Category Archives: Treatments

Case Update, December 1st, 2021; Vaccine against Omicron, Is COVID Endemic?

This is a case update. I’ll also briefly discuss the Omicron variant, the possibility of a vaccine against Omicron, and whether COVID is now endemic.

Cases in the US continue increase, with cases rising particularly in the Northeast, in states like New York, Pennsylvania, Vermont, and Michigan.

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 Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, November 28th, 2021
Endcoronavirus State Level Map, December 1st, 2021

In California and San Diego County, cases are still stable, at a rate about as high as last Summer, but lower than the peak of Delta. Just hours ago, California Public Health and the CDC have announced that a patient with the Omicron variant has been detected in California. They had returned from South African on the 22nd, and the case was detected on the 29th.

_____________________________________
UPDATE: December 1st, 1:00 pm
Just hours ago, California Public Health and the CDC have announced that a patient with the Omicron variant has been detected in California. They had returned from South African on the 22nd, and the case was detected on the 29th.
_____________________________________
UPDATE: December 2nd, 2021
2 more cases of Omicron have been detected, in Minnesota and Colorado. The case in California and Colorado were in individuals who were fully vaccinated. All individuals have had mild symptoms so far.

Hours after reporting the above, another 5 cases of Omicron were reported in New York City. Suffice it to say, it’s now clear that Omicron is in the US and is already nation wide. I’m sure a lot more cases will be reported soon.

Most new cases of a new strain can only be reported after expensive and time consuming sequencing testing has been performed, so these results will come out more slowly than just a COVID detection.

I’m going to stop reporting individual new cases, since the point has been made that Omicron is in the US.
_____________________________________

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 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. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.

World wide, cases are climbing at the moment, with big increases in several European countries. Several countries have reported the detection of the Omicron variant, but so far only a few cases in each country are due to Omicron, so the big increase in cases may be due to Delta and the onset of Winter.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

Vaccine against Omicron: So far, Delta is still the majority of cases world wide. Even in South Africa, only about 20% of the COVID cases are suspected to be due to the Omicron variant as of this writing. But because of the large number of mutations in the Omicron variant, scientists are concerned that the current batch of vaccines will not work against Omicron.

I saw an interview with Albert Bourla, the CEO of Pfizer. He stated that Pfizer could have a vaccine against Omicron ready for distribution in 100 days. Interestingly, Bourla also said in the interview that they had designed a vaccine against Delta, but they hadn’t released it because the original vaccine worked well against Delta. I was very discouraged by this comment. Many countries, including Israel, have been reporting that the vaccines have only been about 40-50% effective against Delta, and even the CDC admitted in July that 15% of COVID deaths have been in vaccinated individuals. I seems the me that the vaccines against the Wuhan strain have not worked well against Delta, and that vaccines against Delta should have been released. The comment seems to be evidence that Pfizer is not fully absorbing data on vaccine effectiveness from around the world.

Is COVID endemic?: I had hoped that once the vaccines came out, we would be able to generate enough immunity (natural and vaccine related) against COVID that it would go away. With 2 major variants that can evade the vaccine already out (Delta and Omicron), I’m becoming more convinced that COVID is indeed endemic at this point, meaning that it will continue to mutate, circulate, and be part of the fabric of life from here on out.

My personal strategy has been to avoid infection and vaccination until it all blows over. I’m becoming convinced that this will not work. So should I get vaccinated now? I’m concerned that Omicron might trigger the ADE pathway and cause worse symptoms for those with immunity to SARS-2. For this reason, I’m going to continue to keep myself SARS-2 free until more is known. Regardless of vaccination status, I encourage you to take some extra precautions until more is known about Omicron. Concern is good, panic is bad.

A glimmer of hope: As stated in Monday’s post, South African Doctor Angelique Coetzee has stated that her COVID patients have had very mild COVID symptoms. Her patients are mostly young people. If symptoms from Omicron are mild in older patients, and the new variant is very infectious, that there is a small chance that it will present a safe and effective way to provide immunity to lots of people. Of course, we will need to wait a few weeks to see.

Don’t fear, but be smart!
Erik

Case Update: November 23rd, 2021; Is Vaccine Effectiveness Going Down?

This is a case update.  I’ll also discuss data suggesting that the v@¢¢¡nes are having a mixed effect.

For the US, new case numbers have begun to creep back up.  Several states like Vermont, Minnesota, Colorado, and West Virginia are experiencing increased cases right now.  This is likely at least partly because colder weather is forcing more people inside. Several states are still enjoying decreasing case numbers after the Summer Delta wave, like Oregon, Washington, Alaska, and the Southern states.

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 Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, November 21st, 2021
Endcoronavirus State Level Map, November 22nd, 2021

Last year’s Fall wave started in October, so it’s good news that a new wave may just be starting now, but keep in mind that new case numbers are just as high now as they were at the peak of last Summer’s wave.

In California and San Diego County, new case numbers are persistent, at around 5000 and 500 new daily cases respectively.  The higher persistent number likely reflects the higher infectiousness of the Delta variant.

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 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. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.

Internationally, several European countries like Germany, the Netherlands, Hungary, and Czechia are experiencing increasing numbers of cases right now.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Daily new cases from Germany, November 23rd, 2021.
Daily new cases from the Netherlands, November 23rd, 2021.
Daily new cases from Czechia, November 23rd, 2021.

