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.

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.

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).

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.

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.

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 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.

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.

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.

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.

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.

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

BACKGROUND: Camps of forcibly displaced populations are considered to be at risk of large COVID-19 outbreaks. Low screening rates and limited surveillance led us to conduct a study in Dagahaley camp, located in the Dadaab refugee complex in Kenya to estimate SARS-COV-2 seroprevalence and, mortality and to identify changes in access to care during the pandemic. METHODS: To estimate seroprevalence, a cross-sectional survey was conducted among a sample of individuals (n = 587) seeking care at the two main health centres and among all household members (n = 619) of community health workers and traditional birth attendants working in the camp. A rapid immunologic assay was used (BIOSYNEX® COVID-19 BSS [IgG/IgM]) and adjusted for test performance and mismatch between the sampled population and that of the general camp population. To estimate mortality, all households (n = 12860) were exhaustively interviewed in the camp about deaths occurring from January 2019 through March 2021. RESULTS: In total 1206 participants were included in the seroprevalence study, 8% (95% CI: 6.6%-9.7%) had a positive serologic test. After adjusting for test performance and standardizing on age, a seroprevalence of 5.8% was estimated (95% CI: 1.6%-8.4%). The mortality rate for 10,000 persons per day was 0.05 (95% CI 0.05-0.06) prior to the pandemic and 0.07 (95% CI 0.06-0.08) during the pandemic, representing a significant 42% increase (p<0.001). Médecins Sans Frontières health centre consultations and hospital admissions decreased by 38% and 37% respectively. CONCLUSION: The number of infected people was estimated 67 times higher than the number of reported cases. Participants aged 50 years or more were among the most affected. The mortality survey shows an increase in the mortality rate during the pandemic compared to before the pandemic. A decline in attendance at health facilities was observed and sustained despite the easing of restrictions.

Prevalence and factors associated with HIV-1 drug resistance mutations in treatment-experienced patients in Nairobi, Kenya: A cross-sectional study.

ABSTRACT: An estimated 1.5 million Kenyans are HIV-seropositive, with 1.1 million on antiretroviral therapy (ART), with the majority of them unaware of their drug resistance status. In this study, we assessed the prevalence of drug resistance to nucleoside reverse transcriptase inhibitors (NRTIs), nucleoside reverse transcriptase inhibitors (NNRTIs), and protease inhibitors, and the variables associated with drug resistance in patients failing treatment in Nairobi, Kenya.This cross-sectional study utilized 128 HIV-positive plasma samples obtained from patients enrolled for routine viral monitoring in Nairobi clinics between 2015 and 2017. The primary outcome was human immunodeficiency virus type 1 (HIV-1) drug resistance mutation counts determined by Sanger sequencing of the polymerase (pol) gene followed by interpretation using Stanford's HIV Drug Resistance Database. Poisson regression was used to determine the effects of sex, viral load, age, HIV-subtype, treatment duration, and ART-regimen on the primary outcome.HIV-1 drug resistance mutations were found in 82.3% of the subjects, with 15.3% of subjects having triple-class ART resistance and 45.2% having dual-class resistance. NRTI primary mutations M184 V/I and K65R/E/N were found in 28.8% and 8.9% of subjects respectively, while NNRTI primary mutations K103N/S, G190A, and Y181C were found in 21.0%, 14.6%, and 10.9% of subjects. We found statistically significant evidence (P = .013) that the association between treatment duration and drug resistance mutations differed by sex. An increase of one natural-log transformed viral load unit was associated with 11% increase in drug resistance mutation counts (incidence rate ratio [IRR] 1.11; 95% CI 1.06-1.16; P < .001) after adjusting for age, HIV-1 subtype, and the sex-treatment duration interaction. Subjects who had been on treatment for 31 to 60 months had 63% higher resistance mutation counts (IRR 1.63; 95% CI 1.12-2.43; P = .013) compared to the reference group (<30 months). Similarly, patients on ART for 61 to 90 months were associated with 133% higher mutation counts than the reference group (IRR 2.33; 95% CI 1.59-3.49; P < .001). HIV-1 subtype, age, or ART-regimen were not associated with resistance mutation counts.Drug resistance mutations were found in alarmingly high numbers, and they were associated with viral load and treatment time. This finding emphasizes the importance of targeted resistance monitoring as a tool for addressing the problem.

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.

Human immunodeficiency virus (HIV) type 1 genetic diversity in HIV positive individuals on antiretroviral therapy in a cross-sectional study conducted in Teso, Western Kenya.

