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

Comparing the accuracy of two diagnostic methods for detection of light Schistosoma haematobium infection in an elimination setting in Wolaita Zone, South Western Ethiopia.

Reagent urinalysis dipstick and filtration have been recommended diagnostic methods for the detection of urogenital schistosomiasis. However, the accurate diagnosis of light infections using these methods presents a major challenge. This study evaluates the diagnosis accuracy of light infection with Schistosoma haematobium in study participants living in Wolaita Zone, an area targeted for sustainable control of Schistosomiasis, and ultimately interrupt transmission. Urine samples were collected from children and adults in surveys carried out during baseline and longitudinal sentinel site surveys conducted from 2018 to 2020. All urine samples were tested using a reagent urinalysis dipstick test (Haemastix) to detect microhaematuria with reference urine filtration technique as a proxy for S. haematobium infection. Sensitivity and specificity were determined in diagnosing urogenital schistosomiasis. Cohen's Kappa statistics was done for the agreement of these diagnostic methods. A total of 12,102 participants were enrolled in the current baseline study. Among them, 285 (2.35%) samples tested positive for microhaematuria and 21 (0.20%) positive for S. haematobium eggs. A total of 4,357 samples were examined in year 1 and year 2 using urine dipsticks, and urine filtration 172 (3.95%) and 2 (0.05%) were positive for microhaematuria and S. haematobium eggs. The reagent urinalysis dipsticks showed the highest sensitivity and specificity for diagnosing light intensity of infection,100% (95% CI:85.18-100.00) and 97.4% (95% CI: 97.10-97.60), respectively. There is a slight agreement between the two methods (Kappa = 0.09, 95% CI: 0.01-0.18). The present study revealed very low prevalence and light intensity of S. haematobium infections. The study also highlights that the dipstick test is considered a useful adjunct diagnostic tool for population-based control of urogenital schistosomiasis