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Alekseenko A, Barrett D, Pareja-Sanchez Y, Howard RJ, Strandback E, Ampah-Korsah H, Rovšnik U, Zuniga-Veliz S, Klenov A, Malloo J, Ye S, Liu X, Reinius B, Elsässer SJ, Nyman T, Sandh G, Yin X, Pelechano V. Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples. Sci Rep 2021; 11:1820. [PMID: 33469065 PMCID: PMC7815738 DOI: 10.1038/s41598-020-80352-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/20/2020] [Indexed: 12/13/2022] Open
Abstract
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.
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Affiliation(s)
- Alisa Alekseenko
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Donal Barrett
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Yerma Pareja-Sanchez
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Rebecca J Howard
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, 17121, Solna, Sweden
| | - Emilia Strandback
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Henry Ampah-Korsah
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Urška Rovšnik
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, 17121, Solna, Sweden
| | - Silvia Zuniga-Veliz
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Alexander Klenov
- Hudak Lab, Department of Biology, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
| | - Jayshna Malloo
- Hudak Lab, Department of Biology, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
| | - Shenglong Ye
- Biotech and Biomedicine Science (Shenyang) Co. Ltd, Shenyang, 110000, China
| | - Xiyang Liu
- Biotech and Biomedicine Science (Shenyang) Co. Ltd, Shenyang, 110000, China
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Simon J Elsässer
- SciLifeLab, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Solna, Sweden
| | - Tomas Nyman
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Gustaf Sandh
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Xiushan Yin
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
- Biotech and Biomedicine Science (Shenyang) Co. Ltd, Shenyang, 110000, China
- Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, 110142, China
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden.
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