Primer Monitor: an online tool to track SARS-CoV-2 variants that may impact primers used in diagnostic assays

ABSTRACT

Nucleic acid diagnostic tests for SARS-CoV-2, whether based on RT-qPCR, RT- LAMP or other amplification technologies, all depend on primers. While the SARS-CoV-2 genome seems to be less variable (1) than some other retroviral genomes, variants with potential effects on amplification efficiency have arisen and become prevalent in local areas. Some regions (e.g., Brazil; Madera County, CA, USA (2)) report greater than 15% of observed sequences with variants in genomic loci commonly used by diagnostic tests. We developed a streaming analysis method to identify variants that may affect specific primers, and an online tool (primer-monitor.neb.com) to allow interested users to register and track primer loci.