COVID vaccine works - we're saved!

Two new variants, close relatives of omicron, have been detected in central New York state. Known as BA.2.12 and BA.2.12.1, they are causing a small and localized surge. They've also been detected in other countries, but the US has the most cases thus far.It's only four days since my previous post, but in that time the case rate in my county has risen from 15 to 16.--Percy

In my opinion optimism has outrun evidence at every step along the way. Over the past six months the expectation has arisen that covid is transitioning from pandemic to endemic. I'm not so sure. Two days ago our county's case rate for a 7-day moving average per 100,000 was 16, it is now 21. The Northeast is currently the nation's most significant covid hotbed.I said a week ago that the Northeast might be a harbinger rather than an anomaly, and now numbers for the country have started rising again.Mask wearing in the grocery store this week? Maybe 10%. But covid doesn't care if you're sick of wearing a mask.Maybe omicron is so much less virulent than the original virus, and maybe our skill at treating covid has improved so much, that catching covid should no longer be a concern, no worse than a cold. Maybe.There are a lot of articles in the press recently about how to balance the risks as things open up, but how does one balance the risk of something that can potentially kill you or leave you long-term debilitated. I've probably already mentioned several times a close friend who has long covid, originally catching it in the early stages of the pandemic about two years ago. He is better now than he was, but he's also so much less than he was. He currently has a cold that would normally just be a nuisance but has wiped him out. A 15-minute walk yesterday exhausted him and he looked it, face red, pained and gaunt.Most people who catch covid will recover just fine (in the near term - an understanding of long term effects will take time), but everyone thinks they're going to be in the "most" category. What if you're not?--Percy

Before I get into the topic, since my last update ten days ago our county's case rate for a 7-day moving average per 100,000 has gone from 21 to 30. The grocery store is still a barren wasteland as far as masks.In the January/February, 2022, issue of American Scientist there was an article about covid's effect on the brain. It described a 2021 preliminary study that relied upon the UK Biobank of 45,000 people in the UK that includes brain imaging data going back to 2014. Many people in the study caught covid, and recent brain images were compared to old. The study found that covid causes a reduction in gray matter tissue in the frontal and temporal lobes:

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The team found marked differences in gray matter—the cell bodies of neurons that process information in the brain—between those who had been infected with COVID-19 and those who had not. Specifically, the thickness of gray matter tissue in the frontal and temporal lobes was reduced in the COVID-19 group, differing from the typical patterns seen in the group that hadn’t experienced COVID-19.

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In the general population, it is normal to see some change in gray matter volume or thickness over time as people age, but the changes in those who had been infected with COVID-19 were larger than normal.

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Severity of the illness was not a factor. Those who had contracted covid processed information more slowly. Long term impact on aging of the brain and the degree of recovery are open questions.--Percy

My county's case rate has risen from 30 to 31 cases per 100,000. Virus mutations aren’t slowing. New omicron subvariant proves it, reports an article in today's Washington Post. New omicron subvariants continue to spawn, like BA.2.12.1, BA.4 and BA.5. We don't know much about these subvariants except that they're more transmissible. This might be good news. Let me explain.The last thing a respiratory virus wants to do is kill the host. A host that's no longer breathing is no longer seeding the air with virus spawn. So lethality is selected against. A host that is too sick to get out and about among other people is not very useful to the virus. Shut-aways or hospitalized people keep the virus from spreading. So making the host too sick is also selected against.What a respiratory virus wants most is high transmissibility combined with minimal impact on the host. A highly infected but completely functioning host is the ideal. The best host is probably one who enjoys running in crowded subways. High transmissibility and minimal severity of illness are the selection pressures on covid variants. The most transmissible variant will have a strong tendency to displace all others. If it also causes the least severe illness then that would be the ideal outcome, both for the virus and for us.We don't yet know the severity of illness caused by the new variants, but if selection pressures can dominate over random outcomes (not guaranteed) then there is reason for hope.In other news, Deborah Birx continues her rehabilitation tour, saying things that make sense. I get the impression that she's aghast at things she said and acceded to under Trump. Right now she's reporting her conclusions that the north should experience winter surges and the south summer ones with a periodicity of four to six months. See Ex-Trump Advisor Birx Warns Of Summer Covid ‘Surge’.--Percy

