Category Archives: Treatments

Fauci’s time with COVID and Paxlovid

This is a post about Tony Fauci’s time with COVID and the drug Paxlovid, which I have discussed in the past.

On June 15th, a story came out about Tony Fauci having contracted COVID, despite having been fully vaccinated and boosted. I didn’t cover this before since I’d already discussed the fact that the vaccines don’t prevent infection by Omicron variants.

However, something else very interesting happened. Dr. Fauci took Paxlovid, which I’ve discussed briefly before, and became COVID negative. But after his 5 day course, he became positive again with worse symptoms. This means that a standard 5 day course of Paxlovid will not necessarily reduce your viral load to zero, and patients may experience “Paxlovid rebound”. Fauci even claims that this kind of rebound with Paxlovid is starting to be seen as “typical” as more patients use it.

The CDC actually issued a warning about Paxlovid Rebound in May, but it was not widely reported.

With so many rebound cases, it’s likely that 5 days is not adequate to eliminate all viruses from the system, allowing rebound. However, Paxlovid does have side-effects, so don’t take it for more than 5 days without consulting your doctor! Hospitals are now only prescribing Paxlovid to high risk patients.

Whenever taking anti-viral or anti-bacterial medications, always take the full course of treatment. If any virus or bacteria survive treatment, they may give rise to a more resistant strain. Don’t just stop your treatment when you feel better. I take anti-biotics as a last report, but when I do, I take the full course. I even made a doctor give me the full 10 day course when she just wanted to give me a half course!

Just to repeat the point on the vaccines, I still hear ads on the radio encouraging vaccination. At this point, the vaccines are really not doing anything against the current COVID variants. There is really no benefit to getting a vaccine or a booster. If you haven’t had COVID yet, I would simply recommend preventative measures. Wear an N95, KN95, or KF94 mask when indoors in public. Cloth and surgical masks will not prevent infection.

Don’t fear, but be smart!
Erik

Kim Iversen’s more in-depth discussion of Dr. Fauci’s rebound.

The Next Pandemic

In yesterday’s post, I outlined some of the factors that resulted in the very high COVID case rate in the US. Today I will discuss how we can prepare for the next pandemic.

I have a PhD in molecular biology, and I specialize in infectious disease testing. I am not a physician or epidemiologist. I have an informed but not expert opinion.

Identifying the threat:

First, most new infectious diseases do not pose a global threat.  SARS-2 was so dangerous because of its high infectivity, long incubation time, and asymptomatic spread. Most diseases do not have these parameters.  Whenever a new disease comes around, and they will, we should soberly and cautiously assess the real threat.  Coming to the wrong conclusions about the threat will lead to the wrong conclusions about combating it.

There have been several important new infectious disease outbreaks in the last few years, including Hantavirus (1993), SARS (2003), Avian Influenza (2004), H1N1 Swine Flu (2009), Ebola (2013), Zika (2015), and of course HIV in the 80s.  They all have different disease parameters which make them behave very differently.  Most of these diseases did not have global impact.  The first SARS for example was much less infectious than SARS-2, but much deadlier, so it was contained quickly and didn’t spread much beyond Asia.  HIV can be spread by asymptomatic victims for a full 8-10 years, avoids the immune system, and evades vaccination efforts, so it has become endemic in much of the world.

The following parameters determine how a new disease will behave:

  • Mechanism of spread
  • Infectivity
  • Asymptomatic/ambulatory spread – can the victim walk around and spread disease?
  • Incubation period
  • Fatality rate
  • Vector – what carries the virus to a new host
  • Non-human reservoir – diseases that come from non-humans are harder to control and cannot be eradicated.

Obviously, we cannot respond to different diseases in the same way. Part of the reason we failed to contain the virus was that we used measures that were designed for viruses that spread by droplet transmission against a virus that spreads through aerosol transmission.  Using the wrong measures was less effective.

Much of my concern with the SARS-2 virus was the Antibody Dependent Enhancement issue, which is very uncommon among viruses, so is not usually a concern.

Be cautious.
Whenever a new threat arises, it is wise to be extra cautious until information can be gathered.  Although many of our precautions turned out to be unnecessary, I still support taking extra precautions early on.  Remember that early estimates were that the fatality rate for COVID was 3.68%.  With the 82 million confirmed cases in the US, this would have been over 3 million deaths if the fatality rate had really been this high.  As it stands, we have had almost 1 million COVID related deaths, a death rate of approximately 1.2%.  Yes, I know we can debate how many of these are deaths really resulted from COVID and how many infections there really were.  But we cannot discount that COVID had an enormous impact.

