News roundup for Friday, Dec 3, 2021

Fascinating. Thank you for sharing the link.

Yes, the world is a big place. I agree that fixing many of the big problems would be good. But I don’t control everything. I work to spend effort choosing and focusing most on things I can control.

Start where you are.
Use what you have.
Do what you can.

I agree with the fox, I can’t control what so and so company does but I can control what me and my family does. And maybe if every family did a little bit better it would make a bit of a difference. 

Same with all this covid stuff going on. I can’t control people getting vaccinated or wearing a mask, but I can get vaccinated myself and wear a mask in hopes that I am not the one spreading things around. Hopefully my little actions will do a little bit of good in this world.

I read it as a reference to this quote from the article: “It is not yet clear whether the people concerned [in the earlier cases] have also been to southern Africa”.

It’s certainly interesting to find Dutch cases from 11 days ago, doubly so if they turn out to be community spread (which is not confirmed). But it’s extraordinarily unlikely that South Africa was Omicron-free 11 days ago, when its current Omicron-fueled outbreak looks like it started ramping up around 20 days ago.

Two days ago, Nigeria found an Omicron case from October. So Omicron has definitely been spreading for a while before we knew about it.

https://www.forbes.com/sites/roberthart/2021/12/01/omicron-case-in-nigeria-dates-back-to-october-weeks-before-it-was-first-reported-in-south-africa/?sh=2818a11f2abc

I also noticed that and that there were many articles online today saying that Omicron didn’t start in South Africa. I agree that it clearly did. There is nothing that one should be sensitive about. Original started in China, Alpha in theUK, Beta in South Africa, Gamma in Brazil, Lambda in Peru, and Delta in India.

“saying that Omicron didn’t start in South Africa. I agree that it clearly did.”

Not necessarily South Africa. It’s quite likely to have started in another nearby African country that was less vigilant with testing/sequencing/reporting. And such details matter. We’ll never be able to trace the original origin of COVID-19 – that trail is cold. But the emergence of Omicron is another major that we might still be able to investigate. Find out how it happened so we can prevent a repeat. I would start with collecting lots of random COVID-19 sequences all, use those to estimate spread patterns and the likely starting point, then start searching for likely reservoirs in that area.

“There is nothing that one should be sensitive about.”

The original breakout was in China. In my own country (USA) anyone who looks Chinese is still paying the price for that, with a sharp rise in racist harassment, and I suspect there are similar issues elsewhere. So yes, there’s very good reason for such sensitivity.

They say that they believe that the immunocompromised are the most likely to have such a complicated, mutated new variant put itself together over several months. They say that they’ve observed such mutations arising in patients with very complicated chronic conditions. I had I had said south Africa with a little s, but my phone doesn’t think I have any grasp of the nuances of English. They believe that the large number of AIDS patients in that region would be very likely to give rise to such variants.  Also true that other countries have also seen new variants appear.

“They say that they believe that the immunocompromised are the most likely to have such a complicated, mutated new variant put itself together over several months.”

That explains half of what we see in Omicron: how lots of mutations could have accumulated in a short period of time. What it doesn’t explain is how Omicron could be descended from a variant that we haven’t seen since 2020. This only makes sense if there were some separate population where Omicron could have evolved in parallel over the last year, then jumped back into the rest of the population.

There’s more than one way that you can have a virus evolving separately from the larger human population of this planet. It could have happened in a remote village, or in a laboratory, but neither of these seems likely. I think the most likely possibility is that Omicron evolved in an animal population that mostly does not interact with humans. Last year, a human infected an animal, who went on to spread last year’s COVID among other animals. After a year of parallel evolution among animal hosts, one of those animals returned the favor and infected a human this October.

