Laboratory experience in massive SARS-CoV-2 mutation screening using laboratory-developed tests

ABSTRACT

Objectives. The main goal of the study was to develop laboratory-developed tests (LDT) for monitoring SARS-CoV-2 variants of concern (VOC) currently present in Latvia. METHODS. We have studied the latest scientific articles to prognose specific mutations that could be indicators of VOC. Mutations responsible for immune escape were chosen as targets for our LDTs. Multiple TaqMan RT-PCR LDTs detecting alfa, beta, gamma, delta and omicron strains in nasopharyngeal swab and saliva samples were developed and validated in our laboratory. RESULTS. More than 15,000 SARS-CoV-2 positive samples were tested. In total, 10,874 different VOCs of SARS-CoV-2 were found by our LDTs. Beta, delta and omicron strains were first detected in Latvia by E. Gulbis Laboratory. Sanger sequencing methods for RT-PCR result confirmation were also developed. The first cases of VOCs detected by the RT-PCR method were also confirmed in our laboratory by Sanger sequencing. Our results were later confirmed by the National Reference Laboratory. CONCLUSIONS. Using our laboratory capacity and intellectual potential, we have developed skills for an urgent response to future VOCs of SARS-CoV-2 or other potentially harmful infectious diseases.