Category Archives: Omicron

Case Update, May 6th, 2022; Yet Another Omicron Sub-Variant, New Drug Paxlovid.

This is a case update.  I’ll also give an update on new Omicron variants and briefly discuss a new anti-Coronavirus drug, Paxlovid.

In the US, cases continue to increase modestly, and may have peaked.  This increase in cases are likely due to Omicron sub-variants BA.2 and BA.2.12.1 (more on these later). However, new deaths are still decreasing.  I will caution that a rise in new deaths often trails new cases by 2-5 weeks. For the first Omicron wave, deaths followed cases by 2 weeks, and we are currently 4 weeks in to the BA.2 wave.

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.
Endcoronavirus County Level Map, May 6th, 2022
Endcoronavirus State Level Map, May 6th, 2022

In California and San Diego County, cases are up modestly.  Again, new deaths have not yet begun to rise.

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. Starting on May 2nd, 2022, San Diego County 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. Starting on May 2nd, 2022, San Diego County only releases information Monday and 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.

New Omicron sub-variants, BA.2 and BA.2.12.1: BA.2 has been well known for a few weeks.  I’ve stated before that BA.2 is very similar to the first Omicron variants, and predicted that it will not have a large impact.  A new variant BA.2.12.1 likely falls into the same category.  These variants now dominate the current cases with 98% of new cases being due to one of these variants. 

From the CDC page on Variant Proportions. Accessed May 6th, 2022.

These variants are more infectious than the first Omicron sub-variants, but it is still unknown if they are more or less pathogenic.  Viruses tend to become more infectious and less pathogenic over time.

Some Eastern states like New York were the first to see modest new waves due to BA.2.  New York has yet to see a significant increase in deaths.

From Worldometer, Daily New Cases, New York State.
From Worldometer, Daily New Deaths, New York State.

All this to say, for now, the BA.2 and BA.2.12.1 wave still appears to be somewhat insignificant.

If you had COVID from mid-December to now, you probably had Omicron.  Because BA.2 and BA.2.12.1 are very similar to Omicron, you should not be concerned about reinfection until a significantly new variant arises.  Some people who had Delta have also been infected with Omicron.

Omicron sub-variants get a lot of press, much more than previous sub-variants.  I’ll let you guess why that is. For now, don’t be alarmed about a new Omicron sub-variant.  They will probably all fall into the “don’t stress about it” category.

The pandemic isn’t quite over. If you don’t have immunity, you may want to continue to take precautions by wearing an N95, KN95, or KF94 when indoors in public. Cloth masks or blue surgical masks will not protect you from Omicron variant SARS-2 viruses.

Paxlovid:  2 friends of mine got COVID just this week.  They were both prescribed Paxlovid, a new anti-SARS medication.  The drug is a protease inhibitor, which prevents viruses from maturing as they are formed inside a human cell.  Protease inhibitors do not prevent infection, but they can significantly reduce viral load and improve symptoms.  Both of my friends are doing well now, one feeling significantly better within just 24 hours.  2 people is a very small sample size so this should not be taken as an endorsement. I’m just pointing out that there is a new therapeutic available.

I will point out that Paxlovid is a Pfizer product.  For some, this will cause concern because Pfizer has lost significant trust due to the vaccine mandates and the attending creepiness.

Don’t fear, but be smart,
Erik

Case Update, April 20th, 2022; Mask Mandates End on Airplanes

This is a case update.  I’ll also have a comment about the recent end of the mask mandate on airplanes.

The BA.2 variant is now causing a very modest uptick in cases in the US.  93.4% of cases in the US are now caused by BA.2, some caused by a new subvariant called BA.12.1.  Most of the uptick in cases in the US is driven by a rise in cases in Northeast states like New York, New Jersey, Massachusetts and Vermont.  Cases remain flat in the rest of the country. 

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.
Endcoronavirus County Level Map, April 20th, 2022
Endcoronavirus State Level Map, April 20th, 2022
Endcoronavirus State Level Map, April 20th, 2022
Endcoronavirus State Level Map, April 20th, 2022
From the CDC page on Variant Proportions. Accessed April 20th, 2022.
Hospitalizations, from the CDC website.

In California, we may be seeing a rise in cases, but reporting has become sporadic, so it’s hard to say for sure. Some days show zero new 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 linear format.

Cases are dropping in San Diego County, and are lower than they were between the Delta and Omicron waves.

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 presented in a linear format.

World wide, cases are dropping quickly, reflecting the drop in Omicron cases in many countries.

