Performance of two SARS-CoV-2 rapid antigen detection tests in resource limited settings, the case of Mali.

Introduction: While real-time reverse transcription PCR (RT-PCR) is the recommended laboratory method to diagnose severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection, its use in resource limited settings can be difficult to maintain due to high testing demand and shortage of reagents. The aim of this study was to evaluate the performances of Realy Tech™ and Standard Q™ in comparison to RT-PCR in a relatively low COVID-19 prevalence setting, Mali. Methods: We conducted a cross-sectional study between January and April 2021 in Bamako and Kati regions to evaluate both rapid tests during a large SARS-CoV-2 prevalence study in Mali. Results: Of the 390 samples tested, the sensitivity and specificity of Realy Tech™ and Standard Q™ were 57.1% (95%CI: 44.1-69.2), 95.8% (95%CI: 93.1-97.5); 61.9% (95%CI: 46.8-75.0), and 94.1% (95%CI: 89.5-96.8) respectively. Using RT-PCR, the global prevalence of SARS-CoV-2 was 14.4% (56/390). In both rapid antigen tests, the performance was better when used in suspected patients compared to positive patients under treatment. Moreover, higher viral loads equivalent to Ct < 25 were associated with better detection rates. Conclusion: While waiting for more complete data, these preliminary studies suggest that Realy Tech™ and Standard Q™ should not be used alone for COVID-19 diagnosis in Mali.

Diagnostic Laboratories' Capacities and Preparedness for Emerging Viral Diseases in Guinea and Mali.

The 2014-2016 Ebola epidemic in Guinea highlighted the need for more extensive evaluation of laboratories diagnostic capacities and preparedness in anticipation of future emerging viral disease outbreaks. We developed a questionnaire to assess the diagnostic capacities and preparedness of the four major medical laboratories in Guinea and Mali that are responsible for the provision of Ebola, Lassa, and Dengue diagnostics. The questionnaire inquired about the current state and need for equipment and reagents and adequacy of equipment and training received. In Guinea, all three diagnostic laboratories have the capacity and are well-prepared to perform Ebola diagnostics, however, only two have the capacity and trained staff to diagnose Lassa and none are currently prepared to diagnose Dengue infection. In Mali, the University Clinical Research Center (UCRC) laboratory, which was in charge of Ebola diagnostics during the last epidemic, currently has the capacity and is prepared to diagnose Ebola, Lassa, and Dengue infections. Combined, Guinea and Mali appear to have complementary capacity and preparedness to diagnose these Category A Priority Pathogens. While, the equipment, reagents and training efforts should be maintained, the gap in Dengue diagnostic capability in Guinea should be addressed with further equipping and training of additional district laboratories to strengthen the public health response for all viral diseases in these high-risk, yet, low-resource settings.

Competitive fitness of Mycobacterium tuberculosis in vitro.

Background: While, bacteria resistance mutations can affect competitive fitness, given our multidrug-resistant (MDR) prevalence, we conducted this study to determine the impact of MDR on the competitive fitness of Mycobacterium tuberculosis (MTB) complex MDR strains. We conducted a cross-sectional study at the University Clinical Research Center (UCRC) from January to December 2017. New TB patients over aged of 18 were recruited at University teaching hospital and health reference centers of Bamako in USTTB Ethical committee approved protocols. Methods: MDR and drug-susceptible (wild-type [WT]) MTB strains (T1 and Beijing) and MTB H37Rv were competed on solid media in UCRC's Tuberculosis Laboratory. Competitive and individual cultures were incubated for 14 days at 37°C with 7% CO2. Number of generation, generation time, and relative competitive fitness (W) of the strains were calculated. Data were analyzed with Epi-Info 7.1.5.2 software (CDC). P value was considered significant when it was <0.05. Scientific calculator (CS-82TL) was used for competitive fitness parameters calculations. Results: We performed 24 competitive cultures and 10 individual cultures. In individual cultures, strains' generation number was for Beijing (WT: 4.60 and mutant MR: 4.40), T1 (WT: 2.69 and MR: 2.37), and H37Rv: 2.91. Generation number of WT strains was less than those of MDR strains in both individual and competitive culture. Relative competitive fitness was below 1 (W<1) in 83.3%. Conclusion: MDR strains were less competitive than WT strains in 83.3% of cases. Resistant mutation impacts bacteria fitness.