The continued waves of the COVID-19 pandemic have repeatedly strained public health systems’ capacity to provide efficient and actionable SARS-CoV-2 testing. To help address this challenge, the Propagate Network – a collaboration of public health and research laboratories from Brazil, Chile, France, Malawi, Nigeria, Trinidad and Tobago and the U.S., was convened by the nonprofit Health and Environmental Sciences Institute. Via the Propagate Network, the participants tested the reproducibility of a more rapid and lower resource methodology (“direct-PCR”) for detection of the SARS-CoV-2 virus in patients. The results of this study, published this month in PLOS ONE, demonstrated that the method is highly reproducible and thus a feasible option for more efficient COVID-19 screening around the world.
“Being part of the Propagate Network was not only a great opportunity for benchmarking our academic labs according to international standards,” said Roger Chammas - University of São Paulo, “but it also increased the awareness for the need of innovative strategies focusing on cost reduction, which are critical for low and middle income countries like Brazil.”
The participating labs used a “direct” RT-qPCR test (Bruce et al., 2020), which was sensitive enough to detect the viral RNA of SARS-CoV-2 but also required less processing time and reagents than the standard RT-PCR test. The “direct” RT-qPCR test differs from the standard three-step test (1- swab, 2- extract viral RNA, 3- amplify RNA) in that it skips step two, the RNA extraction step, which requires equipment and reagents that are not readily available worldwide. By skipping the extraction step, the testing procedure becomes more affordable and requires less equipment and processing time, feasibly making it more accessible worldwide.
“RNA extraction is time-consuming and expensive, and it generates hazardous waste that must be disposed of properly,” said Margaret Mills. “We originally conceived of this project as being helpful in resource-poor settings, but even we at the University of Washington Virology Laboratory have found ourselves resource-poor at points during the pandemic. Supply chain shortages and infection surges have sometimes made it difficult for us to test all the specimens coming in. The direct RT-qPCR test is a great alternative, and it was an honor to put our clinical specimen remnants to use assembling kits for partner laboratories to test this method.”
The Propagate Network tested the same series of positive and negative samples sent from the University of Washington to see if they could replicate results across locations. The study observed 100% concordance across laboratories in the correct identification of all positive and negative samples suggesting that a “direct” RT-qPCR test can be clearly translated across sites utilizing readily available equipment without having to purchase scarcely available reagents. Therefore the “direct” RT-qPCR test is a feasible option for more efficient COVID-19 testing which is globally in high demand.
An international, interlaboratory ring trial confirms the feasibility of an extraction-less “direct” RT-qPCR method for reliable detection of SARS-CoV-2 RNA in clinical samples. Mills et. al. January 13, 2022. PLOS ONE. https://doi.org/10.1371/journal.pone.0261853
About the Health and Environmental Sciences Institute (HESI)
HESI is a non-profit scientific foundation based in Washington, DC, USA which brings together scientists from around the world to collaboratively identify and help resolve global health and environmental challenges through the engagement of academia, government, industry, NGOs, and other strategic partners.
Syril Pettit, DrPH, MEM
Executive Director, Health and Environmental Sciences Institute (HESI)