34 (0.92-1.95) for Wild-type vs. Omicron. These were 1.21 (0.81-1.82), 1.21 (0.68-2.17), and 0.98 (0.53-1.82) among unvaccinated participants. When comparing Omicron sublineages, the aSHR for BA.1 was 1.92 (1.43-2.58) compared to BA.2 and 1.52 (1.11-2.08) compared to BA.5. Interpretation: The herein observed decrease in in-hospital mortality seems to reflect a combined effect of immunity from vaccinations and previous infections, although differences in virulence between SARS-CoV-2 variants may also have contributed. Funding: European Union's Horizon Europe Research and Innovation Programme.

A Machine Learning Approach to Predict HIV Viral Load Hotspots in Kenya Using Real-World Data.

Background: Machine learning models are not in routine use for predicting HIV status. Our objective is to describe the development of a machine learning model to predict HIV viral load (VL) hotspots as an early warning system in Kenya, based on routinely collected data by affiliate entities of the Ministry of Health. Based on World Health Organization's recommendations, hotspots are health facilities with ≥20% people living with HIV whose VL is not suppressed. Prediction of VL hotspots provides an early warning system to health administrators to optimize treatment and resources distribution. Methods: A random forest model was built to predict the hotspot status of a health facility in the upcoming month, starting from 2016. Prior to model building, the datasets were cleaned and checked for outliers and multicollinearity at the patient level. The patient-level data were aggregated up to the facility level before model building. We analyzed data from 4 million tests and 4,265 facilities. The dataset at the health facility level was divided into train (75%) and test (25%) datasets. Results: The model discriminates hotspots from non-hotspots with an accuracy of 78%. The F1 score of the model is 69% and the Brier score is 0.139. In December 2019, our model correctly predicted 434 VL hotspots in addition to the observed 446 VL hotspots. Conclusion: The hotspot mapping model can be essential to antiretroviral therapy programs. This model can provide support to decision-makers to identify VL hotspots ahead in time using cost-efficient routinely collected data.

Accreditation of a molecular HIV diagnostic laboratory following the Strengthening Laboratory Management Towards Accreditation (SLMTA)-Stepwise Laboratory Quality Improvement Process Towards Accreditation (SLIPTA) approach in Kenya: an implementation science study.

Introduction: accreditation is the most effective approach to ensure the quality of services. Laboratory performance can be evaluated using the World Health Organization (WHO)-SLIPTA checklist, which checks a laboratory´s compliance with ISO 15189 on a five-star score scale and improved using the SLMTA approach. Compliance is assessed by an external body and can result in accreditation. In this paper, we describe the steps taken by the Kenya Medical Research Institute (KEMRI) HIV Laboratory, Alupe, a resource-limited public entity, towards accreditation, and discuss the lessons learned. Methods: the laboratory adopted a SLMTA-SLIPTA approach that included targeted mentorship, on-site workshops, and training. Mentorship-based interventions were used to establish a robust quality management system. Targeted mentorship, on-site workshops, and training were conducted between September 2015 and July 2016. Audits used the SLIPTA checklist to detect gaps in 12 quality system essentials. Performance indicators including turnaround time, external quality assurance, sample rejection rates, and corrective actions were tracked. An external assessment by the national accreditation body was conducted between September 2016 and November 2016. Results: training and mentorship-based interventions were successfully conducted. Quality management systems aligned with ISO 15189 were established. Baseline, midterm, and exit audits yielded scores of 47%, 75%, and 94% respectively. Early infant diagnosis external quality assurance scores were 100% in 2014-2016, while average viral load scores were at 60%, 70% and 90% during the same period. Turnaround time from September 2015 surpassed the 80% target. Accreditation was awarded in March 2017. Conclusion: the SLMTA-SLIPTA approach is suitable for quality improvement in resource-limited laboratories.

Discrepant test findings in early infant diagnosis of HIV in a national reference laboratory in Kenya: challenges and opportunities for programs.

BACKGROUND: In Kenya, the availability of a cheap diagnostic service for HIV-exposed infants has helped scale-up access to treatment, and provided a means by which programs that support Prevention of Mother to Child Transmission of HIV can be evaluated. As expected for any large testing program, discrepant and indeterminate results present a significant challenge. METHODS: Dried Blood Spots were collected from health centers countrywide and couriered to four laboratories for tests. Results were dispatched either by email, telephone, GSM SMS printer or courier. Between 2006 and 2009, tests were conducted with the Manual Roche v. 1.5 Assay. In 2010 the labs switched fully to the Cobas® AmpliPrep/ Cobas® TaqMan® HIV-1 Qual automated Roche Test. RESULTS: Between 2006 and 2010, the KEMRI CVR EID Lab conducted 64 591 HIV tests in on children <18 months of age. HIV tests (38 834) used the manual assay, while 17 133 tests used the automated assay. Overall, 10.7% (6915) of the samples tested positive, while 86.6% (55 967) tested negative. A total of 1.6% (1041) tested indeterminate and required a re-bleed of the infant. Two hundred positive tests by the manual assay were retrieved randomly and retested using the automated assay. Among them, 192 (96%) remained positive, 5 (2.5%) were negative while 3 (1.5%) failed. A total of 160 negative samples by the manual assay were retrieved and retested with the automated assay. Among them, 154 (96.24%) remained negative, 3 (1.88%) tested positive while 3 (1.88%) failed. A total of 215 samples that gave indeterminate results by the manual assay were retested using the automated system. Among them, 62 (28.8%) gave positive results, 144 (66.97%) negative and 6 (2.8%) samples still gave discrepant results. Three (1.4%) did not amplify successfully. A few infants who were apparently positive appeared to test HIV negative with age. CONCLUSIONS: Indeterminate results are a significant challenge for HIV diagnostic services, as seen in the Kenyan EID Program. In our experience, they are more often negative than they are positive. False positive and false negative results can arise from clerical error, contamination and limitations of the technologies available. To forestall the consequences of such outcomes, the sensitivity and specificity of available assays must be further improved. All HIV positive samples should be retested for confirmation, and if confirmed, a new sample must be drawn and tested for DNA at the time the infant receives their initial results or starts antiretroviral therapy. Viral clearance is a phenomenon that requires further studies.

