All posts by Erik P. Johnson

Case Update, January 13, 2023; New Variant XBB.1.5, California Physician Misinformation Act Goes into Effect, the Twitter Files and COVID

Friends,

Happy New Year!  I have a brief COVID update for you.  Then I’ll talk about a new variant, XBB.1.5.  I’ll also have comments on a smattering of evolving stories, like California AB 2098, “Physicians and surgeons: unprofessional conduct”, and a new Twitter Files thread on vaccine misinformation.

We have already reached the peak of the December wave.  Cases in the US, California, and San Diego, and even world wide, peaked at around Christmas.  Deaths never really had a peak during this December wave, except in San Diego County. 

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Daily Confirmed Cases – United States, March 16, 2022 to January 12, 2023. Peak of the first Winter Wave was on around Christmas Day. We may already be seeing the start of an XBB.1.5 peak.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Hospitalizations, from the CDC website.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information on Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information on Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

However, we may see a second Winter wave this year…

New Variant XBB.1.5:  A new variant is spreading extremely rapidly in the US right now.  Variant XBB.1.5 is about 43% of the SARS-2 virus in the US right now.  A UK study suggests that this new variant is the most transmissible yet.  John Campbell, in another excellent analysis, suggests that about 80% of us will get it.  Antibody studies suggest that even those with prior COVID infections do not produce many antibodies that can neutralize XBB.1.5, so even those who have had COVID before are likely to get it again. The good news is, XBB.1.5 is another Omicron strain, and will produce very mild symptoms in the vast majority of cases.  I’ve had COVID twice already, and I will treat XBB.1.5 as a chance to get a free booster.

From the CDC page on Variant Proportions for the United States. Updated for January 14th.
From the CDC page on Variant Proportions for the United States. Updated for January 14th.
XBB.1.5 is the most infectious of the current variants, and perhaps the most infectious variant to date. From the UK Health Security Agency, Technical Briefing 49.

Despite the likely mildness of XBB.1.5, do others a favor and stay at home if you have COVID.  The over-the-counter antibody based COVID tests do not work very well, so if you are sick but have a COVID negative antibody test, you should assume you have COVID.  Only a PCR test can tell you if you’re really negative.

If you haven’t yet had COVID, I can no longer recommend that you get a vaccination or a booster, even if you are in an at-risk group.  If you are concerned about getting COVID, consider taking precautions instead.  Wear a N95, KN95, or KF94 rated medical respirator when indoors in public.  It’s also important to make sure your mask fits snugly.  The mask must filter air coming into your nose and mouth.  Loosely fitting masks with large gaps will not do this.  Do not wear a cloth or surgical mask.  These masks will not protect you from XBB.1.5.

California Physician Misinformation Act:  On October 4th, 2022, I wrote about California AB 2098.  This new law went into effect on January 1st and adds “the dissemination of misinformation or disinformation related to the SARS-CoV-2 coronavirus” to the definition of unprofessional conduct for physicians in California.  Unprofessional conduct can result in the suspension or loss of license for physicians in California.

Just yesterday, I had lunch with a friend of mine who is a doctor in California.  I asked him how he is dealing with this new law.  He said most of the doctors at his hospital follow the official guidance promoting vaccination, and the few who don’t have become very quiet about vaccines.  Doctors can’t say anything negative about the vaccine, for the risk of their medical license.

In 2021, this same doctor was coerced into getting the vaccine to retain his position at the hospital.  He got a booster later in the year.  A month after receiving his booster, despite being very physically fit for his age, he had a heart attack.  His cardiologist said he had none of the arterial plaques that typically cause heart attacks.  My friend cannot prove this, but he strongly suspects that clotting due to the vaccine contributed to his heart attack.  Despite all this, he does not feel at liberty in California to give information to patients that would reflect negatively on the vaccines.

Because this law is so new, I don’t yet know how it will be handled by the Medical Board of California.  If they choose to ignore it, then doctors won’t be under threat.  However, doctors and pharmacists have lost their licenses in the last few years for violating CDC guidelines, so the threat is a real one.

If you live in California, you cannot expect your doctor to give you their honest opinion about vaccines.  This is literally illegal now. Consider writing your state senator or assemblymember and ask them to support the repeal of AB 2098.

The Twitter Files have exposed a trove of evidence that official government agencies have been coercing several social media companies to censor COVID related information.  In an amazing post from Michael Shellenberger, a F@¢eb00k official recently revealed that F@¢eb00k was reducing content not because they thought it was misinformation, but simply because it had a sensationalist tone.  In an email to a Whitehouse official, the F@¢eb00k employee wrote:

“As you know, in addition to removing vaccine misinformation, we have been focused on reducing the virality of content discouraging vaccines that does not contain actionable misinformation.  This is often-true content, which we allow at the post level because experts have advised us that it is important for people to discuss both their personal experiences and concerns about the vaccine, but it can be framed as sensation, alarmist, or shocking.”

Obviously, these efforts to limit expression by a government agency is a violation of the first amendment, our most important freedom.  There are now many, many examples of this in the Twitter files, relating to COVID, and other matters.

From the Michael Shellenberger Twitter Files post, January 11th, 2023.

