The world seemed to have a time in 2020 when it's message was unified: "flatten the curve".
But with the benefit of hindsight, we should have been saying "crash the curve". Instead we all kinda went our separate ways after Wave 1.
Some of us got back to baseline, or very close, before "opening up". Others instigated a percent positive threshold below which it was magically okay to get back out & about (as if 1 case wouldn't start it all again) but that left lots of virus spreading throughout the community.
Others encouraged everyone to get back out & save the economy.
Some had a plan for what to do next which included increasing testing & communication & border controls. Some had no plan, waiting for a vaccine. Travelling as usual, because holidays! Sun!
The result was that most places have had a ratcheting curve where the original baseline was never seen again only built upon, instead creating massive spread & more chances for a novel human virus, regardless of season, to spread rapidly and further mutate. At the same time
we build an increasingly immune population - within which some are likely to be more or less susceptible to reinfection (a perhaps rare event that will scale with infection numbers). Add to that a gradually immune population due to spike-targeted vaccines. Chances for SARS-CoV-2
..to mutate to escape that immune pressure (on-the-fly or during a reinfection, but also in new infections of those with immune compromise) abound. I don't really give two figs about whether a polymerase is or isn't more likely to introduce more mutations in this or that virus,
...because of these circumstances. We simply don't care enough to identity & communicate on a similar process occurring in our old viral enemies as they escape vaccines every damn season. Because we didn't have a global plan for what to do next, we've left ourselves in a
right mess. Smash the curve should have been followed by, "zero covid is better than rolling lockdowns, fear & widespread death & disease". High level messaging. With hindsight again, the justification should have included warnings about the risk of mutation. But it didn't.
We retreated to our own jurisdictions and, it seems to me anyway, many really didn't even bother to look out the window again to see or copy what others who were running a host of real-time experiments, could teach them. This is a pandemic but many have spent months reacting as
if it was only a local problem that could only be solved by (reinventing) creating brand new local responses. Leadership was essnetiwal for local responses but also to global ones. Next we need global leadership on whether to invest in mRNA vaccine production capacity for the
the future. Or shall we just wait and see if something better happens, as humans are so great at doing?
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On this "Australia" day I'm extremely grateful for the jurisdictional across which advised State leaders on COVID-19. I'm also grateful that State leaders listened & acted on that advice. I'm grateful for our established health systems that could support that advice.
We never have openly chased down eradication (local elimination) of SARS-CoV-2 transmission, but in saving lives, reducing fear & protecting livelihoods, Australia got to the same point just via a different route.
By aiming to address fear, prevent illness and support jobs, Australia's leaders really couldn't have ended up anywhere but eradicating SARS-CoV-2 from within its borders. That's what was needed to meet those goals. We've seen that "living with the virus" is actually
What is a PCR cycle? 🧵
We sciencey types throw in words that we use for a specific purpose, but which also have other everyday meanings among most of the people on the planet.
We don't see that we do this ALL. THE. TIME.
"Cycle" is one of these words.
Here we're using "cycle" as it relates to the PCR = Polymerase Chain Reaction - a small, enzyme-driven cyclical DNA amplification reaction that we use to detect virus & do other sciency things (longer story)
When we do PCR to detect an otherwise undetectably teensy amount of DNA, we run 40 to 50 cycles of PCR. These 40 to 50 cycles (precise number varies by lab & kit) = the whole experiment (or "PCR run"), all of it.
Anatomy of a real-time PCR or RT-PCR (PCR or RT-rPCR) curve.
Two things to highlight using these stylised rPCR curves.
First.
The yellow arrows highlight threshold cycles.
These are the "results". The number from the point at which each curve crosses that arbitrary horizontal threshold are recorded by the lab and reported as "detected"
Second.
These values are *not* the same numbers as the TOTAL number of cycles that the rPCR is run for (you can read about cycles here if of interest virologydownunder.com/the-mechanics-…)
That website opinion attack piece on the Corman/Drosten RT-rPCR tests has a few confused & sometimes very wrong comments.
I'll preface this thread with a *presumption* I'm making - these authors haven't worked on or with this test themselves. And that matters a lot if true.
I'm not going through everything but here's one from their "Top10 things I hate about this test" list.
From Number 5. "nor does it contain any other negative controls"
But Corman et al. are actually very clear that negative controls were included.
"all assays were tested 120 times in parallel with water and no other nucleic acid except the provided oligonucleotides. In none of these reactions was any positive signal detected"
But even better, they tested primer specificity on a lot of human viruses, including CoVs: