This is not a "bombshell", at least not as presented.
PCR doesn't just have to match on a primer. It has to match on two primers, and the number of nucleotides between those two primers has to be about the same between two different genomes to get a false positive PCR result.
The primers being a perfect match is much less important than two primers being a partial match among two approximately equal length sequences.
For example, if I have a sequence
ACTGAAAAAAAAAAAAACTG
and another sequence
GCTGCCCCCCCCCCCCACAG
you will notice the first four and last four of each are close to each other, and the length is close, but the actual sequence in between is completely different.
If I use the primers TGAC and CAGT it will perfectly match the first one, and partially match the second one. It will match the second one well enough that it will get built by the polymerase and will, with enough cycles, produce a signal close to the first one on a gel (how we determine sequence length) that it will be basically impossible to tell the difference.
In the case of the Nucleocapsid protein, which the CDC recommended primers look for, the sequence similarity may be similar enough to other viruses that the primers match. Having looked up the lengths of a couple RNA virus nucleocapsids here (page 4) and here (page 11), the length of the sequence is similar enough (about 1250 ish base pairs) that if the primers are close enough, its going to get a positive signal from many possible viruses.
I do not know if the sequences where the CDC recommended primers are is similar enough. I should do a comprehensive analysis at some point, but the protein size is close enough between viruses, and such nucleocapsid proteins are reasonably well conserved, so its entirely possible that the CDC test is producing false positives from nearly every similar RNA virus including maybe all the influenza variants. That is a supposition, not a statement.
This is not a "bombshell", at least not as presented.
PCR doesn't just have to match on a primer. It has to match on two primers, and the number of nucleotides between those two primers has to be about the same between two different genomes to get a false positive PCR result.
The primers being a perfect match is much less important than two primers being a partial match among two approximately equal length sequences.
For example, if I have a sequence
ACTGAAAAAAAAAAAAACTG
and another sequence
GCTGCCCCCCCCCCCCACAG
you will notice the first four and last four of each are close to each other, and the length is close, but the actual sequence in between is completely different.
If I use the primers TGAC and CAGT it will perfectly match the first one, and partially match the second one. It will match the second one well enough that it will get built by the polymerase and will, with enough cycles, produce a signal close to the first one on a gel (how we determine sequence length) that it will be basically impossible to tell the difference.
In the case of the Nucleocapsid protein, which the CDC recommended primers look for, the sequence similarity may be similar enough to other viruses that the primers match. Having looked up the lengths of a couple RNA virus nucleocapsids here (page 4) and here (page 11), the length of the sequence is similar enough (about 1250 ish base pairs) that if the primers are close enough, its going to get a positive signal from many possible viruses.
I do not know if the sequences where the CDC recommended primers are is similar enough. I should do a comprehensive analysis at some point, but the protein size is close enough between viruses, and such nucleocapsid proteins are reasonably well conserved, so its entirely possible that the CDC test is producing false positives from nearly every similar RNA virus including maybe all the influenza variants. That is a supposition, not a statement.