Some experts suggest Omicron variant may have evolved in an animal host

I’ll have to read and think about it. Look at the family tree of Omicron. Covid Original was very different than any coronavirus which infected animals. Humans have infected animals with Covid. Most deer in the US. Many kinds of zoo animals. Many pets. Has it been shown that any human caught CV from an animal? Hundreds of sub variants of Covid have been identified. If some of them are similar to Omicron in causing few to no symptoms, they could have mutated and spread quite a bit before being identified.

“Has it been shown that any human caught CV from an animal?”

Humans aren’t that special. It would be absolutely amazing if a dog with COVID couldn’t spread it to a human by licking and breathing on their human’s face, as they so often do. But this mostly doesn’t matter, because a dog isn’t the most likely member of the household to bring the virus home by going out and spending 8 hours per day in a shared office environment.

Pets aren’t a separate population – they’re just an extra member in mostly-human households. Zoos are irrelevant because there are so few animals in each. Deer could have been the reservoir for this, because they mostly live in a separate place (forest) where they more often run into each other than humans. But we know it wasn’t USA deer because then the Omicron epidemic would have exploded in the USA before Africa.

“If some of them are similar to Omicron in causing few to no symptoms, they could have mutated and spread quite a bit before being identified.”

(Omicron’s symptoms aren’t substantially different, but that wouldn’t affect this particular issue anyway.) If anything similar arose here, we would have caught it both from sequencing and rise in hospitalization. We have in fact caught new variants in USA, all of which were minor changes from the current dominant variant. Omicron is very different in that respect, in a way that requires a mostly isolated population for over a year of isolated evolution. An animal reservoir is not the only way to get those conditions, but just seems like the most likely.

Just a hypothesis at this point. It is provable by (1) pinpointing Omicron’s breakthrough time/location to humans and (2) further tracing into wild animal populations in that area. Both require lots of sampling and sequencing throughout Africa. If we wait too long, the trail will go cold.

The importance of solving this mystery is that we could prevent it from happening again. Find out the full story of why this particular animal population was more likely to create such a variant and spread it back to humans, then figure out which step in that story would be the most efficient to interrupt.

There is a limited number of diseases which animals get (usually distinct species) which may be transmitted to humans, called zoonotic diseases. In most cases diseases do not easily make the species leap. As it turned out, the theory that Covid came from horseshoe bats which somehow transmitted Covid to pangolins not found within hundreds of miles of their habitat, was incorrect, just a red herring. Cats and dogs can get coronaviruses: there is a coronavirus vaccine for dogs which Dr. Don Hamilton called a vaccine in search of a disease, it being so rare and mild in dogs. In March 2020 I bought two coronavirus nosodes online: one from Australia for feline Cv and one from the UK for bovine CV, knowing that the diseases were species-specific, I still thought that there would be cross-species effect on general terms. 

We got a rescue kitten in March who had intractable severe diarrhea for over two months, despite being wormed three times and my suggesting ponazuril off-label, which worked after two week-long rounds. She was tested and positive for a coronavirus not specified and the vet thought it meant fatal FIP. I thought it did not: most cats are exposed to that Cv and develop immunity. In only a few does it mutate and take a fatal form. The vet said that types of coronavirus which animals get cannot spread to humans. I said that the animals in zoos dying of Covid had caught it from humans. But notice that it’s only some species. Even within felines, several snow leopards died when other felines did not. 

I considered whether it was possible that Kahlua caught a human type CV in her early life. She was very sick for a long time and the vet never figured it out. We saw last year that diarrhea can be a symptom of human CV. In any case, we did not become I’ll from close contact with her. 

I would be cautious about this hypothesis: I would not want for any animals of any species to be slaughtered on the suspicion that they might transmit it to humans. Humans are doing that just fine among ourselves. And it looks as though Omicron continues to be mild, and if it chokes out Delta, we may be tankful wherever it came from.

“There is a limited number of diseases which animals get (usually distinct species) which may be transmitted to humans, called zoonotic diseases.”