V@¢¢¡ne effectiveness:  A pile of new papers have come out regarding v@¢¢¡ne effectiveness.  A few weeks ago, I discussed Subramanian et al which claimed that v@¢¢¡nation rates are not correlated to case numbers internationally.  New papers from Britain, Germany, and even a story on msn.com are claiming that v@¢¢¡ne effectiveness is becoming reduced. 

The British paper states something I’ve suspected for a long time, that most SARS-2 transmission takes place in households, explaining why lockdowns are not an effective means of controlling COVID. They also claim that v@¢¢¡nation status is nearly irrelevant in a household setting, because of long term exposure to family members.

A Swedish paper (Nordström et al) suggested that v@¢¢¡ne effectiveness is reduced over time, especially for elderly men and those with co-morbidities. Effectiveness against severe symptoms begin to be reduced after about 9 months.

From Chris Martenson, using data from Nordström et al.

Disturbingly, some have suggested that v@¢¢¡nation is doing more harm than good.  A set of British data claims that v@¢¢¡nated individuals are dying at twice the rate of the unv@¢¢¡nated.

A German analysis of national data comparing German states is claiming similarly that excess mortality is actually due to v@¢¢¡nation.

Meanwhile, in the US, the CDC is claiming that v@¢¢¡nation greatly reduces the chances of hospitalization and death, although not to zero.  The agency currently claims that the unv@¢¢¡nated are 5.8 times more likely to become infected and 14 times more likely to die than v@¢¢¡nated individuals.

What are we to make of all this?  Is the v@¢¢¡ne really making people sicker?  Are things different in the US and Europe?  It’s hard to know right now.  We are in a period when v@¢¢¡ne effectiveness may be going down right now, so we may be getting mixed signals because we’re seeing this in real time.  The Delta variant is certainly exacerbating the issue, eluding antibodies developed against the Wuhan strain. We also have to consider that we may be seeing the effect of Antibody Dependent Enhancement (ADE), which may cause greater symptoms in those already infected with a related strain.

The present confusing situation is a great example of why it’s so crucial to accumulate as much data as we can, and to be as objective as possible about the results.  US agencies are still openly admitting that they have as a goal to promote vaccination (see slide 2),

From CDC powerpoint, July 29, 2021, slide 2. Red oval is mine.

and even to suppress information that works against this goal (see “Are adverse reactions …”). 

Screenshot from OSHA FAQ on vaccines. Accessed November 23rd, 2021

I cannot stress strenuously enough that if we work from incomplete or faulty data, we have no hope but to come to faulty conclusions and bad solutions.  If you have a hole in your gas tank, it doesn’t matter how much gas you put in it.  You will still have no gas.  You have to deal with the real problem first. 

The CDC has one and only one job.  To produce data and guidance on how to fight disease. But the very sad fact is that I don’t trust the CDC to produce truthful and/or complete data.  This is why we are relying on papers from foreign sources like Britain, Israel, and Japan to inform us on how to approach COVID.  With all the cases here, and 53 different approaches to the virus, we should have the best and most complete data set for figuring out what to do.  But politics continues to make this impossible. I hope this will change.

As discussed in the paper by Liu et al, boosters against the Wuhan strain will likely not offer long term protection against the Delta strain.  Instead, those who have been v@¢¢¡nated should get a v@¢¢¡ne against the Delta strain as soon as it is available.

Most people with severe symptoms are Vitamin D deficient. If you aren’t already, remember to be supplementing with Vitamin D, Vitamin C, and Zinc in order to reduce symptoms and viral load if you should be infected. Most Americans, especially those with darker skin, are Vitamin D deficient, since we spend so much time in doors. Alternatively, make your own by spending 30 minutes outside per day in shorts and a T-shirt!

Don’t fear, but be smart,
Erik

Indefinite stay on Vaccine Mandate issued by the 5th Circuit.

No COVID case update this week. Like last week, new cases are persistent in the US, California, and San Diego County. 

However, just wanted to note that the 5th circuit has placed a second stay on the OSHA vaccine mandate until further notice.  OSHA has suspended efforts to enforce the mandate. Text on the OSHA website reads:

“On November 12, 2021, the U.S. Court of Appeals for the Fifth Circuit granted a motion to stay OSHA’s COVID-19 Vaccination and Testing Emergency Temporary Standard, published on November 5, 2021 (86 Fed. Reg. 61402) (“ETS”). The court ordered that OSHA “take no steps to implement or enforce” the ETS “until further court order.” While OSHA remains confident in its authority to protect workers in emergencies, OSHA has suspended activities related to the implementation and enforcement of the ETS pending future developments in the litigation.”

Don’t fear, but be smart,
Erik

Case Update, November 5, 2021; Vaccine mandate details released, Should you get a booster, do vaccines cause new variants?

This is a case update. I’ll also talk about the newly release v@¢¢¡ne mandate from OSHA, whether you should get a booster, and the question of whether v@¢¢¡nes lead to new SARS variants.

New cases in the US, California, and San Diego County are all fluctuating right now.  It’s hard to say if this represents the beginning of a new wave.  Most of us are feeling like the pandemic is basically over, but I will point out that in the post-Delta trough, we still have as many new cases per day as we did at the peak of last Summer’s wave.  Minnesota, Colorado, New Mexico, and Arizona are all experiencing increases in cases right now.