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

A friend of mine pointed out to me today that more COVID is being detected in waste water, suggesting another upcoming wave.  The only authoritative looking story I’ve seen on this is out of date, from mid-March, so I don’t know how much of an impact this will have.

Mask mandate ends on planes: On Monday, a federal judge struck down the mask mandate for airplanes and other transportation.  The judge ruled that the mandate exceeded the CDC’s authority under the Public Health Services Act. Within hours, the news was announced to cheers on aircraft across the country. I’m sure flight attendants are happy to have fewer arguments with passengers!

I was actually all for the mask mandate for most of the pandemic because I traveled a lot and it was kind of alarming to be on a full plane during COVID.  I did find it troubling, however, that the mandates allowed nearly useless masks like the blue surgical masks, and did not require the much more effective N95s, KN95s, and KF94s. Why require masks if you aren’t going to require useful masks?

In my last several trips, just in the last few weeks, I went into restaurants, hotel lobbies, stores, gas stations, and everywhere else.  The only places still requiring masks were airports, airplanes, and some laboratories.  This is especially ironic since the air on an airplane is HEPA filtered and is some of the safest air you will encounter in your life.

Omicron is the last gasp of the pandemic, and cases are now very low.  Some estimate that 90% of the American population now has vaccine mediated or natural immunity.  I am now in favor of ending the mask mandate on airplanes.  If you need to travel by air, haven’t had COVID yet, and are concerned about getting COVID on the plane, I strongly encourage you to wear an N95, KN95, or KF94 while you travel.  Don’t bother with a cloth mask or blue surgical mask.

Also, as I’ve stated before, studies now show that vaccine effectiveness drops after 3 months. Also, those with multiple vaccinations, more than a few months old, are now 3x more likely to get an Omicron infection than those who haven’t been vaccinated. For details, see my March 25th post. This is because of Antibody Dependent Enhancement. So if you’re in a high risk category and were vaccinated more than 3 months ago, consider getting a booster. Consult your doctor when making medical decisions.

Don’t fear, but be smart,
Erik

Case Upate, April 8th, 2022; Pfizer Docs Released

This is a case update.  I’ll also talk about a report from Kim Iverson from The Hill regarding finding in the trove of documents release by Pfizer in March and April.

Cases are currently flat in the US.  During the Omicron wave in December and January, the US lagged behind cases in the UK by 2 weeks.  While the Omicron subvariant BA.2 produced a wave in the UK, it has not yet produced a wave in the US, despite it being 5 weeks since the BA.2 wave started in the UK.  I’m going to go out on a limb and say that the slowing of the decrease of cases in the US is all we are going to see of the BA.2 wave in the US. I’ll let you know if this changes. BA.2 cases now constitute 72% of cases in the US.

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.
Endcoronavirus County Level Map, April 7th, 2022
Endcoronavirus State Level Map, April 7th, 2022
From Worldometer.
From the CDC page on Variant Proportions. Accessed April 8th, 2022.

Cases continue to go down in 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 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 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 linear format.

XE variant: Just a few days ago, news emerged of a new COVID variant called XE in the UK.  The variant is a hybrid of Omicron variants BA.1 and BA.2 and is more transmissible than BA.1.  Since XE is very similar to other Omicron variants, I don’t expect it to cause a large wave of cases in the US.

Pfizer Document Analysis from Kim Iverson: Kim Iverson of The Hill released a video claiming that newly released documents from Pfizer confirm what many knew already.  The shocking claim is that Pfizer has known the following for a long time:

  1. Natural immunity is as effective as vaccine mediated immunity.
  2. The rate of adverse events is at least 10/100,000 (33,000 for the US population). It’s unclear from Iverson if this is just for Myocarditis or for all adverse events.
  3. It is unknown if the reproductive systems of women are impacted by vaccination.  This contradicts public claims that vaccination does not affect reproduction.
  4. A more severe case of COVID triggered by Antibody Dependent Enhancement could not be ruled out.  The Lewnard et al paper a surveillance report from the UK have confirmed that higher Omicron infection rates in vaccinated people are likely due to ADE.  As far as I’ve seen so far, ADE has not lead to more severe cases.

The documents were obtained because of a Freedom of Information Act (FOIA) lawsuit which required the FDA to produce the documents.  Yes, this means that the FDA has had this information and did not disclose these conclusions to the public, instead often releasing information which contradicted these conclusions.

There will continue to be more document releases every month until the end of the year.  There will likely be more bombshells, but most of the releases will simply confirm what people have suspected for months but couldn’t prove.  I will discuss the most interesting, but not all of these releases.

Full list of Pfizer Documents released so far. Click “Date Produced” on the top line of the document list to bring April documents to the top of the list.
Request for Priority Review
Sorry, I couldn’t find the link to the consent form.

