Fig 7.
The frequencies of SARS-CoV-2 mutations in genomic regions targeted by the primers and probes of the diagnostic PCR tests A) The regions targeted by popular PCR tests have lower missense mutation rates when those regions are structurally characterized or map to the RdRP structure, and higher missense mutation rates when the regions are structurally disordered. On the other hand, the rate of synonymous mutations remains roughly the same. B) Examples of the effects of constraints imposed by encoded proteins on rates of mutations in regions targeted by the PCR tests. The region targeted by the 2019-nCoV_N1 PCR test (top) encodes the structurally disordered linker region of the Nucleocapsid protein. The region targeted by the nCoV_2019 PCR test (bottom) encodes the RNA-dependent RNA polymerase (RdRP). All reported counts are based on 192,030 high-coverage genomes obtained as of Dec 3rd, 2020 from the GISAID website.