Neisseria gonorrhoeae infection in female sex workers in an STI clinic in Nairobi, Kenya.

BACKGROUND: Gonorrhea caused by Neisseria gonorrhoeae is the second most prevalent curable sexually transmitted infection worldwide. Female Sex Workers (FSWs) are at a higher risk of contracting gonorrhea due to their risky sexual behaviors like inconsistent condom use and multiple sexual partners. We determined the prevalence and risk factors associated with gonorrhea and its antimicrobial susceptibility pattern among symptomatic FSWs attending Sexual Workers Outreach Program (SWOP) city clinic in Nairobi, Kenya. METHODS: Using convenience sampling, we recruited 379 female sex workers from SWOP City clinic in Nairobi County. We administered a semi-structured questionnaire to collect data on socio-demographics and behavioral risk factors associated with gonorrhea. We also conducted three focus groups. Two endocervical swabs were collected from each participant by the attending physician for the laboratory identification of Neisseria gonorrhoeae. An antimicrobial susceptibility test was performed using the disc diffusion method. RESULTS: Twenty-four out of 379 (6.3%) participants tested positive for gonorrhea by PCR. The significant risk factors associated with gonorrhea were having multiple sexual partners in the previous two weeks, primary education, and being in the age group of 38-49 years (p < 0.05). From the qualitative data, sex work disclosure, and difficulty in engaging protected sex with their partner, and unprotected sex with their clients due to more money from the client, PREP, and alcohol use made the female sex workers vulnerable to gonorrhea exposure and or risky sexual behavior. The culture-positive sample result yielded complete (100%) resistance to all the antimicrobials used. CONCLUSION: Neisseria gonorrhoeae infection is prevalent among symptomatic FSWs in Nairobi. Multiple sexual partners, being in age group 38-49 years and having primary education were the factors associated with gonorrhea among the study participants. Based on our identification of a highly resistant isolate, we strongly recommend increasing capacity for culture-based diagnosis and susceptibility testing.

Usability of HIV-1 Assay Using DBS for Early Infant Diagnosis in Field Settings in Kenya.

BACKGROUND: The Xpert HIV-1 Qualitative assay has been in use in Kenya since 2016 for infant diagnosis of HIV. Recently, the assay has been improved and its impact of this on ease of use is yet to be determined. We sought to determine the usability of Xpert® HIV-1 Qual XC assay using dried blood spots (DBS) for early infant diagnosis following this improvement. METHODS: This was a cross-sectional usability study undertaken in 2 selected health facilities in Kenya from October 2020 to February 2021. The laboratory technicians were retrained for this study. HIV-exposed infants were recruited with the consent of their parents. Patient data were recorded, and DBS samples were collected from the infants and tested for HIV on the improved assay. Each laboratory technician performing the assay documented usability characteristics on the provided questionnaire. Data on test errors were collected from the machine logs and analyzed using STATA for Windows. RESULTS: Of 313 test cartridges, 265 (84.66%) were successfully tested on the GeneXpert platform, and 263 valid outcomes were used for comparison with the Roche CAP/CTM HIV-1 Qualitative assay. The sensitivity, specificity, and accuracy of the Xpert HIV-1 Qualitative assay on DBS was 100%. Overall, 48 (15.34%) errors were recorded; 40 (83.33%) were user related and 8 (16.67%) were hardware related. All 4 (4/4, 100%) participating laboratory technicians said the assay had a simple workflow, was easy to use, the tests results were easy to interpret, and the assay throughput was sufficient for their workload. CONCLUSIONS: The improved Xpert HIV-1 Qual XC assay is highly accurate, has a simple workflow, and is easy to use and easy to interpret. Both hardware- and user- related errors are common.

Burden of hypertension and associated factors among HIV-positive adults in Busia County, Kenya.

