Mutational analysis of SARS-CoV-2 hybridization sites for real-time RT-qPCR primers and de novo design of Omicron-specific primers

Identifier:  TFG:5610

Handle: https://hdl.handle.net/20.500.11797/TFG5610

Authors:  Novau Ferré, Nil

Abstract:
SARS-CoV-2 is the cause of the new COVID-19 and there is still no definitive cure for the disease. Therefore, it's critical to study the virus's mutational evolution to spot variants that could develop viral resistance to treatments. In this work, we perform a mutation profiling of more than 4,000,000 SARS-CoV-2 genomes. On the other hand, the RT-qPCR tests for SARS-CoV-2 face several difficulties, because as the virus evolves, the approach may lose sensitivity. We measure the number of mismatches between primer sequence and genomic targets. Additionally, we show variant-specific primer design with high sensitivity and specificity to the Omicron variant.