News roundup for Fri, Nov 26, 2021

There’s a new concerning COVID variant out there, also coming out of South Africa. This one, first dubbed Nu (now Omicron per the WHO) has over 30 mutations to its spike protein. These mutations could lead to immune evasion, meaning neither vaccines nor previous infection would be very protective. There are only about 1,200 cases so far, but it seems to be outcompeting Delta in South Africa. It has spread to Belgium, Hong Kong, and Israel already. Israel, the UK, and the EU have closed air traffic to a number of African countries. Some feel this is an over-reaction given how little we know about the variant. BioNTech is testing whether its current vaccine is protective against it. If it isn’t, a new round of variant-specific boosters may be warranted. We’ll be keeping an eye on this:

Putin has strong words for NATO about crossing red lines—this stems from his perception of NATO expanding assets ever closer to Russian boundaries and his ire with NATO’s use of missile defense systems. It’s possible for some missile defense systems to be used offensively and not just defensively, so Russia is certainly feeling the pressure from encroaching “defensive” capabilities.

Wolf re-entry programs reduce deer v. vehicle collisions so significantly that it saves communities more money than otherwise—even considering the cost of livestock loss to wolf attack:

Labor negotiations at US ports could make the container backup even worse:

Logistics slowdowns could hamper the ethanol delivery chain we rely on to supplement our gasoline. The price of ethanol has also gone up, adding another pressure to the increasing price of gasoline.

Black Friday has turned to Red Friday as stocks suffer secondary to concerning (but preliminary) COVID variant news:

The world has 260.7 million COVID cases. The world has gained 4.4 million cases in the last eight days. There have been over 5.2 million deaths in total. The US has had a cumulative 49 million cases—over 600,000 cases were added in the last week. Nearly 800,000 Americans have died—over 7,000 in the last week. The US added only 27,000 new cases on Thanksgiving Day but there is probably a lag in reporting due to the holiday. The US is still leading global daily case gain.

We have excellent options for antiviral COVID treatments now, but it’s not easy to get them early in the course of the illness because of the failed testing protocols in this country. Tests are not as easy to obtain as they should be, and backlogs of test results mean that folks who do get tests may not get results in a timely enough manner to get antiviral medications on board fast enough to help:

Cases are really rising in Europe again:



    • Eric

      “Israel, the UK, and the EU have closed air traffic to a number of African countries. Some feel this is an over-reaction given how little we know about the variant.”

      We already know enough to wish that containing it was possible. We also know enough to understand that this containment effort will fail. By the time Omicron was detected, it had already spread around the world. Closing borders now is a useless gesture.

      Omicron is at least twice as infectious as delta, probably closer to six times. Immune escape, while still unconfirmed, is very likely. Vaccines will probably still work, but not as well as before. Boosters just became more important, and more potent vaccines will be developed in the coming months. The new antiviral pills may also help.

      I’ll be watching Omicron closely and trying to estimate when the Omicron peak will hit us. My current guess is 1-3 months. When it does come, it will be a bigger peak than we just saw from delta.

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      • Captain Peanut Eric

        I follow you that closing boarders will not 100% prevent it from coming in, but wouldn’t it at least slow it down? During the holiday season if everyone can just travel back and forth however they want it leads to much more possibilities of spreading.

        Buying a little bit of time may help us to have more time to research and know how to treat it and not overwhelm our already hurting healthcare systems.

        So I wouldn’t necessarily call it useless, but also not a foolproof method to prevent it from spreading. 

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      • Eric Captain Peanut

        “I follow you that closing boarders will not 100% prevent it from coming in, but wouldn’t it at least slow it down?”

        That’s an excellent question. Here’s why closing borders won’t slow it down much.

