SARS-CoV-2 variant typing using real-time reverse transcription-polymerase chain reaction-based assays in Addis Ababa, Ethiopia.

Objectives: This study aimed to determine the SARS-CoV-2 variants in the first four COVID-19 waves using polymerase chain reaction (PCR)-based variant detection in Addis Ababa, Ethiopia. Methods: A cross-sectional study was conducted using repository nasopharyngeal samples stored at the Ethiopian Public Health Institute COVID-19 testing laboratory. Stored positive samples were randomly selected from the first four waves based on their sample collection date. A total of 641 nasopharyngeal samples were selected and re-tested for SARS-CoV-2. RNA was extracted using nucleic acid purification instrument. Then, SARS-CoV-2 detection was carried out using 10 µl RNA and 20 µl reverse transcription-PCR fluorescent mix. Cycle threshold values <38 were considered positive. Results: A total of 374 samples qualified for B.1.617 Lineage and six spike gene mutation variant typing kits. The variant typing kits identified 267 (71.4%) from the total qualifying samples. Alpha, Beta, Delta, and Omicron were dominantly identified variants from waves I, II, III, and IV, respectively. From the total identified positive study samples, 243 of 267 (91%) of variants identified from samples had cycle threshold values <30. Conclusions: The study data demonstrated that reverse transcription-PCR-based variant typing can provide additional screening opportunities where sequencing opportunity is inaccessible. The assays could be implemented in laboratories performing SARS-CoV-2 molecular testing.

Medical laboratory accreditation status and associated factors in selected private and government health facilities of Addis Ababa, Ethiopia.

Introduction: quality medical laboratory service(s) is a key to patient safety with a great emphasis on medical diagnoses and treatment. ISO 15189 laboratory accreditation is an effective way to demonstrate competency. Despite the benefits, there are considerable exigent efforts towards achieving its target, mainly in sub-Saharan Africa. Hence, determining those factors that hinder laboratory quality services and the process of accreditation is important to address and resolve. Thus, this study aimed to assess medical laboratory accreditation process and in selected private and government health facility laboratories in Addis Ababa, Ethiopia. Methods: institutional-based cross-sectional study design was conducted in Addis Ababa from July 1 to August 30, 2018. Data was entered into EPI-data version 3.1 and analyzed by SPSS version 23. Data from focus group discussions were categorized and discussed thematically. Additionally, logistic regression analyses were computed to examine the relationship between the explanatory and response variable. Results: a total of 411 professionals participated in this study, of which 117(28.8%) participants were female, 280 (68.2%) participants with a bachelor´s degree, and 352 (85.6%) participants had information about accreditation. The current laboratory accreditation status in Addis Ababa is 3.6%. The primary identified factors were gaps related to method verification/validation, equipment calibration, and continual program quality improvement. Conclusion: strengthening laboratory management standards towards accreditation (SLMTA) will significantly improve the accreditation process. However, there are internal and external factors may hinder the current accreditation process. Therefore, all responsible agencies/services should give more attention to solving those identified major barriers to achieving accreditation.

HIV rapid test performance among health facilities enrolled in HIV rapid test quality improvement initiative (RTQII) in Ethiopia.

BACKGROUND: As the Human Immunodeficiency Virus (HIV) rapid testing services expanded to reach the global target that 95% of people living with the virus will know their status by 2030, ensuring the quality of those services becomes critical. This study was conducted to assess the performance of HIV Rapid testing at sites in health facilities that were enrolled in the Rapid Test Quality Improvement Initiative (RTQII) in Ethiopia. METHODS: Characterized HIV proficiency testing (PT) panels of Dried Tube Specimen (DTS) were prepared, verified, and distributed to testing sites from August to December 2019. In addition on-site evaluation of HIV testing sites (HTSs) was conducted using a checklist to assess testing conditions. For proficiency testing, the study included 159 HIV testing sites (HTSs) in 41 Health facilities (HFs) in five administrative regions and two city administrations. The collected data was analyzed by SPSS version 20 and chi-square test was applied to identify the association between acceptable performance and contributing factors. Testing sites with 100% PT score as well as conducting the test with adherence to the National HIV Testing Algorithm were considered acceptable. RESULTS: The overall acceptable performance (100% PT score with the correct algorithm followed) was found to be 62% while 12% scored 80% and 11% scored between 20 and 60%. The rest 15% were not considered as acceptable due to failure to adhere to the National HIV Testing Algorithm. Testing sites that participated in External Quality Assessment/Proficiency Testing schemes have shown better performance than those that did not participate with 70% and 56% performance respectively (p = 0.057).

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022.

Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499,000 cases, and ~7500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was outcompeted by the Delta variant. Notably, Ethiopia's lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia's role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.

