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.

Prognostic Value of C-Reactive Protein in SARS-CoV-2 Infection: A Simplified Biomarker of COVID-19 Severity in Northern Ethiopia.

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.

Low transcriptomic of PTPRCv1 and CD3E is an independent predictor of mortality in HIV and tuberculosis co-infected patient.

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.

Pre-Treatment Integrase Inhibitor Resistance and Natural Polymorphisms among HIV-1 Subtype C Infected Patients in Ethiopia.

Dolutegravir-based antiretroviral therapy (ART) has been scaled up in many developing countries, including Ethiopia. However, subtype-dependent polymorphic differences might influence the occurrence of HIV-drug-resistance mutations (HIVDRMs). We analyzed the prevalence of pre-treatment integrase strand transfer inhibitor (INSTI) HIVDRMs and naturally occurring polymorphisms (NOPs) of the integrase gene, using plasma samples collected as part of the national HIVDR survey in Ethiopia in 2017. We included a total of 460 HIV-1 integrase gene sequences from INSTI-naïve (n = 373 ART-naïve and n = 87 ART-experienced) patients. No dolutegravir-associated HIVDRMs were detected, regardless of previous exposure to ART. However, we found E92G in one ART-naïve patient specimen and accessory mutations in 20/460 (4.3%) of the specimens. Moreover, among the 288 integrase amino acid positions of the subtype C, 187/288 (64.9%) were conserved (<1.0% variability). Analysis of the genetic barrier showed that the Q148H/K/R dolutegravir resistance pathway was less selected in subtype C. Docking analysis of the dolutegravir showed that protease- and reverse-transcriptase-associated HIVDRMs did not affect the native structure of the HIV-1 integrase. Our results support the implementation of a wide scale-up of dolutegravir-based regimes. However, the detection of polymorphisms contributing to INSTI warrants the continuous surveillance of INSTI resistance.

The serum concentration of vitamin B12 as a biomarker of therapeutic response in tuberculosis patients with and without human immunodeficiency virus (HIV) infection.

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.

Lipid Profile in Tuberculosis Patients with and without Human Immunodeficiency Virus Infection.

BACKGROUND: Understanding whether the preceding low lipid profile leads to active tuberculosis (TB) or active TB leads to low lipid profile is crucial. METHODS: Lipid profile concentrations were determined from 159 study participants composed of 93 active TB patients [44 HIV coinfected (HIV+TB+) and 49 HIV negative (HIV-TB+)], 41 tuberculin skin test (TST) positive cases [17 HIV coinfected (HIV+TST+) and 24 HIV negative (HIV-TST+)], and 25 healthy controls (HIV-TST-). Cobas Integra 400 Plus was used to determine lipid profiles concentration level. RESULTS: The concentrations of total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) in HIV-TB+ patients were significantly lower compared to HIV-TST+ and to HIV-TST- individuals. Similarly, the concentrations of the TC, LDL-C, and HDL-C in HIV+TB+ were significantly lower compared to HIV-TB+ patients. After the 6 months of anti-TB treatment (ATT), the concentration levels of TC, LDL-C, and HDL-C in HIV-TB+ patients were higher compared to the baseline concentration levels, while they were not significantly different compared to that of HIV-TST+ concentration. CONCLUSION: The low concentration of lipid profiles in TB patients may be a consequence of the disease and significantly increased in TB patients after treatment.

The performance of BD FACSPresto™ for CD4 T-cell count, CD4% and hemoglobin concentration test in Ethiopia.

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.

Antiretroviral treatment associated hyperglycemia and dyslipidemia among HIV infected patients at Burayu Health Center, Addis Ababa, Ethiopia: a cross-sectional comparative study.

BACKGROUND: The effects of highly active antiretroviral therapy (HAART) on glucose and lipid metabolism among sub-Saharan Africans, for whom access to antiretroviral therapy is expanding, remain largely unknown. Therefore, the aim of this study was to assess antiretroviral treatment associated hyperglycemia and dyslipidemia among HIV infected patients at Burayu health center, Addis Ababa, Ethiopia. METHODS: A cross-sectional comparative study was conducted among HIV infected adults at Burayu Health Center, Addis Ababa, Ethiopia from September, 2011 to May, 2012. Equal number of HAART naïve and HAART initiated patients (n = 126 each) were included in the study. Demographic data were collected using a well-structured questionnaire. Total cholesterol (TC), Triglyceride (TG), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C) and glucose were determined. The data were analyzed using SPSS version 20 software. RESULT: Of 252 study participants, 72.2% were females; mean age was 35.3 years; mean Body Mass Index (BMI) was 21.4(kg/m2); mean time living with the virus was 20.6 months and 15.5% were TB-HIV co-infected. The prevalence of hyperglycemia, increased LDL-C hypercholesterolemia, hypertriglyceridemia and decreased HDL-C were 7.9%, 23%, 42.1%, 46.8% and 50.8% in HAART and 5.6%, 7.1%, 11.1%, 31% and 73% in non-HAART groups, respectively. First line antiretrovirals were drugs containing 2 nucleoside backbones (from Zidovudine/Stavudine/Lamivudine/Tenofovir) with either Nevirapine or Efavirenz. There was statistically significant increase in serum lipid profile levels among HAART initiated patients than HAART naïve individuals (p =0.01 for TG and <0.001 for others). CONCLUSION: First-line HAART is associated with potentially atherogenic lipid profile levels in patients with HIV infection compared to untreated patients. This indicates glucose and lipid profile levels need to be monitored regularly in HIV infected patients taking antiretroviral treatment.