If you have risk factors like obesity, age, or respiratory problems, you should consider getting a booster.  Also, as I said last week, since vaccine effectiveness is substantially reduced after 3 months, those who have been vaccinated with risk factors will need to get a booster every 3-6 months.  Try and find a provider who will aspirate before injection!  There is no medical reason for someone who has had Omicron or Delta variants to get vaccinated or a booster. Talk to your doctor when making medical decisions.

I am posting about every 2 weeks now instead of every week.  I’ll likely post even less unless interesting news comes out.

Don’t fear, but be smart,
Erik

Other links:
James Cintolo discusses Adverse Events:
Document 5.3.6.

Case Update, March 25, 2022; BA.2 cases in Europe, Persistence of Vaccine mRNA in Lymph Nodes, Higher Omicron Infection in Vaccinated individuals in UK

This is a brief case update. I’ll also make some more comments on BA.2 related waves in Europe, a new paper suggesting that vaccine mRNA persists in the lymph nodes. Also, new evidence from the UK suggests that vaccines lose potency after 6 months and certain vaccinated individuals are more likely to be infected than unvaccinated people.

Cases continue to go down in the US, although the rate of decrease is slowing.  As you’ll read below, some suspect that an Omicron variant, BA.2, may cause cases to rise in the US.

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.
Endcoronavirus County Level Map, March 25th, 2022
Endcoronavirus State Level Map, January 25th, 2022
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. 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 presented in a linear format.

More on BA.2: I have commented on BA.2 before.  This variant is a version of the Omicron variant, which is slightly more infectious than Omicron itself.  It continues to follow the general trend of new variants being more infectious than older ones. Like the original Omicron, equal portions of B.1.1.529 and BA.1.1, BA.2 has a low fatality rate as compared to previous versions, including Delta. 

I originally held that BA.2 is not particularly interesting because of its similarity to the first Omicron strains.  This still may be true, but some countries like the UK and the Netherlands have seen significant new peaks after BA.2 became prominent. BA.2 is likely contributing to rising cases globally.

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

Right now in the US, BA.2 is increasing in prevalence, and is currently 1/3 of SARS-2 found in the US.  It’s similarity to previous Omicron versions means that it is displacing B.1.1.529 and BA.1.1, just like Omicron displaced Delta before it. We now have 0% Delta in the US.

From the CDC page on Variant Proportions. Accessed March 25th, 2022.

Currently, new case numbers in the US are still going down, although the rate of decrease is slowing.  John Campbell, a physician and COVID commentator in the UK, argues that a new peak in the US due to BA.2 is inevitable, and he may be right.  But we aren’t seeing it yet.  We may see it the next few weeks.  Campbell also argues that “cases”, the number of infections recognized by the NHS, is much lower than actual infections.  This is certainly true, but we can’t know how many infections there are, since they aren’t reported. This was almost certainly true in the US as well during the Omicron wave.

Does BA.2 significantly change the picture?  I still say no, since the fatality rate with BA.2 is still very low, perhaps even lower than with other Omicrons.  We may or may not see a significant BA.2 wave, depending on how many Americans already have resistance to BA.2. If you had Delta or Omicron, you almost certainly won’t get BA.2.  Vaccination is only partially effective against Omicron variants.

Most people in my area, northern San Diego County, are basically going back to normal.  This is warranted for most.  If you have risk factors like age, obesity, or respiratory issues, you will want to remain vigilant and consider a booster.  I do not recommend a booster for those without risk factors, and certainly not for those with natural immunity.  Talk to your doctor when making medical decisions.

mRNA and Spike Protein Persist in Lymph System for up to 8 weeks:  The Journal Cell just published a paper (Röltgen et al) which argues that mRNA and spike protein are present in vaccinated individuals for up to 8 weeks after vaccination. Cell is the third most highly respected journal in cell and molecular biology.

The cells in your body are surrounded by a fluid called “interstitial fluid”.  This fluid carries nutrients from nearby blood vessels to your cells, and also carries waste back to the blood vessels.  The lymph system is a one-way circulatory system that carries excess interstitial fluid from the extremities of your body back to veins near your arm pits.  On the way, they pass through the lymph nodes, a biological filter and part of your immune system that checks for invading particles. 

The Röltgen et al paper suggests that vaccine mRNAs from the interstitial fluid collect in the lymph nodes and can persist there for many weeks.  They continue to produce spike protein during this time.  Remember that vaccines are intended to be given in an intra-muscular manner, meaning that they are intended to be injected to a muscle and stay there.  This paper shows that they are able to migrate to the lymph nodes. 