What if COVID were deadlier? Or what if it had selectively killed children, or caused more long-term symptoms like polio did? Things would have been much different.

All this to say, I think caution was warranted in the beginning of COVID, and we should continue to be cautious in future pandemics. On the other hand, we should also learn to abandon precautions that are not effective.  Maintaining ineffective precautions wastes resources, causes extra economic and social suffering, and causes people to lose confidence in government agencies.  It started to become clear to me by May of 2020 that lockdowns were ineffective, and that transmission was happening mostly indoors, but I still see people wearing masks outside to this very day.

Persuasion, not coercion:
From the beginning of the pandemic, public communication was terrible.  Official guidelines were confusing and often contradictory.  Far worse, explanation or evidence was rarely given for policies.  Instead, disagreement was met with accusations of being anti-science, rather than persuasion.  This approach contributed to the loss in confidence in official channels. 

Going forward, officials need far better communication skills when dealing with emergencies.  Give evidence rather name-calling, and respect the population enough to tell the whole truth.

Then came the vaccine mandates.  Many people I know were coerced into getting vaccinated against their will, and many others were fired.  All at a time when information about the vaccines was being hidden from the public.  This is unacceptable, and no way to run an emergency.

Here is a link to my post on science communication:

Restoring Trust:
Both the CDC and FDA hid information from the public.  In order to restore confidence, senior leadership needs to be replaced and new leadership should explain how things will be better in the future.  Is likely to happen?  No, it is not.

Government agencies need to be far more transparent.  Lack of transparency forces people to wonder what is going on, and create their own theories.  Government agencies often decry conspiracy theories, but they had a big role in creating them.

Misinformation:
Freedom of speech, censorship, and misinformation had a major role in the public discussion over the pandemic.  Doctors and scientists were frequently censored, shunned, or fired for sharing ideas that went against WHO or CDC guidelines. This includes ideas like the lab leak hypothesis that later turned out to be likely.

Freedom of speech is a foundational principle of American life.  It’s in our DNA, as some would say.  We are not America without it.  Some will say that too much freedom of speech leads to misinformation and conspiracy theories.  While it’s true that this freedom allows the spread of falsehoods, it also allows all ideas to be debated, true ideas to be raised up, and false ideas to be discredited. Freedom of speech is the solution to misinformation, not the cause.  Most of the leaders in world history that wanted to control freedom of speech had something to hide. It is essential that we maintain this basic right.

State emergency powers:
As discussed in yesterday’s post, the US federal government has surprisingly little power to deal with a public health crisis.  The CDC can develop guidelines, but most of the real work is done at the state and local level.  State officials need to step up and realize it’s their responsibility to respond well.  Citizens need to hold state and local officials accountable.

Manufacturing:
The US needs to maintain manufacturing capacity for certain essential items like personal protective equipment, testing kits and equipment, and medications.  Tax incentives need to exist to encourage companies not to send these functions overseas.

In addition, we should have national and state stockpiles of certain equipment.  I know many hospitals and labs are now creating stockpiles of their own.

Testing:
Most countries that did well produced lots of COVID testing early.  In the US, the CDC tried to manage all the testing themselves, and quickly became overwhelmed.  By the time private labs were allowed to develop their own tests, it was way too late.  Testing capacity didn’t become nearly adequate until at least July of 2020. Next time, the CDC needs to allow testing by private labs right away.  Ideally, anyone who wants a test and anyone potentially exposed to an agent should be tested.

Quarantine, not Lockdown:
Countries that did well did not quarantine healthy individuals, although some of these countries had more restrictions during the big Winter waves.  Instead, only COVID positive people should be quarantined.  This is only effective when tests are readily available.

Later in the pandemic, some outlets acknowledged that most infections were happening in private settings.  Basically, people would get infected outside, then bring COVID home to infect everyone in the household.

Here is a very interesting video using computer models to show why our model of lockdown was not effective.  Computer models are only as good as they are programmed to be, so this is only for demonstration purposes, and is not data.

