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Rapid, low-cost and efficient molecular diagnostics and large-scale population testing strategies for COVID-19 management

Grant number: 20/05949-2
Support type:Regular Research Grants
Duration: July 01, 2020 - June 30, 2022
Field of knowledge:Biological Sciences - Genetics - Human and Medical Genetics
Principal Investigator:Mayana Zatz
Grantee:Mayana Zatz
Home Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Assoc. researchers:Germán Gustavo Sgro ; Maria Rita dos Santos e Passos Bueno ; Michel Satya Naslavsky ; Miguel Mitne Neto ; Shaker Chuck Farah ; Yeda Aparecida de Oliveira Duarte
Associated research grant:13/08028-1 - CEGH-CEL - Human Genome and Stem Cell Research Center, AP.CEPID

Abstract

Successful response to the COVID-19 pandemic caused by the new coronavirus (SARS-CoV-2) has been observed in countries equipped with resources that enable mass testing of the population, such as South Korea (Normile, 2020). With increasing international demand for laboratory supplies, countries such as Germany, Singapore and South Korea have been redirecting their industrial capacity to produce their own supplies and successfully alleviate demand for diagnostic tests (Editorial in Nature, 2020). However, most nations are not technologically self-sufficient to produce reagents, particularly those required for probe-based RT-qPCR (i.e. Taqman®), which is currently widely employed for SARS-Cov-2 diagnostics, as recommended by the CDC (Centers for Disease Control and Prevention, US) (Reusken et al., 2020). Therefore, development of alternative tests that are fast, low-cost and efficient is increasingly urgent. Brazil's high dependency on imported supplies for molecular diagnostics has been a major limiting factor for widespread population testing, as it delays and makes the process costly. Given such limitations, we propose the development of a molecular biology-based diagnostic test with the use of RT-LAMP (reverse transcription loop-mediated isothermal amplification), a sensitive, low-cost method that does not rely on sophisticated equipment or laboratory conditions that can be carried out on any site, even those with minimal infrastructure (Hong et al., 2004; Lamb et al., 2020; Shirato et al., 2014; Silva et al., 2019a; Zhang et al., 2020). This proposal includes in-house production of the enzymes required for RT-LAMP to resolve the reliance on imported supplies. We will also evaluate the sensitivity of RT-LAMP in pool testing (5-20 pooled samples), which will allow mass triage of COVID-19 cases and identification of population groups at higher risk. The development of these protocols will generate technological capacity and knowledge that will enable creation and nation-wide production of fast molecular diagnostics methods for COVID-19, which could be easily adapted to detect other pathogens. The present approach will provide means to prepare Brazil for future crises of similar nature and to develop population triage approaches to guide authorities in the management of SARS-CoV-2. (AU)