Don’t fear, but be smart,
Erik

Case Update, December 18, 2022; A Tridemic and Vaccine Related Blood Clots

This is a COVID update.  Then I’ll discuss the high number of RSV and flu cases right now.  I’ll also discuss the issue of vaccination induced blood clotting and the film “Died Suddenly”.

There has been a modest rise in cases in the past few weeks, suggesting that we will have a winter wave of cases.  So far, this wave is not nearly as high as last December, when the Omicron variant first became dominant in the US.  This is according to official testing data. Many are no longer being testing in a medical setting, so the number is likely much higher.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Hospitalizations, from the CDC website.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information on Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information on Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

Hospitalization data provides a better relative view of cases, since it shows how many are actually entering the medical system with moderate to severe cases, but San Diego County is no longer providing this information on their website.

As we’ve discussed before, the drug store tests are not nearly as sensitive as a PCR test, and I know several people who were negative by this kind of test for days after symptoms began.  The drug store tests can tell you if you have COVID, but false negatives are common, so if you get a negative result, it doesn’t mean much.  If you really need to know if you have COVID, get a PCR test.

The BA.5 variant now represents only 10% of currently circulating COVID variants.  There are currently 12 variants circulating in significant numbers, the most common being BQ.1.1.

From the CDC page on Variant Proportions for the United States. Updated on December 17th.
From the CDC page on Variant Proportions for the United States. Updated on December 17th.

Tridemic: A physician friend of mine who works in urgent care joked that we are currently in a “tridemic”, by which he meant that there a lot of COVID, Flu, and RSV cases right now.  Everyone knows about the flu, but many are unfamiliar with RSV.  Well, actually, you are.  Respiratory Syncytial Virus (RSV) is one of the several viruses that are responsible for what we call the common cold.  You have likely had it many times in your life. 

For most people, RSV is just an annoyance, but it can be serious for infants, causing bronchiolitis, a swelling of lung tissues.  If your infant is coughing a lot, breathing rapidly, wheezing, or just breathing noisily, contact your doctor.  Those with infants in their life may consider taking extra precautions to avoid passing along a cold.  The blue surgical masks are not a good defense against COVID, but they are effective to prevent droplets which transfer colds and flus.

Many guess that RSV has become more serious because we have been so cautious for the last few years.  I don’t know for sure if this is true, but it seems like a reasonable idea.

Long blood clots due to vaccines:  Chris Martenson has a new video regarding the long blood clots that many embalmers have discovered in the arteries of COVID vaccine recipients.  The phenomena started occurring in May of 2021, a few months after vaccination became common. Dr. Martenson is a pathologist and has done many autopsies in his career. 

Chris Martenson on vaccine related blood clots:

In the video, he addresses a recently released documentary called “Died Suddenly”.  The documentary claims that at least 140,000 people have died due to these vaccine induced blood clots.  In Martenson’s video, he points out that detractors of the “Died Suddenly” film argue that these clots are post-mortem, meaning they arise after the person has died. Dr. Martenson argues that the clots in vaccinated patients are definitely pre-mortem (before death), not post-mortem as some have claimed.  He gives specific features that lead him to this conclusion.

Dr. Martenson is one of my favorite commentators.  He is knowledgeable, open-minded, and evidence based.

I got a question about whether these clots only happen in vaccinated people. Late stage COVID disease is well known to cause clotting. But COVID related blood clotting mostly cause strokes and thrombosis. Obviously, these can also be very serious and lead to death. The vaccine related clots are different, completely blocking vessels. It’s not yet known how large they are pre-mortem. Dr. Mortenson argues they are pre-mortem, but that doesn’t mean they won’t continue to grow before an autopsy.

Searching “COVID blood clot” and “vaccine blood clot” on Pubmed will both bring up a lot of papers. I haven’t read enough of these yet to know if the large clots only happen with vaccination. The fact that you don’t need to get COVID to have clotting is obviously very important.

Died Suddenly: Several people have asked my thoughts on this film.  I will say that many COVID-era documentaries have a definite bias, so I always have my guard up when watching them.  Claims without sufficient evidence are common. 

The opening credits juxtapose images regarding blood clots and potential vaccine related deaths with images from other unproven theories, some that most regard as untrue or even ridiculous, like bigfoot and UFOs.  This seems intentional, as if the makers intend for the viewer to pair these ideas.  This seems to me to be ill-advised, if they intend to convince the viewer that blood clots can be tied to COVID vaccines.  It almost begs the viewer to associate their thesis with nonsense.

The basic premise of the film, the phenomena of vaccine related clots, seems to be at this point to be well founded and well evidenced.  The film offers several disturbing images of these clots being removed from cadavers.  The film also shows many examples of individuals passing out suddenly, while driving, speaking in public, even performing surgery.  The existence of this phenomena seems beyond dispute.  Interestingly, the detractors Martenson references in his video claim that the clots are post-mortem, not that the clots don’t exist at all.  Clotting has been a well known aspect of late stage COVID disease.

In addition to the potentially valid idea that vaccines have contributed to blood clotting in patients, the film makes the explosive claim that the deadly effects of the vaccine are actually intentional.  I haven’t seen any data to suggest this connection.  I’m not saying this is untrue, just that I haven’t seen evidence of this yet, so I don’t see a reason to believe it at this time.