Coronavirus wave this fall could infect 100 million, administration warns says the Washington Post headline. The article has little good to say, but it does give some internal indications that it understands it's a pessimistic assessment.It says that as immunity wanes this fall and winter that there could be 100 million cases. An investment in updated vaccines for the new variants (omicron BA.2, BA.4 and BA.5) would probably be prudent. If omicron has a .1% mortality rate (my number, I think I'm being conservative) then that's an additional hundred thousand deaths. There's also the various forms of long covid to consider.Nationally case rates have more than doubled since the end of March. The northeast remains a hotspot and over a slightly longer period case rates in my county are up from 6 to 35 per hundred thousand for a 7-day moving average, an increase of six times. People may be starting to get the message here as the number of masks in the grocery store this week had risen from around 5% last week to maybe 15% this week.Through the first year of covid only a few people we knew contracted covid, but during the past six months or so around 10 to 15 people we know have contracted it. Two people I know have contracted it twice. We have several times learned that someone we'd had contact with only two or three days before had contracted covid. One the contact was outdoors and we paid it no concern, but the other was indoors and we were very concerned. One woman we know insisted on playing in her tennis league even though her husband was home with covid - half the players didn't show up that week. Good for them. Sends the right message.The number of people who contract covid with mild cases and fully recover sends the wrong message. More attention should be paid to those who I don't have mild cases. I don't have exact figures in front of me, but I imagine I'm not too far off to say that around 10% are hospitalized, 5% end up in the ICU, 1% are intubated, and .1% die. This is not a virus you want to mess with.Also, a fair percentage of people who apparently fully recover experience symptoms returning weeks or even months later, even though they didn't catch covid again. The disease is neurological. Yes, it attacks the lungs, but it really likes the olfactory nerve centers when it can affect taste and smell and gain a pathway to the brain. As I reported last week, people who have contracted covid at any level of severity experience reduced brain mass and complete mental tasks more slowly. Some in the neurological field are predicting spikes in Alzheimer's years from now as the neurological effects people suffered years ago eventually catch up with them.My wife and I desperately do not want to catch this virus, but we can only be cautious for so long. When this spike here in the northeast calms down we're returning to normal life, which means eating out inside, visiting family (requires cross country travel), vacations, etc. We'll put the masks back on as necessary and reduce activities whenever things get really bad, but otherwise we're returning to life as normal.We were so close some months ago. Our local case rate was down to 1 per hundred thousand, and we figured one more week at 1 and we'd stop wearing masks. It didn't happen, probably because most of the rest of the county had already stopped wearing masks, allowing it to once again gain a foothold. I don't know what it is about people that leads them to insist on dropping restraints just as things are starting to get better, instead of after they're already better.--Percy

I think you're at 2 per 100,000. Ah, I remember 2. Those were the good old days.--Percy

New York City and environs are all somewhere between 30 and 50 per 100,000. If you're going to be staying around the New York area then just be careful. If you're free to visit anywhere in the country then anywhere that's not New York, New Jersey and New England (the Northeast) is in pretty good shape. Here's the latest map: --Percy

Edited by Percy, : Fix image.

Hope your having fun on your trip. Here again is the 5/7/2022 map of hotspots in the country, and just below it today's map just five days later. The case rate has significantly worsened in the Northeast, by maybe 25%, and have similarly worsened in much of the rest of the country but from a much lower base. Hospitalizations have begun to creep up in all but 12 states. It can be hard to tell what's going on in the Northeast because the states are so small and the text makes the subtle color differences hard to see. The change is easier to see in Minnesota, Wisconsin, Michigan and Illinois. I know the change isn't dramatic, this is over just five days.Worst county in the country? Loving, Texas, but the population's only 163.--Percy

Edited by Percy, : Fix image link.