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 Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, November 3rd, 2021
Endcoronavirus State Level Map, November 5th, 2021
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 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. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

V@¢¢!ne mandate finally drops: In September, the President said he wanted government agencies to produce a mandate for v@¢¢¡nation.  Just this week, OSHA issued an Emergency Temporary Standard. This is official form of the v@¢¢¡ne mandate we’ve been waiting for.  The mandate conforms to the news you’ve heard, all employers with more than 100 employees must get v@¢¢¡nation status from all employees, and those who are not v@¢¢¡nated must be tested weekly.  The testing option means that the standard does NOT require that everyone be v@¢¢¡nated. Enforcement will begin January 4th, 2022.

Full length OSHA Emergency Temporary Standard.

As we saw last week, the CDC has known since July that a significant number of hospitalizations and deaths have occurred in fully v@¢¢¡nated individuals.  In addition to this, a recent Lancet paper from Singanayagam et al suggests that the transmission of Delta is less from v@¢¢inated individuals, but is still very significant. In light of this, I think all employees, regardless of v@¢¢¡nation status, should be tested regularly, although it would be impossible to test everyone every week. Ignoring the transmission threat from v@¢¢inated individuals is likely to lead to trouble. Everyone exposed to someone who tested positive for COVID should also be tested.

I saw a truly amazing thing on an OSHA FAQ page regarding v@¢¢ination. I checked it again just now to make sure it was still there.  Under the item “Are adverse reactions to the COVID-19 v@¢¢¡ne recordable on the OSHA recordkeeping log?” The answer reads:

DOL and OSHA, as well as other federal agencies, are working diligently to encourage COVID-19 vaccinations. OSHA does not wish to have any appearance of discouraging workers from receiving COVID-19 vaccination, and also does not wish to disincentivize employers’ vaccination efforts. As a result, OSHA will not enforce 29 CFR 1904’s recording requirements to require any employers to record worker side effects from COVID-19 vaccination at least through May 2022. We will reevaluate the agency’s position at that time to determine the best course of action moving forward.

In effect, an official government page is saying, we are asking you to ignore health information in order to get people to do what we want.  Some of you may be wondering why so many people are willing to ignore official calls to get v@¢¢¡nated, or are suspicious of government in general.  This is why. This also answers the question as to why it is so difficult to get clear information on adverse events. The government appears to have an official policy of ignoring these events.

Screenshot from OSHA FAQ on vaccines. November 5th, 2021

I’ll say again what I’ve said many times, I am not anti-v@¢¢¡ne.  I think many people with risk factors including age, obesity, respiratory or cardiac issues, those who work closely with the public, etc. should get v@¢¢¡nated. However, I am against a v@¢¢¡ne mandate.  I am not v@¢¢¡nated, mostly because of the ADE issue, and because I think I can avoid being infected.

I will also state what is obvious to many, but not to some that are making policy.  Lying or hiding information from the public will make people mistrust you.  You can sometimes force people to comply, but you cannot, even in principle, force people to trust you.  Trust must be earned. Once you lose it, it is very difficult to get back. 

This rule can be applied to any area of life.  Remember this if you’re a husband, wife, parent, child, pastor, politician, consultant, leader of a company, employee, or anything else where trust is required.  Trust is earned, and once broken, is very hard to get back. 

Should you get a booster?: Several people in the past few weeks have asked me if they should get a booster.  Right now, unfortunately, my best answer is “I don’t know”.  A booster may improve your immune response to the originally Wuhan strain of the SARS-2 virus, but the Spike protein from the v@¢¢¡ne is likely toxic on it’s own. In addition, the paper from Japan I wrote about some time ago suggests that another booster of the current variety is unlikely to provide complete protection against Delta.  Instead they recommend a Delta derived booster. 

Anyone who has had COVID or has been v@¢¢¡nated should get a Delta v@¢¢¡ne as soon as it is available to protect from any ADE related effects. Several companies are currently working on v@¢¢¡nes against Delta.

Does the v@¢¢¡ne create variants?: A nobel prize winning scientist is claiming that v@¢¢¡nation creates SARS variants.  I absolutely agree that v@¢¢¡nation creates selection pressures that can force viruses to gain new forms to avoid neutralization.  However, the very same can be said for natural immunity.  Both natural immunity and v@¢¢¡nation create selection pressures that can lead to new viral variants.  This is true of all viruses and other invading agents. In spite of this, our bodies are designed to use the immune system to fight off infection, and immunity has had a tremendous benefit, despite the selection pressure it poses. ADE is a rare exception to this rule. Our immune systems work much more quickly than viruses can adapt to them, which is why they are so effective at preventing infectious disease.

____________________________________
Updated November 23rd, 2021:

No COVID case update this week. Like last week, new cases are persistent in the US, California, and San Diego County. 

However, just wanted to note that the 5th circuit has placed a second stay on the OSHA vaccine mandate until further notice.  OSHA has suspended efforts to enforce the mandate. Text on the OSHA website reads:

“On November 12, 2021, the U.S. Court of Appeals for the Fifth Circuit granted a motion to stay OSHA’s COVID-19 Vaccination and Testing Emergency Temporary Standard, published on November 5, 2021 (86 Fed. Reg. 61402) (“ETS”). The court ordered that OSHA “take no steps to implement or enforce” the ETS “until further court order.” While OSHA remains confident in its authority to protect workers in emergencies, OSHA has suspended activities related to the implementation and enforcement of the ETS pending future developments in the litigation.”
_______________________________________

Don’t fear, but be smart!
Erik

Case update, October 25th, 2021; Vaccination vs Cases, Do Vaccine Mandates Exist?

This is a case update.  I’ll also discuss a new paper regarding v@¢¢!nation and new cases, as well as v@¢¢!ne mandates.

