Omicron Variant versus Delta Variant: Lessons on What to Expect From Coronavirus Adaptations

My previous blog post described how Coronavirus strains adapt and benefit from their naturally high error rate when they copy their own RNA as more virus particles are produced in an infected cell. (Click to read that posting here.) If these changes cause a particular strain to spread easier among us humans then these new strains quickly take over the infection race. There is no evil plot, just the random events of statistics and bad luck for us as variants like Omicron spread faster. Delta is still around, but Omicron gets to new unvaccinated persons first, and eventually, more of those requiring admissions to our hospitals will have Omicron and not Delta. That said, both Delta and Omicron are killing people inside our hospital ICUs. Why exactly does Omicron spread faster than Delta?

Trojan Horses, Pandora's Box, and Gambling with the Variants of COVID19.

(Updated for Omicron variant, November 28, 2021)

Who are the gamblers? Our leaders at many levels, including those managing our workplaces, towns, cities, counties, and states, continue to underestimate the potential outcomes of COVID variant emergence. What many molecular biologists (scientists who work with DNA and RNA) and mathematicians understand is that the very nature of viral replication makes viruses into ever-changing evolution machines. The strain of COVID19 now running rampant through our network of unvaccinated neighbors is far more infective than the ones we dealt with in early 2020. This is the how and why.

Does the COVID19 Vaccine Booster Work? Judge for yourself with your own eyes.

In my main work as a biomedical research scientist at Oakland University (Oakland.edu) I study mechanisms of how genes are turned on and off in the retina and what causes some diseases to threaten vision in people from infants to adults. I also design the biotechnology production of human proteins in bacteria to make potential future therapeutics (drugs) to repair damaged blood vessels in the retina. Fundamentally, I am first and foremost a biochemist and have been fortunate to have gained experience in most specialities of biochemistry including metabolism, cell physiology, human physiology, DNA, RNA, Proteins, carbohydrates, hormones, cytokines, and some infectious diseases. Even a little past work with aspects of viruses, including HIV. You can do many things over 25-plus years in the lab. When the pandemic shut down non-covid research for some months into summer 2020, statewide, I pivoted, with the help of a few students to start evaluating a mobile fingertip blood test for antibodies to the COVID19 spike protein, from a US company called Epigentek. (Note I do not work for Epigentek, nor own any stock in the company.) As we found that this particular brand of the test was reliable (no false positives) and very specific to detect only antibodies to the COVID19 spike protein, we have used it to get a snapshot of when antibodies are detectable in our community after COVID19 infections (in 2020) and after COVID19 vaccinations in 2021. So, what about vaccination? I knew that even in my own case, before vaccination we cannot detect any antibodies in our blood. What about after vaccination? After 

6 months? After a booster shot? Here are my own tests to share with you to show you why I am quite happy with my vaccinations and my booster shot.

Like Old Jedi, Good Antibodies just Fade Away........

Above is our test of my blood's Covid 19 antibodies (IgG class) at 3 months after my 2nd dose of Pfizer vaccine. Marked with the black dot. The red line to the right is a control line.

Below is my test done today, now about 5.7 months after full vacvination. 

As you can see the relative concentration of my antibodies to the spike protein of Covid 19 is still easy to detect but is about half of what I had at 3 months. 

Now even if my antibodies fade away completely, I will likely have resident immune system clonal cells that are ready to detect and respond more quickly to a Covid 19 infection than I would have prior to being vaccinated. However, in time, the number of those cells will also decrease. 

So we should expect that a yearly vaccine shot to Covid19 will be routine medicine just as the flu shot is too. Generally, our human immune system does not remain primed for more than 6 months against corona-type viruses, which is the class of virus that Covid 19 belongs to. Many coronaviruses are actually cold viruses and we already know that it's possible to get a full-blown cold more than once from the same coronavirus strain within a single winter because coronaviruses trigger a shorter lasting immunity.

The viral RNA polymerase that makes copies of the Covid 19 RNA within infected cells has an error rate of 1/10,000, and the genome of Covid19 is about 30,000 bases long. Thus each new virus made in one of our infected cells has an average of 3 mutations. That is three bases different from the virus that infected the cell. That means that almost all 3,000 to 5,000 copies made in one infected airway cell are all mutated, changed, different from the original infecting virus. That is how viruses change, adapt, and evolve. Most of the mutations will not make much difference, some will make the virus less efficient, but some can make the virus replicate faster and also bind faster and stronger to our airway cells. 

That is why variants like Delta occur and the virus will have opportunities to become even worst if we have large regions of mostly unvaccinated persons. Mutations have changed the Delta variant's spike protein and just one changed link in that protein makes it bind to and infect cells faster than the virus at the start of the pandemic.

As a molecular biologist with expertise in gene expression, genetic diseases, and RNA and DNA polymerases, I am concerned.

