January 3rd 2022
Omicron Overview - The world of omicron as I see it now
OMICRON IS A MORE INFECTIOUS BUT LESS SEVERE VARIANT ACCORDING TO ALL REPORTS - Amen
1) Omicron is everywhere in the US now, as expected.
2) Hospitalizations and deaths remain decoupled from cases meaning that we are on our way to mild COVID endemicity and likely the end of the pandemic as we know it based on Delta and Alpha's severity
3) There are reports out of major cities like NYC stating that Covid disease in children is on a path upward. We have not seen an increased rate of illness and no increased death rate. The volume of illness is now so high that we are by definition going to see more cases in children. The vast majority of cases remain mild or asymptomatic.
4) Your risk of death if you have had covid naturally or been vaccinated appears now to be very very very low with Omicron or Delta.
5) The caveat to number three is that if you are older with co-morbid disease in a significant stage, your risk of death is much higher. But, this is true for influenza and other severe viral illnesses as well at this point because of the inflammation that pervades the body from these diseases over time.
6) Boosting, to me, remains controversial at this time for the young, healthy and previously vaccinated or infected. Omicron is definitely a milder infection from a severity perspective. We still need hospital data based on age and disease risk to better allocate booster doses. A positive test with mild symptoms is just that. As always, to boost is a personal choice based on the science, age and risk. Getting vaccinated if not already vaccinated makes incredible sense at this point.
7) The rest of the world needs vaccine now to slow the mutability of the virus in general.
8) Please keep all schools open regardless of spread unless we see an increase in hospitalizations and deaths as the disease risk for children remains incredibly low.
9) MOST IMPORTANT - Every decision from here on out has to have the mental health of humans as part of the calculus. Fear of COVID is not a good decision making guidance tool now and likely never was. Risk calculation and personal health is important.
10) Read #6 quick hit again this week - too important to only read once.
New CDC guidelines: People with COVID-19 should isolate for 5 days and if they are asymptomatic or their symptoms are resolving (without fever for 24 hours), follow that by 5 days of wearing a mask when around others to minimize the risk of infecting people they encounter. The change is motivated by science demonstrating that the majority of SARS-CoV-2 transmission occurs early in the course of illness, generally in the 1-2 days prior to onset of symptoms and the 2-3 days after. - This is a very welcome admission of change in the face of good science that has been around for a while.
My thoughts at this time about COVID and Omicron in general: This is likely the best case scenario for us moving forward. Omicron is less deadly while being more transmissible. Therefore, we going to see everyone get infected at some point this year, regardless of vaccination status and prior infection, with lower viral loads and hopefully less mutation as it replicates based on the more mild disease. Hopefully, studies will show lower viral loads portending less risk and less mutagenesis. We are absolutely in a different world now with a milder variant coupled to a mostly non SARS2 naive population that has robust T and B cell memory with which to tackle the viral variants. Unless some unimaginable change occurs via a novel mutation or some unforeseen event, we should be heading in the right direction for a normal life with COVID now.
The big issue now based on Omicron infectiousness is the lack of health care and general workers on the job. With so many people testing positive and needing to quarantine from work, we are struggling to keep effective workflows and production that could have serious consequences in the hospital and clinic setting. Hopefully, the lack of severity will balance this equation. Time will tell, but so far so good.
Quick Hits -
1) Current rates of COVID related hospitalization for a vaccinated individuals = 3.9/100,000 vs 67.8/100,000 for unvaccinated. Typical influenza season has more than 20 hospitalizations per 100,000. (CDC site) Again, we see more data that being vaccinated is associated with the best outcome.
2) A new data set from Germany is very very reassuring for children. Hospitalization overall was 36 per 10,000 for children. ICU admission was 1.7/10,000 and death was 0.9/10,000. Further drilling down the data noted that children who were disease free pre infection had almost zero risk of death. The lowest risk age group was from age 5 to 11 years old with no co-morbid disease.
Multi inflammatory syndrome was 1 in 4000 cases of illness. (Sorg et. al. 2021) This is not a trivial number. Our clinic have 5 known MIS cases, all of which survived.
What this data doesn't say is that it overestimates these stats as they cannot expect to have an accurate case volume denominator. They tried very hard to account for missed infections by antibody titers and statistical predictions. However, my take on this data is that it is likely less than all of these known stats., i.e. ICU admission is less than 1.7/10,000. Either way these numbers are very very low.