New cases for the US continue to go down. 

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 Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, October 23rd, 2021
Endcoronavirus State Level Map, October 25th, 2021

For California and San Diego County, however, there is a persistent higher case number, and the numbers for last week may even reflect a very slight increase in new cases.

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 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. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

The very large wave from last Fall and Winter started in October.  We may be seeing the very beginnings of a Fall wave.  Hopefully our Summer Delta wave will have provided some extra immunity.

V@¢¢!nation and new cases:  A paper came out in September regarding the correlation between v@¢¢!nation rates and new cases.  The study compares data in 68 countries and 2947 US counties that had 2nd v@¢¢!ne doses available. 

The most interesting figure features a piece of data called a “linear regression”. This kind of data compares 2 variables and shows visually if they are related.  In the below hypothetical example, the 2 variables, the number of tests in a day and the number of confirmed cases in a day, shows a high correlation between these 2 things. Notice that the line plotting the relationship between data points goes from bottom left of top right as the values of each variable increase.

A linear regression plot with hypothetical data. Good correlation gives an R squared value between 0.95 and 1. If the variables are negatively correlated, the R squared value will be between -0.95 and -1.

The paper shows a linear regression plot with the percent of the population that is fully v@¢¢!nated on the x-axis, and the per capita confirmed case rate on the y-axis. If v@¢¢!nation strongly protects individuals from infection, new cases would go down as v@¢¢!nation went up.  In this case, the plot line would go from top left to bottom right (the green line).  Instead, it appears that there is little correlation between percent v@¢¢!nation and cases, producing the black line.

V@¢¢!nation vs cases produces black line, showing little correlation between the 2 variables. The green line was added by me and shows hypothetical data that would show strong correlation. From Subramanian et al.

They also have a box plot with US counties showing the new per capita case loads arising from counties with various levels of v@¢¢!nation. While counties with high v@¢¢¡nation rates do have fewer cases, the impact is not as profound as might be expected, and the difference between counties above 50% v@¢¢!nation rate is likely not statistically significant.

Box plots showing v@¢¢¡nation vs per capita cases in US counties. V@¢¢¡nation rates are groups in blocks for this view. Notice that very little difference exists between counties above 50%. From Subramanian et al.

It should be noted that this study was performed in September with data mostly from August.  This is during the Delta wave in the US and many Western countries.  The Delta variant may be different enough from the original Wuhan strain to enable the Delta virus to avoid neutralization by Wuhan induced immunization.

It has long been rumored that v@¢¢!nation does not prevent infection, and this paper seems to support this view. In spite of this, most scientists, including me, still hold that v@¢¢!nation does reduce the chance of hospitalization and death in infected patients.  This is still true.  However, a power point published by the CDC shows that this protection is diminishing as well.  In January, hospitalization and death among v@¢¢!nated individuals was essentially 0%, but now 9% of hospitalizations are among v@¢¢!nated people, and 15% of deaths.

From CDC powerpoint.

Why is this happening?  There are likely multiple factors. Certainly, the Delta variant is not the same virus as the Wuhan strain.  The different Spike protein makes it more infectious, and may not be recognized by an antibody against, the Wuhan strain.  It may even be triggering the Antibody Dependent Enhancement (ADE) pathway in some patients.  Also, it is becoming clear that v@¢¢!ne mediated immunity has been going down over time, necessitating a booster.  The paper from Liu et al argued that given the differences in Delta, a booster against Delta would be much more effective than another booster against the Wuhan strain.

V@¢¢!ne mandates: I still believe that v@¢¢!nation is a good choice for some with risk factors like age, obesity, diabetes, or respiratory problems.  However, I remain against v@¢¢!ne mandates because they do not take into account the medical history of individuals, the data that natural immunity is significantly better than v@¢¢!ne mediated immunity, and also the potential danger of ADE.  In addition to these scientific reasons, I have also felt an increasing orneriness on my own part.  Orneriness is not a good reason to make scientific or medical decisions, but policy makers should realize that it is a powerful reason for many.

For myself, I have chosen to not be v@¢¢!nated, but to remain careful to not be infected.  I continue to wear a mask indoors when there is poor ventilation. 

President Biden mandated v@¢¢!nation for federal agencies soon after taking office.  He announced in September that he would seek v@¢¢!nation mandates for private companies with more than 100 employees.  While many assume that a mandate for private companies is in effect now, as of this writing, no such mandate for private companies actually exists, either by law or by executive order. Companies that have enacted v@¢¢!ne mandates as of now have done so voluntarily.

________________________________________________
Update: November 5th, 2021

The official vaccine mandate was released on November 4th 2021 and is scheduled to be enforced starting on January 4th 2022. Details are on my November 5th post.
________________________________________________

Updated November 23rd, 2021:

No COVID case update this week. Like last week, new cases are persistent in the US, California, and San Diego County. 

However, just wanted to note that the 5th circuit has placed a second stay on the OSHA vaccine mandate until further notice.  OSHA has suspended efforts to enforce the mandate. Text on the OSHA website reads:

“On November 12, 2021, the U.S. Court of Appeals for the Fifth Circuit granted a motion to stay OSHA’s COVID-19 Vaccination and Testing Emergency Temporary Standard, published on November 5, 2021 (86 Fed. Reg. 61402) (“ETS”). The court ordered that OSHA “take no steps to implement or enforce” the ETS “until further court order.” While OSHA remains confident in its authority to protect workers in emergencies, OSHA has suspended activities related to the implementation and enforcement of the ETS pending future developments in the litigation.”
_______________________________________

Don’t fear, but be smart,
Erik

Case Update, September 13th, 2021; Israel data, Mu variant

This is a case update. I’ll also discuss a hack for poorly ventilated areas, the paper from Israel everyone is talking about, as well as the new variant, the Mu variant.

