This is a case update. I’ll also talk about a report from Kim Iverson from The Hill regarding finding in the trove of documents release by Pfizer in March and April.
Cases are currently flat in the US. During the Omicron wave in December and January, the US lagged behind cases in the UK by 2 weeks. While the Omicron subvariant BA.2 produced a wave in the UK, it has not yet produced a wave in the US, despite it being 5 weeks since the BA.2 wave started in the UK. I’m going to go out on a limb and say that the slowing of the decrease of cases in the US is all we are going to see of the BA.2 wave in the US. I’ll let you know if this changes. BA.2 cases now constitute 72% of cases in the US.
Cases continue to go down in California and San Diego County.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.
XE variant: Just a few days ago, news emerged of a new COVID variant called XE in the UK. The variant is a hybrid of Omicron variants BA.1 and BA.2 and is more transmissible than BA.1. Since XE is very similar to other Omicron variants, I don’t expect it to cause a large wave of cases in the US.
Pfizer Document Analysis from Kim Iverson:Kim Iverson of The Hill released a video claiming that newly released documents from Pfizer confirm what many knew already. The shocking claim is that Pfizer has known the following for a long time:
Natural immunity is as effective as vaccine mediated immunity.
The rate of adverse events is at least 10/100,000 (33,000 for the US population). It’s unclear from Iverson if this is just for Myocarditis or for all adverse events.
It is unknown if the reproductive systems of women are impacted by vaccination. This contradicts public claims that vaccination does not affect reproduction.
A more severe case of COVID triggered by Antibody Dependent Enhancement could not be ruled out. The Lewnard et al paper a surveillance report from the UK have confirmed that higher Omicron infection rates in vaccinated people are likely due to ADE. As far as I’ve seen so far, ADE has not lead to more severe cases.
The documents were obtained because of a Freedom of Information Act (FOIA) lawsuit which required the FDA to produce the documents. Yes, this means that the FDA has had this information and did not disclose these conclusions to the public, instead often releasing information which contradicted these conclusions.
There will continue to be more document releases every month until the end of the year. There will likely be more bombshells, but most of the releases will simply confirm what people have suspected for months but couldn’t prove. I will discuss the most interesting, but not all of these releases.
If you have risk factors like obesity, age, or respiratory problems, you should consider getting a booster. Also, as I said last week, since vaccine effectiveness is substantially reduced after 3 months, those who have been vaccinated with risk factors will need to get a booster every 3-6 months. Try and find a provider who will aspirate before injection! There is no medical reason for someone who has had Omicron or Delta variants to get vaccinated or a booster. Talk to your doctor when making medical decisions.
I am posting about every 2 weeks now instead of every week. I’ll likely post even less unless interesting news comes out.
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.
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.
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.
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.
This week I’ll have a case update, then discuss variant BA.2, and Dr. Fauci’s announcement about the end of the Pandemic.
Cases in the US, California, and San Diego County are all still going down sharply. Cases are now at the same level as in mid-December. According to Endcoronavirus, most states have decreasing cases.
Variant BA.2: This new variant is now increasing slightly over the original Omicron. This is no reason to be concerned, however, since BA.2 is just a slightly more infectious version of Omicron. Antibodies against Omicron are expected to be effective against BA.2, so this does not represent a new variant that will cause case numbers to rise.
Dr. Fauci announces the end of the Pandemic: In an article in Financial Times, Dr. Fauci stated that he expects that the pandemic phase of COVID will be over in the next few months. I agree, with the exception that I think a reasonable time frame is more like weeks than months.
He also stated that he thinks boosters will continue to be necessary to keep the virus at bay. On this I have to disagree. The vaccines had a minimal impact on new infections due to Omicron, although they probably had a positive impact on disease severity. Given that the new cases are now very low, and the unknown but real danger from adverse reactions, I think there is now almost no reason to get a vaccine booster. For vaccines to continue to be useful, we need a more current version, against something like Delta or Omicron. I don’t expect we’ll be getting that.
Many scientists, including those I respect, think the virus will become endemic, meaning it will continue to circulate at a low level in different forms basically forever. With some trepidation and perhaps over-optimism, I think Omicron will eventually peter out and SARS-2 will be over. We’ll see if that happens.
Just a brief case update today. New cases are still dropping fast in the US, California, and San Diego County. Cases are now about as many as their were just before Christmas when the Omicron wave was just starting in the US.
