I made a sorta New Year’s resolution to post about stuff other than covid, but covid takes up a lot of everyone’s mental space, and I am particularly angry about this latest surge. Maybe the next post will be about Russia.

This morning, one of my go-to virologists, Dr. Angie Rasmussen, tweeted a rage-thread. She gave a nice definition of endemicity, which I plan to use going forward because it works with my emphasis on prevalence.

This isn’t “living with” the virus. That’s not what endemicity means anyway. Endemic means that there is a steady state level of virus circulating. This is explosive exponential, epidemic growth, not a stable level of endemic transmission.

— Dr. Angela Rasmussen (@angie_rasmussen) January 11, 2022

In the rest of the thread, she enumerates policy mistakes. She doesn’t explicitly blame Joe Biden, but she mentions the White House, and others do explicitly blame Biden and “the Democrats.” It’s easy to blame the party in power and easy to believe the President can do anything with a snap of his fingers or by signing a piece of paper, but it’s not true. I agree that I would have preferred some of her policies, but let’s focus on what we actually have to change, not just yell at the easy targets.

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Kevin Drum offers some suggestions as a conversation starter on “living with covid.”

Far too many people using that phrase actually mean “Shut up and sit down because I’m tired of dealing with this and want things back to where they were before the pandemic so I will act that way.” That’s not going to happen, and Kevin recognizes it in his post, but I need to say it again.

At the moment, with something like 600,000+ new infections a day, we must get prevalence down before we can start to think about a more stable situation. The good news is we may see a decline in infections fairly quickly, say by the end of January, as more people become immune via infection or vaccination. At that point, we need to look hard at what we need to do to keep it that way, because immunity via infection seems to wane fairly quickly. Vaccination, obviously, needs to continue and expand.

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Over the last few days, I have thought of at least six posts I might write on the pandemic and started three of them, now trashed by events. I am going to write this one straight through and get it posted before something else happens.

The rapid spread of Omicron and its different characteristics from Delta have changed the game, not to mention that we have viruses in circulation with different characteristics. There is a lot we don’t know yet about Omicron and probably won’t for some weeks.

There is also far too much misinformation, disinformation, and wishful thinking circulating on social media. Please don’t retweet people you don’t know or add your non-expert takes to the din. Please.

The CDC released guidance on recovery and going back to work. Every official decision right now is the result of combining not enough data with public health guidelines with expected political and emotional pushback and professional best judgment. I have given up second-guessing. This thread and the one embedded in it indicate why.

Dr. Rasmussen is one of my go-to people on the pandemic. I think this thread illustrates the difficulties of making decisions on official policies.

1) The sheer number of things we don't know about the virus, which has become much worse with Omicron and its rapid spread. https://t.co/aWM9VAE2WH

— Cheryl Rofer (@CherylRofer) December 29, 2021

It can’t be said enough times that back in June 2021, things were looking up because of the vaccines, and that was when the Republican Party ramped up its hardline push in favor of death and disease. Yes, Delta showed up too, but in a country where public health was uniformly valued, it would have had less of an effect.

I’ve come to look at the pandemic in terms of getting transmission down, and I think that’s still a good frame. The only way we will get back to anything resembling “normal” is to get the transmission down. That’s going to take a while, although what we see of Omicron’s characteristics, it’s possible we could have a peak through January and then be in a much better position by March.

We don’t have enough tests.

We’re not thinking enough about long Covid. More about this later.

Nor are we thinking enough about vaccinating the world. More about this too.

The good thing is that we know what we need to do: Get vaccinated and boosted, mask up around other people, distance as much as possible, avoid large numbers of people indoors.

Stay safe, y’all, and keep the noise down.

Cross-posted to Lawyers, Guns & Money

If you, like me, are puzzled by the wide variety of mask manufacturers you’ve never heard of and have also heard that not all masks being sold as N95s actually are of that quality, here’s some reliable help.

The CDC has a list of approved mask manufacturers.

Project N95 has evaluated a large number of manufacturers and masks and has aids to find the mask that’s best for you. You can order masks through them.

Cross-posted to Lawyers, Guns and Money

With so many people still contracting covid, filling up the hospitals, the fourth wave now, and vaccinations too, we must be getting to a point where there will be no more people to get sick, right?

I’ve had that intuition, but I know it’s mixed with my desire for the pandemic to be over, so I ran some numbers.

From my latest spreadsheet calculations on November 29, I get a figure of about 133 million Americans susceptible to the virus. This is going to be a very approximate calculation, so don’t worry about those three weeks.

There are other inaccuracies in that number, including that I assumed a that 20% of vaccinations have gone to people who have already had the virus. I recently saw a more reliable estimate of 25%. There are also imponderables, like how many have become susceptible because of waning immunity from infection or vaccine and how many, idiosyncratically, haven’t mounted an immune reaction to the vaccine. Then there’s the degree to which Omicron can escape previous immunity. All that makes the 133 million figure larger and the times longer.

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Back in September, I developed a simple model to predict how many more Americans would die from COVID-19. Over this long weekend, I updated the model with numbers from the New York Times on Friday, November 26.

