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.

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!

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.

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.

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