Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics
Chamteut Oh, Palash Sashittal, Aijia Zhou, Leyi Wang, Mohammed El-Kebir, Thanh H. Nguyen
Abstract
Monitoring the introduction and prevalence of variants of concern (VOCs) and variants of interest (VOIs) in a community can help the local authorities make informed public health decisions. PCR assays can be designed to keep track of SARS-CoV-2 variants by measuring unique mutation markers that are exclusive to the target variants. However, the mutation markers may not be exclusive to the target variants because of regional and temporal differences in variant dynamics. We introduce PRIMES, an algorithm that enables the design of reliable PCR assays for variant detection. Because PCR is more accessible, scalable, and robust for sewage samples than sequencing technology, our findings will contribute to improving global SARS-CoV-2 variant surveillance.