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Next stages for Covid
General Boards - COVID
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Next stages for Covid

Sep 28, 2021, 7:45 AM

Below is a cross post from a data scientist I really respect. It's quite thoughtful and insightful I believe and hopefully can get us to a different conversation going forward:

The reproductive rate of a virus, R0, indicates how many people an infected person will infect. The higher the value of R0, the more transmissible the virus. The more transmissible, the more people need to be protected to attain herd immunity, H.

We can estimate H = 1 - 1/R0

The chart plots this out.

"OG" Covid with a 2.5 or so R0 required 60% protection. By June in the US, we were at that point: 10% of the US had a confirmed virus, probably meaning ~25% actually were infected at some point, and 45% fully vaccinated. Even with some overlap, we were close and cases were plunging.

Then Delta came along, with an R0 of 7.5. With much more efficient transmission (getting in the neighborhood of chickenpox), 87% of the population needed to have protection (natural or vaccinated) to stop the spread. So Delta spread.

Nationally, we are now up to 13% of the population with a confirmed case which could mean 33% infected + 55% vaccinated immunity. That's getting closer to that 87% after removing overlaps.

This is putting us pretty close to the herd immunity threshold nationally - though different states are in different spots based on natural infections and vaccination rates and some places will be far closer to herd immunity than others.

So where do we go from here? Here's a little "hopium":

We are vaccinating 700k people a day and new infections (confirmed) are around 120k a day. Both numbers are decreasing however in 60 days this could mean as many as 45 million more people (13%) "protected". If under-12 vaccinations are approved and the vulnerable get boosters, the number will be even higher. That could push us to well above 90% with some protection.

What if a new strain comes along? Well, the opportunity for "worse" strains is limited. Delta required 87% protection for herd immunity. If a strain had an R0 of 16, like the whooping cough, the threshold only goes up to 94%. Basically, you can only get to 100% so it's diminishing returns on H as R0 goes up.

So while more vaccinations and infections create more "protected" people, I think now we need to focus on how immunity wanes. These are the new, critical questions to answer:

How effective are the vaccines as a function of time, brand, age, dosage spacing and comorbidities?

Is natural immunity better than a vax, and how effective is immunity in people who have both?

Is mixing and matching vaccine brands effective? If so, should you get a different type (Moderna/Pfizer vs J&J)?

Are there common trends between the breakthrough cases and can we predict those people and customize a plan of care for them?

THESE are the critical questions we need to start answering now. If we understand these and can optimize shot sequencing, booster timing and prioritization of the patients most at risk for breakthroughs, we will have a really good, data-driven approach to this urgent public health question, and understand where this pandemic goes in the future.

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Herd immunity, there's that term again

Sep 28, 2021, 9:26 AM

Where is the herd immunity to the common cold? Where is the herd immunity to influenza? Where is the herd immunity to tons of seasonal viruses? The chart is accurate for herd immunity that you posted. Herd immunity to delta was actually reached months ago, if you count antibodies. 90% of UK citizens, in a randomized study, had immunity/antibodies, like 2 months ago. Now, look at their case chart. Israel, heck there are countries 90% vaxxed, still, they have cases.

You really need to understand covid is not a normal virus. A normal virus, for it to go from Alpha to Delta with that much higher of an R0, the classic virus mutates (usually in the spike protein) to accomplish that increased transmission. That's how normal viruses (subject to herd immunity) evolve. That's not covid. In a dish in a lab, our vaccine induced antibodies are still VERY effective against Delta, and Alpha, and every variant. So how does covid go from an R0 of 2.5 to 7? If that was accomplished through spike mutations, then our vaccines would not be as effective as they still are. The increased transmissibility from Wuhan to B.117 to Delta, from 2.5 to 7, is accomplished not through the spike protein changing, but from increased immune suppression, specifically interferon suppression. This is why there is and will be no herd immunity. The virus can do everything it NEEDS to do to transmit and propagate before our immunity (period) can respond. Our immunity only comes into play later, after peak viral loads, after peak transmission levels, and THEN the vaccines make a difference, and prior immunity makes a bigger difference. This is why covid has ended up being FAR less contagious for hospitals and medical staff. Most people, by the time they're hospitalized, are shedding far less virus. Many hospitalized covid patients are not even contagious at all.

We simply can't beat covid on the front end. Nature can't beat covid on the front end. Our immune systems can't beat covid on the front end. There isn't a vaccine, or any knowledge to even make one, that beats covid on the front end, because we don't know exactly how covid suppresses our interferon signals we have evolved to rely on (our very first line of defense). All we can do is evolve to beat it on the back end, AFTER infection, and after transmission. We have reached herd immunity to Delta already in the US. With that R0, and our level of openness, it's long since happened. If you dig down though, you see something else, a disturbing trend seen in Brazil and South America mostly. There are technically now 33 Delta variants, and climbing almost daily. When the original Delta has run its course and there is herd immunity to Delta, other sub-variants of delta then move in and infect more people. AY.4, AY.12, and AY.25 are the main "cleanup" variants now, and they can keep cases high. This is what happened with the P.1 variant in Brazil. AY.4 is dominant in the UK now. They have not had a large drop in cases. Delta is through there, but AY.4 is still causing their cases to be near their highs with Delta. Israel, AY.12 there. Same deal. Pick a place where Delta has run through and cases are dropping, and you see the sub variants are causing most cases, not the original Delta.

