Background Early detection of pathogens is of outmost importance for managing epidemic outbreaks. Primary healthcare laboratories in low-and middle-income countries often lack comprehensive diagnostic and surveillance capacities due to limited resources and infrastructures. The Gates Foundation supported the International Centre for Genetic Engineering and Biotechnology (ICGEB) in establishing a platform for the sustainable transfer of diagnostic and surveillance technologies to community laboratories in Africa. The technology transfer is facilitated through an initial testing at ICGEB followed by a multicentric clinical trial in recipient countries, while support for regulatory approval is also provided. This workflow was successfully applied to an isothermal amplification colorimetric molecular assay (RT-LAMP) for RNA viral detection.

Methods The testing of RT-LAMP for SARS-CoV-2 developed by New England Biolabs was based on a multicentric observational and cross-sectional clinical study on 1657 prospective swabs collected in four African countries and Italy. The sample size included 25% negative, 50% positive and 25% weakly positive samples, while extracted RNA was tested in parallel with the diagnostic standard RT PCR. The test was rolled out to six additional African countries and a further optimized version allowing to skip RNA extraction was tested in four countries, such that the current field trial tested 2419 swabs and 589 saliva samples.

Results RT-LAMP from swabs resulted highly specific (98%), with positive predictive value 99%, and 87% sensitive with negative predictive value 70% compared to standard RT PCR. Stratification of RT-PCR data showed superior sensitivity achieved with a cycle threshold (Ct) below 35 (97%), which decreased to 60% above 35. Similar values were obtained with saliva direct testing. The test was approved in Kenya and Nigeria.

Conclusion RT-LAMP performance is comparable to RT-PCR, particularly with medium-high viral loads, hence it can be deployed in resource-limited settings for timely management and prevention of COVID-19 and other diseases.