For the US, it definitely looks like we’ve cleared the peak for the US. Cases in many states have started to go down. States in which case numbers are still rising include Utah, West Virginia, Maine, and Pennsylvania. A word of caution is that COVID spreads indoors in poorly ventilated areas. Last Summer, we had large case loads in the South, and the winter had even larger case loads starting in the North. Both phenomena were probably caused by the virus spreading indoors, where there was air-conditioning and heating respectively. As Summer ends, we may end up seeing a large number of cases starting from the Northern states and spreading south, just like we did last Fall. If this happens, it will likely begin in October.

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 Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, September 13th, 2021
Endcoronavirus State Level Map, September 13th, 2021

Cases continue to fall for California and 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.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. 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. See also regularly updated slides from SD County.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

Indoor virus filter: I recently heard a podcast from physician Mike Osterholm (Osterholm Update, Episode 66). He argued that indoor ventilation was actually much more protective than masks. For those who can’t ventilate a space well, he suggested making a large scale air filter (Corsi box) using a box fan and a MERV 13 air filter. This is equivalent to a number 10 Honeywell furnace filter like you’d get at Home Depot. If you have a space where people gather that you can’t ventilate, buy a filter roughly the same size as your fan and tape it firmly to the front of the fan. Make sure the filter supports are toward the fan blades. On a side note, he also argues as I do that loose fitting masks are nearly worthless, but N95, KN95, and KF94 respirators are very good.

Data from Israel: Lots of folks are talking about the pre-print paper from Israel (Gazit et al) on vaccination vs natural immunity (infection by COVID). The data was from a database of patient information. They compared breakthrough infections (a person who was vaccinated and later was infected with Delta) to reinfection (a person who was infected with a previous SARS-2 variant and was then infected with Delta). They did this as a whole and also in a time matched way, meaning that the date of likely infection was around the same as the date of the 2nd dose of vaccine. Note that the vaccines are against the original Wuhan strain, so the paper is also discussing the rate at which Delta infects those who had natural vs vaccine exposure to non-Delta strains.

The results show that naturally infected people were almost 6 times less likely to get infected by Delta than vaccinated people, and 7 times less likely to have symptoms. The results are even more striking for the time matched data. For these patients, naturally infected people were 15 times less likely to get infected, and 27 times less likely to be symptomatic. Over all, it looks like natural immunity is better than vaccination for resistance to the Delta Variant.

Protection from Delta infection from vaccination and natural immunity. Protection from vaccination is arbitrarily given a value of 1, while other categories are shown in fold increased protection.

They did another study comparing natural immunity to natural immunity plus 1 dose of vaccine. Those previous infected with COVID AND having 1 dose of vaccine were about half as likely to be infected with Delta. Or you could say that having 1 dose of vaccine made them almost twice as resistant to reinfection.

Protection from Delta infection from vaccination and natural immunity. Protection from natural immunity is arbitrarily given a value of 1. Natural immunity plus 1 dose of vaccine gives 1.88 fold increased protection.

Some cautions are in order. Countries are not responding to the Delta Variant in exactly the same way. As discussed before, countries with large vaccination programs are seeing much fewer deaths due to Delta than other countries. However, rates of infection in vaccinated people by Delta seem to be higher in Israel, suggesting a slightly different version of Delta is in that country. Some reports suggest the Pfizer vaccine is only 39% effective against Delta in Israel.

The Mu Variant: News is only starting to circulate regarding the Mu variant (pronounced “mew”). First detected in Colombia in January 2021, this variant is currently classified as a Variant of Interest, not a Variant of Concern, suggesting it does not have characteristics that are very different from other versions, and may not have a large impact. A recent paper from Italy suggests that currently available vaccines do neutralize Mu, although with less efficiency. On the other hand, a WHO press release suggested that it may be able to escape immune responses raised to other variants. Since there is some disagreement, more studies will need to be done.

Don’t fear, but be smart!
Erik

Case Update, September 1st, 2021; FDA approval for Pfizer vaccine, 2 shots of vaccine, or 1 after COVID infection improve protection from Delta.

This is a case update. I’ll also discuss the potential for a Fall peak, new branding for the approved Pfizer vaccine, and whether you should get a vaccine shot if you’ve had COVID.

In the US, cases continue to rise, but the rise is slowing. Numbers from this last weekend suggest we may be seeing a peak in cases, but it’s too early to say. Deaths from the Delta peak are increasing also, but are proportionately less than for previous peaks.

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 Johns Hopkins University COVID site. Graph is presented in a linear format.

We are starting to see fewer cases in the South. Last year, the Summer peak was centered in the warmer states, California to Florida, and then we had a very large wave starting in the North starting in October. With cases still high at the start of September, we may see another large surge of cases in the North as we head into Fall.

Endcoronavirus County Level Map, August 31st, 2021. New cases slowly receding in the South and growing in the North. Michigan, Missouri, Nebraska still appear to not have strong outbreaks as of now, likely because of large case numbers during the UK variant wave in the Spring of 2021.
Endcoronavirus State Level Map, August 31st, 2021

New cases continue to fall in California and San Diego. Tentatively, it even looks like deaths are falling as well.