Evaluating diagnostic accuracies of Panbio™ test and RT-PCR for the detection of SARS-CoV-2 in Addis Ababa, Ethiopia using Bayesian Latent-Class Models (BLCM).

BACKGROUND: Rapid diagnostics are vital for curving the transmission and control of the COVID-19 pandemic. Although many commercially available antigen-based rapid diagnostic tests (Ag-RDTs) for the detection of SARS-CoV-2 are recommended by the WHO, their diagnostic performance has not yet been assessed in Ethiopia. So far, the vast majority of studies assessing diagnostic accuracies of rapid antigen tests considered RT-PCR as a reference standard, which inevitably leads to bias when RT-PCR is not 100% sensitive and specific. Thus, this study aimed to evaluate the diagnostic performance of Panbio™ jointly with the RT-PCR for the detection of SARS-CoV-2. METHODS: A prospective cross-sectional study was done from July to September 2021 in Addis Ababa, Ethiopia, during the third wave of the pandemic involving two health centers and two hospitals. Diagnostic sensitivity and specificity of Panbio™ and RT-PCR were obtained using Bayesian Latent-Class Models (BLCM). RESULTS: 438 COVID-19 presumptive clients were enrolled, 239 (54.6%) were females, of whom 196 (44.7%) had a positive RT-PCR and 158 (36.1%) were Panbio™ positive. The Panbio™ and RT-PCR had a sensitivity (95% CrI) of 99.6 (98.4-100) %, 89.3 (83.2-97.6) % and specificity (95% CrI) of 93.4 (82.3-100) %, and 99.1 (97.5-100) %, respectively. Most of the study participants, 318 (72.6%) exhibited COVID-19 symptoms; the most reported was cough 191 (43.6%). CONCLUSION: As expected the RT-PCR performed very well with a near-perfect specificity and a high, but not perfect sensitivity. The diagnostic performance of Panbio™ is coherent with the WHO established criteria of having a sensitivity ≥80% for Ag-RDTs. Both tests displayed high diagnostic accuracies in patients with and without symptoms. Hence, we recommend the use of the Panbio™ for both symptomatic and asymptomatic individuals in clinical settings for screening purposes.

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Medical laboratory waste generation rate, management practices and associated factors in Addis Ababa, Ethiopia.

BACKGROUND: Biomedical wastes (BMWs) generated from medical laboratories are hazardous and can endanger both humans and the environment. Highly infectious biomedical wastes are produced at an unacceptably high rate from health laboratories in developing countries with poor management systems, such as Ethiopia. The purpose of this study was to assess the rate of biomedical waste generation, management practices, and associated factors in public healthcare medical laboratories in Addis Ababa, Ethiopia. MATERIALS AND METHODS: From July 13 to September 25, 2020, a health institution-based cross-sectional study was conducted in 6 hospital laboratories and 20 health centres laboratories in Addis Ababa, Ethiopia. Data on socio-demographic characteristics, knowledge and practice of biomedical waste management and generation rate were collected d in health facilities using pre tested data collection tools. SPSS version 20 was used to manage the data. To identify independent predictors of the dependent variable, descriptive statistics, Pearson correlation, linear, and logistic regression analysis were used. The strength of the association was determined using an odds ratio with a 95% confidence interval. RESULTS: In this study, the mean ± SD daily generation rate of biomedical wastes was 4.9 ± 3.13 kg/day per medical laboratory. Nineteen medical laboratories (74.3%) had proper biomedical waste management practice, which is significantly associated with professionals' knowledge of biomedical waste management policies and guidelines, the availability of separate financial sources for biomedical waste management, and the level of training of professionals. CONCLUSION: The study found that medical laboratories in Addis Ababa's public healthcare facilities generate a significant amount of biomedical waste. Nearly two-thirds of hospitals performed proper waste segregation, collection, storage, and treatment procedures for biomedical waste generated in their laboratories. However, there was a poor transportation and disposal method. As a result, paying special attention and implementing the current national guidelines for biomedical waste management is recommended.

Diagnostic accuracy of three commercially available one step RT-PCR assays for the detection of SARS-CoV-2 in resource limited settings.

