Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

A Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants of Concern and Lineages from Direct Nasopharyngeal Swab Samples without RNA Isolation

Santiago Enrique Werbajh
ORCID logo ,
Luciana Larocca
,
Carolina Carrillo
,
Fabiana Stolowicz
,
Lorena Ogas
,
Sergio Pallotto
,
Solange Cassará
,
Lilia Mammana
,
Inés Zapiola
,
María Belén Bouzas
ORCID logo ,
Adrián Alberto Vojnov
*
Version 1 : Received: 26 July 2023 / Approved: 27 July 2023 / Online: 28 July 2023 (13:29:56 CEST)

A peer-reviewed article of this Preprint also exists.

Werbajh, S.; Larocca, L.; Carrillo, C.; Stolowicz, F.; Ogas, L.; Pallotto, S.; Cassará, S.; Mammana, L.; Zapiola, I.; Bouzas, M.B.; Vojnov, A.A. Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation. Viruses 2023, 15, 1910. Werbajh, S.; Larocca, L.; Carrillo, C.; Stolowicz, F.; Ogas, L.; Pallotto, S.; Cassará, S.; Mammana, L.; Zapiola, I.; Bouzas, M.B.; Vojnov, A.A. Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation. Viruses 2023, 15, 1910.

Abstract

A large population has been infected by COVID-19 (Coronavirus disease-19) and it has been necessary a rapid and simple diagnostic method to detect the SARS-CoV-2and control its spread. We developed a colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) kit that allow the detection of SARS-CoV-2 from nasopharyngeal swab samples without the need of RNA extraction. The kit utilizes three sets of LAMP primers targeting two regions of ORF1ab and one region in the E gene. The results are reported using colorimetric change of hydroxynaphthol blue, enabling visual interpretation without the need for expensive instrument. The kit demonstrated sensitivity to detect between 50 and 100 copies of the viral genome per reaction. The kit was authorized by the National Administration of Drugs, Food and Technology (ANMAT) of Argentina after validation using samples previously analyzed by gold standard RT-qPCR. The results showed sensitivity of 90,6 % and specificity of 100%, consistent with conventional RT-qPCR. In silico analysis confirmed the recognition of SARS-CoV-2 Variants of Concern (VOCs) B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427, B.1.429and lineages of variant Omicron (B.1.1.529) with 100% homology. This rapid, simple, and sensitive RT-LAMP method paves a way for a large screening strategy to be carried out at locations lacking sophisticated-instrumental and trained-staff, as particularly happen at regional hospitals and medical centers from rural areas.

Keywords

COVID-19; SARS-CoV-2; LAMP

Subject

Biology and Life Sciences, Virology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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