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G/meskel W, Desta K, Diriba R, Belachew M, Evans M, Cantarelli V, Urrego M, Sisay A, Gebreegziabxier A, Abera A. SARS-CoV-2 variant typing using real-time reverse transcription-polymerase chain reaction-based assays in Addis Ababa, Ethiopia. IJID Reg 2024; 11:100363. [PMID: 38634071 PMCID: PMC11021353 DOI: 10.1016/j.ijregi.2024.100363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024]
Abstract
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.
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Affiliation(s)
- Wodneh G/meskel
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Kassu Desta
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Regasa Diriba
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Mahlet Belachew
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Martin Evans
- Global Public Health Programs, American Society for Microbiology, Washington, USA
| | - Vlademir Cantarelli
- Global Public Health Programs, American Society for Microbiology, Washington, USA
| | - Maritza Urrego
- Global Public Health Programs, American Society for Microbiology, Washington, USA
| | - Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | | | - Adugna Abera
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
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Gebrecherkos T, Challa F, Tasew G, Gessesse Z, Kiros Y, Gebreegziabxier A, Abdulkader M, Desta AA, Atsbaha AH, Tollera G, Abrahim S, Urban BC, Schallig H, Rinke de Wit T, Wolday D. Prognostic Value of C-Reactive Protein in SARS-CoV-2 Infection: A Simplified Biomarker of COVID-19 Severity in Northern Ethiopia. Infect Drug Resist 2023; 16:3019-3028. [PMID: 37215303 PMCID: PMC10199690 DOI: 10.2147/idr.s410053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
Purpose To evaluate the role of C-reactive protein (CRP) in predicting severe COVID-19 patients. Methods A prospective observational cohort study was conducted from July 15 to October 28, 2020, at Kuyha COVID-19 isolation and treatment center hospital, Mekelle City, Northern Ethiopia. A total of 670 blood samples were collected serially. SARS-CoV-2 infection was confirmed by RT-PCR from nasopharyngeal swabs and CRP concentration was determined using Cobas Integra 400 Plus (Roche). Data were analyzed using STATA version 14. P-value <0.05 was considered statistically significant. Results Overall, COVID-19 patients had significantly elevated CRP at baseline when compared to PCR-negative controls [median 11.1 (IQR: 2.0-127.8) mg/L vs 0.9 (IQR: 0.5-1.9) mg/L; p=0.0004)]. Those with severe COVID-19 clinical presentation had significantly higher median CRP levels compared to those with non-severe cases [166.1 (IQR: 48.6-332.5) mg/L vs 2.4 (IQR: 1.2-7.6) mg/L; p<0.00001)]. Moreover, COVID-19 patients exhibited higher median CRP levels at baseline [58 (IQR: 2.0-127.8) mg/L] that decreased significantly to 2.4 (IQR: 1.4-3.9) mg/L after 40 days after symptom onset (p<0.0001). Performance of CRP levels determined using ROC analysis distinguished severe from non-severe COVID-19 patients, with an AUC value of 0.83 (95% CI: 0.73-0.91; p=0.001; 77.4% sensitivity and 89.4% specificity). In multivariable analysis, CRP levels above 30 mg/L were significantly associated with an increased risk of developing severe COVID-19 for those who have higher ages and comorbidities (ARR 3.99, 95% CI: 1.35-11.82; p=0.013). Conclusion CRP was found to be an independent determinant factor for severe COVID-19 patients. Therefore, CRP levels in COVID-19 patients in African settings may provide a simple, prompt, and inexpensive assessment of the severity status at baseline and monitoring of treatment outcomes.
