If you're baking a cake, maybe one you haven't tried before, do you set the oven at a temperature, cook it for exactly xyz minutes, then turn the oven off, pull the cake out and eat it? Or do you leave the oven on while you check the cake is baked, and if it isn't leave it in?
In PCR'land we don't take our tubes out & test them, but we "set and forget" to a MAX baking time (=total number of cycles; at 40-50). We come back at the end & see the results. Virus positive samples show up *before* the run is completely finished (15-30 cycles, with some later)
In the real-world RT-PCR result below you can see a bunch of positive curves for flu (the negatives are the flat lines underneath the red threshold).
Doesn't matter what the final cycle number is (how long the oven was on), just that it allows all the ingredients to be cooked.
Leaving the cake analogy now (because it would just get confusing).

Where the curve for each sample crosses that red threshold 👆is called the "threshold cycle", or Ct.
You can see that the Cts are very different in cycle number from the final cycles (the endpoint of the PCR).
In fact, every patient sample in that real-world example👆 has a slightly different Ct, just reflecting that every person has a slightly different amount of virus in their sample (affected by lots of things); sometimes not so slight!
Some other info and a stylised PCR curve showing the endpoint (starred; what most non-users confuse with Ct when talking about cycles)

Happy to answer real questions.

Resources...
🧬
🧬
🧬virologydownunder.com/putting-pcr-in…

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More from @MackayIM

Aug 16, 2023
For the AJ Leonardi fans recent quote posts of me (he blocked me, so it took others to point them out🙏; I've returned the favour now), I'll add that the definition of "immune" or "immunity" does not imply never getting infected. It's a term scientists use & it can differ from..
..that used by you in the wider community.
To us, if I can speak for all scientists (!I can't🙂), it means your body has mounted an immune *response*. That response - such as the one _most humans_ mount to SARS-CoV-2 after infection (whole virus) or vaccination (mainly Spike...
..protein) generally make future infection by the same thing, less severe. Having immunity (producing or 'mounting' an immune response) protects you from serious disease (hospital-level stuff) & death. It may protect you from less severe disease too. Not all vaccines are as..
Read 17 tweets
Apr 4, 2023
#COVID19 in Australian hospitals over the last 12 months.
Creeping up from the lowest base over that period.
But what is the State of Queensland doing?
I don't think anywhere else in Aus has had this strange little peak and drop at this time.
If look at the entire pandemic in Australia, we see there's still a *long* way to go before we see a 'flu-like' pattern of a between-peak drop to a baseline of basically zero hospitalisations.
If it ever drops to that of course.
Read 5 tweets
Mar 9, 2023
😷Respiratory virus data in these tweets are from Sullivan Nicolaides Pathology (SNP) lab weekly report.
😷They service #Queensland, northern New South Wales and wider Darwin area and Alice Springs
•Reports: snp.com.au/clinicians/res…
•SNP locations:snp.com.au/our-locations/
😷A reminder that whatever respiratory signs & symptoms bring a patient in for a test/Doctor's visit - many very different respiratory viruses can cause that disease. Only a good pathology laboratory test has a hope of identifying a cause.
🧬Detailed public-facing PCR data from a private lab in Queensland, Australia (thankyou🙏) showing #Flu % positivity around 6%↔ (about 1 in 16 samples tested are FluA or FluB positive).
•FluB showing its spiky face but FluA dominating
•RSV and rhinovirus number⬆
Read 5 tweets
Feb 11, 2023
Equatorial Guinea quarantines 200 after unknown hemorrhagic fever deaths.
reuters.com/world/africa/c…
"Equatorial Guinea said on Wednesday that it had registered the "unusual epidemiological situation" over the past weeks in Kie-Ntem province's Nsok Nsomo district that caused nine deaths in two adjacent communities over a short period."
Read 9 tweets
Feb 4, 2023
🔅What follows is not to minimise serious impact of COVID-19. Because many things are true at once. 🔅

Pre-pandemic, excess deaths from heart & other issues were associated with respiratory virus seasons-Flu, RSV, MPV etc.
Cleaned air & 😷 will also reduce risk of those harms
We've never succeeded in removing those harms or, in many nations, made serious non-vax efforts to reduce the risks, although a well matched flu vaccine likely helps them for flu.
But now SARS-CoV-2 has added more harms to the pile.
We have plenty of evidence of airborne spread for all respiratory viruses. Including SARS-CoV-2. We have plenty of evidence of how to interfere with that without needing to lockdown.
Yes, even masks (despite some poorly thought out studies) have a role.
Read 4 tweets
Jan 27, 2023
We are all playing Covid roulette. Without clean air, the next infection could permanently disable you.
-a pretty full summary of the worst of it all.
1/7
theguardian.com/commentisfree/…
"Do we really mean to sit and watch as this infection encroaches on our freedom to be well, brutal winter after brutal winter?"
🦠Of course "No", but I can't square that with the fact that in my lifetime, there's been no action but a vaccine for the same question about influenza
Because we prove again & again that we have short memories. We'd rather fight than learn/progress.
We're easily distracted & don't care about the death of our elderly (we do seem to care about neonate & infant deaths)
Not very hard to see why we *must* have leadership.
3/7
Read 7 tweets

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