A Web-based Method for Designing and Validating Primer-probe Sets for SARS-CoV-2

Abstract

Coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread around the world with high mortality rates. Since this virus constantly mutating rapidly, it causes different kinds of variants such as the Delta Plus variant, and this variant even dominated the original Delta variant. Thus, designing a new primer-probe set is required to cope with the new variant effectively. However, the existing primer-probe set design tools are also effective in designing for a given sequence, but it is difficult to consider all variants or off-target. Here, we introduce a web-based method for designing and validating primer-probe sets for SARS-CoV-2. Through the web server we built, a user could get results of the binding site matching, homology tests, and variant coverage calculation of the primer-probe set they designed. Moreover, a user also could find the primer-probe sets which bind as many SARS-CoV-2 variants as possible by using the user-input FASTA sequence. We believe that our web service would help researchers by reducing the difficulty of designing primers and probes of SARS-CoV-2. © 2021 IEEE.