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Affiliation(s)
- Teklay Gebrecherkos
- Department of Medical Microbiology and Immunology, College of Health Sciences (CHS), Mekelle University (MU), Mekelle, Tigray, Ethiopia
| | - Feyissa Challa
- National Reference Laboratory for Clinical Chemistry, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Geremew Tasew
- Department of Bacteriology, Parasitology and Zoonosis, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Zekarias Gessesse
- Department of Internal Medicine, College of Health Sciences, Mekelle University, Mekelle, Tigray, Ethiopia
| | - Yazezew Kiros
- Department of Internal Medicine, College of Health Sciences, Mekelle University, Mekelle, Tigray, Ethiopia
| | | | - Mahmud Abdulkader
- Department of Medical Microbiology and Immunology, College of Health Sciences (CHS), Mekelle University (MU), Mekelle, Tigray, Ethiopia
| | - Abraham Aregay Desta
- Public Health Research and Emergency Management, Tigray Health Research Institute, Mekelle, Tigray, Ethiopia
| | - Ataklti Hailu Atsbaha
- Department of Microbiology, Tigray Health Research Institute, Mekelle, Tigray, Ethiopia
| | - Getachew Tollera
- Research and Technology Transfer Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Saro Abrahim
- HIV/TB Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Britta C Urban
- Department of Clinical Sciences, Respiratory Clinical Research Group, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Henk Schallig
- Department of Medical Microbiology and Infection Prevention, Experimental Parasitology Unit, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Tobias Rinke de Wit
- Amsterdam Institute of Global Health and Development, Department of Global Health, Amsterdam University Medical Center, Amsterdam, the Netherlands
- Joep-Lange Institute, Amsterdam, the Netherlands
| | - Dawit Wolday
- Department of Medical Microbiology and Immunology, College of Health Sciences (CHS), Mekelle University (MU), Mekelle, Tigray, Ethiopia
- HIV/TB Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
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Gebremicael G, Gebreegziabxier A, Kassa D. Low transcriptomic of PTPRCv1 and CD3E is an independent predictor of mortality in HIV and tuberculosis co-infected patient. Sci Rep 2022; 12:10133. [PMID: 35710869 PMCID: PMC9203579 DOI: 10.1038/s41598-022-14305-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022] Open
Abstract
A comprehensive assessment of immunological profiles during HIV-TB co-infection is essential to predict mortality, and facilitate the development of effective diagnostic assays, therapeutic agents, and vaccines. Expression levels of 105 immune-related genes were measured at enrolment and 6th month follow-up from 9 deceased HIV and TB coinfected patients who died between 3 and 7th months follow-up and at enrolment, 6th and 18th month from 18 survived matched controls groups for 2 years. Focused gene expression profiling was assessed from peripheral whole blood using a dual-color Reverse-Transcription Multiplex Ligation-dependent Probe Amplification assay. Eleven of the 105 selected genes were differentially expressed between deceased individuals and survivor-matched controls at baseline. At baseline, IL4δ2 was significantly more highly expressed in the deceased group than survivor matched controls, whereas CD3E, IL7R, PTPRCv1, CCL4, GNLY, BCL2, CCL5, NOD1, TLR3, and NLRP13 had significantly lower expression levels in the deceased group compared to survivor matched controls. At baseline, a non-parametric receiver operator characteristic curve was conducted to determine the prediction of mortality of single genes identified CCL5, PTPRCv1, CD3E, and IL7R with Area under the Curve of 0.86, 0.86, 0.86, and 0.85 respectively. The expression of these genes in the survived control was increased at the end of TB treatment from that at baseline, while decreased in the deceased group. The expression of PTPRCv1, CD3E, CCL5, and IL7R host genes in peripheral blood of patients with TB-HIV coinfected can potentially be used as a predictor of mortality in the Ethiopian setting. Anti-TB treatment might be less likely to restore gene expression in the level expression of the deceased group. Therefore, other new therapeutics that can restore these genes (PTPRCv1, CD3E, IL7R, and CCL5) in the deceased groups at baseline might be needed to save lives.
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Affiliation(s)
| | | | - Desta Kassa
- Ethiopian Public Health Institute (EPHI), P.O.Box: 1242, Addis Ababa, Ethiopia
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Gebremicael G, Alemayehu M, Sileshi M, Geto Z, Gebreegziabxier A, Tefera H, Ashenafi N, Tadese C, Wolde M, Kassa D. The serum concentration of vitamin B 12 as a biomarker of therapeutic response in tuberculosis patients with and without human immunodeficiency virus (HIV) infection. Int J Gen Med 2019; 12:353-361. [PMID: 31571974 PMCID: PMC6759284 DOI: 10.2147/ijgm.s218799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 09/03/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Prior to clinical trials of new tuberculosis (TB) drugs or therapeutic vaccines, it is necessary to develop monitoring tools to predict treatment outcomes in TB patients. METHODS Micronutrients concentration level was determined from a total of 262 study participants with five clinical groups: 57 TB patients coinfected with HIV (HIV+TB+), 87 active TB Patients (TB cases), 71 HIV infected without active and latent TB infection (HIV+TST-), 22 latent TB infection (TST+) and 25 healthy controls (TST-). Vitamin A concentration was measured using high-performance liquid chromatography (HPLC), whereas iron and vitamin B12 concentrations were measured using Cobas® 6000 analyzer. RESULT The serum concentration levels of iron, vitamin A and vitamin B12 had a significant difference between active TB and latent (LTBI) or healthy controls. Six months after treatment, the serum concentration levels of vitamin A, vitamin B12 and iron in tuberculosis became indistinguishable from the levels of LTBIs and healthy control individuals. The concentration levels of iron and vitamin B12 in HIV+TB+patients at the end of TB treatment were normalized to the levels observed in healthy controls (TST-) regardless of HAART treatment. However, the concentration level of vitamin A in HIV+TB+patients HAART untreated at the end of TB treatment was not normalized to the levels observed in healthy controls (TST-) or HAART untreated HIV+TST-. CONCLUSION Detecting serum concentration levels of vitamin B12 and vitamin A might be used as a biomarker of the diagnostic method of active TB regardless of HIV-infected individuals. Moreover, detecting serum concentration of vitamin B12 might also be used for TB treatment responses monitoring biomarker in TB-HIV-co-infected individuals regardless of HAART (in)eligibility and therapy.
