Guy, thank you for your excellent and informative answers much appreciated.
Have looked a bit more into this claim that you might be more likely to get a false positive if you are infected with another coronavirus that isn't SARS2.
It seems this mostly comes from a controversial off-guardian article called something like "COVID19 PCR Tests are Scientifically Meaningless". That article is full of distorted and misleading claims, one of which is that the test may confuse SARS2 with other coronaviruses and that the WHO seem to be encouraging this.
What seems to have happened is that a German lab developed a SARS2 test before SARS2 had even been sequenced, by looking for bits of SARS1 that they had in common (which presumably they found by guessing). The test found bits of the "E" gene that SARS1 and SARS2 share. But the sequences they were looking for are not found in any other known human coronaviruses.
Newer tests also look for other parts of the genome (most tests look for a few). So the question arose what conclusion should you draw if you match on 'E' but not on anything else? Either you have SARS1 (or some other unknown related virus) or, which is far more likely, the test just didn't find enough of that other gene to pass the threshold. The WHO concluded that if you match only on E then you might as well call that a match.
If you're using the test to decide whether to quarantine or trace contacts during an epidemic (such as happened in Iceland) it makes sense to treat an 'E' gene only match as a positive. You will not match on 'E' if you have any other cold (any more than the normal false positive rate). The bits they're looking for are only shared between SARS1 and SARS2 out of known coronaviruses. You probably don't have SARS1 but if you do, you should quarantine yourself anyway, since it's like SARS2 only worse. On this occasion the WHO are giving good advice.
The test is highly specific and will not match on other common cold viruses. It's not 100% specific because nothing is. Contamination and human error are the most likely causes of false positives. The false positive rate is low, nobody knows exactly how low-- certainly less than 5% but more than 0%. This just means that when prevalence is down to less than that you need to treat the results with a lot of caution. The low sensitivity is generally considered a bigger problem, but this matters when prevalence is high, which in the UK it isn't. But it will be a problem in Australia for example where the epidemic is just starting to kick off.
Interesting article yesterday by Prof. Carl Heneghan:
https://www.cebm.net/covid-19/covid-cases-in-england-arent-rising-heres-why/
The more you test the more you find. But are the results significant?
Yes, very good article. He's put his finger on the real problem, which is very real, impossible to argue with, and doesn't rely on outlandish claims about the test being "scientifically meanginless" or anything.
"The potential for false-positives (those people without the disease who test positive) to drive the increase in community (Pillar 2) cases is substantial, particularly because the accuracy of the test and the detection of viable viruses within a community setting is unclear."
This is exactly the problem.
What I can't get my head around is why Pillar 2 testing gives far more positive results per 100,000 tests when the tests are done on a Wednesday, and fewest positive results when done on a Sunday or Monday??
There's definitely a weekly pattern; why should far more positive test results occur mid-week compared to the beginning?