The SARS-CoV-2 Spike protein has several toxic effects.  First, it causes an inflammatory response in many tissue types in the body, leading to diverse symptoms, including myocarditis, inflammation of heart tissue. This new phenomena shows that the spike protein can also cause blood proteins like fibrin to form an amyloid, an unnatural collection of proteins. Amyloid plaques also have a role in Alzheimer’s disease.

Should you get the updated booster?  COVID vaccines appeared to be working well in the Spring of 2021, but their effectiveness began to wane with the Delta variant.  When Omicron became the dominant variant, vaccine effectiveness dropped even further.  As knowledge of possible harms due to the spike protein has increased, I now think the harms of vaccination outweigh benefits in our current environment.  In my opinion, there is no longer any reason to get a vaccine or booster, even for those with risk factors. 

If you’ve been vaccinated, this information will likely cause you some concern.  I don’t know how long vaccine related spike protein has the potential to cause injuries.  Blood clots appear to form around 5 months after vaccination.  If you haven’t been vaccinated or boosted in the last 7 months or so, you may be in the clear. I’m sorry I don’t know more.

I have to point out that official channels claim that the information in “Died Suddenly” has been de-bunked. When posting this information on Facebook, I was met with several warnings about posting.  To be fully informed on this issue, you should read several sources of information and judge for yourself which are most reliable.

Don’t fear, but be smart,
Erik

COVID Update, November 17th, 2022; Is COVID Endemic Yet?

This is a COVID Update.  I’ll also ponder again if we have entered the endemic phase of COVID.

In the US, and San Diego County, case numbers are beginning to climb slightly, perhaps suggesting the start of a fall wave of new cases.  California isn’t showing this trend yet.  Hospitalizations are not rising for the time being, so all this means more people are entering the medical system with COVID, but this isn’t yet translating into more hospitalizations.  So current cases are more mild and moderate than severe.  This trend is new, so we may see this change later.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Hospitalizations, from the CDC website.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information on Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information on Thursday each week. Data points shown are extrapolated using this information.
Hospitalizations in SD County, July 10th to October 10, 2022. Gray area represents time-frame in which data is still being collected. Note that a significant number of hospitalizations are among the vaccinated.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

Is COVID endemic yet?  An epidemic is an outbreak in a larger region like a state, country or even continent.  A pandemic is an outbreak that spans multiple continents.  An outbreak becomes endemic when it becomes widespread in an area and is beyond control by disease prevention means.  For example, flu and HIV are both endemic, a now permanent part of life in the world.  Many people I have spoken to have believed that COVID has been endemic for a long time, and perhaps was always destined to be. I was optimistic for a long time, thinking that our immune systems would be able to eventually catch up with it and make it extinct.  Unfortunately, I think I lost hope in that this week.  Some of you are saying “what took you so long?”  I get it.  But I think it’s important to have good reasons for why we believe something.

We have generally had single dominant COVID variant in each region, with a few less important versions going around too.  In the US, we had Wuhan, then Alpha, Delta, Omicron, then Omicron BA.5. Currently, BA.5 has become a minority variant, with several others growing in prevalence.  There is no single variant that dominates, and none are clearly growing faster than others.  Importantly, new variants are arising more quickly that our collective immune system can keep up with them, and re-infections are now common. Happily, none of these new variants appear to be very pathogenic, and are not increasing the number of deaths, perhaps because natural immunity against COVID is becoming common.

From the CDC page on Variant Proportions for the United States. Updated on November 12th.
From the CDC page on Variant Proportions for the United States. Updated on November 12th.

In light of all this, I’m becoming more convinced that COVID is now endemic, and we won’t get rid of it.  Viruses have a tendency to become more infectious and less pathogenic (disease causing) over time, and we’ve certainly seen that happen during COVID.  New COVID variants will likely continue this trend. So we most likely will never return to the days when there are very large numbers of COVID hospitalizations and deaths.

Fewer posts from me: During most of the pandemic, I posted every week.  In the last few months, I’ve been posting only every 3 weeks or so.  Because I believe COVID is now endemic, and most are only minimally concerned, I will probably be posting even less now, only when there is some significant COVID news.

Don’t fear, but be smart,
Erik

Case Update, October 21st, 2022; Lab Creates Hybrid SARS-2 Virus, Spike Protein Causes Inflammation, How Many have had COVID?

Even though many think the pandemic is basically over in the US, there was still a ton of COVID news this last week.  As usual, I’ll tell you what I’m going to talk about in the intro, and you can check the headlines down below to read what interests you.  Some sections will be more detailed than many care about, and I have labeled those sections.

This is a COVID case update. I’ll also discuss yet more COVID variants, and a new paper from Greece about vaccines and inflammation.  I’ll also discuss a preprint paper from Boston University in which they claim to have created a hybrid SARS-2 virus. Last, I’ll talk about a recent study which sheds some light on the number of people in the US who have actually had COVID as of February.

