A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS-CoV-2 in seven Sub-Saharan African countries: Lessons from the field.

BACKGROUND: The COVID-19 pandemic led to severe health systems collapse, as well as logistics and supply delivery shortages across sectors. Delivery of PCR related healthcare supplies continue to be hindered. There is the need for a rapid and accessible SARS-CoV-2 molecular detection method in low resource settings. OBJECTIVES: To validate a novel isothermal amplification method for rapid detection of SARS-CoV-2 across seven sub-Sharan African countries. STUDY DESIGN: In this multi-country phase 2 diagnostic study, 3,231 clinical samples in seven African sites were tested with two reverse transcription Recombinase-Aided Amplification (RT-RAA) assays (based on SARS-CoV-2 Nucleocapsid (N) gene and RNA-dependent RNA polymerase (RdRP) gene). The test was performed in a mobile suitcase laboratory within 15 min. All results were compared to a real-time RT-PCR assay. Extraction kits based on silica gel or magnetic beads were applied. RESULTS: Four sites demonstrated good to excellent agreement, while three sites showed fair to moderate results. The RdRP gene assay exhibited an overall PPV of 0.92 and a NPV of 0.88. The N gene assay exhibited an overall PPV of 0.93 and a NPV 0.88. The sensitivity of both RT-RAA assays varied depending on the sample Ct values. When comparing sensitivity between sites, values differed considerably. For high viral load samples, the RT-RAA assay sensitivity ranges were between 60.5 and 100% (RdRP assay) and 25 and 98.6 (N assay). CONCLUSION: Overall, the RdRP based RT-RAA test showed the best assay accuracy. This study highlights the challenges of implementing rapid molecular assays in field conditions. Factors that are important for successful deployment across countries include the implementation of standardized operation procedures, in-person continuous training for staff, and enhanced quality control measures.

Vitamin D level and its determinants among Sudanese Women: Does it matter in a sunshine African Country?

BACKGROUND: Vitamin D deficiency is a worldwide concern. The aim of the current study was to determine the vitamin D level and its contributing factors in Sudanese women. METHODS: In this cross-sectional study, 251 Sudanese women attending Family Health Centers in Khartoum, Sudan were interviewed. Following the exclusion of confounding factors, samples from 190 women were analzsed. Serum 25 hydroxyvitamin D "25(OH) D" was quantified using competitive electrochemiluminescence immunoassay. RESULTS: Participants' age ranged from 18 to 85 years with a mean age (±SD) of 40.2 (±14.06) years. The mean (±SD) vitamin D level was 13.4 (±6.72) ng/ml, ranged 3.00-36.5 ng/ml and the median was 12.7 ng/mL. In total, 157 out of 190 (82.6%) had vitamin D serum levels below 20 ng/ml (deficient); of whom, 52 (27.4%) were in the age group 21-30 years (P value = 0.228). The correlation between vitamin D level and residence outside Khartoum, sun-exposed face and hands, and face and limbs in comparison with being completely covered were found to be statistically significant (p values 0.008, 0.023, and 0.036). CONCLUSION: This study displayed a high percentage (82.6%.) of vitamin D deficiency among women in Sudan, and this in part may indicate that sunshine alone cannot guarantee vitamin D sufficiency in the tropics. Family physicians in tropical countries should screen those with clinical presentations related to vitamin D deficiency.

Serum vitamin D level, sun-exposed area, dietary factors, and physical activity as predictors of invasive breast cancer risk among Sudanese women: A case-control study.

BACKGROUND: The role of vitamin D in the development, progression, and prognosis of breast cancer, though widely studied worldwide, has been inconclusive. This study intended to assess the role of some factors (including serum vitamin D level, sun-exposed area, dietary factors, and physical activity) as predictors of the development of invasive breast cancer (IBC) among Sudanese women. METHODS: A case-control study was conducted on 200 Sudanese women (100 with newly diagnosed IBC and 100 matched healthy females). Serum 25-hydroxyvitamin D was measured through a competitive electrochemiluminescence immunoassay. Matching analysis was adopted by R version 3.4.1 making use of the "MatchIt" package for calculating propensity scores to build a confounder-adjusted, multiple generalized, linear logistic regression model. RESULTS: Participants' age ranged from 28 to 85 years with a mean [±standard deviation (SD)] of 48.10 (±12.11) years. The mean (±SD) serum vitamin D level was 12.97 (±8.60) and 13.79 (±6.79) ng/mL in breast cancer and noncancer Sudanese women, respectively [P = 0.013; odds ratio (OR) 0.862; 95% confidence interval (CI) 0.766-0.969; ß = 0.149)]. Sun-exposed area (P = 0.038; OR 0.013; 95% CI 0.000-0.782; ß = 4.339) is significantly and negatively associated with breast cancer development. While moderate physical activity (P = 0.0008; OR 2625.430; 95% CI 26.647-258673.001; ß = 7.873) is significantly and positively associated with IBC risk. Occasional consumption of milk, dairy products, eggs, and fish reduces the risk of developing IBC by 78.1%, 75.0%, 78.4%, and 76.4%, respectively. CONCLUSION: The higher the plasma vitamin D level by one unit, the lower the risk of breast cancer by 13.84%. Sedentary lifestyle, reduced sun-exposed skin area, and low serum vitamin D levels can be considered as predictors of IBC. Encouraging moderate physical activity and consumption of certain foods may, in part, decrease the precipitating risks of breast cancer. More studies and research are needed to confirm these findings.