Contact tracing:
Contact tracing was very successful in some countries, but the long incubation time of COVID made this difficult.  Successful programs involved tracking of individuals by cell phone and credit card data, practices that would probably not be tolerated in the US. Such programs would need to be voluntary to not trigger the creepiness factor and violate constitutional rights.

Masking:
I was a big proponent of wearing a medical grade respirator (N95, KN95, or KN94) indoors during the pandemic.  Because COVID spread as an aerosol as well as droplet form, cloth and blue surgical masks were ineffective.  Simpler masks can be effective against colds and flu, however.  So the choice of mask depends on the agent in question.  CDC guidelines need to reflect the method of spread of the agent in question. 

So what should Dr. Fauci have said early on?  Something like this:

N95 masks offer the best protection against infection by the SARS-2 virus. However, our current supply is very low, and we desperately need to save these masks for our medical professionals.  Please do not purchase N95 masks at this time.  In the mean time, there are some options that will help reduce the risk…

In actuality, of course, I didn’t see an N95 in a store from March 2020 until at least February of 2021, so I couldn’t have bought one if I’d wanted to!

Treatment:
Most medical facilities in the US didn’t treat COVID until a patient was experiencing respiratory distress.  By then, treatment options were limited.  To their credit, intubation was largely abandoned by the medical community when it was learned that this treatment was largely ineffective.

However, controversy swirled over potential treatments that became disfavored by the medical community.  Doctors are usually granted the right to prescribe “off label” medications, meaning they can use medications for treatments outside the guidelines of the manufacturer.  But drugs like Hydroxychloroquine, Ivermectin, and others quickly become forbidden, and some doctors even got fired for prescribing them.  Research on these drugs were minimal.

I am not arguing here that these drugs are effective against COVID.  I’m simply saying that forbidding doctors from working with or publishing papers about these drugs was a big mistake.  While it is of course wise for a doctor to consider guidelines, treating a novel virus may require some “outside the box” thinking.

Let me know in the comments if I missed something important!

Don’t fear, but be smart!
Erik

What Went Wrong?

Today I’ll discuss the approach to the pandemic in the United States, and all the factors which contributed to our very high case load during the pandemic.  This article ended up being longer than I thought, so I’ll have a separate post later in the week about how we can prepare for the next pandemic. I have a PhD in molecular biology, and I specialize in infectious disease testing. I am not a physician or epidemiologist. I have an informed but not expert opinion.

The COVID-19 pandemic finally seems to be drawing to a close.  For most of the pandemic, the US had the highest number of daily cases, and has had the most cases over all.  As I write this on May 17th, 2022, the US has 82,629,736 total confirmed cases, approximately 25% of the population, and an unknown but likely very large number of unconfirmed infections.

Meanwhile, the US has the most technologically advanced and well funded medical system in the world.  So what happened? This is a very important question because answering it correctly will help us respond to the next pandemic.

First, we can ask what policies the US had in place, and contrast them with policies that were successful.

Countries that initially did well were Taiwan, Japan, Singapore, and South Korea.  These countries are right next to China, which is the natural source for the seasonal flu.  This is because flu viruses exist natively in aquatic birds from southern China, and there is no practical way to eradicate the flu. We can expect dangerous respiratory viruses to arise from China from time to time.  Neighboring countries know this and are naturally vigilant.  The citizens of Asian countries are used to wearing a mask whenever they have the sniffles, and they are prepared for local epidemics. 

South Korea had the following strategy:

  • Early free testing for anyone who wanted a test.
  • Contact tracing of people exposed to infected individuals. Cell phone and credit card data was used to track residents and produce contact information for infected people.
  • Quarantine COVID positive patients at home, fines imposed for breaking quarantine.
  • Nearly all citizens wore masks in public.
  • Treatment of patients with moderate symptoms.
  • No “Lockdowns”, that is quarantining COVID negative individuals, but schools, cinemas, and gyms were closed. Most stores were open.  Vaccine passports allowed access to high risk areas during the Fall and Winter of 2021/22.

By contrast, the US, and most of the Western world, had the following policies:

  • Testing only for symptomatic people.
  • Treatment only for severe cases.
  • Early “Lockdowns” of all but essential workers.
  • Contact tracing applied too late to be effective.
  • Early communication on masks was incorrect and even deceptive to avoid a run on N95s which happened anyway.  Mask wearing remained controversial and unevenly applied, medical grade respirators unavailable or rarely used for most of the pandemic.

