Validation and operationalization of LAMP assays for COVID-19 diagnosis in low-resourced health facilities in Ghana

The rapid spread of the novel coronavirus disease, COVID-19, necessitates early detection of infected persons as part of strategies to identify and control community transmission. The current 'gold-standard' method for detection of SARS-CoV-2 is based on RT-qPCR. Although this technique is sensitive, the turnaround time (TAT) takes several hours, often days, limiting its use as a quick test for clinical management, and also makes it less suitable for mass screening. Our ultimate goal is to seek a COVID-19 diagnostic method that can be used at all levels of the health system and for field research. We will evaluate a one- and two-stage loop mediated isothermal amplification (LAMP) assay that allow samples to be run within an hour at constant temperature(s). These assays do not require high throughput sample processing, hence reducing the time required for refined nucleic acid extraction. The newly developed LAMP methods will be validated using nosocomial, nasopharyngeal/oropharyngeal and sputum samples previously collected and tested for SARS-CoV-2 using RT-qPCR. Using RT-qPCR as the gold standard, sensitivity, specificity and, negative and positive predictive values will be compared with the LAMP results. In addition, the processing time will be evaluated in real-time and a cost-benefit analyses using the two diagnostic methods will be performed. Once validated and found to be affordable for use in low-resourced settings, capacity will be built through training of hospital laboratory staff to use the assays. There will be further evaluation of the methods as a point-of-care tool at lower levels of the health-care system and for mass COVID-19 screening. Expected Outputs At the end of this study, the effective and most sensitive LAMP assay would be determined as a rapid method for detection of SARS-CoV-2 in clinical samples. In addition, the use and cost-effectiveness of lyophilized reagents for the assay intended particularly for use in lower healthcare settings and field screening of COVID-19 would be determined. We would also build the capacities of laboratory/technical staff in performing LAMP assays for COVID-19, which could potentially be replicated across Africa and other low- and middle-income countries.