The paper does not discuss the medical importance for this in terms of adverse events.  Given the relative rarity of adverse events, I would guess that the presence of vaccine mRNA does not produce adverse events, and that these events are caused by vaccine injection into a vein. Again, the data is not conclusive on this, so this is just my guess at this point.

mRNA technology note:  At this point, I have no evidence to suggest that the problem with the new vaccines is the mRNA technology.  In my estimation, the likely reason the new vaccines lead to adverse events is that they produce the SARS-2 Spike protein which likely causes inflammation throughout the body.  This may only be in vaccine recipients who receive a vaccination in a vein rather than an intra-muscular injection.  If you choose to get a vaccination or booster, ask the health care provider to aspirate before injection.

Certain vaccinated individuals are more likely to be infected by Omicron than the unvaccinated:  A UK surveillance report shows that vaccine effectiveness against symptomatic Omicron infection goes from around 65% effective soon after 2 doses of vaccine, to around 5% 6 months later.  Protection from hospitalization goes down to just 35% after 6 months. These findings suggest that to maintain full protection against Omicron, a vaccinated person will need to get a booster every 3 to 6 months.

From UK Surveillance Report, March 17, 2022, Table 1b. Effectiveness of Pfizer vaccine at preventing symptomatic COVID infection after 2 doses, and after a Pfizer or Moderna booster.
From UK Surveillance Report, March 17, 2022, Table 2b. Effectiveness of Pfizer vaccine at preventing hospitalization after 2 doses, and after a Pfizer or Moderna booster.

In another finding from the report, people with 3 doses of vaccine are 3x more likely to be infected with Omicron than unvaccinated individuals.  This is the clearest evidence yet that Omicron may be using Antibody Dependent Enhancement (ADE) to infect people. The Lewnard et al paper from a few months ago has a similar finding.  For both studies, a certain number of vaccine doses are more likely to increase the chance of infection.  If viruses are using the ADE pathway, this effect would be explained more by the timing than by the number of doses per se.  For ADE to work, a person needs to have a mediocre immune response to an agent, not a strong or weak one. Since we know vaccine mediated immunity goes down over time, then a person becomes more likely to be reinfected as their immune response goes from strong to mediocre.

From UK Surveillance Report, March 17, 2022, Table 13. New case rates among UK residents with at least 3 doses of vaccine, and with no vaccination. Numbers are normalized for the percentage of people in each group.

So should you get a booster? Again, if you have risk factors like age, obesity or respiratory problems, you might want to get a booster every 3 – 6 months. Otherwise, you may choose instead to just take extra precautions as Omicron cases continue to fall in the US. If you choose to get a booster, ask them to aspirate before injection. Talk to your doctor when making medical decisions.

I know this is all very complicated.  Your questions will help me make this more clear.

Don’t fear, but be smart,
Erik

Case Update, February 14, 2022; Variant BA.2, Dr. Fauci Announces the End of the Pandemic.

This week I’ll have a case update, then discuss variant BA.2, and Dr. Fauci’s announcement about the end of the Pandemic.

Cases in the US, California, and San Diego County are all still going down sharply. Cases are now at the same level as in mid-December. According to Endcoronavirus, most states have decreasing 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.
Endcoronavirus County Level Map, February 14th, 2022
Endcoronavirus State Level Map, February 14th, 2022
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.
Hospitalizations, from the CDC website.

Variant BA.2: This new variant is now increasing slightly over the original Omicron. This is no reason to be concerned, however, since BA.2 is just a slightly more infectious version of Omicron. Antibodies against Omicron are expected to be effective against BA.2, so this does not represent a new variant that will cause case numbers to rise.

From the CDC page on Variant Proportions. Accessed February 5th, 2022.

Dr. Fauci announces the end of the Pandemic: In an article in Financial Times, Dr. Fauci stated that he expects that the pandemic phase of COVID will be over in the next few months. I agree, with the exception that I think a reasonable time frame is more like weeks than months.

He also stated that he thinks boosters will continue to be necessary to keep the virus at bay. On this I have to disagree. The vaccines had a minimal impact on new infections due to Omicron, although they probably had a positive impact on disease severity. Given that the new cases are now very low, and the unknown but real danger from adverse reactions, I think there is now almost no reason to get a vaccine booster. For vaccines to continue to be useful, we need a more current version, against something like Delta or Omicron. I don’t expect we’ll be getting that.

Many scientists, including those I respect, think the virus will become endemic, meaning it will continue to circulate at a low level in different forms basically forever. With some trepidation and perhaps over-optimism, I think Omicron will eventually peter out and SARS-2 will be over. We’ll see if that happens.