Case Update: Cases continue to go down in the US, California and San Diego County. This has been a steady trend since mid-July.  Cases are about the same as in the Spring, before BA.5 arose.  Despite several new variants, deaths have not had a new peak, and are still relatively low, but not as low as the Summer of 2021, before the Delta variant arose.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information on Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information on Thursday each week. Data points shown are extrapolated using this information.
Hospitalizations in SD County, July 10th to October 10, 2022. Gray area represents time-frame in which data is still being collected. Note that a significant number of hospitalizations are among the vaccinated.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

New variants:  There are more new variants.  They continue to follow the trend of being more infectious than previous versions.  Some outlets are raising alarms about these new variants (BF.7, BQ.1, XBB), but there is not yet concrete evidence that they are more pathogenic than other recent versions.  There was concern that BA.5 was truly more pathogenic than other Omicron versions, but it still didn’t produce a new wave in deaths, perhaps because so many Americans now have either vaccine or natural immunity. How many? See below!

From the CDC page on Variant Proportions for the United States. Updated on October 15th.
From the CDC page on Variant Proportions for the United States. Updated on October 15th.
From the CDC page on Variant Proportions for the United States, by region. Updated on October 15th.

Spike protein may contribute to adverse events:  A July opinion paper from Greece claims that the Spike protein produced by vaccines cause inflammation and may be responsible for adverse events. The paper was published by Cell Press, one of the premiere science journal publishers.

If you’ve been reading my posts for a while, you will know that I first wrote about the link between the Spike protein and adverse events way back July of 2021.  For many months, the idea that vaccines were causing a lot of adverse events, and that the Spike protein itself was toxic was considered misinformation by the American medical establishment, yes, even by me.  Now this idea is becoming a topic of debate and perhaps even accepted. 

If you look up the words “adverse events covid vaccine” on PubMed, the site biologists use to search scientific articles, you will now see dozens of papers linking vaccines, the spike protein, inflammation, and adverse events.  Sorry, I still do not know just how many adverse events there are, as this information has not been adequately collected and/or shared by the CDC.

Detailed analysis by High Intensity Health.

Details: Many scientists are now suggesting that the vaccine should have used the Nucleocapsid protein rather than the Spike protein.  Nucleocapsid is a SARS-2 protein that helps package the RNA genome.  It does not change as rapidly as the Spike protein and does not interact directly with human proteins, so is not toxic.  For these reasons, it would have been safer to use the Nucleocapsid protein instead.

Structure of SARS-2. Spike is the tall outer protein, Nucleocapsid is the internal pink protein. From Sriwilaijaroen, N.; Suzuki, Y. Host Receptors of Influenza Viruses and Coronaviruses—Molecular Mechanisms of Recognition.

The downside is that a vaccine using Nucleocapsid would not have prevented initial infection.  Why would it have been useful then?  When the immune system destroys a virus, proteins from the virus end up getting displayed on the outside of cells, either infected cells, or immune cells.  This gives the immune system a chance to either detect these viral proteins and use them or make antibodies, or as a signal that a cell is infected and needs to be destroyed.

If the Nucleocapsid protein were used in a vaccine, SARS-2 could still infect human cells, since Nucleocapsid is inside the virus where the immune system can’t see it.  However, after a cell is infected, it displays Nucleocapsid on the outside.  If a person is immunized, immune cells will detect these proteins and destroy the infected cell.  While using Nucleocapsid in a vaccine wouldn’t prevent infection, it would probably greatly reduce viral load and symptoms.

Keep in mind that this is Monday morning quarterbacking.  Scientists didn’t know that the Spike protein itself was toxic when they created the vaccines, and internal viral proteins aren’t generally used in vaccines, so it didn’t occur to anyone to do this at the time. It is being discussed now, though, and may change vaccine design in the future.

Of course, we all now know that the Spike vaccines did not prevent infection by the Delta and Omicron variants.

Hybrid SARS-2 Virus Created in the Lab: This Monday, a lab at Boston University reported that they had created a strain of SARS-2 virus that killed 80% of infected mice.  The internet freaked out and subsequent reports said that it wasn’t all that bad, etc.  So I wanted to discuss this paper, tell you want exactly they did, and what I think about it.  There will be some detail, but I’ll give you a summary at the end if you want to skip to that.

The Boston group led by Mohsan Saeed took the Spike protein from an Omicron variant, and knitted it into the backbone of the original Wuhan virus.  The goal was to see what made the Wuhan virus more pathogenic, and the Omicron virus less pathogenic.  Was it the Spike protein, which determines transmissibility, or the internal viral proteins which determine other factors like how fast it replicates in a cell.

The resulting virus, called Omi-S was in fact much more pathogenic than Omicron, but not as pathogenic as the original Wuhan strain.  In the now infamous 80% kill rate experiment, it is important to know that the mice were infected in a very efficient manner, so that they were likely to have a severe case.  Also, the ancestral Wuhan strain killed 100% of these mice (6 mice died out of 6 mice tested).  The Omicron strain killed 0%.  So if Omi-S were to escape into the population, it wouldn’t kill 80% of the population, only 80% of the number that Wuhan killed.  So if Wuhan killed 1 – 3% of victims, Omi-S might only kill 0.8 – 2.4%.  Using several measures, Omi-S was much more pathogenic than Omicron, but less pathogenic than the Wuhan strain.

