Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples

• Published in: Scientific reports Vol. 11; no. 1; pp. 1820 - 10
• Main Authors: Alekseenko, Alisa, Barrett, Donal, Pareja-Sanchez, Yerma, Howard, Rebecca J., Strandback, Emilia, Ampah-Korsah, Henry, Rovšnik, Urška, Zuniga-Veliz, Silvia, Klenov, Alexander, Malloo, Jayshna, Ye, Shenglong, Liu, Xiyang, Reinius, Björn, Elsässer, Simon J., Nyman, Tomas, Sandh, Gustaf, Yin, Xiushan, Pelechano, Vicent
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19.01.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/1647/1513/2216; 692/699/255/2514; COVID-19; COVID-19 - diagnosis; COVID-19 - virology; Displacement activity; DNA-directed DNA polymerase; Hot Temperature; Humanities and Social Sciences; Humans; Molecular Diagnostic Techniques - methods; multidisciplinary; Nasopharynx - virology; Nucleic Acid Amplification Techniques - methods; Reagent Kits, Diagnostic; Reagents; Ribonucleic acid; RNA; RNA, Viral - metabolism; RNA-Directed DNA Polymerase - metabolism; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Science; Science (multidisciplinary); Sensitivity and Specificity; Severe acute respiratory syndrome coronavirus 2; Virus Inactivation
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-80352-8

RT-LAMP detection of SARS-CoV-2 has been shown to be a valuable approach to scale up COVID-19 diagnostics and thus contribute to limiting the spread of the disease. Here we present the optimization of highly cost-effective in-house produced enzymes, and we benchmark their performance against commercial alternatives. We explore the compatibility between multiple DNA polymerases with high strand-displacement activity and thermostable reverse transcriptases required for RT-LAMP. We optimize reaction conditions and demonstrate their applicability using both synthetic RNA and clinical patient samples. Finally, we validate the optimized RT-LAMP assay for the detection of SARS-CoV-2 in unextracted heat-inactivated nasopharyngeal samples from 184 patients. We anticipate that optimized and affordable reagents for RT-LAMP will facilitate the expansion of SARS-CoV-2 testing globally, especially in sites and settings where the need for large scale testing cannot be met by commercial alternatives.