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Affiliation(s)
- Gebremedhin Gebremicael
- HIV and TB Research Directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Mihret Alemayehu
- Department of Medical Laboratory Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Meron Sileshi
- HIV and TB Research Directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Zeleke Geto
- HIV and TB Research Directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Atsbeha Gebreegziabxier
- HIV and TB Research Directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Hulumtaye Tefera
- Nutrition and Food Science Research Directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Nigat Ashenafi
- Nutrition and Food Science Research Directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Chere Tadese
- Nutrition and Food Science Research Directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Mistire Wolde
- Department of Medical Laboratory Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Desta Kassa
- HIV and TB Research Directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
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Gebremicael G, Belay Y, Girma F, Abreha Y, Gebreegziabxier A, Tesfaye S, Messele Z, Assefa Y, Bellete B, Kassa D, Vojnov L. The performance of BD FACSPresto™ for CD4 T-cell count, CD4% and hemoglobin concentration test in Ethiopia. PLoS One 2017; 12:e0176323. [PMID: 28448581 PMCID: PMC5407647 DOI: 10.1371/journal.pone.0176323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 04/07/2017] [Indexed: 11/19/2022] Open
Abstract
Introduction In Ethiopia, CD4+ T-cell counting is still required for all patients at baseline before antiretroviral therapy (ART) and to determine eligibility and follow-up of opportunistic infection prophylaxis. However, access to CD4+ T cell count in rural health facilities remains a major challenge in Ethiopia like other resource-limited settings. Methodology Both capillary and venous blood was drawn from each of 325 study participant recruited in Addis Ababa and surroundings. The CD4+ T-cell count, CD4%, and hemoglobin (Hgb) were tested at one of the four study health facilities using capillary blood and BD FACSPresto™ device. These tests were also done at the national HIV reference laboratory, using venous blood with BD FACSCalibur™, Sysmex XT-1800i™, and BD FACSPresto™. Results BD FACSPresto™ had an absolute mean bias of -13.3 cells/ul (-2.99%) and 28.3 cells/μl (6.4%) using venous and capillary blood, respectively, compared with BD FACSCalibur™. The absolute CD4 assay on the BD FACSPresto™ had a regression coefficient (R2) of 0.87 and 0.92 using capillary blood and venous blood samples, respectively, compared with BD FACSCalibur™. The percentage similarity of the BD FACSPresto™ using capillary and venous blood was 105.2% and 99.3%, respectively. The sensitivity of the FACSPresto™ using threshold of 500 cells/μl for ART eligibility using capillary and venous blood was 87.9 and 94.3%, while the specificity was 91.4 and 83.8%, respectively. Furthermore, the BD FACSPresto™ had an absolute mean bias of -0.2 dl/μl (0.0%) (95% LOA: -1.7, 1.3) and -0.59 dl/μl (0.1%) (95% LOA: -1.49, 0.31) for Hgb using capillary and venous blood compared with the Sysmex XT-1800i™, respectively. Conclusion Our results showed acceptable agreement between the BD FACSPresto™ and BD FACSCalibur™ for CD4+ T-cell counting and CD4%; and between the BD FACSPresto™ and Sysmex XT-1800i™for measuring Hgb concentration.
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Affiliation(s)
- Gebremedhin Gebremicael
- HIV and TB diseases research directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
- * E-mail:
| | - Yohanes Belay
- HIV and TB diseases research directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Fitsum Girma
- HIV and TB diseases research directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Yemane Abreha
- HIV and TB diseases research directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Atsbeha Gebreegziabxier
- HIV and TB diseases research directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Simret Tesfaye
- HIV and TB diseases research directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Zelalem Messele
- Clinton Health Access Initiative, Inc. (CHAI), Addis Ababa, Ethiopia
| | - Yibeltal Assefa
- HIV and TB diseases research directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Bahrie Bellete
- Clinton Health Access Initiative, Inc. (CHAI), Addis Ababa, Ethiopia
| | - Desta Kassa
- HIV and TB diseases research directorate, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Lara Vojnov
- Clinton Health Access Initiative, Boston, Massachusetts, United States of America
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Kebede A, Kebede Y, Desale A, Mulugeta A, Yaregal Z, Gebreegziabxier A, Tedla Y, Zeh C, Ayana G. Quality assurance for point-of-care testing: Ethiopia's experience. Afr J Lab Med 2016; 5:452. [PMID: 28879127 PMCID: PMC5433826 DOI: 10.4102/ajlm.v5i2.452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/11/2016] [Indexed: 11/27/2022] Open
Affiliation(s)
| | - Yenew Kebede
- Centers for Disease Control and Prevention, Ethiopia Laboratory Branch, Ethiopia
| | | | | | | | | | - Yared Tedla
- Centers for Disease Control and Prevention, Ethiopia Laboratory Branch, Ethiopia
| | - Clement Zeh
- Centers for Disease Control and Prevention, Ethiopia Laboratory Branch, Ethiopia
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