For assessment of sequence variability in primer/probe binding regions of diagnostic PCR assays you may use
- Ready-to-use MSA file (see components section)
- Our step-by-step protocol published in bioprotocols
**References:**
Kashif Aziz Khan and Peter Cheung. 2020 Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome. R. Soc. open sci. 7:200636
https://doi.org/10.1098/rsos.200636
Kashif Aziz Khan and Peter Cheung. 2020 Evaluation of the Sequence Variability within the PCR Primer/Probe Target Regions of the SARS-CoV-2 Genome. Bio-protocol 10(24): e3871. https://doi.org/10.21769/BioProtoc.3871