Don’t fear, but be smart,
Erik

Case Update, February 8th, 2022.

Just a brief case update today. New cases are still dropping fast in the US, California, and San Diego County. Cases are now about as many as their were just before Christmas when the Omicron wave was just starting in the US.

The great news is, deaths appear to have peaked in the US 2 weeks ago, and were indeed very low, about as many as last Winter when the cases were far fewer than in the Omicron wave. A little math says that Omicron is roughly a quarter as deadly as the Alpha variant from last Winter.

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, February 8th, 2022
Endcoronavirus State Level Map, February 8th, 2022
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.

Another plug for data: Last week I asked for folks to answer the following questions:

1) Have you ever had COVID? If so, when?

2) Have you been vaccinated? When?

3) Have you had COVID multiple times? If so when? What were your symptoms like each time? Were you hospitalized? If so for how long?

4) Is there anything else you’d like to share?

Obviously, a lot of people don’t want to go public with this information. You can post below or direct message me. I want to get an idea of how vaccination and previous infection produced protection for future infection. When you were infected will tell me what SARS-2 variant you had, and whether that variant protected you from future versions.

So far, I’ve only gotten about 30 responses, too few to be useful. If you want chime in, please do so! Thanks!

Don’t fear, but be smart,
Erik

Case Update: January 29th, 2022; The end of COVID for me, Final thoughts on ADE.

Just as the Pandemic seems to ending with a bang, so my personal COVID story ended dramatically. But first, the case update for this week.

The US, California, and San Diego County are all well past the peak of Omicron cases, and cases are dropping rapidly. In some Northeastern states like New York, New Jersey, and Vermont, the Omicron wave is already nearly over.

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, January 25th, 2022
Endcoronavirus State Level Map, January 29th, 2022
Endcoronavirus State Level Map, January 29th, 2022
Endcoronavirus State Level Map, January 29th, 2022
Endcoronavirus State Level Map, January 29th, 2022
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.

According to the CDCs variant proportion site, Omicron is now 99.9% of new cases. I will not report on this again, since this has now become uninteresting. There have been reports of a new subcategory of Omicron, BA.2, which is even more infectious than Omicron, but just as mild.

From the CDC page on Variant Proportions. Accessed January 29th, 2022.
Hospitalizations, from the CDC website.

The end of my COVID story: I tested Positive for COVID on Friday the 14th, and finally tested Negative this Thursday morning, the 27th, almost exactly 2 weeks later. COVID actually got worse for me during course of the 2 weeks, with me getting more fatigued as time passed. Thursday night and yesterday were particularly bad, with extreme fatigue, sleeplessness, dehydration, uncontrollable shaking, and finally mental incoherence on Thursday night and Friday. Finally last night I was able to sleep for 11 hours and I finally feel like I’m recovering. I ate a full breakfast this morning and am actually doing some chores around the house.

I really only have 1 co-morbidity, celiac disease, an auto-immune disease. Unfortunately, I’ve never seen research on how auto-immune diseases interact with COVID or vaccination. It may be safe to assume for now that my auto-immune disease put me at greater risk from an immune system intensive disorder, but I don’t know for sure. While most of my COVID symptoms were indeed very mild, I was very surprised by the severity of my fatigue, which had multiple other negative effects. I sought medical attention twice, but they were never nearly as concerned as I was.

The “Final” Verdict on Antibody Dependent Enhancement: As most of you know, ADE has been a major concern of mine from almost the beginning. I’m finally willing to give an assessment of how ADE impacted the pandemic. There were a smattering of cases in previously infected people who may have had more severe cases because of possible ADE, but not more than a smattering. It’s also becoming well acknowledged that Omicron infected everyone regardless of vaccination status and may have even preferentially infected vaccinated people. I know MANY people who are double vaxxed and boosted who got Omicron.

All that being said, I never saw any evidence that conclusively suggested that ADE was causing more severe symptoms because of natural or vaccine mediated immunity. In fact, even during Omicron, during which ADE was most likely to be operating, those with previous immunity clearly fared better than those without. Because I think Omicron is the death rattle of the pandemic, I’m willing to say that ADE never became the threat I was concerned about. For this reason, IF I didn’t already have natural immunity because of Omicron, I might actually get vaccinated IF I could find someone who would aspirate before injecting!

I never saw any paper that dealt with the issue of ADE, not even a little. Those that mentioned it did so only in passing.