On the other hand, Omicron was well known to be much more transmissible than the Wuhan strain.  Presently, even countries that did well early in the pandemic have been unable to control Omicron and have experienced big outbreaks this year.  So it is likely that Omi-S could spread extremely rapidly, and still kill more people than the original Wuhan strain.

So was this result worth the risk?  Most infectious disease scientists know that the 1918 flu was so dangerous not just because of its unique surface proteins, but also because the internal proteins were especially robust.  The result with Omi-S paper shows much the same thing.  To me, the paper gave a result which was unsurprising. Scientists will disagree on whether this new variant should have been created. In my view, it was not worth the risk to create such a potentially dangerous variant to get a “water is wet” result.

Does Omi-S still pose a threat?  Experiments like this in the US are usually monitored by the CDC or other agencies.  Labs are generally required to destroy dangerous agents when the experiment is over.  It is likely that Omi-S no longer exists.  But given the unintentional release of SARS-2 in the first place, I think Americans may feel justified in being a little nervous about these experiments.

As an aside, in many infectious disease experiments, scientists go through a lot of effort to create test viruses or bacteria that cannot survive outside the lab environment. They do this by making versions that are incomplete, or need to be provided specific nutrients to survive.

For more detail, see this analysis by Mobeen Syed.

Summary of the Hybrid SARS-2 virus:  The Boston lab created a virus that combined the internal workings of the more pathogenic Wuhan strain with the more transmissible Omicron Spike protein.  They found that the internal proteins were likely responsible for the higher pathogenicity of the Wuhan strain.  In light of what is known about the 1918 flu virus, this result is not surprising.  While this hybrid virus likely no longer exists, my view is that the incremental knowledge gained was not worth the risk of creating this strain.

Headlines that the virus killed 80% of mice were true but misleading.  Under the conditions of the experiment, 80% of mice were killed by the new virus, but 100% of mice were killed by the original Wuhan strain. So this virus would be approximately 80% as deadly in infected people as the Wuhan strain.

How many people have had SARS?  The CDC published a paper in April describing “Seroprevalence” in the American population.  “Seroprevalence” basically means the number of people who have antibodies for a particular virus.  The study detected antibodies against the Nucleocapsid protein in patients between September 2021 and February 2022.  They did not have a random sample of patients, but rather used lab samples gathered when the people tested went to the doctor for any reason. So the subjects were skewed to people who were sicker or otherwise more engaged with health care than others. 

Because they detected antibodies against Nucleocapsid and not Spike, the study did not detect vaccinated people, only those who have had COVID.  Interestingly, the results showed that 75% of children up to 11 have had COVID, and the number was lower in each higher age group.  Of those 65 and older, only 33% have had COVID.

Graph by me with data from Clarke et al. 2022.

I know this post had a lot of detail!  Congratulations to those who read the whole thing!  Your questions will help me make it all more clear!

Don’t fear, but be smart,
Erik

New California law seeks to punish Doctors for Spreading Misinformation

This post is about a new California law seeking to limit misinformation.

California’s Governor Gavin Newsom signed AB 2098 into law on Friday. The new law allows the Medical Board of California to punish health care providers for spreading misinformation.  The law does this by adding the act of spreading misinformation to the definition of “unprofessional conduct” used by the Medical Board of California.  Unprofessional conduct is punishable in California by up to the suspension or loss of a license to perform medicine.

The law defines “misinformation” as “false information that is contradicted by contemporary scientific consensus contrary to the standard of care.”

There are many, many examples of ideas in science and medicine that were opposed by the scientific consensus and later accepted as true.  There are so many examples of this, that it should be considered as a normal part of the scientific process.  Examples include:

  • The Earth revolves around the Sun
  • Not cleaning surgical tools between operations can lead to increased mortality in patients
  • Ulcers are caused by the bacteria H. pylori, not by spicy food
  • Viruses can cause cancer
  • Cells produce energy by passing electrons through a membrane
  • The universe began at a discrete moment, and then expanded to its current form, creating both space and time in the process
  • The SARS-2 virus was created in a laboratory in Wuhan*

The idea that misinformation can reasonably be defined as an idea that is contradicted by scientific consensus is itself contradicted by centuries of scientific practice.

Scientific ideas come to be seen as true not merely by achieving consensus, but also by surviving challenge by new ideas.  No scientific idea is immune to this process. Science is not a set of facts set in stone, but a constantly changing set of ideas guided by the scientific process, a process which includes debate among scientists.  Requiring that new ideas achieve consensus immediately would freeze the advance of science in place, the current, and often wrong, ideas remaining dominant forever.

Of course, I have not yet addressed the obvious First Amendment violation this new law creates.  The First Amendment clearly allows freedom of speech, a cornerstone of American life.  This law will quickly be challenged by First Amendment advocates and will almost certainly be struck down.

As I’ve stated before, freedom of speech is not the cause of misinformation. It is the antidote.  Only if we allow the free flow of ideas can these 3 things happen:

All ideas to be aired
Good ideas to be confirmed and adopted
Bad ideas to be discredited

The correct way to battle misinformation is clear and persuasive communication, not censorship.

Dr. Mobeen Syed points out several other negative impacts this law will have:

  • Doctors will be suspicious of their patients, compromising the doctor/patient relationship.
  • Doctors will only give consensus advice, making going to the doctor more like going to a call center.
  • Laws will expand to include other kinds of “misinformation” further compromising the exchange of ideas.
  • Law will be used unequally to silence only certain kinds of speech.
  • Doctors may choose not to practice in California.