I will point out that most countries, even Japan, South Korea, and Taiwan, had major outbreaks during the Omicron wave.  These countries did have some COVID related restrictions during the Winter of 2020/21 and during the Omicron wave.  I leave China out of the analysis because I don’t trust their data.

Most respiratory viruses like cold and flu are spread by droplet or contact transmission.  However, SARS-2 is spread by aerosol transmission.  Droplets and aerosols are similar, but an aerosolized droplet is much smaller and can linger in the air for much longer than a droplet, more like a cloud than a spray.

Several precautions than became common and even required are designed to prevent droplet transmission rather than aerosol transmission.  These precautions include 6 foot distancing, cloth and blue surgical masks, and those plastic shields at the store.  These measures are mostly ineffective at preventing the spread of aerosols because they do not prevent the movement of small particles.  As you know, I was a strong advocate of masks indoors during the pandemic, but only the medical grade respirators like N95s, KN95s and KF94s.

Peculiarities of the US:
In addition to prevention policies, the US has several cultural and demographic factors which contribute to our high infection numbers. 

Population: Americans know that the 2 most populace countries in the world are China and India, with about 1 billion people each.  These populations appear to dwarf our own estimated population of 330 million.  But we forget that the US is the 3rd most populace country in the world, with number 4 being Indonesia at 272 million. Japan has 125 million, and the most populace European country, aside from Russia is Germany at only 82 million.

Mobility: The US is an enormous country, and Americans are used to traveling much more than other peoples.  We may not fly to other continents as much as the Germans do, but we don’t hesitate to drive several hours for the weekend, or fly across the continent. I was having lunch with an Englishman once who said they might plan for weeks to take a trip that would involve a 3 hour drive.  Many Americans may only plan for a few hours for such a trip. Our high mobility certainly contributed to our high COVID numbers.

Independence:  Our independent nature has been an enormously useful quality, contributing to our high innovation, personal freedom, and economic prosperity.  So I’m certainly not arguing against American individualism.  But I have to acknowledge that our fierce sense of independence did contribute to non-compliance with government recommendations.  And yes, I totally understand that many official recommendations were ineffective or unlawful. But this factor is part of the equation that we will need to consider in order to deal with future pandemics.

Federalism: The US Government has a lot less power than most people think.  The 10th amendment states:

The powers not delegated to the United States by the Constitution, nor prohibited by it to the States, are reserved to the States respectively, or to the people.

This means that the only powers the federal government has are those expressly given to it in the Constitution. Much of what the US government does now goes beyond the powers given by the Constitution, and is only done because no one has stopped them.  New federal powers are often popular, so they go forward unchecked. 

The pandemic has caused many to lose trust in several previously trusted federal agencies, and States have started to pull back power from the US.  Many were surprised to discover how limited the President’s power was during the pandemic, limited to suggesting guidelines and creating regulation for federal property and interstate travel.  The vaccine mandate attempted to use private companies to enforce vaccination, but even this was struck down by the Supreme Court. 

Emergency powers outlined in the Constitution only apply in the case of an insurrection or invasion. Unless a Constitutional amendment is passed, the Federal Government can only impose martial law if an emergency forces the courts to close (Duncan v. Kahanamoku, 1946).

States have much broader powers.  In California, the Emergency Services Act allows the Governor to declare a state of emergency at any time, a state which grants him broad powers, including the power to suspend certain laws.  Some have said that this state can only last 90 days without approval from the Assembly, but the ESA allows the Governor to end the state of emergency whenever he deems it necessary, “at the earliest possible date that conditions warrant.” (§8629).

All this to say, the states have much more power to address a pandemic than does the federal government.  Whether you find this good or bad news depends on your own political leanings, and the state you live in!

Manufacturing:
The national shortage of N95 masks early on in the pandemic painfully revealed that our domestic capacity for manufacturing certain necessary items fell woefully short. Other items in short supply were hospital gowns, gloves, disinfectant, certain medications, and yes, even toilet paper. 

This shortage meant that almost no-one had effective masks early on.  In addition, confused messaging from Dr. Fauci and the CDC later produced a condition in which ineffective masks were common in public areas.  This certainly had a big negative impact on our case load.

Misinformation and freedom of speech:
I have written on this before, so I won’t repeat this now.  Suffice it to say that many Americans lost confidence in government agencies, including the CDC and FDA during the pandemic.  Lost trust is hard to regain and it can take a long time to get back.  I’ll discuss this more in my next post.