BACKGROUND: COVID-19 is an ongoing public health pandemic regardless of the countless efforts made by various actors. Quality diagnostic tests are important for early detection and control. Notably, several commercially available one step RT-PCR based assays have been recommended by the WHO. Yet, their analytic and diagnostic performances have not been well documented in resource-limited settings. Hence, this study aimed to evaluate the diagnostic sensitivities and specificities of three commercially available one step reverse transcriptase-polymerase chain reaction (RT-PCR) assays in Ethiopia in clinical setting. METHODS: A cross-sectional study was conducted from April to June, 2021 on 279 respiratory swabs originating from community surveillance, contact cases and suspect cases. RNA was extracted using manual extraction method. Master-mix preparation, amplification and result interpretation was done as per the respective manufacturer. Agreements between RT-PCRs were analyzed using kappa values. Bayesian latent class models (BLCM) were fitted to obtain reliable estimates of diagnostic sensitivities, specificities of the three assays and prevalence in the absence of a true gold standard. RESULTS: Among the 279 respiratory samples, 50(18%), 59(21.2%), and 69(24.7%) were tested positive by TIB, Da An, and BGI assays, respectively. Moderate to substantial level of agreement was reported among the three assays with kappa value between 0 .55 and 0.72. Based on the BLCM relatively high specificities (95% CI) of 0.991(0.973-1.000), 0.961(0.930-0.991) and 0.916(0.875-0.952) and considerably lower sensitivities with 0.813(0.658-0.938), 0.836(0.712-0.940) and 0.810(0.687-0.920) for TIB MOLBIOL, Da An and BGI respectively were found. CONCLUSIONS: While all the three RT-PCR assays displayed comparable sensitivities, the specificities of TIB MOLBIOL and Da An were considerably higher than BGI. These results help adjust the apparent prevalence determined by the three RT-PCRs and thus support public health decisions in resource limited settings and consider alternatives as per their prioritization matrix.

Diagnostic Performance of SARS-CoV-2 IgM/IgG Rapid Test Kits for the Detection of the Novel Coronavirus in Ethiopia.

PURPOSE: Rapid severe acute respiratory syndrome coronavirus 2 test kits are crucial for bridging diagnostic gaps in health facilities and community screening mainly in resource limited settings. However, there is no objective evidence on their diagnostic performance. Thus, the study aimed to evaluate comparative diagnostic performance of three selected SARS-CoV-2 IgG/IgM rapid test kits in Ethiopia. METHODS: A cross-sectional study was conducted among 200 clients between May and July 2020 in Addis Ababa, Ethiopia. The performance of three SARS-CoV-2 rapid test kits EGENE, CTK BIOTECKs Onsite, and ACON Biotech were evaluated using blood specimens against RT-PCR on respiratory swabs. Sensitivity, specificity, and agreement with each other and to RT-PCR were computed using Vassarstats, MedCalc and SPSS version 23 statistical software. RESULTS: Test kits showed a heterogeneous comparative diagnostic performance in their sensitivity and specificity. The sensitivity was 61.18% (95% CI: 49.96-71.37%), 74.12% (95% CI: 63.28-82.74%) and 83.53% (95% CI: 73.57-90.38%) for kit A, B and C, respectively. Similarly, the specificity was 96.52% (90.81-98.88%), 94.78% (88.52-97.86%) and 94.78% (88.52-97.86%) for test kit A, B and C, respectively. The test kits have an agreement with RT-PCR with kappa value of 0.60 (0.48-0.83), 0.71 (0.65-0.93), and 0.80 (0.76-1.04) for A, B, and C, respectively. There was a significant difference on diagnostic performance among the three test kits and PCR with a p-value < 0.001 Cochran's Q test. CONCLUSION: The diagnostic performance of the test kits was promising and recommended for COVID-19 diagnostics in combination with RT-PCR to detect more infected patients. It allows determining the seroprevalence of the virus and true extent of SARS-COV-2 community spread in resource limited settings. We underline countries to evaluate rapid diagnostic test kits before diagnostic use.

Evaluation of Laboratory Performance, Associated Factors and Staff Awareness Towards Achieving Turnaround Time in Tertiary Hospitals, Ethiopia.

BACKGROUND: WHO recommends that each laboratory should establish turnaround time (TAT) to monitor and evaluate performance throughout processes. The status of established TAT was not yet assessed in Ethiopian Armed Force Comprehensive Specialized Hospital. The aim of this study was to evaluate the laboratory performance and associated factors towards achieving TAT in clinical chemistry and hematology tests at Armed Force Comprehensive Specialized Hospital, Addis Ababa, Ethiopia. METHODS: Hospital-based cross-sectional study was conducted from April 2019 to June 2019. Standardized questionnaire was designed to collected data on awareness of laboratory staffs about TAT. The data was entered, cleaned and analyzed using SPSS version 24.0 Software. Logistic regression analysis was done to find out statistically significant association and strength of association between dependent and independent variables at pvalue <0.05. RESULT: A total of 422 test results were systematically selected with 100% response rates. Of these, 253(59.9%) were chemistry tests. From the expected < 90min TAT clinical chemistry tests, only 41(16.2%) and from < 60min TAT time for hematology tests, 37(21.9%) met the target. The laboratory TAT was affected by factors including high work load, laboratory information system problem, power interruption and sample collection time. Moreover, the level of knowledge, attitude and practices of laboratory staffs towards laboratory TAT were 60%, 85.7% and 62.9% respectively. CONCLUSION: Overall achievement of clinical Chemistry and hematology tests TAT was poor. The finding might reflect other public hospital situation in Addis Ababa. Thus, additional large scale studies need to conduct.