INTRODUCTION: high HIV-1 infection rates and genetic diversity especially in African population pose significant challenges in HIV-1 clinical management and drug design and development. HIV-1 is a major health challenge in Kenya and causes mortality and morbidity in the country as well as straining the healthcare system and the economy. This study sought to identify HIV-1 genetic subtypes circulating in Teso, Western Kenya which borders the Republic of Uganda. METHODS: a cross-sectional study was conducted in January 2019 to December 2019. Sequencing of the partial pol gene was carried out on 80 HIV positive individuals on antiretroviral therapy. Subtypes and recombinant forms were generated using the jumping profile hidden Markov model. Alignment of the sequences was done using ClustalW program and phylogenetic tree constructed using MEGA7 neighbor-joining method. RESULTS: sixty three samples were successful sequenced. In the analysis of these sequences, it was observed that HIV-1 subtype A1 was predominant 43 (68.3%) followed by D 8 (12.7%) and 1 (1.6%) each of C, G and B and inter-subtype recombinants A1-D 3 (4.8%), A1-B 2 (3.2%) and 1 (1.6%) each of A1-A2, A1-C, BC and BD. Phylogenetic analysis of these sequences showed close clustering of closely related and unrelated sequences with reference sequences. CONCLUSION: there was observed increased genetic diversity of HIV-1 subtypes which not only pose a challenge in disease control and management but also drug design and development. Therefore, there is need for continued surveillance to enhance future understanding of the geographical distribution and transmission patterns of the HIV epidemic.

Prospective evaluation of accuracy of HIV viral load monitoring using the Aptima HIV Quant Dx assay with fingerstick and venous dried blood spots prepared under field conditions in Kenya.

Quantification of HIV-1 RNA is essential for clinical management of HIV patients. The limited throughput and significant hands-on time required by most HIV Viral load (VL) tests makes it challenging for laboratories with high test volume, to turn around patient results quickly. The Hologic Aptima HIV-1 Quant Dx Assay (Aptima), has the potential to alleviate this burden as it is high throughput and fully automated. This assay is validated for both plasma and dried blood spots (DBS), which are commonly used in resource limited settings. The objective of this study was to compare the performance of Aptima to Abbott RealTime HIV-1 Assay (Abbott RT), which was used as reference. This was a cross-sectional prospective study where HIV VL in finger stick (FS) DBS, venous blood (VB) DBS and plasma, collected from 258 consenting adults visiting 5 medical facilities in Kenya, Africa were tested in Aptima. The results were compared to plasma VL in Abbott RT at the medical decision point (MDP) of 1000 copies/mL and across Aptima assay range. The total agreement at MDP between plasma HIV VL in Abbott RT and plasma, FS and VB DBS tested in Aptima were 97.7%, 92.2% and 95.3% respectively with kappa statistic of 0.95, 0.84 and 0.90. The positive and negative agreement for all 3 sample types were >92%. Regression analysis between VL in Abbott RT plasma and various sample types tested in Aptima had a Pearson's correlation coefficient ≥0.91 with systematic bias of < 0.20 log copies/mL on Bland-Altman analysis. The high level of agreement in Aptima HIV VL results for all 3 sample types with Abbott RT plasma VL along with the high throughput, complete automation, and ease of use of the Panther platform makes Aptima a good option for HIV VL monitoring for busy laboratories with high volume of testing.

Two-Step Reverse Transcription Droplet Digital PCR Protocols for SARS-CoV-2 Detection and Quantification.

Diagnosis of the ongoing SARS-CoV-2 pandemic is a priority for all countries across the globe. Currently, reverse transcription quantitative PCR (RT-qPCR) is the gold standard for SARS-CoV-2 diagnosis as no permanent solution is available. However effective this technique may be, research has emerged showing its limitations in detection and diagnosis especially when it comes to low abundant targets. In contrast, droplet digital PCR (ddPCR), a recent emerging technology with superior advantages over qPCR, has been shown to overcome the challenges of RT-qPCR in diagnosis of SARS-CoV-2 from low abundant target samples. Prospectively, in this article, the capabilities of RT-ddPCR are further expanded by showing steps on how to develop simplex, duplex, triplex probe mix, and quadruplex assays using a two-color detection system. Using primers and probes targeting specific sites of the SARS-CoV-2 genome (N, ORF1ab, RPP30, and RBD2), the development of these assays is shown to be possible. Additionally, step by step detailed protocols, notes, and suggestions on how to improve the assays workflow and analyze data are provided. Adapting this workflow in future works will ensure that the maximum number of targets can be sensitively detected in a small sample significantly improving on cost and sample throughput.