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 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. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

The Pfizer vaccine recently received FDA approval. The confusing part, is that legally speaking, the approved vaccine is not the same legal entity as the Emergency Authorized vaccine. The Pfizer vaccine we’re used to is called “Pfizer-BioNTech COVID‑19 Vaccine”. The FDA approved one is called “COMIRNATY (COVID-19 Vaccine, mRNA)”. I’m not a legal expert at all, but my understanding from watching some legal analysis is that the original vaccine is still only EUA authorized, and has some liability protection for Pfizer. However, Pfizer does not have liability protection for the COMIRNATY vaccine. According to the approval letter from the FDA, the formulations of the 2 vaccines are the “same formulation” and “can be used interchangeably”.

So why the name change? An analyst I watched said that Pfizer would like to continue to use the original vaccine under the new approval, but avoid liability. So those getting the vaccine now would still be getting the vaccine with liability protection for Pfizer. If you want to get a 3rd shot, you may want to wait until the legally approved COMIRNATY vaccine is available. Again, I am not a legal expert, so my analysis may be wrong on this.

If all this is true, you may regard this as a dirty trick by Pfizer. I try not to be cynical about things that I have only a vague understanding of, but if you thought that, I couldn’t disagree with you.

2nd shot improves protection against Delta, even for those with natural immunity. In a video by Dr. Roger Seheult, he argues that another shot greatly improves the immune response to the Delta variant. This follows both for those with only a single shot of the Pfizer vaccine, or with natural immunity. All this to say, if you’ve had COVID, 1 shot of a vaccine will help protect you from a breakthrough infection from the Delta Variant.

From Planas et al, 2021. Data suggests boosted binding of antibodies to Delta Variant after natural immunity (COVID infection) and 1 shot of the Astra Zeneca or Pfizer vaccine.
From Planas et al, 2021. Data suggests boosted binding of antibodies to Delta Variant after 2 shots of Pfizer vaccine.

Don’t fear, but be smart,
Erik

Possible low efficacy of current vaccines against Delta, possible Delta enhancement in the future.

This post is detailed, but adds an important new set of facts regarding the Delta Variant, the current vaccines, and prospects for a new booster shot.

You may have heard commentators in the last few days talking about the reduced efficacy of the current set of vaccines. There has also been a lot of discussion about a study from Israel about relatively high numbers of Delta COVID cases among vaccinated individuals.

First a little background on antibodies. Your immune system is making a random set of new antibodies all the time. In an ingenious mechanism, your immune cells “mix and match” pieces of a gene in your immune cells, producing the ability to make a zillion (scientific language for a whole lot) of different antibodies. Your body is basically making different “keys” that can fit into the “lock” of some new protein.

When you get an infection, several different antibodies may bind to the invading agent, on different regions, so you may be protected by several different “keys”. When this happens, a bunch of different things happen, including the manufacture of Memory B cells which makes just the antibody that binds to a particular protein. These cells get activated if you get re-invaded by something with that protein. All this to say, if you’ve had COVID, or been vaccinated, your body will have B cells with antibodies on them that bind to different parts of the Spike protein.

Before I say anything else, I want to repeat that I have not been vaccinated, but have recommended that high risk individuals get vaccinated! I’ve also pointed out many times in the past few weeks that countries with large vaccination programs have lower death rates due to Delta than other countries!

Literally 30 minutes after Thursday’s post on vaccine myths, a doctor friend of mine sent me a pre-print paper from a lab in Japan. Please note, this is a pre-print paper and has not yet finished peer review! The paper describes experiments using antibodies derived from patients infected with the Wuhan strain, as well as with the Delta Variant. They then studied binding of these antibodies to artificial viruses. The paper argues that Delta variant viruses are less neutralized by vaccines against “wild-type” or Wuhan strain vaccines. While the “wild-type” antibodies against Wuhan can neutralize a region of the Delta Spike protein called the Receptor Binding Domain (RBD) (Figure 1C), other antibodies binding to another region of Delta Spike protein actually enhance infectivity. Figure 1D from the paper shows negative levels of “neutralization” for antibodies that bind the N-terminal domain of the Spike protein. The paper calls this “enhanced”. Yes, this is the ADE I’ve been talking about.

Figure 1 from Liu et al 2021.

They suggest that with rapid changes in COVID variants, a new version of Delta is going to be able to use the ADE pathway in the near future, when Wuhan era antibodies will no longer be able to neutralize a mutated Delta strain.

To sum that all up in simpler language, it basically says that Delta is more infectious because it is partially using the ADE method of infection. Future versions may be less prone to be neutralized by Wuhan antibodies, making them fully enhanced. If this happens, we may have more severe disease in those who get infected with this new enhanced Delta.

They conclude by saying a booster against the Wuhan strain will not be effective in improving protection from Delta, and that a new vaccine against Delta will be required.

The material in the paper may help to explain why we have been seeing lowering levels of vaccine effectiveness in some countries.

Just to be very clear, they are not saying that this new enhanced Delta exists now, just that it may exist in the future.

I will pay close attention to this issue. If you have already been vaccinated or had COVID, a new Delta vaccine will be your best defense against possible ADE arising from a possible enhanced Delta.

If an enhanced Delta arises, and you have had Wuhan COVID or a Wuhan vaccine, and you haven’t had Delta, then you may be at greater risk for severe disease.

If you have had COVID since July 2021, you are likely already immune to the Delta variant, and this will not be an issue for you.