If I’m being too subtle, I’ll just say that this is a bad, unconstitutional law and should simply be ignored.

Don’t fear, but be smart,
Erik

* I’m taking a little liberty on this one.  This idea was rejected totally early in the pandemic.  It is not yet universally recognized as true, but many scientists, including me, see it as most likely to be true.

Another excellent video by Dr. Christy Risinger.

Case Update, September 28th, 2022; Variants BA.4.6 and BF.7, New Booster including Omicron Strains, President Biden Announces the Pandemic is Over.

This is a case update.  I’ll also comment on new variant, new boosters, and the President’s announcement that the pandemic is over.

Cases continue to go down in the US, California and San Diego County.  Again, since most people are now testing themselves using over the counter tests, the official case numbers are probably a gross underestimation of actual cases.  Hospitalizations are a better measure, and they are also going down.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Hospitalizations, from the CDC website.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information on Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information on Thursday each week. Data points shown are extrapolated using this information.
Hospitalizations in SD County, June 19th to September 14, 2022. Gray area represents time-frame in which data is still being collected. Note that a significant number of hospitalizations are among the vaccinated.

Variants BA.4.6 and BF.7:  In my last post, I introduced a new variant BA.4.6.  While hospitalizations are down, this new variant is now 11% of COVID cases in the US, and 20% of cases in the Midwest.  Still, I don’t think this new variant is likely to have a big impact on the pandemic at the moment, and I expect cases to continue to go down. Deaths remain relatively low compared to the Omicron variant in April after the Winter wave.  A newer variant, BF.7, is already growing in prevalence, but so far, there isn’t a lot of news about it.

From the CDC page on Variant Proportions for the United States. Updated on September 24th.
From the CDC page on Variant Proportions. Updated on September 24th. Notice that BA.4.6 (dark blue wedge) is most prominent in the Midwest.
From the CDC page on Variant Proportions for the Midwest. Updated on September 24th.

New boosters including Omicron strains:  In August, the FDA announced emergency authorization of new boosters by Pfizer, Moderna, and Novavax.  This new class of boosters produces spike proteins from the original Wuhan strain, but also from Omicron variants BA.4 and BA.5.  People have been asking me my opinion about these new boosters.  To preface my comments, I’ll say again that I am not a physician, epidemiologist, or immunologist, so my opinion is informed but not expert.

While the inclusion of BA.4 and BA.5 targets will make these new boosters an improvement over previous versions, I think most people will not benefit from them.  For anyone who has had COVID, which is now arguably most of us, they will not really benefit you.  Natural immunity has been shown in many studies to be equal or superior to vaccine mediated immunity in preventing infection and severe disease.

If you have never had COVID, you may benefit from the new booster.  Keep in mind however that we have never really gotten clear data about adverse events after vaccination.  In fact, Pfizer documents suggest that adverse events have been much more numerous than have been officially acknowledged.  The new boosters have not yet been FDA cleared, and according to a video by John Campbell, Pfizer’s testing only included eight mice in their testing group.  No human testing has yet been performed.  Because variants are arising so quickly these days, I think the usefulness of new boosters is effectively over.

I suggested that my own parents get vaccinated in the Spring of 2021.  But I am not suggesting that they receive the new booster.  If you do choose to get the new booster, try and find a provider who will aspirate before injection.

President Biden announces that the pandemic is over: On September 19, CBS News released a video in which President Biden stated that the pandemic is over. In the interview, the President said “The pandemic is over. We still have a problem with COVID. We’re still doing a lotta work on it. … But the pandemic is over.” Of course, this triggered a debate on whether the pandemic is really over.  At least a few health care officials said the health crisis is still ongoing, and that caution is still warranted.  Debates are now ongoing as to the appropriateness of ongoing emergency measures like vaccine mandates and emergency use authorizations.

As for me personally, I had difficult time with COVID in January, and a much more mild case in July.  I am basically behaving normally at this point. Most places I go, even in California, are basically going back to normal.

On other hand, hospitals are still seeing COVID patients and laboratories are still doing lots of COVID testing, so for them, COVID is still a reality they have to deal with.

If you’ve never had COVID, I would still recommend wearing a high quality medical respirator indoors in public (N95, KN95, or KF94).  Blue surgical and cloth masks are not effective against Omicron variants.

Don’t fear, but be smart,
Erik

Case Update, September 8th, 2022; Variant BA.4.6, Hurricane Kay will pass near San Diego

This is a COVID case update. I’ll also have a brief warning about Hurricane Kay, which I’ve heard very little about in the news.

Confirmed cases continue to decrease in the US, California, and San Diego County. Hospitalizations are down too, especially in San Diego County.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Hospitalizations, from the CDC website.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Hospitalizations in SD County, May 29th to August 21st, 2022. Gray area represents time-frame in which data is still being collected. Note that a significant number of hospitalizations are among the vaccinated.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

A newly recognized variant, BA.4.6 is growing relative to BA.5, so is likely more infectious. I haven’t been able to determine from news stories if it is more or less pathogenic (disease causing) than BA.5. BA.5 never caused an increase in deaths, despite it being more dangerous than previous Omicron strains.