More data from which to make your decisions regarding children, schools, vaccines and other COVID related questions.
3) "Our results indicate that systematic surveillance of asymptomatic vaccinated HCWs uncovers many times more cases of Vaccine Break Throughs or VBT infection than symptom-based testing. The incidence of asymptomatic VBT infections seemed to depend on the frequency of testing and not occupational risk or community prevalence; once corrected for frequency of testing, incidence was similar in the high- and moderate-risk groups. Asymptomatic cases seemed to clear much more quickly and had higher mean antibody levels than symptomatic cases. Because of the rapid viral clearance in asymptomatic VBT infections, our surveillance program likely missed many other such infections."(Novazzi et. al. 2021)
This study was performed with delta as the prominent variant. If you look for it routinely, you will find more cases, but that is almost assuredly unrelated to significant transmission. This is very different than super spreaders and ill people in general. Asymptomatic cases are not the problem and never have been in children who are low risk spreaders. We need to steer away from this testing metric especially in schools. Symptomatic testing remains the route of Omicron discovery and quarantine protocol. Avoid the desire to test everyone in schools as you will likely find a lot of asymptomatic cases that are not causing disease spread. The removal of a child from school for a positive test is not fruitful but will continue as long as we keep testing non ill people.
Imagine that you can get this infection 2-3 x a year just like a common cold. Are we going to keep these children, their siblings and parents quarantined every time from now on for each true asymptomatic case and the false positive cases. That is an unbelievable volume of missed school, work and life in general. We need to focus on illness and spread risk first and foremost.
4) Rapid testing is useful at home if you are trying to determine the disease possibility when you start to have symptoms. The home tests are based on picking up antigen or viral protein fragments in nasal secretions. If you have a reasonable viral load, there will be larger amounts of antigen present and thus the test is likely to be positive. If you test too early or too late, it will be negative despite being infected. Omicron is infecting at a quicker rate than Delta meaning that early testing is more likely to be positive if you are symptomatic as the viral load of antigen ramps up faster. Unlike a Polymerase Chain Reaction test that amplifies the viral RNA making lower viral loads detectable, at home antigen kits cannot do this making them less sensitive. Thus, if you want to know for sure that you have COVID, use a PCR based test.
The current antigen home tests, BinaxNOW and QuickVue are both able to detect Omicron per the companies and the FDA.
If you are exposed to COVID directly and want to know for sure whether you have contracted the virus, you can use a rapid at home test 3 and 6 days after exposure which will significantly increase the likelihood of picking it up.
5) Monika Gandhi has written an excellent article in Time Magazine on the new metrics of Omicron. "If public health officials tie policies to hospitalizations, not cases, the media’s obsession with case counting will likely abate and help refocus attention on serious illness alone. With this sharper focus, our time can be better spent on vaccinating the unvaccinated and boosting as soon as possible the most vulnerable, such as residents of nursing homes, persons over age 65, and those with chronic health issues. However, this new strategy highlights the need for the CDC to increase its tracking and reporting of severe breakthrough infections by the health status of individuals so that the most vulnerable can be rapidly identified and prioritized for life saving treatment." (Gandhi M. 2021)
This is incredible! A logical approach to testing and reporting. How this is not happening remains a major mystery. If we knew that all vaccine breakthroughs that lead to hospitalization and death were in a certain subgroup of less healthy or at risk individuals, than we could target all therapy their way and stop worrying about everyone else. I would also love to see genomic analysis in the future finding these targeted groups through SNP analysis for defects in innate immunity against viral pathogens.
I have noted in the past that large numbers of mildly infected vaccinated individuals are likely our foreseeable future with this virus. Thus, it makes little logical sense to treat a mild breakthrough infection in a vaccinated or previously infected individual as a major problem. The issue has to be that we spend our energy protecting the vulnerable through booster vaccinations and drug treatment when ill. We have to get away from this reality that any positive case is the same. They are clearly not anymore. This is not March of 2020.
On masking: "Protecting those at risk of severe breakthroughs also means the end of blanket mask mandates. Our adult population has had access to highly effective vaccines for almost a year, and more recently, all children ages 5 and older became eligible for vaccination. Use of N95, KN95, KF94, FFP2, or even double masking, should be encouraged among select high-risk populations, but perpetual masking of entire populations is not sustainable or necessary. Our children, the demographic group at lowest risk of serious COVID-19 illness, continue to endure more hours of uninterrupted masking than higher risk adults. This strategy would mean making child masking optional at 12 weeks after the last school-age child became eligible for vaccination."