Political polarization:
Similar to the erosion of trust in government agencies, the response to the pandemic quickly became a “team sport” with some responses being typical of the “blue team” and others typical of the “red team”.  Unfortunately, both sides often opposed reasonable ideas simply because they came from the other side.  Also, some terrible ideas had a longer life span than they should have because they were favored by certain political groups.  As I’ve said many times before, science and politics are a terrible combination.  When politics gets involved in science, the results are usually terrible. 

Frankly, things have become so polarized that I am pessimistic about the future.  Republicans and Democrats seem to disagree strongly about nearly everything these days, having fundamental worldview differences, not just differences in approach. I know lots of people who lost contact with friends and even family during the pandemic, as have I myself.

Let me know in the comments what factors you think contributed to our response. Later this week, I’ll post on the next pandemic, and how we can prepare.

Don’t fear, but be smart,
Erik

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

______________________________________________
Important Update on Paxlovid, from July 2nd, 2022:

This is a post about Tony Fauci’s time with COVID and the drug Paxlovid, which I have discussed in the past.

On June 15th, a story came out about Tony Fauci having contracted COVID, despite having been fully vaccinated and boosted. I didn’t cover this before since I’d already discussed the fact that the vaccines don’t prevent infection by Omicron variants.

However, something else very interesting happened. Dr. Fauci took Paxlovid, which I’ve discussed briefly before, and became COVID negative. But after his 5 day course, he became positive again with worse symptoms. This means that a standard 5 day course of Paxlovid will not necessarily reduce your viral load to zero, and patients may experience “Paxlovid rebound”. Fauci even claims that this kind of rebound with Paxlovid is starting to be seen as “typical” as more patients use it.

The CDC actually issued a warning about Paxlovid Rebound in May, but it was not widely reported.

With so many rebound cases, it’s likely that 5 days is not adequate to eliminate all viruses from the system, allowing rebound. However, Paxlovid does have side-effects, so don’t take it for more than 5 days without consulting your doctor! Hospitals are now only prescribing Paxlovid to high risk patients.

Whenever taking anti-viral or anti-bacterial medications, always take the full course of treatment. If any virus or bacteria survive treatment, they may give rise to a more resistant strain. Don’t just stop your treatment when you feel better. I take anti-biotics as a last report, but when I do, I take the full course. I even made a doctor give me the full 10 day course when she just wanted to give me a half course!

Just to repeat the point on the vaccines, I still hear ads on the radio encouraging vaccination. At this point, the vaccines are really not doing anything against the current COVID variants. There is really no benefit to getting a vaccine or a booster. If you haven’t had COVID yet, I would simply recommend preventative measures. Wear an N95, KN95, or KF94 mask when indoors in public. Cloth and surgical masks will not prevent infection.

Don’t fear, but be smart!
Erik

Kim Iversen’s more in-depth discussion of Dr. Fauci’s rebound.

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, March 14th, 2022; Continued Enforcement of Vaccine Mandates

Here’s a brief case update. I’ll also have a brief comment about vaccine mandates.

Cases continue to come down in the US, California and San Diego County. Cases in the US are now approaching being as low as they were in the Spring before Delta started. The only current outbreaks, according to endcoronavirus, is in the Twin Falls area in Idaho. Cases are dropping in San Diego County too, but unfortunately, not as fast as other places. LA and San Diego Counties are now #1 and #2 for new case numbers 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 10th, 2022
Endcoronavirus County Level Map, March 10th, 2022
Endcoronavirus State Level Map, March 12th, 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.

World wide, the US is now in 8th place for countries with the most new COVID cases in the last month. This is a welcome change, since the US has spent large majority of the pandemic in 1st place. Ironically, the country in first place right now is South Korea, which has been doing well for the majority of the pandemic, serving as an example for other countries to follow. The majority of cases country wide have happened in the last month, due to the super infectious but less virulent Omicron variant.

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

Vaccine mandates still enforced: In January 2022, the Supreme Court struck down the vaccine and testing mandate for all but a few health care workers. Mandates for federal workers are still working their way through the courts. In spite of this, some companies and municipalities are still enforcing the mandates. They often cite vaccine mandates, but the vaccine mandates still do not officially exist, having been struck down. So these entities are enforcing mandates entirely on a voluntary basis, and of their own volition. These entities do not acknowledge the now well known data that natural immunity is better than vaccine mediated immunity at preventing infection and the spread of SARS-2.