From the CDC page on Variant Proportions. Updated on September 3rd.
From the CDC page on Variant Proportions. Updated on September 3rd. Most BA.4.6 cases are in the center and East Coast of the country.

My guess is that BA.4.6 will be less dangerous than BA.5, and that we’ll see fewer hospitalizations and deaths. This is just my speculation at this point.

Important Hurricane Kay warning for San Diego: Last weekend and this week, our increased heat and humidity was caused by Tropical Storm Javier, which traveled up the coast just west of Baja California before heading out to sea. Following closely after is Kay, currently a Hurricane off of Southern Baja. Kay will likely get much closer to San Diego than Javier did. San Diego is likely to see rain and even winds up to 23 miles and hour on Friday, according to the Weather Channel on Thursday morning. Kay will likely be downgraded to Tropical Storm by the time it gets to the waters West of San Diego, but it will still likely bring rain and stronger than normal winds. Consider securing loose items like patio furniture, tarps, and garden gnomes. No one likes a flying garden gnome.

National Oceanic and Atmospheric Administration site on Hurricane Kay, accessed at 7:30, Thursday Morning, September 8.

Don’t fear, but be smart,
Erik

Case Update: August 27th, 2022; Changes at the CDC, New COVID Guidance

This is a COVID case update. I’ll also discuss the CDC’s recent changes in policy.

We have some good news this week. New cases are going down by every available metric. New confirmed case numbers are coming down in all 3 regions. More importantly, hospitalizations are coming down as well, sharply in San Diego County. BA.5 continues to be the most common variant in the US by far. BA.5 was feared to be more dangerous than previous variants, but deaths have not risen significantly since BA.5 appeared.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Hospitalizations, from the CDC website.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Hospitalizations in SD County, May 22nd to August 14th, 2022. Gray area represents time-frame in which data is still being collected. Note that a significant number of hospitalizations are among the vaccinated.

World wide, new cases are coming down. After spending most of the pandemic at the top of the list of countries with the most new cases, the US is now at #3 on John’s Hopkins list, behind both Japan and South Korea, and at #7 on Worldometer’s list. Sorry, the US still has double as many total cases as #2, India.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Worldometer, Daily new cases in Japan.
Worldometer, Daily new cases in South Korea.

Changes at the CDC: Several news outlets reported on August 17th that CDC Director Rochelle Walensky has finally admitted that the CDC made significant mistakes in the agency’s response to COVID. She said, “For 75 years, CDC and public health have been preparing for COVID-19, and in our big moment, our performance did not reliably meet expectations. My goal is a new, public health action-oriented culture at CDC that emphasizes accountability, collaboration, communication, and timeliness.”

I’ve discussed several times before that the CDC is primarily responsible for the poor US response to the pandemic. Even worse, they have done great damage to the public’s trust in the medical community and in science in general. I’m glad she intends to fix the agency, but I’m afraid this will not be a speedy process and may essentially be impossible. In order to be successful, they will need to be transparent, and probably fire some people top leadership in order to regain the public’s trust.

Changes to CDC guidance: They also made some changes to CDC guidance on COVID. These changes include the following:

• Those exposed to COVID need not quarantine. Test on day 5, and wear a mask in public for 10 days.

• If you test positive for COVID, quarantine for 5 days. If after 5 days you are fever-free for 24 hours without the use of medication, and your symptoms are improving, or you never had symptoms, you may end isolation after day 5. Wear a mask until day 11, and stay away from high risk people.

• Vaccinated and unvaccinated people will not be treated differently.

Some of these changes are in response to the improving situation, while others are long overdue.

If you think you may have been exposed to COVID, review the changes on the CDC website.

Also, you can review the full COVID 19 page.

Don’t fear, but be smart,
Erik

Case Update, August 12, 2022, Monkeypox Update.

This is a case update. I’ll also have an update on the Monkeypox epidemic.

Not much has changed in the last 2 and a half weeks. Cases are still at a moderate level, at least according to official case numbers in the US, California and San Diego County. However, deaths in all 3 regions are still relatively low. This situation has persisted since early May. Even the more dangerous BA.5 has not really produced a large increase in official cases.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.

Most people are not getting tested in a medical setting right now, preferring to test themselves with over the counter antigen tests. As I posted a few weeks ago, these tests are producing a lot of false negatives right now, so many with COVID think they just have a cold. I believe I had COVID in mid July, but I tested negative twice, and never tested positive.

A better measure of case load is hospitalizations. In the US, hospitalizations likely peaked just a few weeks ago, and are now headed down. In San Diego County, hospitalizations likely peaked on around July 10th.

Hospitalizations, from the CDC website.
Hospitalizations in SD County, May 1st to July 30th, 2022. Gray area represents time-frame in which data is still being collected.

Right now, 89% if the COVID in the US is of the BA.5 variant. This variant is theoretically more dangerous than previous Omicron variants, but has not had a large impact, likely because of a lot of immunity in the population, either vaccine or naturally acquired. As for me, my case in January was much more severe than my case in July, despite my case in July being a more “dangerous” variant.

