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

WERBAJH SANTIAGO; LAROCCA LUCIANA; CARRILLO CAROLINA; STOLOWICZ FABIANA; OGAS, LORENA; SERGIO PALLOTTO; SOLANGE CASSARA; MAMMANA LILIANA; ZAPIOLA INÉS; BOUZAS MARÍA BELÉN; VOJNOV ADRIAN

Viruses

Multidisciplinary Digital Publishing Institute (MDPI)

Lugar: Basel; Año: 2023 vol. 15

Since, during the Coronavirus disease 19 (COVID-19) pandemic, a large part of the humanpopulation has become infected, a rapid and simple diagnostic method has been necessary to detectits causative agent, the Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2),and control its spread. Thus, in the present study, we developed a colorimetric reverse transcriptionloop-mediated isothermal amplification (RT-LAMP) kit that allows the detection of SARS-CoV-2 fromnasopharyngeal swab samples without the need for RNA extraction. The kit utilizes three sets ofLAMP primers targeting two regions of ORF1ab and one region in the E gene. The results are based onthe colorimetric change of hydroxynaphthol blue, which allows visual interpretation without needingan expensive instrument. The kit demonstrated sensitivity to detect between 50 and 100 copies of theviral genome per reaction. The kit was authorized by the National Administration of Drugs, Foodand Technology (ANMAT) of Argentina after validation using samples previously analyzed by thegold standard RT-qPCR. The results showed a sensitivity of 90.6% and specificity of 100%, consistentwith conventional RT-qPCR. In silico analysis confirmed the recognition of SARS-CoV-2 variants ofconcern (B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427, and B.1.429), and lineages of the Omicron variant(B.1.1.529) with 100% homology. This rapid, simple, and sensitive RT-LAMP method paves the wayfor a large screening strategy to be carried out at locations lacking sophisticated instrumental andtrained staff, as it particularly happens in regional hospitals and medical centers from rural areas.