As I entered the numbers and watched the changes, I had questions about some of my assumptions, so I won’t post the whole spreadsheet the way I did in September. I think the bottom lines are no worse than any other projection. Across the US, 133,859,829 people remain susceptible. That’s 40% of the population. We need that to be closer to 10%. In September, the number was 147,194,141.

Although unvaccinated people have been filling hospitals, their numbers are not enough to make a big difference in those remaining susceptible to the disease. Additionally, evidence is mounting that having been infected with the virus produces less, shorter-lasting immunity than vaccination does.

I did not do a formal sensitivity analysis, but watching the numbers in the spreadsheet change made it clear that vaccination is the biggest factor in decreasing the numbers of susceptible people. Over the next few weeks, we will see large numbers of children vaccinated, which will help, but children in the age group newly opened for vaccination number about 33 million.

South Africa has one of the best surveillance programs for the virus, and they have found a new variant, which the WHO has called Omicron. None of the things that we want to know – NOW! – are available, and they won’t be available for weeks. Omicron has many more mutations than previous variants, which means it’s been hiding out somewhere as those mutations piled up.

Which means that the earlier variants weren’t as transmissible as Delta. One of the things I am watching for is Omicron’s transmissibility relative to Delta. If it’s much less, it won’t replace Delta, no matter what its other characteristics.

Here’s a good summary of what is known about Omicron. And here’s WHO’s update. What you need to do is the same as before – get vaccinated, mask up, use testing before getting together with people. And tell your legislative representatives we need to vaccinate the world.

Cross-posted to Lawyers, Guns & Money

I was surprised last week to see one of the epidemiologists I follow admonishing those who think that covid’s “becoming endemic” is a good thing for humans. It is a good thing for SARS-CoV-2, because endemicity means it persists in the human population, although at a mostly steady state. I didn’t realize that some thought it was a good thing for the rest of us.

SARS-CoV-2 is pretty much everywhere that humans go now, and maybe further than that. Covid has even reached Antarctica. There have been several narrative descriptions of what we can expect in the mid-term future, but I am wary of those.

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A while back, when it seemed like a lot of people were becoming ill with covid, I wondered how long it would take to get to herd immunity the hard way. It turned out that, although it seems like horrendous numbers are becoming ill, the percentages of the population were much smaller than I had intuited.

It’s time to do another calculation. IIRC, we didn’t have vaccines when I last did that calculation, and it was before Delta made its appearance. There’s not much talk about herd immunity these days because of Delta’s much higher transmissibility and maybe because it’s gotten mixed up in the “let it rip” crowd. I hope to write a post on R and those calculations one of these days.

I built a VERY simple Excel model. The point is to get a handle on the numbers, and two significant figures are good enough for that. If anything, it may overpredict deaths, which would be a change from our expectations of the last almost two years.

The state population numbers are from the World Population Review. The covid numbers are from last night’s New York Times tracking.

I converted the cases and deaths per 100,000 to percentages. I assumed that 10% of those vaccinated had been infected and removed that overlap. I also assumed that 10% of those vaccinated were still susceptible to serious cases of covid. I added the percent of cases to the adjusted 0.8 of vaccinated to get the immune %. The susceptible are thus everyone else. I multiplied the death percentage times the susceptible (this is probably the largest source of pessimism) to get the expected deaths.

The bottom line, expected deaths for the US, is close to 300,000, which will give a total close to a million dead from covid. That doesn’t count excess deaths from the overloading of the medical system. Combined immunities from illness and vaccination are not too different from the percent of vaccinations. The pandemic is far from over.

Photo: The Guardian

Cross-posted to Lawyers, Guns & Money

This may be simple and obvious, but it’s worth saying.

The more virus there is around, the more danger to all of us, including the vaqccinated. That’s why nonpharmaceutical interventions (NPIs) like masks and distancing are important.

The more virus you encounter, the more likely it is that one of those encounters will go well for the virus and badly for you. So when case numbers go up, it makes sense to take more precautions.

The reason that anti-vaxxers are often able to avoid having their children infected with measles is that there is usually no measles virus circulating. An immune system that can’t handle the virus is safe as long as it doesn’t confront the virus.

This ties into speculation on the endemic endgame for SARS-CoV-2, although I haven’t seen anyone consider it explicitly. We can, through a combination of vaccines, natural immunity, and NPIs, get the virus down to the levels we’re accustomed to with measles. At current rates, however, that will take years. It might be instructive to look at how measles cases declined after vaccination became available.

Cross-posted to Lawyers, Guns & Money

I’ve had a vision of writing a magisterial series to clarify everything about the mathematics of the pandemic, but it looks more like I will, hit-or-miss, do one issue at a time.

I’ve worked with mathematical models for chemical reactions. The math is identical to that of a pandemic – coupled differential equations describing the transformation of one set of things into other things. In the case of the pandemic that transformation is

susceptible people -> infected people -> immune or dead people

Sets of coupled differential equations have become popular for such things since we have gotten enormous computing power. Solving them isn’t easy to do by hand. Epidemiology (and chemical kinetics) grew up with simpler equations to model their processes. And those simpler equations can be good for some things!

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