Don’t go looking for Omicron: Lastly, I’ll just say that while most of my friends had an undramatic time with Omicron, I did not. If you haven’t gotten Omicron yet, don’t go out looking for natural immunity from an Omicron infection. For me, it was no fun at all, and not worth the lost time and anxiety, even though I’m glad to now have hard earned natural immunity. The vaccines may not actually help you against Omicron infection, but they do seem to help you have an easier time of Omicron. Also, if you haven’t gotten Omicron yet, I recommend taking precautions and wearing an N95, KN95, or KF94 when in public.

Precautions against Delta are not adequate for Omicron, so kick it up another notch if you haven’t had Omicron yet.

Don’t fear, but be smart,
Erik

Aspiration during Vaccination.

After 12 days of symptoms, I still have COVID. My symptoms are considered mild, but I’m still tired, have no appetite, and am frequently feverish, so writing a long post is not my favorite activity right now. I also have a small amount of viral pneumonia, but not enough to be treated for. For an update, I’ll just state for now that cases are coming down rapidly in the US right now. I may add a real update to this post later.

Aspiration by vaccinators: I did want to point out that I saw a very interesting video recently from John Campbell that is very instructive. He points out that vaccines are intended to be given in an “intra-muscular” fashion, meaning the injection is supposed to remain in the muscle it’s injected into. If this happens, the vaccine makes Spike protein just in that localized area, and your immune system finds it there and mounts a response. Unfortunately, if a vaccine is injected into a blood vessel, the vaccine can travel throughout the body, making adverse events much more likely. For the flu, this is still not a big risk because the flu proteins only really interact with respiratory cells. But for COVID, the Spike protein can interact with cells all over the body and cause various effects including inflammation.

There is a simple way to avoid injecting in to blood vessels. A vaccinator can simply push the needle in, then pull back slightly to make sure there is no blood, then inject (Demonstration of this process starts at 22:00 of the video). This eliminates the possibility of a blood vessel injection. Unfortunately, this procedure is standard practice in just a few countries like Denmark, S. Korea, and Japan. Most countries including the US, UK, Canada, and many others do not practice this. John Campbell is very pro-vaccine, but wishes aspiration was standard.

My doctor friends tell me blood vessel vaccine injections are very rare.

In the US, lots of people in the health care industry basically ignored adverse events due to COVID vaccination. This includes me for a time. The CDC is still not capturing all of the available data on adverse events. Many of these events could have been avoided with a small change in policy.

Vaccination has helped a lot of folks have milder COVID symptoms. It’s too bad that the lessons from adverse events were not absorbed sooner. If you get vaccinated or get a booster, see if you can get them to aspirate before they inject!

The UK drops COVID restrictions: The Omicron wave has come and gone in the UK, and the country has basically dropped all COVID related restrictions. The US is a few weeks behind the UK, so we may be able to drop restrictions here soon too.

Omicron is milder, but I certainly haven’t had an easy time of it, so I wouldn’t recommend running out and getting your natural immunity by getting Omicron. If you haven’t had it yet, continue to wear your N95, KN95, or KF94 while indoors in public. Or even outdoors in groups. I probably got COVID outside but in close proximity to someone with COVID. The stuff that worked with previous versions doesn’t necessarily work with Omicron.

Don’t fear, but be smart,
Erik

Case Update: January 18, 2022; Omicron now 99.5% of cases, Infection rate by Delta and Omicron, new CDC mask guidance

This is a case update. I’ll also give an update on the state of Omicron in the US, and show some data from a great new paper from California. I’ll also comment on the new mask guidance by the CDC.

New cases have apparently peaked in the US over the past week, reaching a high of 1.5 million cases in 1 day. Cases are now declining for the US as a whole, driven by declines in several Eastern states like New York, New Jersey, and Florida. Cases have not yet declined in most US states, although many may be peaking right now as new cases have slowed. So far, deaths are only slightly up for the US. Hospitalizations appear to have peaked as well.

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.
Endcoronavirus County Level Map, January 17th, 2022
Endcoronavirus State Level Map, January 18th, 2022
Hospitalizations, from the CDC website.
Endcoronavirus State Level Map, January 18th, 2022
Endcoronavirus State Level Map, January 18th, 2022

California and San Diego County new cases appears to be still going up, but new cases have slowed, and I suspect will start declining soon, maybe this week. Again, deaths have not yet started to increase. Deaths usually follow cases by between 2 and 4 weeks.

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. 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 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.

Omicron Update: Omicron infections now represent 99.6% of infections in the US. Omicron has now almost completely eliminated Delta in the US. It continues to appear that Omicron represents the end of the pandemic, although it will go out with a bang!

From the CDC page on Variant Proportions. Accessed January 18th, 2022.
From the CDC page on Variant Proportions. Accessed January 18th, 2022.