As you may have noticed, I’ve been tapering off the frequency of my updates as the pandemic recedes. As things continue to improve, I will post more infrequently.

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 4th, 2022; Omicron update, US Omicron Proportion Estimated at 95%.

This is a case update. I’ll also give an update to the Omicron wave we are experiencing.

On Monday, the new case numbers were approximately 3 times the single day case number from last Winter, with over a million new cases in 1 day. Cases are skyrocketing in many states across the country, in particular in the Northeast where Omicron cases are tremendously high. Of course, the very high 1 day number is partially due to the lower rate of reporting over the holiday weekend. I’m switching back to a logarithmic format for some of my graphs because the new high numbers make my linear graphs a little meaningless.

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 Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, January 1st, 2022
Endcoronavirus State Level Map, January 4th, 2022

Deaths have not yet started to rise in response to new Omicron wave, at least here in the US. Deaths tend to follow cases by between 2 and 5 weeks, although this time frame will be shorter for Omicron because both incubation time and disease duration are shorter for Omicron. In South Africa, where the Omicron wave is almost over, deaths are up very modestly during the Omicron wave.

From Worldometer.
From Worldometer.

Hospitalizations in the US are up, but notice from the CDC graph that this is explicitly “Patients with Confirmed COVID-19”. Since all patients are screened for COVID, even those who were admitted for non-COVID reasons may be registered as a COVID admission. John Campbell has stated that about half of recent hospital COVID patients are “incidental”, meaning they were admitted for something else. For most Omicron patients, the symptoms are like a cold. Is is certain that many who have Omicron are not entering the medical system and are not seen in the new case numbers.

Hospitalizations, from the CDC website.

California and San Diego County are likewise experiencing very high numbers, although the case numbers in California are only just as high as last Winter, not higher.

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 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, new cases are very high, again mostly due to Omicron. Fully half of new cases over the weekend are from the US alone!

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

Omicron update: The CDC updated their page on variant proportions again just this morning. The estimate for the week ending 1/1/2022 is 95.7% Omicron, and just 4.6% Delta. The estimate for last week was upgraded from 58% to 77%. Remember that the last 2 weeks of data include “Nowcast” numbers based on computer modeling, and computer modeled numbers are only as good as the algorithm and the data that go into them.

From the CDC page on Variant Proportions. Accessed January 4th, 2022.
From the CDC page on Variant Proportions. Accessed January 4th, 2022.

The very high proportion of Omicron cases is very good news. Omicron is much less pathogenic (disease causing) than Delta. Most experience mild cold-like symptoms, and few experience fever, loss of taste and smell, inflammatory events, or blood clots.

My wife and I both experienced mild cold-like symptoms last week, and I think we both had Omicron. My symptoms were mild, even for a cold.

In addition, new data suggests that Omicron is in fact displacing Delta, and even that Omicron immunity protects against Delta infection. This is all fantastic and suggests that Omicron is in fact ending the Pandemic! Just a little cautionary note. I have a close friend who got COVID over the weekend, and she says it was Delta. No, I don’t know how she knows it was Delta. Her symptoms were severe, but not enough to be hospitalized. She was very sick for a few days, but is on the mend. So Delta is still lurking about.

Should you get a booster?: I’m going to say something you definitely won’t hear on the news right now. A study from Denmark suggests that the vaccines are about 55% effective against Omicron, and that effectiveness wanes quickly afterward. Given the possibility of an adverse reaction from the vaccines, mostly because of the Spike protein itself, my opinion is that vaccines are not an effective measure for Omicron infection. In a cost/benefit analysis, the costs of a booster outweigh the benefits. If you are in an at risk group, I would advise instead simply taking precautions like mask wearing indoors and avoiding indoor gatherings. If you wear a mask, use a medical grade mask like an N95, KN95, or KF94. Blue surgical masks, neck gators, and cloth masks are ineffective in protecting against infection. Of course, always consult your doctor when making medical decisions. I am a molecular biologist, not a physician, or an epidemiologist. This is my informed but not expert opinion.

Also, remember to keep supplementing Vitamin C, Zinc, and especially Vitamin D! Data keep rolling in that Vitamin D deficiency is heavily correlated to severe COVID symptoms!