It’s entirely true that many viruses can infect one species but not another. In this case, we already know that COVID-19 can infect humans, and dogs, and deers, and a variety of other mammals. Are you thinking that the virus somehow loses the ability to infect humans if its latest host wasn’t human?

“I would be cautious about this hypothesis: I would not want for any animals of any species to be slaughtered on the suspicion that they might transmit it to humans.”

Even if the species were confirmed, that sounds like an overreaction. There are many other approaches to mitigate risk. We can’t take any of them now due to lack of information. I prefer to know the truth first, then consider alternative options for responding. Unfortunately, it is likely that this trail will grow cold, as already happened for the original zoonotic crossover, unless those samples are collected now.

I don’t have enough information to say. No, it might be possible for susceptible humans to be infected by a strain of Covid mutated in animals. But it remains possible that it mutated in one or more immunocompromised humans. It was contemptible that certain experts spent months blaming horseshoe bats and pangolin when the genomes didn’t match at all.

“But it remains possible that it mutated in one or more immunocompromised humans.”

Yes, that is also possible. Here’s what that story would need to look like, and why I think it sounds unlikely.

In summer 2020, an HIV patient catches COVID-19. They caught it fairly early in the pandemic, suggesting that they hadn’t been taking substantial precautions to avoid infection. Then they remained infected with COVID-19 for over a year, while completely isolating so that they don’t infect anyone else for over a year. Throughout this year their infection gets more and more infectious (more than 4x) yet they still manage to avoid infecting anyone for all this time. Also, throughout this time no one sequenced the patient’s infection to see that it was very different than everyone else’s infections. Then finally in September 2021 (estimated) someone slips up and finally gets infected from this person. Suddenly there’s an Omicron outbreak that won’t be noticed until a couple months later.

It seems like an odd sequence of events. It’s very rare for an HIV patient to incubate a virus that ends up being a major new, highly infectious variant. What are the odds that one of these rare events happens in someone who is so well isolated that this extra contagious variant doesn’t infect a single other person over the course of a year? Are HIV patients typically held in such extreme isolation? I would think probably not in a country where such a large portion of people have HIV.

Now consider that it’s very rare for an HIV patient to manufacture a major new variant. This has happened only a handful of times in the entire world, and at most twice in Africa. What are the odds that the patient involved would be so extremely isolated?

https://www.washingtonpost.com/health/2021/03/11/immunocompromised-patients-covid-variants/

This article discusses many cases in which that happened, immunocompromised people who had the virus for a long time, when it had mutations. I think others may have been infected by them, but may have gotten mild or asymptomatic cases and stayed under the radar.

“I have not seen or read of harassment of Chinese people because of the origins of Covid.”

I’m surprised you haven’t heard of this. Perhaps I’m just more sensitive to it because my wife is part Chinese. She has personally noticed an increase in unfriendly behavior from random strangers, and is also alarmed by news of anti-Asian hate crimes.

BTW, I posted a response to your proposed explanation of Omicron emergence, but that post is “awaiting moderation”. I think you’ll find it interesting if it survives that process. I really hope the site figures out soon that I don’t post spam and carefully avoid spreading misinformation, but I recognize that some of the words I used are often found in misinformation.

Many of my comments have been put into moderation, both here and elsewhere. 

I just looked for hate crimes against Asians in US because of Covid, but just found some articles on surveys which found that in general hate and disapproval crimes against Asians in the US were in eighth place. Hate crimes against Jews are always in the first place. Almost all such crimes are verbal, not physical. Physical attacks are carried out against so many people of all different types, always by unsavory groups and individuals,, that it would be hard to construct an ideological motivation. Normal people just don’t go out and attack someone for that. Not even after 9–. And when you can construct an ideological motivation, Wauk… 

I’d like to read your explanation. I read nearly a year ago, pre Omicron, about variants being thought to develop in the chronically I’ll over many months to end with a much-mutated variant. It would be hard to disprove, as it would only take one such chronically-I’ll person, to be found everywhere. I think a place with a huge number of AIDS patients just has better chances. And no, S Africa is not the only such place. I have a friend who has two sisters who work in AIDS hospitals in Zambia, both physicians. In s Africa, not South A.