I am fully aware this complicated. Also, the CDC has rarely if ever discussed this possibility, so unfortunately, most of the people you talk to about this will not believe it. I am sharing this with you so you can make wise decisions for you and your family.

Some companies are already working on Delta versions of the vaccine. If you have had the current vaccines, or had COVID, you should get the Delta vaccines as soon as they are available.

Of course, discuss your medical history with your doctor before making medical decisions.

Another note on misinformation: My post from last Thursday generated a lot of discussion regarding censorship and misinformation. I argued strongly that the dangers of misinformation do not outweigh the benefits of free speech. Many of you are pro-vaccine and others are suspicious of the vaccine. I would simply urge this:

1) If you use the words “misinformation” and “disinformation” in a post or in a discussion, please come ready with evidence to support whatever claim your making! Don’t just throw out this word, support it!

I recently saw a video with a pro-vaccine medical person saying “we just need to keep pounding this information into people”. That is the wrong approach. With someone who is not yet convinced to get a vaccine, “pounding” away on them is just going to raise their defenses and exasperate you. Instead, gently show them your reasons for believing what you do! Explain to them what the data means. You may not convince them, but you may move them toward being more open to your view.

2) If someone makes a claim that sounds unfounded or that you don’t trust, don’t just tell them they’re wrong or make a counter claim, ask them to provide evidence, or where they got their information. You don’t have to do their homework for them! If they can’t produce any evidence, you are under no obligation to counter it. I’ve saved myself A LOT of work with this approach. It’s OK that they just heard it somewhere IF their source is reliable and has evidence themselves. You can still ask them to provide you with a link or something to that person’s statement. However, “I just heard it somewhere” is not evidence.

Part of the reason I’m not so worried about “misinformation” for myself is because of my regular use of suggestion #2.

Don’t fear, but be smart!
Erik

Video: “Top 3 vaccine Myths” and Tech Censorship

In the interest of openness and full disclosure, I need to share a video with you that I just watched. Dr. Zubin Damania is a Youtube commentator that I actually listen to a lot, and I find him more reliable than many. He just posted a video “Top 3 COVID Vaccine Myths“. Two of his myths are:

2) The Spike protein is toxic.
3) Antibody Dependent Enhancement may cause vaccinated individuals to experience more severe disease if infected with SARS-2.

If you have been reading my posts, then you know I have been concerned about both these issues. So am I spreading myths?

2). My concerns about Spike protein toxicity are based on persistent rumors of people having moderate severe reactions to the vaccines. For awhile, I dismissed these as just the standard reaction that some have had to any vaccine, including those for flu. But more and more rumors piled up and made me wonder if something else was going on. Then I saw the video by Bret Weinstein and Robert Malone. Dr. Malone is the inventor of the mRNA vaccine technology. The video argues that the Spike protein itself is toxic. Dr. Malone’s credentials are at least as good as Dr. Damania’s on this matter, likely better, so I can’t dismiss his view.

Unfortunately, I haven’t yet been able to find enough reliable information on adverse events to form my own opinions based on the data, so I’ve been relying on others to inform me. Frankly, because of the politicized nature of the vaccine issue, I don’t feel at all confident that I can get reliable information. So I may never be able to develop an informed opinion on this matter.

Dr. Damamia claims that convincing evidence exists that demonstrates that Spike protein is not toxic, but he doesn’t give it in this video. This of course is very common.

3) I’ve talked a lot about the ADE issue. In this video, Dr. Damania claims that ADE has not been an issue in the vaccine roll out, and the new variants have not caused more severe symptoms. I agree with both of these points. I point these out in my November 2020, December 2020, and April 2021 updates to my ADE post. I am still concerned about that new variants may someday arise that can use the ADE pathway, or that a new SARS strain, a hypothetical “SARS-3” will arise that will be different enough to trigger ADE. So while I agree with Dr. Damania’s point on ADE, it’s not quite the point that I’m still concerned with.

As I’ve stated many times, the vaccines are likely to help you if you have a risk factor and I have several friends and family members that I have recommended get the vaccine. So I am not anti-vax per se. But I don’t think it’s the obvious choice for everyone, and I’m staunchly for personal medical freedom in regards to COVID vaccines.

So what do I do now? What should a thinking person do when confronted with new information from a trusted source that you’re not sure about? These things are all true when dealing with complicated issues:

People you generally agree with may say something you don’t agree with.
People you generally disagree with may say something you agree with or makes you think about an issue in a new way.

Both of these are normal. When dealing with a complicated issue like COVID, race relations, worldview, politics in general, it is critical to keep an open but critical mind. You have to read widely from both your side and others to hope to get a clear view of the issues involved.

I respect Dr. Damamia. He might be right! I’ll have to think about his points, do some more homework, and reassess my opinion. There are 3 possibilities.

I will abandon my position and accept his.
I will learn new things that will reinforce my position.
I will do a bunch of research, but will not find conclusive information that will allow me to form a new opinion either way.

If I can arrive at a place closer to the truth, then the exercise will be a good one. If I decide I think Dr. Damania is wrong on these points I’ll likely still watch his videos, since I think he is right more often than he is wrong, and he’s more open minded than most, so I think he is at least being honest about what he believes, which is a very valuable trait! Dr. Damania is both for COVID vaccination and against vaccine mandates.

I started out posting on COVID because as a scientist I felt a responsibility to help my non-scientific friends and family members make some sense of the pandemic, especially when scientific communication is so often poor. I hope I have done that. I can’t claim to always be right, and have changed by view several times. But I have given you the truth as best as I can find it, and supported it with evidence.