This doesn't end. We either all get vaccinated, then get covid, or get covid without a vaccine. Or we get a vaccine, get covid, get a booster, then get covid again, and get covid again. Natural antibodies last longer, but they too wane. 9-10 months on the natural immunity, and maybe 5-6 months for the vaccines. But once you've had a vaccine, and then covid, etc. you will just be able to handle it eventually, and it will end up being a cold someday years in the future. Covid is a pandemic (novel) virus with a completely new trick that sets it apart from others. We can see what the trick is, what it does, but we are clueless HOW it does the trick or how to stop that part of the virus, and that's the problem. Get a vaccine, then get covid and not die. Then get a booster. Then get covid and get less sick. Then get covid again. Then get it again. This is the plan, and scientists know this, and it's why they want the vaccines used so badly. They know everyone, EVERYONE, will get covid. Without the vaccine immunity (helps you not die, otherwise does nothing to stop covid) there will be a lot of death. But WITH the vaccine, and then you get covid and survive, that sets up a scenario where we can let it become endemic and return to normal. THink of the vaccine as a complimentary first case of covid. A mild one, that sets you up to survive your next infection. After that next infection, you're better able to survive the next, and so on. That was the plan, and IS the plan, but we're not following that because politicians don't want to tell people bad news and want people to think they're saving lives (liberals), or it's all fake and doesn't exist (conservatives).

This is the science, on the virus itself. And countries know this. Singapore, England, US, Israel, most of Europe, heck even Australia knows this. The plan is to get vaccinated and carry on. If 90% get vaccinated, you can carry on without a hospital crisis. If 47% are vaccinated, then you carry on with a lot more death and a hospital crisis (US), or stay locked down like Australia. Highly vaccinated countries have shown how this is done. In fact, it's beneficial to get Delta after your vaccine, and then you have natural and vaccine immunity, and then you likely (hopefully) won't die the next time. It's why they're not making Delta-specific vaccines. They can easily, but haven't. We don't need it. Structurally the virus does not mutate much, it's the interferon suppression where the mutations are making the difference. As such, this IS something we CAN live with, with immunity.

All this being said, we need to pay careful attention to the virus mutations we can address. The ORF sections of the genome are where scientists are studying the virus the most right now. That is the section where the virus is evolving with the most success. That is the section that impacts the proteins that inhibit interferon expression (the trick) that brought us from 2.5 to 7. And ORF is totally NOT impacted whatsoever by our vaccines. For scientists it's counterintuitive and goes against decades of science NOT to concentrate on the spike protein, as that's what the virus uses to infect another cell. BUT, we know how that works very well. We don't know how interferon suppression occurs, and that's a largely chemical process, and less structural than the spike protein. And if this was a lab leak, the Chinese found a way to produce a gain of function in a new area. When it was "proposed" to make a coronavirus that's 1,000 times more transmissible, I expect they may have been onto something in the ORF section of the genome, and I'd wager that's where they were experimenting.

LSS - Covid bypasses our immune system for a period of time. It has since day one. Main difference is that period of time is much longer now, and the virus replicates faster (incubation period decreased to two days with Delta). It literally has explosive replication during the exact time of suppression, causing the high viral loads. It becomes more transmissible by pure volume of virus, not by a spike mutation that sticks better. When our immunity (whatever we have) responds, it's deluged with an infection that's far more severe and widespread in the body than we know what to do with. It's also why almost all treatments (Regeneron, ivermectin, HCQ, WHATEVER) is used as early as possible on the first sign of symptoms. Ideally, if you had a way to detect the infection before your immune system does (symptoms), there are antivirals that can make a big impact on the level of virus you end up having to clear, and hence you get a less severe infection and better recovery. But without symptoms and immune recognition for such a long time, that's difficult.

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Tough times create strong men.
Strong men create easy times.
Easy times create weak men.
Weak men create tough times.

So the good news is that the pandemic is probably over....

Sep 28, 2021, 11:02 AM

...and the bad news is that covid is endemic.

You are right, we don't have much of a choice. We will just adapt to it over time.

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Re: Herd immunity, there's that term again

Sep 28, 2021, 11:26 AM

Great post and honestly I don't think what you said and my post are significantly different.

I think the term "herd immunity" is the trigger phrase here as I don't believe covid is going away either. But become a manageable problem over time. So I think in this sense "herd immunity" is speaking to deaths a d collapse of the health care system in that we are unlikely to see a wave as bad as Delta again in the next year.

So the next phase is how to manage it. And that's what we have to focus on now

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