Laboratory biomarkers associated with mortality in COVID-19 patients in Addis Ababa, Ethiopia (preprint)

Background: Laboratory biomarkers are amongst the best imperative predictors of disease outcomes in hospital-admitted COVID-19 patients. Although data is available in this regard at a global level, there is a paucity of information in Ethiopia. Thus, this study aimed to assess the laboratory biomarkers association with death among COVID-19 patients in Ethiopia. Methods: A health facility-based longitudinal study was conducted from 2020 to 2022 among RT-PCR-confirmed COVID-19 patients admitted and on treatment follow-up at COVID-19 treatment hospitals in Addis Ababa. A robust Poisson regression model was fitted to assess the association between demographic, clinical, and laboratory factors and death. Significance was determined at p<0.05, and variables with p < 0.15 in bivariate analyses were included in the final multivariable models. Incidence rate ratio (IRR) with a 95% confidence interval (CI) was used to describe associations. Results: Of the 2357 COVID-19 patients, 248 (10.5%) died. The median age of participants was 59 (IQR= 45- 70) years, and the majority (64.9%) of them were male. Lower median RBC was observed among those who died at 4.58 (4.06-5.07) as compared to those who survived at 4.69 (4.23-5.12) whereas high median (IQR) WBC was a predictor of mortality with 11.2 (7.7-15.9). After adjusting for confounders, death was associated with age >74 years having adjusted incidence rate ratio [aIRR (95%CI): 2.46 (1.40-4.34)], and critical clinical situations [aIRR (95% CI): 4.04 (2.18-7.52)]. Conclusion: Our results demonstrate that abnormal liver function tests, abnormal white blood cells, age of the patients, and clinical status of the patients during admission are associated with unfavorable outcomes of COVID-19. Hence, timely monitoring of these laboratory results at the earliest phase of the disease was highly commendable.

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022 (preprint)

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 ~7 500 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 out-competed by the Delta variant. Notably, Ethiopia 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 role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.

Evaluating diagnostic accuracies of Panbio™ COVID-19 rapid antigen test and RT-PCR for the detection of SARS-CoV-2 in Addis Ababa, Ethiopia using Bayesian Latent-Class Models (BLCM) (preprint)

Background Rapid diagnostics are vital for curving the transmission and control of 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 gold 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 COVID-19 rapid antigen test jointly together 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 rapid antigen test 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 Ag-RDT positive. The Ag-RDT 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), 99.1 (97.5- 100) respectively. Most of the study participants, 318 (72.6) exhibited COVID-19 symptoms and the most reported was cough 191 (43.6). Conclusion The diagnostic performance of Panbio COVID-19 Ag RDT is coherent with the WHO established criteria of having a sensitivity [≥]80% for Ag-RDTs. Superior performance of the Panbio RDT was documented in samples with the lowest cycle-threshold RT-PCR values and clients with confirmed clinical symptoms. Thus, we recommend the use of the Panbio RDT for both symptomatic and asymptomatic individuals in clinical settings for screening purposes.