I will get my Covid-19 booster as soon as I am eligible. 

Ken Mitton

PS. I got my flu shot last week and have done so every year for over 15 years. I have not had the flu in that time.

Delta: COVID19 Cases and Deaths for Any Country

Sadly, in August 2021, here I am making an update to this post, which I first added here over a year ago, way back in 2020. Here in the United States, as in several other countries, conservative political leaders have gone almost insane. They have conned so many Americans into walking right into a COVID19 pandemic that is now killing off mostly unvaccinated republican voters in counties with low vaccination rates. 

I am a scientist in North America, who has lived and worked on both sides of the US/Canada border, and as a medical research professor, I felt it my duty to use my blog here to provide more awareness with access to numbers that you can trust. This data visualization lets you follow the progress of COVID19 in the USA and other countries, and visualize it over time. I have included some iFrame code to this blog post to give you the ability to change the time frame and even the selection of countries you may be interested in. You can adjust the graph views to suit your need for knowledge.

Currently, in addition to my eye research, I also manage a small local research study in Oakland County, Michigan, to monitor the presence of antibodies to the COVID19 spike protein in persons. My students and I have found that vaccines from Moderna, Pfizer, and J&J, do well at producing antibodies in our test volunteers, including ourselves. We are all vaccinated at this point. So keep wearing a mask, get vaccinated, and think about the people who will not get harmed because you buffer them from this pandemic disease.

The "delta" variant is simple and dangerous. 

I can understand why, because I often make proteins and custom modifications to the structure of proteins for medical research. The purpose of my research at Oakland University is to understand how specific proteins work for vision.  I engineer human proteins, which are required to develop structures in our retinas, for bacterial factory production as potential therapeutics to repair damaged human retinas. For conditions such as Retinopathy of Prematurity and Diabetic Retinopathy. In the 90s I briefly got to do some research on how the HIV protease can also harm a cell's proteins in addition to simply processing the making the more HIV virus. Since then we have the knowledge of the human genome. 

So now I can also tell you that viruses generally replicate their own DNA or RNA sequences with low fidelity. That is the DNA or RNA Polymerases that replicate their DNA/RNA tend to make frequent mistakes, to change their genetic code. This, in turn, changes the components that make up the virus's proteins, including the spike protein you hear about on the news. This "spike protein" is used by the virus to bind to cells that line our sinuses and respiratory tract (lungs). This high error copy rate creates hundreds of variations of the COVID19 spike protein in every person who is infected with COVID19. Most of the errors will result in a less infectious virus but once in while, versions like the delta variant evolve to spread faster and more efficiently. This is the case now in 2021, August. So I am updating and reposting this blog, as we all need to watch how numbers rise again. Numbers of cases and numbers of deaths. As 99.9% of persons entering ICU and 99.9% of those dying from Delta variant in the ICU are unvaccinated, I suggest you get vaccinated ASAP. 

Here are graphs that you can adjust to look at different timelines for cases of illness and deaths for any country. I embedded iFrame code in this posting to give you graphs that you can also adjust. Table and MAP views are also available. Book mark this blog posting so you can return here. The data in these graphs will update automatically. 

Bad Pharma Good Pharma: how Patients and their Doctors are fooled about the drugs sold to them.

Snake oil salesmen are alive and well in the 2000's.
They know how to use the Congress to overturn FDA new
review panel recommendations and market away.

Bad Science is simply not doing science right. If you cut corners, never repeat experiments to confirm they are reproducible, bury negative results, then you can end up with egg on your face as a scientist. At best, the target for teasing by your colleagues, or at worst a biomedical company that contributes to the illness or deaths of many people and who will never be trusted again in the science or medical world. As it should be. 


Bad science or medicine seems to happen when money is part of the motivation equation in the form of "for profit". Unfortunately, that is the context where most commercial Pharma research occurs, including clinical trials. With shareholders to pay, there is a strong executive pressure to get the product developed and flying out of the pharmacy on Doctor's prescription pads as soon as possible. This factor, profits, are one of the greatest conflicts of interest (COI) we must manage.

For all of us, as the patient, this can have bad consequences. For our Doctors, they may be making prescription decisions based on information that is skewed or incomplete. They can be in a position where they cannot even get the full story on many of the drugs they must choose from. The Pharmacist will be in the same position as your Doctor. The problem that is keeping all three of us in the dark is reporting bias on the part of the drug developer. That is, under-reporting of negative trial results, and basic cherry-picking of trial results. While we have currently, in the United States, a political effort to reduce government regulations, we already suffer commercial lobbying and political overriding of FDA biomedical science recommendations on drug approvals. This includes ignoring expert panel recommendations to not approve a drug and instead let the company market away. Essentially neutering the ability of the FDA to save us all from snake oil salesmen, even in 2018.