Fast, low-cost and highly specific colorimetric RT-LAMP assays for inference of SARS-CoV-2 Omicron BA.1 and BA.2 lineages

Abstract

Two lineages (BA.1 and BA.2) of the Omicron variant are the main ones responsible for the recent COVID-19 pandemic waves worldwide. Monitoring the prevalence and spread of these variants is important as the presence of mutations might lower the efficacy of vaccines and hinder the benefits of monoclonal antibody therapies. Although the need to screen these new lineages is emerging, genetic sequencing is scarce due to its high cost. Alternatively, we propose using reverse transcription loop-mediated isothermal amplification (RT-LAMP) to infer the prevalence of these lineages and aid in genomic surveillance in countries with limited genetic sequencing capacity. For this, we designed specific primers and tested them on a panel of 267 sequenced RNA genomes from different lineages. The test for BA.1 and its descendants showed 96.63% sensitivity, 100% specificity, and 98.85% accuracy, and the test for BA.2 and descendants showed 90.00% sensitivity, 98.85% specificity, and 98.52% accuracy. These results demonstrate the potential of RT-LAMP to be an alternative to help monitor variants, especially in countries with scarce resources.