        Imagine that one infected person per day has been arriving for the past month. Also imagine that each infected person causes 2 other people to be infected 4 days later. The person who arrived 30 days ago has already spread the infection to 2^7 = 128 people by now. The person who arrived 29 days has already spread the infection to around 128 people by now. Those 30 people that arrived over the past month have spread the infection to many thousands of people in our country by now. So each day, those thousands of people each infect thousands more people, and one more person arrives from overseas… The new arrivals just can’t make much difference compared to the thousands that are already being infected within our country every day.

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      • Eric Eric

        Possible flaw in my reasoning…

        My basic claim was that closing the gates after the variant got in doesn’t help much. But that’s not quite the situation. The US already had some defenses against international spread: the requirement that all incoming international travelers be vaccinated. We’re not closing the gates – we’re strengthening them!

        I still think it’s too late, but I could be wrong. I hope I’m wrong.

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      • Hardened Eric

        I just listened to an interview of Dr. Fauci and he said the border closings are intended to buy us more time to study the impact of the new variant.

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      • Cia Hardened

        I think it’s reasonable to close the borders until we know what we’re dealing with. Deaths from Covid would have been much higher than they were had most countries in the world not enacted all the protective measures we did. Just letting people die while making no effort to shield them bc would have been and would still be, callous and irresponsible. Economies and schools would not have trundled along as normal in the midst of pervasive sickness and death.

        Charts on the variants seem to show that Delta choked all of them out in every country in the world. Now Omicron seems to be doing the same to Delta, at least in the few cases which have been observed so far. I think extreme caution is warranted at this time, but it’s possible that our deliverance is at hand. Maybe.

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      • Eric Cia

        I’m all in favor of protective measures. The question is whether a travel ban is an efficient way to do that.

        If our country is already seeded with Omicron, then it’s too late for a travel ban to help. In this situation, a travel ban is useless. It will not even buy us one extra day of time.

        If our country is not already seeded, then we should ban all international travel, not just from a few specific countries. Banning just some African countries would buy us a week, forcing the virus to follow an indirect route through other countries. Banning all international travel could buy us months.

        I would actually be in favor of travel bans (or quarantining 5 days on arrival, with testing) if we used the possible extra time to ramp up other protective measures. Good focus areas would be increased vaccination rate, building ventilation, and variant-focused contact tracing. And of course any travel bans should be stopped immediately if we later find, as is likely, that community spread is already outpacing the number of cases that travel would add.

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      • Cia Eric

        A ban on all international travel would be a good idea. I think buying time is worthwhile, until we know more about what we’re dealing with. Even if it has been seeded here, several countries were able to stop further spread with extensive contact tracing and quarantine or isolation of contacts. In this case, I would be in favor of vaccine mandates for virtually everyone, the way Austria says it is planning to do in the next two months. Those who can’t be vaxxed should have to stay alone at home until this is over. Maybe it will be soon, although it seems hard to believe that maybe Omicron really will be mild, but so transmissible that it will choke out Delta.

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      • Eric Cia

        I’m not expecting Omicron to be milder than Delta, though it’s certainly still possible. I think that part will be clear within a week from now.

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      • Cia Eric

        I agree with you. I was just reading the whole thread on Twitter starting with the tweet by Eric Feigl-Ding. We know close to nothing about it at this point. Extreme caution is advised. 

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      • Stephanie ArnoldContributor Eric

        I saw this as well. I’ll mention it on the next roundup–everything needs to be taken with a proverbial grain of salt until we know more. It’s going to take a few weeks. 

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      • Cia Eric

        How do you think vaccine resistance should be handled? Federal courts are striking down mandates. I’m against mandates in general, but this pandemic is a special case.

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      • Eric Cia

        Vaccine resistance is just one of the symptoms of rampant misinformation. The solution is for more people to learn how to vet information sources. I don’t expect any fast progress on that.

        In terms of the pandemic, we can also look at vaccines as just one layer of defense, and put more effort into strengthening the other layers. Ventilation, for example, is a defense option that I think hasn’t gotten enough attention.