The great news is, deaths appear to have peaked in the US 2 weeks ago, and were indeed very low, about as many as last Winter when the cases were far fewer than in the Omicron wave. A little math says that Omicron is roughly a quarter as deadly as the Alpha variant from last Winter.
Another plug for data: Last week I asked for folks to answer the following questions:
1) Have you ever had COVID? If so, when?
2) Have you been vaccinated? When?
3) Have you had COVID multiple times? If so when? What were your symptoms like each time? Were you hospitalized? If so for how long?
4) Is there anything else you’d like to share?
Obviously, a lot of people don’t want to go public with this information. You can post below or direct message me. I want to get an idea of how vaccination and previous infection produced protection for future infection. When you were infected will tell me what SARS-2 variant you had, and whether that variant protected you from future versions.
So far, I’ve only gotten about 30 responses, too few to be useful. If you want chime in, please do so! Thanks!
Just as the Pandemic seems to ending with a bang, so my personal COVID story ended dramatically. But first, the case update for this week.
The US, California, and San Diego County are all well past the peak of Omicron cases, and cases are dropping rapidly. In some Northeastern states like New York, New Jersey, and Vermont, the Omicron wave is already nearly over.
According to the CDCs variant proportion site, Omicron is now 99.9% of new cases. I will not report on this again, since this has now become uninteresting. There have been reports of a new subcategory of Omicron, BA.2, which is even more infectious than Omicron, but just as mild.
The end of my COVID story: I tested Positive for COVID on Friday the 14th, and finally tested Negative this Thursday morning, the 27th, almost exactly 2 weeks later. COVID actually got worse for me during course of the 2 weeks, with me getting more fatigued as time passed. Thursday night and yesterday were particularly bad, with extreme fatigue, sleeplessness, dehydration, uncontrollable shaking, and finally mental incoherence on Thursday night and Friday. Finally last night I was able to sleep for 11 hours and I finally feel like I’m recovering. I ate a full breakfast this morning and am actually doing some chores around the house.
I really only have 1 co-morbidity, celiac disease, an auto-immune disease. Unfortunately, I’ve never seen research on how auto-immune diseases interact with COVID or vaccination. It may be safe to assume for now that my auto-immune disease put me at greater risk from an immune system intensive disorder, but I don’t know for sure. While most of my COVID symptoms were indeed very mild, I was very surprised by the severity of my fatigue, which had multiple other negative effects. I sought medical attention twice, but they were never nearly as concerned as I was.
The “Final” Verdict on Antibody Dependent Enhancement: As most of you know, ADE has been a major concern of mine from almost the beginning. I’m finally willing to give an assessment of how ADE impacted the pandemic. There were a smattering of cases in previously infected people who may have had more severe cases because of possible ADE, but not more than a smattering. It’s also becoming well acknowledged that Omicron infected everyone regardless of vaccination status and may have even preferentially infected vaccinated people. I know MANY people who are double vaxxed and boosted who got Omicron.
All that being said, I never saw any evidence that conclusively suggested that ADE was causing more severe symptoms because of natural or vaccine mediated immunity. In fact, even during Omicron, during which ADE was most likely to be operating, those with previous immunity clearly fared better than those without. Because I think Omicron is the death rattle of the pandemic, I’m willing to say that ADE never became the threat I was concerned about. For this reason, IF I didn’t already have natural immunity because of Omicron, I might actually get vaccinated IF I could find someone who would aspirate before injecting!
I never saw any paper that dealt with the issue of ADE, not even a little. Those that mentioned it did so only in passing.
Don’t go looking for Omicron: Lastly, I’ll just say that while most of my friends had an undramatic time with Omicron, I did not. If you haven’t gotten Omicron yet, don’t go out looking for natural immunity from an Omicron infection. For me, it was no fun at all, and not worth the lost time and anxiety, even though I’m glad to now have hard earned natural immunity. The vaccines may not actually help you against Omicron infection, but they do seem to help you have an easier time of Omicron. Also, if you haven’t gotten Omicron yet, I recommend taking precautions and wearing an N95, KN95, or KF94 when in public.
Precautions against Delta are not adequate for Omicron, so kick it up another notch if you haven’t had Omicron yet.
After 12 days of symptoms, I still have COVID. My symptoms are considered mild, but I’m still tired, have no appetite, and am frequently feverish, so writing a long post is not my favorite activity right now. I also have a small amount of viral pneumonia, but not enough to be treated for. For an update, I’ll just state for now that cases are coming down rapidly in the US right now. I may add a real update to this post later.