Survey-Defined and Interview-Elicited Challenges That Faced Ethiopian Government Hospital Laboratories as They Applied ISO 15189 Accreditation Standards in Resource-Constrained Settings in 2017.

OBJECTIVES: The World Health Organization African Regional Office recommends ISO 15189 standards to improve performance quality in sub-Saharan African laboratories. We specify challenges Ethiopian laboratorians encountered applying ISO 15189 standards. METHODS: From a structured survey at 12 Ethiopian government hospitals, 175 laboratory staff replied; all were aware of the ISO standards and 138 had been involved in the ISO 15189 inspection process. In addition, 11 laboratory heads, 10 quality officers, and three medical directors were interviewed in depth. RESULTS: Half or more respondents identified six challenges obstructing accreditation to a "large" or "very large" degree: (1) low management support, (2) inadequate training, (3) insufficient infrastructure, (4) excessive documentation, (5) little mentorship, and (6) increased accreditation-related workload. Interviewees added (7) poor equipment, (8) unavailable/poor-quality reagents, and (9) high staff turnover. CONCLUSIONS: The survey and interviews specified nine major challenges for Ethiopian government hospital laboratories that seriously obstruct meeting ISO 15189 demands.

Assessment of the magnitude and associated factors of immunological failure among adult and adolescent HIV-infected patients in St. Luke and Tulubolo Hospital, Oromia Region, Ethiopia.

INTRODUCTION: The use of antiretroviral therapy (ART) has become a standard of care for the treatment of HIV infection. However, cost and resistance to ART are major obstacles for access to treatment especially in resource-limited settings. In this study, we aimed to assess the magnitude and associated factors of Immunological failure among adult and adolescent HIV infected Patients (with age '15 yrs) on Highly Active Antiretroviral Therapy (HAART) in St. Luke and Tulu Bolo Hospitals, Oromia Region, Ethiopia. METHODS: A retrospective follow-up study was conducted among HIV-infected patients initiated 1st line ART at St. Luke and Tulu Bolo Hospitals, South West Shoa Zone, Oromia, Ethiopia. RESULTS: A total of 828 patient charts were reviewed. 477(57.6%) were female and the median age was 32 years. The median baseline CD4 count was 148cells/mm3. The most common prescribed ART was TDF based (36.7%). Out of 828 patients chart reviewed 6.8% (56) were developed immunological failure. Out of them only 20 (2.4%) were detected and put on second line regimen. The incidence of immunological failure was 1.8 cases per 100 person years of follow-up. Patients who had not disclosed their HIV status to any one had high risk of immunological failure compared with patients those who had disclosed their HIV status (AHR, 0.429; 95% CI 0.206 - 0.893; P-value=0.024). CONCLUSION: Non disclosures of HIV status and with ambulatory of baseline functional status were found to be predictors of immunological failure. Most of the immunological failure cases were not detected early and not switched to second line ARV regimen. So patients with the above risk factors should be considered for a timely switch to second line HAART.

Assessing the outcome of Strengthening Laboratory Management Towards Accreditation (SLMTA) on laboratory quality management system in city government of Addis Ababa, Ethiopia.

INTRODUCTION: Strengthening Laboratory Management Toward Accreditation (SLMTA) is a competency-based management training programme designed to bring about immediate and measurable laboratory improvement. The aim of this study is to assess the outcome of SLMTA on laboratory quality management system in Addis Ababa, Ethiopia. METHODS: The study used an Institutional based cross sectional study design that employed a secondary and primary data collection approach on the participated institution of medical laboratory in SLMTA. The study was conducted in Addis Ababa city government and the data was collected from February 'April 2014 and data was entered in to EPI-data version 3.1 and was analyzed by SPSS version 20. RESULTS: The assessment finding indicate that there was a significant improvement in average scores (141.4; range of 65-196, 95%CI=86.275-115.5, p=0.000) at final with 3 laboratories become 3 star, 6 laboratories were at 2 star, 11 were 1 star. Laboratory facilities respondents which thought getting adequate and timely manner mentorship were found 2.5 times more likely to get good success in the final score(AOR=2.501, 95% CI=1.109-4.602) than which did not get it. CONCLUSION: At the end of SLMTA implementation,3 laboratories score 3 star, 6 laboratories were at 2 star, 11 were at 1 star. The most important contributing factor for not scoring star in the final outcome of SLMTA were not conducting their customer satisfaction survey, poor staff motivation, and lack of regular equipment service maintenance. Mentorship, onsite and offsite coaching and training activities had shown a great improvement on laboratory quality management system in most laboratories.