Testing: I know several people with clear Omicron-like symptoms who were negative for COVID after using an at home rapid test. Is it clear that these tests are doing a poor job detecting the Omicron variant. If you need to know if you have COVID, you’ll need to get a PCR based test. Even those are missing some cases right now, but they are much more sensitive for Omicron than the rapid tests.

What if we get another variant?: Variants have had a huge impact these year. The vaccines were working great until the Delta variant appeared and messed everything up. Then Omicron showed up and changed everything again, this time for the better. Viruses tend to become more infectious and less pathogenic over time, and Omicron certainly fits that pattern. I’ve been asked “what if we have another variant?” The potential exists for another variant to come along and ruin the party like Delta did, but more likely, it will be less pathogenic than Omicron, especially since it will probably be most related to Omicron. So I’m not worried about new variants for the time being.

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 suggests that Omicron deaths will be low, even in older populations.

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!

Don’t fear, but be smart,
Erik

Case Update, December 21st, 2021; Omicron overtakes Delta in the US!

This is a case update. I’ll also discuss the new Omicron numbers in the United States, and reevaluate if Omicron will represent our way out of the pandemic.

In terms of whole numbers, cases are still increasing in the US, mostly in the Northeast. In some amazing news, most of the cases in the Northeast are now from Omicron and not Delta (more detail on this below).

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, December 20th, 2021
Endcoronavirus State Level Map, December 21st, 2021

In California, cases are still at a persistent number, at around 5,000 new cases a day.

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.

San Diego is continuing to experience a burst in cases right now.

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.

Omicron rapidly overtakes Delta!: In amazing news, cases from Omicron already outnumbers cases due to Delta in the US, and are 90% of new cases in some regions. Last week, the CDC was reporting that 3% of US cases were from Omicron. This week, they revised that number upward to 12%, but also reported that for 12/18, 73% of COVID cases in the US were caused by Omicron, 60% in the Southwest. I expect 95% of cases in the US to be Omicron by next week, and virtually 100% by New Years. This is potentially great news!

From the CDC page on Variant Proportions. Accessed December 20th, 2021.
From the CDC page on Variant Proportions. Accessed December 20th, 2021.

While still very early, a few other countries have started to produce data that can tell us what we might expect. In South Africa, the peak of new cases is already coming down. In previous waves there, peak deaths have trailed peak case by about 10 days. But for the Omicron wave, there is only a modest increase in deaths 10 days after peak new cases. This seems to confirm reports that Omicron produces very mild disease.

From Worldometer.
From Worldometer.

In the UK, Omicron cases are surging dramatically, with cases doubling every few days. In spite of this, there were 909 COVID deaths last week. In total, only 14 people have died from an Omicron infection this far. As Omicron spreads in the UK, we will likely see hospitalizations and deaths go down dramatically. I will caution that in the UK, deaths trail cases by about 12-20 days, and we are still early in the Omicron wave in the UK.

From Worldometer.
From Worldometer.

Back in the US, 90% of new cases in the Northeast are due to Omicron right now. In spite of this, total case numbers in New York are roughly double what they were a week ago. This means that of the 20,000 new cases daily in New York State, only 1600 are from Delta, the rest are from Omicron. So Delta cases in New York have gone down by 80%! Indeed, Omicron appears to be displacing Delta!

From Worldometer.
From Worldometer.

Keep in mind that we are only a few weeks into the Omicron wave, and things are still early. I will also caution that there are still a few people dying due to Omicron, so it’s not all over. Cases may be extremely high in the next few weeks. That being said, Omicron definitely has the potential to essentially end the pandemic, maybe in just a few weeks! If you’re one of my colleagues in the medical industry, start polishing up your post-COVID business models now!

I am NOT saying you should run out right now and get a nice case of Omicron. It’s still to early to say if that will be a good idea. For now, keep it together and stay cautious for just a few more weeks until we know more. I will also caution that I have a track record of being overly optimistic on my expectations of when the pandemic will end!

Given that the vaccines have some inherent risks of their own, and that Omicron appears to have very mild symptoms and completely ignores previous immunization, I do not recommend a booster to prevent Omicron infection at this time. Instead, those with risk factors should simply take precautions until the Omicron wave is over, or until more is known. As always, consult with your medical provider when making health care decisions. I am a molecular biologist, not a physician.