Aspiration by vaccinators: I did want to point out that I saw a very interesting video recently from John Campbell that is very instructive. He points out that vaccines are intended to be given in an “intra-muscular” fashion, meaning the injection is supposed to remain in the muscle it’s injected into. If this happens, the vaccine makes Spike protein just in that localized area, and your immune system finds it there and mounts a response. Unfortunately, if a vaccine is injected into a blood vessel, the vaccine can travel throughout the body, making adverse events much more likely. For the flu, this is still not a big risk because the flu proteins only really interact with respiratory cells. But for COVID, the Spike protein can interact with cells all over the body and cause various effects including inflammation.
There is a simple way to avoid injecting in to blood vessels. A vaccinator can simply push the needle in, then pull the plunger back slightly to make sure there is no blood, then inject (Demonstration of this process starts at 22:00 of the video). This eliminates the possibility of a blood vessel injection. Unfortunately, this procedure is standard practice in just a few countries like Denmark, S. Korea, and Japan. Most countries including the US, UK, Canada, and many others do not practice this. John Campbell is very pro-vaccine, but wishes aspiration was standard.
My doctor friends tell me blood vessel vaccine injections are very rare.
In the US, lots of people in the health care industry basically ignored adverse events due to COVID vaccination. This includes me for a time. The CDC is still not capturing all of the available data on adverse events. Many of these events could have been avoided with a small change in policy.
Vaccination has helped a lot of folks have milder COVID symptoms. It’s too bad that the lessons from adverse events were not absorbed sooner. If you get vaccinated or get a booster, see if you can get them to aspirate before they inject!
The UK drops COVID restrictions: The Omicron wave has come and gone in the UK, and the country has basically dropped all COVID related restrictions. The US is a few weeks behind the UK, so we may be able to drop restrictions here soon too.
Omicron is milder, but I certainly haven’t had an easy time of it, so I wouldn’t recommend running out and getting your natural immunity by getting Omicron. If you haven’t had it yet, continue to wear your N95, KN95, or KF94 while indoors in public. Or even outdoors in groups. I probably got COVID outside but in close proximity to someone with COVID. The stuff that worked with previous versions doesn’t necessarily work with Omicron.
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.
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!
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.
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.
This is a case update. Cases continue be super high in the US. Over the past 2 years, the Sunday numbers are always the lowest of the week, but they also usually predict what will happen to the number in the following week. If you look closely at the case graph for the US, you can easily see the weekend dips in numbers. For this Sunday’s number, the rise in cases is much lower relative to the previous week than the number for the 26th. Because of this, I expect new case numbers in the US to peak this week or next.
All that being said, cases are still extremely high in every state in the US right now, and still rising. Only Washington DC appears to be seeing a drop in cases right now. Deaths have not yet started to increase in the US. Deaths have tended to increase between 2 and 5 weeks after the start of a peak, so it’s still too early to know how high they will be.
California and San Diego County are of course also experiencing extremely high numbers of cases right now. LA County again has the highest number of cases in the US, with a staggering 384,000 active cases right now.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
In Denmark, which has a lot of testing and virus surveillance, deaths are up but at a very moderate rate. At the peak of last year’s Winter surge, the COVID fatality rate was 0.94% (deaths/confirmed cases). For the Omicron wave in Denmark, the rate has been only 0.053%. This rate is very small, but it’s still not zero, so if you have COVID risk factors, continue to take precautions.
Omicron Update: The CDC recently released an update on variant proportions. Omicron is now 98% of SARS-2 cases for both the US and the Southwest region This is great news.
Omicron infections are proving to be very mild in most patients. That being said, there are a tremendous number of cases right now. I have lots of friends and family who have had COVID in the last 2 weeks, and several businesses near me have had closures or reduced hours because of under staffing. Additionally, hospitalizations are way up, and doctors and nurses are pretty exhausted taking care of all the sick people.
Managing COVID right now: Hospitalizations are way up, and lots of people are getting tested, either in a health care setting or with home rapid test a drug store. For this reason, tests are now in short supply everywhere. If you don’t need a test to go back to work or school, please consider NOT testing yourself just to satisfy your curiosity. If you do need to test yourself, please don’t test yourself every day, and try to reduce the number of tests you use. Since current tests are based on the Wuhan strain, there are lots of false negatives right now, especially with the rapid tests, since Omicron is the dominant strain. So a negative test is not very meaningful if you have symptoms. Most people’s Omicron symptoms last between 2 and 5 days.