“I read nearly a year ago, pre Omicron, about variants being thought to develop in the chronically I’ll over many months to end with a much-mutated variant.”

That was a good explanation for previous variants, but Omicron has a big difference that makes that less plausible. The patient would need to have gotten sick in mid-2020 and kept it to themselves this entire time, then suddenly infected someone else after all that time. And during that time also developed a 4x more infectious variant that somehow never infected anyone in that time.

My more complete explanation just passed moderation if you scroll up a bit.

The WaPo article I linked this morning said that the immunocompromised patients it discussed continued to be infected with the same early strain for as long as a year or more. They would test positive, then negative when their struggling immune system fought it back, only to later test positive again, some of them going from negative to positive to negative over and over. We saw last year that a cycle count was used for a long time in many places which was believed to be too high, meaning that people were testing positive for Covid when they had so low a count of virus as to be what was considered irrelevant since they never got very sick or symptomatic at all. But it may be that even a low level of virus can rev up again and cause a positive read and symptomatic illness. And the latent virus may have undergone significant mutations. Etc.

“The WaPo article I linked this morning said that the immunocompromised patients it discussed continued to be infected with the same early strain for as long as a year or more. They would test positive, then negative when their struggling immune system fought it back, only to later test positive again, some of them going from negative to positive to negative over and over.”

That at least partially addresses the issue I raised about this person not infecting anyone else over the course of over a year. If their infection ramped up and down, they may have been non-infectious for most of that year.

South Africa is definitely where it’s hopping off, but it’s not necessarily the place of origin. I’m not saying this to be politically correct or because I fear demonization of a region (although that happens), I’m saying it because I’m not sure we’ve pin-pointed the exact origin. It’s all over the place. If Europe had been doing more sequencing they would have found it first (or at least much earlier), but that doesn’t mean it originated there, either. 

Stephanie, I don’t mean any offense. I appreciate your articles overall, and everything you just said is true. The first sentence of your article is probably false, and I would recommend replacing it, perhaps with a more specific statement about a much earlier Dutch case being identified.

I have changed the sentence to the actual CBS News article title and quoted it with attribution to the news outlet. Beyond this you may take it up with CBS News. 

The word “detected” makes all the difference. Thanks Stephanie.

Very good point regarding the importance of moving quickly. There are a variety of treatments available which work best if taken as early as possible, within the first 1-3 days of symptom onset. Everyone should have a clear emergency plan for how they would handle an infection, including testing, isolation, prescription, and treatment. It’s way too much to figure out after you’re already infected, especially considering that brain fog is sometimes one of the symptoms.

For Delta, the best available post-exposure treatment was antibody injection. That may or may not still be the case with Omicron.

Other treatments to consider include Merck’s Molnupiravir (EUA just granted) or Pfizer’s Paxlovid (more effective, expect EUA soon). These are both pills, so should be much easier to get your hands on.

I think that’s going to be a problem. I think in most cases, it would be more than three days after infection, or maybe symptoms, before you really admitted to yourself that this might be Covid. If you tested positive on day 3, I think they’re going to need to set up an expedited system to send Paxlovid to your house right away, same day as you notify them of test results. Would they take your word for the positive home test? If not, there would be a dangerous delay.

“Would they take your word for the positive home test? If not, there would be a dangerous delay.”

I have no idea. That sounds like an important question to get answered before being in that situation.

I’m fairly sure the answer will be no. After getting a positive result on your home test, you’d STILL have to make an appointment with a health care professional (sarc implied) to get your amateur reading confirmed, before they would deign to give you a prescription for Paxcovid or antibodies. That means it would take well over the initial three days? Oh, well. 