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      • Cia Eric

        I don’t think misinformation is a good characterization. The Covid vaccine, like all others, can kill or disable (paralysis etc.) Those who refuse it for that reason are correct as far as that goes. They may or may not be correct in assessing their personal risk from the vaccine as opposed to the disease. At a societal level, it is better for everyone to be vaxxed (drafted), even though a certain number will be personally harmed, even killed, by it. 

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      • Cia Eric

        This was a discussion here from last summer. I thought I’d better put the link in a reply rather than add it to my reply below.

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    • brownfox-ff

      What you can do about it:

      • Practice gratitude. What is one thing you’re grateful for this week? Practicing gratitude helps train our brains to recognize the positive, and recognize progress.
      • Take a deep breath. It’s going to be okay. You’ve got this.
      • Get some sleep. Getting enough sleep not only helps brain happiness, it also makes you better able to tackle challenges and prepare.
      • Get some exercise. Good health helps whether prices rise, or don’t. It helps whether ports close, or don’t. It helps whether big events happen, or don’t.
      • Keep working on that pantry.
      • Connect with someone. Is there someone in your community or family you would enjoy catching up with? Building and strengthening our social connections is a healthy activity.
      • Keep filling up your car when you get down to half a tank.
      • Consider working on your finances.
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      • Eric brownfox-ff

        What you can do about it – COVID addendum:

        • Stay relaxed. Shamelessly stolen from brownfox’s list because it’s so important. Just take one step at a time, trying not to worry about whether it’s enough.
        • Get vaccinated, including boosters. That’s 2 shots for J&J or 3 shots for Pfizer/Moderna.
        • Upgrade your mask to N95, which provides much stronger protection than the cloth masks that most people wear.
        • Learn to wear your mask properly. The mask should seal around the edges, so that air passes through the mask rather than around it. The best masks are moldable to fit the shape of your nose.
        • Avoid crowds, especially indoors. If this is impossible due to your job, talk to your employer about…
        • Ask your employer to improve ventillation in your workplace. This could be anything from opening windows, to meeting customers outside, to installing UV in the air conditioning.
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      • brownfox-ff Eric

        Excellent, practical list. Thanks for posting.

        Here is the guide on masks and how to wear them.

        It looks like HEPA-quality filters may help in several cases.

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      • Eric brownfox-ff

        That’s an excellent guide that I hadn’t seen before. The donning/doffing video is especially well done.

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      • Karl Winterling Eric

        Booster advice is complicated, but here goes:

        1. If you’re “fully vaccinated” (2 doses mRNA or 1 dose J&J), you can choose any approved booster 6 months after finishing mRNA doses or 2 months after J&J.
        2. If you’re a woman under age 50 and got the J&J vaccine, you should get an mRNA booster because we’re not sure about blood clot risk with additional doses.
        3. The Moderna booster had a somewhat higher rate of myocarditis in men aged 18-30 than the Pfizer booster, but that isn’t likely to be something you should worry about.
        4. If you had something like Sinovac/Sinopharm, talk to a doctor about getting either an mRNA booster or possibly the full Pfizer or Moderna vaccine sequence.
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    • Karl Winterling

      My understanding of the omicron variant is:

      1. It could be between 2x and 5x more transmissible than delta, but we don’t know for sure because there aren’t many cases. We also don’t know whether the higher transmission is based on a biological advantage, lax public health restrictions, or something like a superspreader event.
      2. Most (so far) cases are in young people in South Africa. Young people in South Africa are highly vaccine-hesitant (the rate is 25% in 18-34), for what it’s worth, but there’s also been a high estimated level of natural infection in South Africa.
      3. Experts are hopeful that vaccines will remain effective against severe disease and death (they might not be, given that we have 30 spike protein mutations) but think they won’t be as effective against infection/spread. So get your vaccine or booster if you haven’t already.
      4. Updated doses of vaccines can be ready in 100 days, but the process of stuff like FDA approval means it would take until the Summer before doses are available.
      5. Travel bans will delay the “case curve” by about a week but will damage South Africa’s economy. I’m not sure that’s a justified tradeoff.
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      • Stephanie ArnoldContributor Karl Winterling

        Virtually all of the people in South Africa who came down with the Omicron variant were unvaccinated, so it’s possible that vaccines are still protective. We won’t know for sure for a few weeks. 