The covid case rate is beginning to rise more rapidly in the US, not just in the Northeast and the northern Midwest, but everywhere, just from a lower base. Here's images of the nationwide county case rate map for the 7th and the 14th of May. With just a casual glance they appear the same, but look more carefully. This is what the beginning of a surge or outbreak looks like. Here's the recent Covid case rate graph for the nation, just the last six months or so: Grocery store mask rate was maybe 10% yesterday, possibly 15%. It's going to get worse before it gets better. The only question is how much worse.We took advantage of the good weather the last couple days to eat lunch out on outdoor patios. It was nice to be doing something normal again. None of our friends who recently caught covid had a severe case.--Percy

Edited by Percy, : Typo.

This is from today's NYT (How America Lost One Million People): --Percy

As my relative has made clear to me, information like that graph is just propaganda from the liberal news media, combined with their censoring of what's really going on. Covid's just an excuse for the Dems to impose their tyrannical authoritarianism. Twitter and Facebook ban anyone who tells the truth about covid. Fauci admitted he funded the covid research in Wuhan. Any covid was brought in by the Dems by importing illegal immigrants.I think that about covers it.--Percy

I don't know why I haven't posted my county's covid case rate in the past couple weeks, but this morning it is 46. Here's an Excel table of the values I've happened to note here since March. The numbers are a 7-day moving average of the number of cases per day. Here's a graph of the same data showing a slowly accelerating rate of increase: Mask wearing in the grocery store is still around 10%-15%. People are largely unaware of the state of the pandemic in our area.The rate is likely far higher since many people now take home tests and don't report positive results to anyone. There's an article in today's Washington Post describing how we no longer have a handle how good/bad things are in the various regions of the country: How big is the latest U.S. coronavirus wave? No one really knows.. Since the article's behind a paywall and most people don't have access, here are a few excerpts:

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With public health authorities shifting their focus to covid-related hospitalizations as the pandemic’s U.S. death toll hits 1 million, people are largely on their own to gauge risk amid what could be a stealth surge.

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Experts say Americans can assume infections in their communities are five to ten times higher than official counts.

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“Any sort of look at the metrics on either a local, state or national level is a severe undercount,” said Jessica Malaty Rivera, an epidemiologist at the Pandemic Prevention Institute housed at The Rockefeller Foundation. “Everyone knows someone getting covid now.”

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Hospitalizations nationally have increased 50 percent since bottoming out six weeks ago. But the roughly 23,000 patients with covid in hospitals over the last week still represent near the lowest hospitalization levels of the entire pandemic. The recent increase is driven by the Northeast, where hospitalization rates are almost twice as high as any other region.

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Reported cases of covid have also tripled in the Northeast in just over a month, driving much of the growth nationally, according to the Centers for Disease Control and Prevention. The country has averaged nearly 90,000 new cases each day over the past week — three times higher than the lowest point in March.

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Covid hospitalizations have increased but remain low

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Covid hospitalization have dipped to levels similar to early last summer just before the delta surge, matching the lowest levels of the pandemic.

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--Percy

With covid case rates reported by states becoming an unreliable indicator of the pandemic's severity, I'm switching to hospitalizations. Here's the national map. The worst part of the country is the Northeast, with the Midwest next worse, but overall the country looks very good for hospitalizations, near the lowest levels since the pandemic began.Though we can no longer get an accurate read on case rates, they're probably pretty high, probably at least 100 cases per 100,000 per day as a 7-day moving average nationwide, about half the highest rate from last winter.There are several reasons I can think of that hospitalizations are low:

• More than half the country is vaccinated, and vaccinated people are hospitalized at about 1/10th the rate of unvaccinated people.
• We have better outpatient treatments than earlier in the pandemic, such as Paxlovid pills.
• The medical establishment has a lot more experience dealing with covid now.
• Omicron might be milder.

Here is today's map of current hospitalizations from the NYT: --Percy

Yeah, that too.That reminds me, a coupled days ago a NYT article reported that it is becoming increasingly apparent that covid does not appear to be settling into a flu-like pattern as many expected. Rather than a once a year surge, it seems to be settling into a 2-3 times a year surge that doesn't align with the seasons and that can follow different patterns in different regions of the country or world.And the protection provided by infection and vaccination appears to begin waning after three months and is mostly gone after six months.--Percy

