In late November 2022, representatives from ten African laboratories and partners of the COVID-19+ project met in Addis Ababa, Ethiopia, for the first “RT-LAMP and Community Laboratories Diagnostic Empowerment” workshop.
Co-organised and hosted by the Bio and Emerging Technology Institute (BETin), the workshop represented an opportunity for African partners and ICGEB scientific and project management teams to meet in person for the first time, since the commencement of the project in 2020, to discuss the progress of the clinical study on RT-LAMP in each partner country.
More than 30 participants recounted country-specific experiences and challenges during the testing phase, reflecting great committed to find solutions to common issues related to the assay and its management.
Dr. Eric Agola from Kenya, commented “this technique is very straightforward, particularly when it comes to the interpretation of results. Because we are just using the naked eye to read the colour change, the expensive equipment needed in PCR is not required.” In Ethiopia, RT-LAMP has been tested in ten labs and, as reported by Dr. Molalegne Aserese, it was found that “the test was very powerful, almost similar to RT-PCR”.
Testing performed in nine African countries confirmed the reliability of RT-LAMP for detection of SARS-CoV-2. African partners believe RT-LAMP can be used interchangeably with RT-PCR, which is acknowledged to be more precise and sensitive and therefore should be maintained as the reference method.
The short reaction time of RT-LAMP (30 minutes) and the colorimetric readout makes it perfectly tailored to emergency cases and when situations require quick and reliable diagnostics.
Overall, the consortium believes RT-LAMP will help LMICs mitigate supply chain challenges for RT-PCR reagents, most of which are not available on local markets or are received as donations from abroad.
The main goal of the COVID-19+ project is the diagnostic and surveillance empowerment of community labs in Sub-Saharan Africa. In the coming months project activities will expand beyond RT-LAMP testing and COVID-19.
From discussions, it emerged that partner countries are facing constant challenges in the diagnostics of Arboviruses, which are frequently mis-diagnosed due to the prominence and co-existence of Malaria in Sub-Saharan Africa. At the same time, the lack of surveillance programmes for arboviral diseases results in knowledge gaps regarding circulating variants in the African Continent.
The consortium considered an adaptation and further development of RT-LAMP for the detection of arboviruses would greatly help to fill the existing gap and would empower community labs in providing rapid and correct diagnosis to local populations. ICGEB is currently developing the assay in collaboration with NEB for the detection of Zika – this is the starting point for further adaptation to other arboviruses, such as Dengue or Chikungunya.
Looking to the future: in order to overcome the limited access to reagents for diagnostics of many community labs, ICGEB proposed to test in a field trial the Sustainable LAMP protocol, which is under development and stems from the protocol designed by Andy Ellington from the University of Texas for the development of cellular reagents via expression on bacteria (E. coli). The polymerase expressed could be used for the development of LAMP kits to be deployed for diagnostic purposes. The starter kit, comprising bacteria and reagents, will be tested on SARS-CoV-2 and, if shown successful, the approach can conceivably be extended to other pathogens, such as Arboviruses.
The SARS-CoV-2 experience demonstrated the importance of performing genomic sequencing at multiple levels in public health for a prompt management of the pandemic. Partners will test the ONT Mk1C MinION using a tailored ARTIC protocol for SARS-CoV-2 sequencing, which thanks to its portability and rapidity in data elaboration and sharing, should facilitate empowerment of community labs for the performance of decentralised and low-cost genomic sequencing.