A part of the emergency plan should include having powers of attorney for legal, financial, and medical matters. The time to do that is when you are well, not when you’re dealing with a health crisis. Having this paperwork in place was immensely helpful to loved ones who recently had a health crisis (non-Covid) and would not have been able to navigate the medical system without the paperwork.

Ideally have copies of the paperwork on file with all of your healthcare and financial providers pre illness – hospitals in this area will only take originals, not copies, but once they’ve scanned the originals into their systems they give the originals back and you no longer need to have them with you.   

“For Delta, the best available post-exposure treatment was antibody injection. That may or may not still be the case with Omicron.”

Regeneron and Eli Lilly have both reported that their antibody treatments will be less effective against Omicron, because it is resistant to antibodies that target the original strain. These are preliminary results based on lab tests. I expect that, like the vaccines, it will take some months to develop and test replacement versions that target the Omicron variant.

https://www.wsj.com/articles/covid-19-antibody-drugs-are-challenged-by-omicron-preliminary-testing-indicates-11638270003?mod=hp_lead_pos3

Same, waiting for them to be free and available to all. Our local library was giving away free at-home tests but they keep running out of stock so I have decided to buy a box anyway while I wait for more availability.

It seems to be the case that Biden is not giving everyone free tests? It looks to me as though if you have insurance, you have to submit your receipts forms the tests you bought to your insurance company (would that be worth your time to recoup twenty dollars?), but if you don’t have insurance you just have to buy them yourself. Oh, well, I’m used to that. At least the shots were free

Added just now:

https://www.politico.com/amp/news/2021/12/03/biden-free-at-home-covid-test-523727

Ah. Will lead to higher prices for tests and higher health insurance premiums. Why didn’t I think of that?.

I would hope that pharmacies would take your insurance card and take care of the insurance claim, just like they do for any prescription.

They do that for you? I didn’t know. I have MS and was never able to afford even the very expensive Obamacare. I 

Red tape and the need for reimbursement are not what people need. They need free or very low cost tests that are ubiquitous. I’m disappointed that this is the way they chose to go. 

“I’m disappointed that this is the way they chose to go.”

I think this is mostly a side effect of Biden trying to make unilateral decisions, and therefore being restricted to changes that do not require congressional authorization. He already had some knobs to turn on an existing piece of legislation, and he turned them. Congress typically takes months to act, and that could be too late. That said, I think you’re right, and it would be good if congress followed up with a better replacement.

I agree. The vaccine has been free for all Americans and most of the world has followed suit. Since it is obvious that control of the virus depends on early detection, a public good, tests should be provided free of charge, no bureaucracy, to everyone in the country. I read that that would require passing a law which would require the cooperation of legislators, which I would think would be easy, but maybe not. I think, though, that it could be easily enacted through an executive order.

I am very grateful that the vaccine has been available to all for free. If people had to pay for it, vaccination rates would be much lower.

Has anyone heard how much each dose of vaccine costs the government? Just out of curiosity I wonder how much it was for me to get vaccinated.

“Has anyone heard how much each dose of vaccine costs the government?”

Each government negotiates a price on each large order, so prices can vary a lot. I think they’re all quite inexpensive compared to the value. Here are some estimates.

Moderna: $25-37

Pfizer: $19.50

J&J: $10

AstraZeneca: $2-5

https://www.biospace.com/article/comparing-covid-19-vaccines-pfizer-biontech-moderna-astrazeneca-oxford-j-and-j-russia-s-sputnik-v/

My view is that Biden is mostly trying to do the best he can in terms of the policy knobs available to him. He already used the Defense Production Act in September to try to make more at-home OTC tests cheaper.

The FDA waited to authorize more home tests because of the “false sense of security” line. IIRC, we have data now showing that infection rates are lower in areas where the government gave free rapid test kits to every household. So at least the “false sense of security” argument doesn’t seem to hold up.