Introduction: the use of antiretroviral (ARVs) for the management of HIV (human immunodeficiency virus) infection has resulted in a prolonged lifespan among HIV-positive individuals. Both HIV infection and ARVs treatment put this population at a greater risk of developing hypertension. The study aimed at establishing the burden of hypertension and associated factors among HIV-positive population. Methods: a cross-sectional design was employed where a total of 280 HIV-positive adults in Busia County were selected in a multi-stage sampling procedure between March and August 2020. Sociodemographic, economic and behavioral information was collected using a structured questionnaire. Anthropometric measurements were taken using standard methods while clinical data were extracted from patients´ medical records. Proportion was used to establish hypertension burden. Analyses were done using the T-test, Chi-square, and odds ratio. Results: among the 280 study participants, 194 (69.3%) were females, and 239(85.4%) over 35 years of age. Hypertensive cases were 55 (19.6%). The hypertensive group had a significantly higher mean age (52.25±10.4 vs 44.9±11.3; p=0.002), waist-to-hip ratio (0.93±0.09 vs 0.89±0.07; p=0.016), HIV duration (8.64±4.63 vs 6.86±4.04; p=0.014) and cumulative ART treatment duration (8.31±4.61 vs 6.68±3.93; p=0.018). Factors found to be significantly associated with hypertension in the bivariate analysis included age (p=0.003); family history (p=0.024); duration of alcohol intake (p=0.034); HIV duration (p=0.033) and treatment duration (p=0.043). In the multivariate analysis, only age (p=0.045) and family history (p=0.018) contributed significantly in the logistic regression model. Conclusion: the study revealed a slightly lower burden of hypertension among HIV -positive adults in Busia County. Age and family history were the factors independently associated with hypertension in this study.

Comparison of the performance of Aptima HIV-1 Quant Dx Assay with Abbott RealTime HIV Assay for viral load monitoring using plasma and Dried Blood Spots collected in Kenya.

INTRODUCTION: HIV-1 viral Load (VL) testing is recommended for the monitoring of antiretroviral treatment. Dried Blood Spots (DBS) are an effective sample type in resource limited settings, where safe phlebotomy and reliable shipping are hard to guarantee. In HIV high burden countries, high throughput assays can improve access to testing services. The Hologic Aptima HIV-1 Quant Dx Assay (Aptima Assay) is a high throughput assay that runs on the CE-IVD approved Panther platform. The objectives of this study were to assess the performance characteristics of Aptima for VL monitoring using plasma and venous DBS specimens and to determine the stability of HIV-1 RNA in DBS. MATERIALS AND METHODS: This was a cross-sectional study of 2227 HIV infected adults visiting health facilities in Nairobi and Busia, Kenya. Each provided a venous blood sample; plasma was prepared from 1312 samples while paired DBS samples and plasma were prepared from the remaining 915 samples. The agreement between the Aptima assay and the Abbott RealTime HIV-1 Assay (Abbott RT) was analysed by comparing the HIV-1 VL in both assays at the medical decision point of 1000 copies/mL. To assess stability of HIV-1 RNA in DBS, VL in DBS spotted on day 0 were compared with that from the same DBS card after 21 days of storage at room temperature. RESULTS: Overall, 436 plasma samples had quantifiable results in both Aptima and Abbott RT. The agreement between the two assays at 1000 copies/mL was 97.48% with a Pearson's correlation coefficient (r) of 0.9589 and gave a mean bias of 0.33 log copies/mL on Bland-Altman analysis. For fresh DBS, the agreement in both assays was 94.64% at 1000 copies/mL, with an r of 0.8692 and a mean bias of 0.35 log copies/mL. The overall agreement between DBS tested in Aptima on day 0 versus day 21 was 95.71%, with a mean bias of -0.154. CONCLUSION: The Aptima HIV-1 Quant Dx assay is an accurate test for VL monitoring of HIV-1 using DBS and plasma sample types in Kenya.

Correlation of HIV-1 drug resistant mutations and virologic failure.

INTRODUCTION: mutations are important by ensuring that the HIV-1 agent remains fit in the environment and evades drugs that are developed purposely to kill them. In Kenya, mutations conferring resistance to available ARVs have been reported in previous studies. However, there is a paucity of information on whether these previous studies have reported all mutations conclusively that confer resistance to available drugs leading to virologic failure. Therefore, this study was sought to identify the current HIV-1 drug-resistant mutations attributable to virologic failure among adults on various ARV regimens. METHODS: the samples were collected March to June 2020. Analysis of viral loads and HIV-1 drug-resistant mutations through sequencing of the pol region of HIV-1 were done. Alignment of the cDNA sequences was done by Recall (beta version 3.05) software. HIV-1 resistant mutations were identified by Stanford University HIV drug resistance database. RESULTS: most of the participants had viral loads of more than 1000 copies/ml during all the three visits. Out of 125 mutations identified, 83 mutations resulted in virologic failure. Out of 17 new mutations, 14 resulted in virologic failure and included NRTIs (L74I, L74V, T69D, V65R); NNRTIs (A98G, V179E, V179F, V179D, 179F); PIs (I54V3, F53L2, L89T, G48A). CONCLUSION: the study reveals new HIV-1 drug-resistant mutations which have never been reported in Kenya as well as old and both resulted in virologic failure. This calls for frequent monitoring and profiling of mutations that will enable decision-making in the drugs and vaccine design and development.