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      • There’s some (theoretical) indication that very high antibody levels could help. Moderna is testing both its standard booster and a high-dose booster.

        The two people who got the Omicron variant in the “quarantine hotel” in Hong Kong were vaccinated more than 6 months ago. Both had mild flu-like symptoms.

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      • Eric Stephanie Arnold

        That’s worse than I was expecting. 🙁

        I just watched the video linked by that Twitter thread. He said they were seeing one vaccinated hospital admission for every 4 non-vaccinated hospital admissions. Considering that only 28% of South Africans are vaccinated, that translates into a vaccine efficacy of 29% against hospitalization.

        There’s still some reason to be hopeful. We don’t know if those vaccinated hospitalizations had received one shot or two, or were overdue for a booster. It’s also likely they used Astrazenca, which is somewhat less potent than the Moderna/Pfizer that are common here in USA. Still, 29% efficacy is ridiculously low.

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      • Eric Karl Winterling

        Most of what you said sounds right. I’m fairly confident, however, that Omicron’s transmission advantage is biological. Take a look at this graph of the percentage of variants over time in South Africa. That blue slice on the right is Omicron, and it almost completely replaced Delta in even less time than it took for Delta to do the same to Beta. Public health restrictions would have affected all variants equally, not allowed one to rise above the others. And if that spike were caused by a superspreading event, it would need to be a single event big enough to triple South Africa’s total COVID infections overnight, and also just happen to only involve people with this one very mutated variant. That would be an extraordinarily unlikely coincidence.


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      • Karl Winterling Eric

        I’m under the impression that spread/hospitalization is mostly young people whereas older people have higher vaccination rates (like 60%).

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      • Eric Karl Winterling

        Higher vaccination rate among older people could certainly throw the numbers off and make vaccines appear less effective than they are. Have you found a breakdown by age that would make a more accurate calculation possible?

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      • Karl Winterling Eric

        My understanding is:

        1. Anecdotally, spread and severe cases are mostly in unvaccinated populations.
        2. The details of the limited data South African scientists have suggest that Pfizer and J&J work to some degree, but we’ll have to wait for more people to look at that data.
        3. About 65% of hospitalizations are unvaccinated people, while many of the 35% vaccinated had only one dose. (no clear breakdown yet). It isn’t clear how long ago they got the doses.
        4. You can’t figure out vaccine efficacy just by a numerical comparison, you have to wait and see how the spread and hospitalizations play out over time. You need the lab tests and long-term hospitalization data.
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      • Eric Karl Winterling

        Found a reference and more details regarding your note that vaccinated, hospitalized patients tend to be half-vaccinated.

        “Young people, in their 20s to just over their late 30s, are coming in with moderate to severe disease, some needing intensive care. About 65% are not vaccinated and most of the rest are only half-vaccinated,” said Mathivha.

        Found via

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    • Cia

      Eric Topol said today that the report on Omicron’s causing milder cases was the best news of the day, that no one had thought that the mutation-laden variant could include reduced virulence. However, if the severe fatigue is like long Covid and can continue for years in many patients, it would mean indefinite and excruciating disability. Similar for the tachycardia.

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      • Eric Cia

        You’ve raised a good point regarding how Omicron will affect the likelihood and severity of long COVID. Unfortunately, that’s one of the most difficult questions to answer quickly. We’ll need months of data for that.

        Until then, it’s mostly a good sign that we aren’t seeing more severe disease. It’s even possible that Omicron infections will be less severe. Until we know more, I’m assuming similar severity as Delta.

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