A word on tech censorship: The WHO said 2 false things early on:

SARS-2 is not human to human transmissible
SARS-2 is not transmissible as an aerosol.

Both of these things were demonstrably false, and perhaps politically motivated, even at time the WHO stated them. In in spite of this, the social media platforms came to hold the WHO as the gold standard for the truth on COVID matters. To this day, F@¢3b00k may place a tag on the end of this post claiming the WHO as the authority on COVID matters. Most platforms would delete or restrict anything that ran against the WHO. Yes, computer programmers in Silicon Valley are still pulling down information posted by medical doctors and scientists. Even Dr. Damania has had videos censored!

One of the worst results of the pandemic in the US is censorship of divergent opinions. Freedom of speech allows 3 things:

All opinions to be held up to public scrutiny.
True things to rise to the surface.
False things to be discredited.

When freedom of speech is restricted, none of these can happen. If a wrong thing becomes the “orthodox” view, and no other views are permitted, then the orthodox view will always be wrong, and we will end up solving all of the wrong problems. If there is a hole in your gas tank, it doesn’t matter how many times you put gas in it. It will always be empty. Fix the real problem first.

This is why all the claims of misinformation, from all sides, are so insidious. When you claim misinformation, you are claiming to have the whole truth on an issue. Sure, we can and should argue against views we think are false. But we must also protect the right to air all views! Or we are doomed only to have the first view that becomes dominant, and we are less likely to find the truth!

I also found an article on why some are still vaccine hesitant. For those of you who are wondering, you should read it.

As always, Don’t fear, but be smart!
Erik

Case Update, August 19th, 2021, Is COVID Endemic?, Mandatory Vaccination.

This is a case update. I’ll also briefly discuss the future of the pandemic.

Numbers continue to rise in the US, but are definitely slowing in their increase. New cases are most prominent in the West and Southeast. New deaths are rising, but much more slowly than for other waves.

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 Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, August 19th, 2021
Endcoronavirus State Level Map, August 19th, 2021

For California and San Diego, it looks like we have crested the wave and new cases are starting to head down. In both of these regions, new deaths are not really increasing at all. This supports the pattern that in vaccinated areas, large numbers of new cases due to the Delta Variant are not followed by large numbers new deaths. I mentioned a few weeks ago that deaths can trail new cases by as much as 4 weeks, but we are now 6 weeks into the Delta Wave in California and San Diego without seeing a significant rise in new deaths.

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 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. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.

Internationally, new cases appear to perhaps have peaked world wide, but it will take some time to see if cases start to go down. As stated above, countries with vaccination programs are experiencing almost no new deaths due to Delta Variant. Numbers for the Netherlands are striking, and other countries like the UK, Sweden, Japan, and South Korea show a similar pattern.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
New daily confirmed cases in the Netherlands, from Worldometers.
New daily deaths in the Netherlands, from Worldometers.

Several sources I listen to are now saying that SARS-2 is now or will be endemic. For some background, an epidemic is an outbreak of a disease in a small area or region. Avian influenza and the first SARS outbreaks were epidemics, since they didn’t leave Asia. A Pandemic is an outbreak in a large area including several continents. A disease becomes endemic when it becomes a constant feature of life in an area. I would include malaria, seasonal flu, and HIV in the list of endemic diseases. Interestingly, Wikipedia still considers HIV to be a pandemic.

I have resisted calling COVID endemic. I don’t think it fits the criteria at this point. While there have been several new variants that have caused additional waves of cases, they are all at least partially impacted by the available vaccines, and presumably by natural immunity as well. While this is the case, I still think it is possible that we can eradicate the virus from the world at some point.When might SARS-2 become endemic? For me, that would happen if either new variants arose that were not mitigated by natural or vaccine driven immunity, or if immunity in vaccinated or naturally immune people ceased to be effective in preventing new infection. Both of these would allow SARS-2 to continue to circulate indefinitely.

Some have argued that vaccine mediated immunity is not as long lived as hoped. This may be why there have been many “breakthrough” cases in the last few weeks. However, Youtuber Dr. Zubin Damania suggests that while protected from new infection wanes over months, vaccine protection against severe disease is persistent, at least against the Delta Variant. This may explain our current pattern of low deaths despite high cases in vaccinated regions.

So is COVID endemic? I still say no, and hope it can be eradicated. However, some municipalities, including Norway and the state of Iowa, have declared that is endemic and will be a permanent feature of the world. If I decide that the data shows that SARS-2 is endemic, then that is the day that I will get vaccinated. ‘Cuz I do want to go back to normal life someday, but I don’t want to actually get COVID. Obviously, many vaccinated and unvaccinated folks have decided to go back to living normally, despite official calls to maintain vigilance.

Vaccination mandates: I have not been in favor of requiring vaccination in order to return to work, fly on commercial aircraft, or other activities. While I am all for precautions and continue to wear a KN95 indoors while in public, healthcare is a personal choice and should not be coerced. Some have even claimed that it is illegal to coerce a measure that does not have FDA clearance. While vaccination is a good choice for many, it does have liabilities that have made many resistant to vaccination. This should be honored.

I know several people in the healthcare industry who have not wanted to be vaccinated, and have quit or been fired from technical or nursing jobs. While an argument could be made that those working with patients should be vaccinated, it seems misguided to be letting go of nursing staff when there has been a long standing nursing shortage.

Don’t fear, but be smart,
Erik