From the CDC page on Variant Proportions. Updated on August 13rd.

Most in the public are acting as if the pandemic is basically over. For the vast majority, there is really no longer a danger of severe disease or death. If you have not yet had COVID, you may still want to take precautions to prevent infection. Wear a medical respirator (N95, KN95, or KF94) when indoors in public.

Monkeypox Update: Despite being only moderately infectious, Monkeypox has continued to spread in many countries. There are now 11,000 confirmed cases in the US. The disease is similar to Smallpox, but is much less severe. It is spread primarily by skin to skin contact. With medical attention, Monkeypox is very rarely fatal, with currently only 3 fatalities in Europe. Monkeypox is endemic in central Africa, and occasionally produces outbreaks.

From the CDC website on Monkeypox cases, accessed August 12th, 2022.
From a UK government website on Monkeypox accessed August 12, 2022.

Monkeypox virus has been found on surfaces and in airborne droplets, so it is theoretically possible to contract it via these routes. However, there have been no confirmed cases of airborne transmission in the UK, according to a UK government document.

Some people living with infected persons have also contracted Monkeypox, so it appears that prolonged indirect contact can also spread this disease.

At the moment, 95.3% of cases in the UK are in a category called “men who have sex with men” (MSM), and this rate is likely similar in the US, but if cases continue to go up in the US, we will likely see more cases in the broader community. The good news is, new daily cases in the UK peaked in early July and are coming down now, so the US will likely start seeing a reduction in cases soon. Hopefully, the Monkeypox epidemic will be short lived.

A note on symptoms. Most of the public and even physicians assume that Monkeypox produces boils similar to smallpox or chickenpox. While it often does, it commonly seems to produce small rashes instead, leading to misdiagnosis. So if you or someone you know has small rashes, they should assume Monkeypox, isolate themselves, and seek medical attention. Smallpox vaccine appears to be effective against Monkeypox, so a vaccine is already available, but it is in short supply right now.

Monkeypox rashes, from Wall Street Journal video, Why Monkeypox is a Global Health Threat.

Don’t fear, but be smart,
Erik

Do the Antigen Tests Work for BA.5?

This post is about the over the counter Antigen tests that a lot of us have used in the last few months, and whether they really work.

As we’ve discussed, BA.5 is re-infecting lots of people, even those who’ve had Omicron just a few months ago. Those with recent cases generally have a mild case the second time around, even with BA.5

I just got back from summer camp with a bunch of high school students. I knew I could get COVID again, but since I had Omicron in January, I figured I’d be OK, even if I got BA.5. One of our counselors got sick while we were there, and tested negative for COVID, with an antigen test. I got sick on Sunday morning, after we were back, and also tested negative for COVID using an antigen test. On Sunday I just had a sore throat, Monday and Tuesday morning I had fatigue, sore throat, and just a little coughing. My sore throat felt very similar to the one I had in January, kind of like a weird heart burn, so I tested myself again on Monday. Still negative.

Meanwhile, the other counselor tested negative again when he got home, but then tested positive after that. His wife too. So he had 2 negative tests before testing positive.

So did I have COVID again? I still don’t know. I’m at the “just getting over a cold” stage right now and am feeling pretty normal. I had 2 negative tests and I’m not going to test myself again.

Doing a good scientific study is a slow process, and we’re probably unlikely to get good scientific articles on how well the antigen tests work for every new variant. The only articles I could find on BA.5 and antigen tests were from Slate and CNET. I usually don’t bother to read popular level articles on COVID since journalists often get things wrong, but that’s all we have. Both basically say that yes, they work, but you may need to take several tests. Well, that’s kind of like saying they don’t work very well.

How Antigen tests work: There are 2 kinds of tests that use antibodies for testing. One is an Antibody test. This kind of test looks for human antibodies against SARS-2 proteins. It actually determines whether you’ve been infected at some point in the past. IgM antibodies appear after a few days and persist for about a week. IgG antibodies appear after about a week and persist for weeks or months. So a positive SARS IgM tests says you basically have COVID right now, while a positive IgG test you have it now, or had it weeks or months ago. An IgG test is not useful if you want to know if you have COVID now.

An Antigen test detects actual SARS-2 proteins. They usually detect the Nucleocapsid protein (N), a protein on the inside of the virus which does not mutate rapidly. In theory, these tests should work well even if the Spike protein changes, which is by far the most common changes in new variants. They are not usually thoroughly tested with each new variant.

The Slate article suggests the tests may not be working as well because the BA.5 variant may not be as present in the nostrils as previous variants. Scientists know that a Nasopharyngeal (back of the nose/throat) site is better, but patients far prefer a nostril test. So this may be why the tests are not working as well for BA.5.

Antigen tests are less sensitive than a PCR test, but they are far cheaper, faster, and easier to use, which is why they are so common now. If you really need to know if you have COVID, a PCR test is the way to go. I frankly am pretty disappointed that a clearly symptomatic person can test negative for COVID right now with an Antigen test.

All this to say, if you have cold-like symptoms in the next few weeks, you’re better off staying at home and laying low for a few days, even if you have a negative Antigen test. You may actually have COVID.

Happily, if I indeed have COVID now, it’s a very mild case.

Don’t fear, but be smart,
Erik