Couldn't agree more. The whole article deserves your attention - it is fully copied in section II below.
6) Dr. Wu writes a nice article on the importance of cytotoxic killer T cells in the fight against omicron and any future variants. These cells have a natural capability to kill any cell that has viral particles attached to it. These cells and our other T cells and B cells will give us the ability to handle most variants to the level that moderate to severe disease is rare after vaccination and or natural infection in the past. You may contract omicron as it has evaded the antibodies that you made to date, but it will likely be a mild and shorter illness based on your T and B cell activity. (Wu K. 2021)
Another study in preprint has excellent data that the cytotoxic T cells from Delta are well conserved against omicron. They state: "This analysis examined if the previously identified viral epitopes targeted by CD8+ T-cells in these individuals (n=52 distinct epitopes) are mutated in the newly described Omicron VOC (n=50 mutations). Within this population, only one low-prevalence epitope from the Spike protein restricted to two HLA alleles and found in 2/30 (7%) individuals contained a single amino acid change associated with the Omicron VOC. These data suggest that virtually all individuals with existing anti-SARS-CoV-2 CD8+ T-cell responses should recognize the Omicron VOC, and that SARS-CoV-2 has not evolved extensive T-cell escape mutations at this time." (Redd et. al. 2021)
This is likely the most important study in this newsletter. This is likely the main reason behind milder disease in individuals that get reinfected with COVID omicron and have symptoms. Remember that when we review all of this data regarding waning antibodies and reinfected individuals, we have to look at the totality of the immune response to have a full picture of risk and safety.
7) Neurological disorders are becoming a major problem for providers of care as their patients are struggling with neuropsychiatric changes during and post COVID illness. While we all are well aware of the loss of taste and smell, we are less aware of the rare but devastating acute psychiatric conditions that produce psychosis and mood disorder conditions. Many of these changes are autoimmune in nature, but the underlying cause in unremitting inflammation of the brain space as the immune system's cells that reside in the brain including microglial cells and peripheral macrophages fight the attacking SARS2 virus. The individuals as discussed in the past that have defects in viral surveillance and killing capacity will have higher viral loads in the brain leading to increased activation of microglial cells that swoop in to engulf and kill the virus. The process of killing is infused with inflammatory chemicals that also damage local tissue not just the virus. Thus, the more viral particles that make it to the brain the more self tissue that is collaterally damaged. This is akin to Alzheimers, Parkinsons, PANS, PANDAS, Lyme disease, etc.....over time.
The key to preventing these issues is multi factorial assuming that you do not have a genetic SNP that predisposes to this risk damage state and is not modifiable. To control the inflammatory process, we want to reduce all upstream triggers of inflammation and immune dysregulation pre infection, during infection and post infection.
My basic tenets of achieving this goal are:
a) avoid all refined carbohydrates especially liquid sugars and high fructose corn syrup. Try to avoid coupling them or any high carbohydrate load with large amounts of fat that also drive insulin resistance
b) avoid sedentary behavior that drives insulin resistance, obesity and mental stress
c) eat a high quality mostly vegetarian diet chock full of micronutrients like zinc, magnesium, vitamin A,B,C,D and E for immune cellular activity
d) avoid all toxins, drugs and chemicals that promote oxidation, DNA damage and cellular stress that can drive a passive macrophage M2 type.
e) avoid mental stress overload through meditation and prayer keeping the pro-inflammatory hormone cortisol in check
f) make sure to treat your allergies and food intolerances appropriately through elimination diets and targeted medicines/supplements
g) take fiber supplements and prebiotics to enhance high quality microbes in your microbiome which in turn enhances mucous production, micronutrient synthesis and inflammatory LPS reductions
h) consider taking N-acetyl cysteine, a precursor to glutathione, for enhanced TH1 cell type activity
i) avoid low oxygen states that drive HIF1a and inflammation
j) obtain effective daily sleep volume for stress reduction
k) fast or time restrict your feedings to induce counter regulatory hormones and immune activity that is pro pathogen killing
In my mind, the greatest risk of poor pathogen killing is chronic insulin resistance and obesity which are primarily a result of poor refined processed food consumption habits. Sugar, fructose, HFCS and saturated fats taking in concert are the recipe for disaster.