Omicron scorecard: Here’s my revised “scorecard” from last week. 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, while Omicron may preferentially infect those who have been previously infected, 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.

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. With the super high infectiousness of Omicron, it might just do that. Total Delta cases are currently down 80% since the start of the Omicron wave in New York State. This is very encouraging. This criteria is provisionally met.

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.

Don’t fear, but be smart!
Erik

Case Update, December 15th, 2021; Omicron update, will Omicron end the Pandemic?

This is case update.  I’ll also give an Omicron update, and discuss the criteria that must be met if Omicron is to be a blessing rather than put us back to square one.

For the US, the Northeastern states are continuing to see increased cases in states like New York, Michigan, Pennsylvania, Ohio, and Illinois. This is at least partially because of colder temperatures leading to more people being indoors. Last year, the Winter wave spread from Northern states like Wisconsin, Michigan, and Minnesota. Just like last Winter, Cook County, the home of Chicago, has the most active cases in the US 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, December 15th, 2021
Endcoronavirus County Level Map, December 15th, 2021
Endcoronavirus State Level Map, December 15th, 2021

In California, new cases remain at a persistent level after the Delta wave. 

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.

San Diego County experienced a burst in cases in the last few weeks.

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.

Globally, new cases are at a peak, but reducing for now.  However, many countries are starting to experience increasing numbers of Omicron cases.

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

Omicron update: Information on Omicron infection continues to come in from South Africa, and now from the UK and Denmark.  In South Africa, most new cases are now from Omicron, but fatalities are only 4% of what they were during the Delta wave there.  In the UK, it is estimated that fully 50% of new cases are from Omicron.  At this point, there are 1 million new Omicron cases every day.  Omicron is proving to be explosively infectious.  John Campbell says the US is about 3 weeks behind the UK, and we’ll see 1 million new cases of Omicron per day by the first week of January.

Surveillance is very good in Denmark, and a lot of isolated strains are being sequenced.  It appears in Danish data that previous vaccination or infection status has almost no bearing on whether someone is infected by Omicron, so we can’t expect vaccines to prevent infection.  However, it does appear that previous infection or vaccination reduces the chance of hospitalization or death from Omicron.

From Statens Serum Institut, part of Denmark public health.

Commentators warn that because of its very high infectiousness, nearly everyone will be infected with Omicron at some point. However, the fatality rate is very low compared to other strains, although not zero.  In order to reduce your symptoms, continue to supplement with Vitamin D, Vitamin C, and Zn.  Costco carries a supplement with all 3 in the same pill! If you’re in a Northern state, you can also make Vitamin D by having an extended snowball fight with your kids on a sunny day. Don’t throw at the face, or it’ll be a short fight.

While Omicron now exists in 36 US states, Omicron currently represents 3% of COVID in the US.

From the CDC page on Variant Proportions.

Will Omicron be a blessing?: Several commentators like John Campbell, Chris Martenson, and Mobeen Syad are feeling optimistic that Omicron really may represent the end of the pandemic. Here’s what needs to be in place for this to be a reality, and how the data stands right now. 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, while Omicron may preferentially infect those who have been previously infected, 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. At this point, it appears preliminarily in the UK that fatality rates are lower than with Delta, so I’m going to say this criteria is met with some caution.

    The next 3 are related, but not exactly the same.
  3. Displace Delta: Delta is currently the most common strain in the world, and almost 100% of COVID in the US right now.  Omicron must displace Delta as the dominant strain.  Binding of a more infectious SARS-2 strain to cells will prevent others from binding instead, so this criteria will likely be met.
  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.  Right now, most guess that Omicron will not be independent from Delta, but we’re not sure yet.
  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.
These are my criteria for whether Omicron is likely to end the pandemic. If all criteria are met, we may see a large reduction in COVID cases world wide in the coming months. I am not an epidemiologist, I am a molecular biologist. This is my informed but not expert opinion.

As of right now, I’m actually feeling optimistic about chances that Omicron will end the pandemic!  It’s still too early to tell for sure.  For myself, I continue to take precautions until more is known.  Keep in mind that Delta is still almost all of the SARS-2 virus in the US right now, so it’s not time to run out and get your natural immunity to Omicron.  Also, when Omicron hits hard in the US, a lot of people will be at home sick at once, so expect some economic disruption, and be prepared for colleagues to not be at work.

Don’t fear, but be smart,
Erik