I finally got COVID!: Last Friday I tested positive for COVID! I almost certainly got it while in a “gray area” situation that had some risk, but might have been OK with a previous variant. Most symptoms have been very mild, but I was super achy for a day. I’m still not feeling strong and I nap a lot. No loss of taste and smell, or shortness of breath, but I did have a fever during my achy day. As of yesterday, I still test positive, so my body is still fighting.

Omicron much milder than Delta, but evades vaccines much more: As I’ve stated before, it’s a little scandalous how few useful papers have come out of the US this last year. But a UC Berkley lab has a great new paper in pre-print right now. They had the foresight to collect data for a time period in December when both Delta and Omicron were present in the population. The paper is a little opaque because much of the information is in dense tables, with less than useful headings (SGTF = Omicron, non-SGTF = Delta) but has some great information nonetheless.

Table S10 is the most interesting to me. I’ve turned some of the data into graphs to make the meaning more clear. The table compares the number of infections by Delta or Omicron in unvaccinated persons, those with differing levels of vaccination, and with documented previous infection (natural immunity). Vaccination definitely helps prevent infection by the Delta variant, but Delta still infects vaccinated individuals. This may be because vaccine efficacy goes down over time, the Delta variant is too different to be completely stopped by the Wuhan based vaccines, or some combination of both.

Graph is by me, from data in Lewnard et al, Table S10. Cases with Natural Immunity were multiplied by 6 to normalize for the number of documented infected individuals in the population. In San Diego County, there are roughly 500,000 documented COVID-19 cases, out of a population of approximately 3 million in the county.
Graph is by me, from data in Lewnard et al, Table S10. Cases with Natural Immunity were multiplied by 6 to normalize for the number of documented infected individuals in the population. In San Diego County, there are roughly 500,000 documented COVID-19 cases, out of a population of approximately 3 million in the county.

Omicron is far more infectious in general, and also is far more infectious in vaccinated individuals. In fact, more people in this study were infected by Omicron if they had 2 doses of the Pfizer or Moderna vaccines. Since a majority of Southern Californians are vaccinated, it this does not necessarily mean that vaccination made it more likely to be infected by Omicron, but it’s a striking result. Yes, Antibody Dependent Enhancement may play a role in this result, although the exact reasons are likely a complicated combination of factors.

Another interesting result is that infections are far lower among those with previous infections. For the graphs I include, I’ve even normalized this number for the proportion of people who have been infected by multiplying the given number by 6 (see graph for details). In spite of this, infections are FAR lower in those previously infected. This is consistent with the data from Israel suggesting that natural immunity is far better than vaccination at preventing future infection.

Most European countries and Israel include previous infection in immunity requirements. The US still does not accept previous infection as prove of immunity. As we continue to argue about vaccine mandates, it would be wise to include previous infection as proof of immunity.

See a video by Dr. Mobeen Syed for a detailed analysis of this paper.

Better super late than never I suppose: After many months of treating all masks as essentially equal, the CDC released new guidelines regarding masks that points out that simple cloth masks are not as effective as medical grade respirators like N95s, KN95s, and KF94s. They still don’t go far enough in my opinion, since they still promote surgical masks as effective. Blue surgical masks are loose fitting on the side and allow air to enter and exit without being filtered. If you wear a mask, wear a medical grade respirator, not a blue surgical mask.

I believe we are a few weeks away from the end of the pandemic! As for me, I’m really looking forward to eating indoors at a restaurant again!

I know a lot of this post is dense and complicated. Your questions will help me be more clear.

Don’t fear, but be smart,
Erik

Case Update, January 12, 2022; Omicron Update, Omicron now at 98% of COVID cases.

This is a case update. Cases continue be super high in the US. Over the past 2 years, the Sunday numbers are always the lowest of the week, but they also usually predict what will happen to the number in the following week. If you look closely at the case graph for the US, you can easily see the weekend dips in numbers. For this Sunday’s number, the rise in cases is much lower relative to the previous week than the number for the 26th. Because of this, I expect new case numbers in the US to peak this week or next.

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.
Endcoronavirus County Level Map, January 12th, 2022
Endcoronavirus State Level Map, January 12th, 2022

All that being said, cases are still extremely high in every state in the US right now, and still rising. Only Washington DC appears to be seeing a drop in cases right now. Deaths have not yet started to increase in the US. Deaths have tended to increase between 2 and 5 weeks after the start of a peak, so it’s still too early to know how high they will be.

California and San Diego County are of course also experiencing extremely high numbers of cases right now. LA County again has the highest number of cases in the US, with a staggering 384,000 active cases right now.