Using Moose's county as an example, 3 cases/day is undoubtedly a severe underreport because all across the country most people now take home tests and don't report positive results. Mostly the only cases coming to light are those of people whose symptoms are so serious that they go to a doctor, urgent care or emergency room. Something around 20 cases/day is more likely for Moose's county.With a population of 11,000 that puts the probability of any individual catching covid today at around .0018. That sounds like very little and nothing to worry about, but if the rate remains roughly constant, sometimes a little higher, sometimes a little lower, then tomorrow the probability is again around .0018. And the next day, too. What's the probability that an individual will catch covid once during the year if the rate remains roughly the same? That would be 1-(1-.0018)³⁶⁵, which is .482.Put in percentage terms, the probability of any given person catching covid in Moose's county over the course of the next 365 days if the rate remains roughly the same is around 50%. Around half the people in his county are going to catch covid over the next year. Naturally the brunt of infection will be felt by those who don't vaccinate or mask, and/or are older.With a mortality rate of around .1% (we still don't have an accurate measure for omicron) and a population of 11,000, that's 5 or 6 deaths. Somewhere around 20% of covid patients come down with long-covid, if not immediately afterward then within six months, so that's around 1100 people with long covid symptoms.The conclusion to take from this is that what sounds like a low case rate is actually going to have dire consequences.I don't want to seem to be singling out Moose's county, so let's go through the same exercise for my county here in New Hampshire, where there are very few masks, maybe 10% at most. We're at 40 cases per 100,000 right now, so the actual rate is probably around 300 cases per 100,000, which translates to 1242 actual cases per day or a probability of any individual catching covid at .003. What's the probability that an individual will catch covid once during the year if the rate remains roughly the same? That would be 1-(1-.003)³⁶⁵, which is .666.Put in percentage terms, the probability of any given person catching covid in my county over the course of the next 365 days if the rate remains roughly the same is around 67%%. More than half the people in my county are going to catch covid over the next year. Naturally the brunt of infection will be felt by those who don't vaccinate or mask, and/or are older.Using the same mortality rate as before, around .1%, and a population of around 400,000, that's around 270 deaths, and 53,000 people with long covid symptoms.The number of people who catch covid will be underreported because of people like my long-covid friend who three weeks ago undoubtedly came down with his second case of covid, but refused to be tested. We can't know for certain he had covid, but if he did the national statistics don't reflect it.And he's complacent about both protection and treatment. He is now weaker than ever. He still refuses to get vaccinated or wear masks. Over the course of the past two years the virus has forced him prematurely into retirement, left him with a pacemaker, rendered him unable to play the sport he loves, and has turned him into a recluse, yet he still does nothing. He's probably a bit toward the extreme end of the spectrum, but not by that much.And we now know that the protection provided by vaccines and infections begins to wear off after three months and have almost completely worn off after six months. Hence it isn't enough to catch covid once or vaccinate once like we do with the MMR shot (measles, mumps, rubella). Those who wish vaccination protection covid will have to get shots twice a year, or at least that's how it looks right now.At present California is around 70% vaccinated, one of the highest rates in the country, but unless the people of California get revaccinated about twice a year, within a year that rate will be much lower. It's probably already much lower.We can't blame the CDC for the high case rates and low vaccination rates because much of the country just won't listen, but we can blame the CDC for not sending the right message about best practices. Once they get the message right maybe they'll be able to figure out how to get people to listen.As I said, the country's covid rate is much higher than case rates indicate (waste water measures have been much more reliable here in the Northeast in places where they're available, for instance like Boston where rising case rates were indicated well before the reported numbers started rising). Everyone indoors, not at home, and not alone, should be wearing a mask. Everyone should get vaccinated twice a year, not just the "vulnerable population", because the "vulnerable population" is exposed to the "not vulnerable population." And the "not vulnerable population" label doesn't mean they're at lower risk of contracting the virus. It just means they're less likely to get very sick or die when they catch it. They'll still be a vector for the virus to people who are in the "vulnerable population." Half the country is acting like they don't care if old or vulnerable people die, especially including their own Mom and Dad and Grandpa and Grandpa and aunts and uncles and so forth. These people are a conundrum and a puzzlement. Mostly they just don't believe what they're being told about the virus. Many don't even believe it's real. We know who we have to blame for this.If our goal were to keep covid going at a much higher rate than necessary, then we're doing a great job.--Percy