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. 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 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.

In Denmark, which has a lot of testing and virus surveillance, deaths are up but at a very moderate rate. At the peak of last year’s Winter surge, the COVID fatality rate was 0.94% (deaths/confirmed cases). For the Omicron wave in Denmark, the rate has been only 0.053%. This rate is very small, but it’s still not zero, so if you have COVID risk factors, continue to take precautions.

From Worldometer.
From Worldometer.

Omicron Update: The CDC recently released an update on variant proportions. Omicron is now 98% of SARS-2 cases for both the US and the Southwest region This is great news.

From the CDC page on Variant Proportions. Accessed January 12th, 2022.
From the CDC page on Variant Proportions. Accessed January 12th, 2022.

Omicron infections are proving to be very mild in most patients. That being said, there are a tremendous number of cases right now. I have lots of friends and family who have had COVID in the last 2 weeks, and several businesses near me have had closures or reduced hours because of under staffing. Additionally, hospitalizations are way up, and doctors and nurses are pretty exhausted taking care of all the sick people.

Hospitalizations, from the CDC website.

Managing COVID right now: Hospitalizations are way up, and lots of people are getting tested, either in a health care setting or with home rapid test a drug store. For this reason, tests are now in short supply everywhere. If you don’t need a test to go back to work or school, please consider NOT testing yourself just to satisfy your curiosity. If you do need to test yourself, please don’t test yourself every day, and try to reduce the number of tests you use. Since current tests are based on the Wuhan strain, there are lots of false negatives right now, especially with the rapid tests, since Omicron is the dominant strain. So a negative test is not very meaningful if you have symptoms. Most people’s Omicron symptoms last between 2 and 5 days.

Although Omicron causes less severe disease in general, there are a huge number of cases right now and some are still severe. If you don’t think you need medical attention, and are just experiencing cold-like symptoms, consider NOT going to the hospital for a test or to be treated. Please keep space open for those with more severe symptoms. However, if you have one of the classic COVID symptoms, like shortness of breath, don’t hesitate to check in with your doctor.Please don’t assume your vaccination, even with booster, will prevent you from getting COVID right now. Many fully vaccinated and boosted people are getting COVID right now because the Omicron variant is so different from the Wuhan strain used to make the vaccines.

Also, I still usually wear a mask indoors. If you choose to wear a mask, wear an N95, KN95, or KF94. Don’t imagine that a blue surgical mask, cloth mask, or neck gator is going to prevent infection. These masks are ineffective against Omicron. Effective medical grade masks are easily available at stores and online right now.

Remember to supplement with Vitamin C, Zinc, and especially Vitamin D! This is for everyone, to prepare your body should you get infected, or if you have Omicron right now.

Omicron scorecard: Here’s my “scorecard” for this week. The new data from South Africa suggests that Omicron infection is “back compatible” with Delta, preventing Delta infection. This is great news and suggests Omicron infection will prevent future infections from other variants. As a reminder, I am not an epidemiologist, I’m a molecular biologist. This is my informed but not expert opinion.

1) Omicron must not use the ADE pathway to produce more severe cases: Looking at the available data so far, Omicron may preferentially infect those who have been previously infected, but cases are still mild, and fatality rates very low. So for now, this criteria is met.

2) Low fatality in older populations: South Africa has a relatively young population, so reports of mild symptoms may not carry over to countries with older populations. The UK data from this week suggests that Omicron deaths will be low, even in older populations. We are seeing a slight drop in deaths already.

3) Displace Delta: Delta has a much higher case fatality rate in the US than Omicron appears to have. For Omicron to end the pandemic, it must displace Delta from the COVID population of strains. Data from the US and UK suggest this is happening!

4) Omicron must not circulate independently from Delta: Related to the above, if Omicron is very different from Delta, it may act as a completely different virus. There’s a chance that Omicron may displace Delta on the short term but still allow Delta to persist. Since Omicron is displacing Delta, it looks like this criteria may be met, but we won’t know for sure until we can see if Delta pops back up after the Omicron wave is over.

5) Omicron infection must immunize against future SARS-2: Since Omicron appears to infect those with immunity to Delta, it may be that it is different enough that it will not provide immunity to Delta or other SARS-2 strains. This criteria is not strictly necessary if Omicron completely displaces other SARS-2 strains (see 3 above), but it would be really nice to have some protection against future strains. We won’t know for sure about this one until a new version of COVID arises. The new data from Denmark suggests this criteria is met!

I believe that the Pandemic is almost over, but there’s one big final push! Continue use your head, but be encouraged!

Don’t fear, but be smart!
Erik