Although Omicron causes less severe disease in general, there are a huge number of cases right now and some are still severe. If you don’t think you need medical attention, and are just experiencing cold-like symptoms, consider NOT going to the hospital for a test or to be treated. Please keep space open for those with more severe symptoms. However, if you have one of the classic COVID symptoms, like shortness of breath, don’t hesitate to check in with your doctor.Please don’t assume your vaccination, even with booster, will prevent you from getting COVID right now. Many fully vaccinated and boosted people are getting COVID right now because the Omicron variant is so different from the Wuhan strain used to make the vaccines.
Also, I still usually wear a mask indoors. If you choose to wear a mask, wear an N95, KN95, or KF94. Don’t imagine that a blue surgical mask, cloth mask, or neck gator is going to prevent infection. These masks are ineffective against Omicron. Effective medical grade masks are easily available at stores and online right now.
Remember to supplement with Vitamin C, Zinc, and especially Vitamin D! This is for everyone, to prepare your body should you get infected, or if you have Omicron right now.
Omicron scorecard: Here’s my “scorecard” for this week. The new data from South Africa suggests that Omicron infection is “back compatible” with Delta, preventing Delta infection. This is great news and suggests Omicron infection will prevent future infections from other variants. As a reminder, I am not an epidemiologist, I’m a molecular biologist. This is my informed but not expert opinion.
1) Omicron must not use the ADE pathway to produce more severe cases: Looking at the available data so far, Omicron may preferentially infect those who have been previously infected, but cases are still mild, and fatality rates very low. So for now, this criteria is met.
2) Low fatality in older populations: South Africa has a relatively young population, so reports of mild symptoms may not carry over to countries with older populations. The UK data from this week suggests that Omicron deaths will be low, even in older populations. We are seeing a slight drop in deaths already.
3) Displace Delta: Delta has a much higher case fatality rate in the US than Omicron appears to have. For Omicron to end the pandemic, it must displace Delta from the COVID population of strains. Data from the US and UK suggest this is happening!
4) Omicron must not circulate independently from Delta: Related to the above, if Omicron is very different from Delta, it may act as a completely different virus. There’s a chance that Omicron may displace Delta on the short term but still allow Delta to persist. Since Omicron is displacing Delta, it looks like this criteria may be met, but we won’t know for sure until we can see if Delta pops back up after the Omicron wave is over.
5) Omicron infection must immunize against future SARS-2: Since Omicron appears to infect those with immunity to Delta, it may be that it is different enough that it will not provide immunity to Delta or other SARS-2 strains. This criteria is not strictly necessary if Omicron completely displaces other SARS-2 strains (see 3 above), but it would be really nice to have some protection against future strains. We won’t know for sure about this one until a new version of COVID arises. The new data from Denmark suggests this criteria is met!
I believe that the Pandemic is almost over, but there’s one big final push! Continue use your head, but be encouraged!
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.
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.
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.
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.
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.
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!
This is case update. I also have a slightly disappointing and confusing update on Omicron.
The presence of Omicron is definitely appearing in the numbers for the US. After the Christmas weekend, case reports were unnaturally low because of the holiday, and certainly unnaturally high yesterday. That being said, there were a record number of new daily cases yesterday, mostly due to the Omicron variant (more on that later). Also, as has been seen in many countries, the daily number of deaths is actually starting to trend down. This is great news of course. It appears that the Omicron variant is resulting in a huge number of new cases, but fewer deaths. The incubation time for Omicron is just 2 days, so we will start to see an increase in cases due to holiday gatherings immediately.
New cases are particularly high in the Northeast. Cases are also increasing in urban areas throughout the country. Hospitalizations are currently trending down.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.Endcoronavirus County Level Map, December 27th, 2021Endcoronavirus County Level Map, December 27th, 2021Endcoronavirus State Level Map, December 28th, 2021Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format. Positive tests are way up over the last few weeks. The highest of these data points are actually outliers, being far above 30%. The very high number from last week was 234%. Very high numbers are produced in part by reporting practices and some of the positives are really spread over a longer time period.Hospitalizations due to COVID, CDC website.
In California, new cases are trending upward, and deaths are trending slightly downward.
It is great news that deaths are starting to come down, and I certainly hope this trend continues. But I don’t want to overstate the good news. With a huge number of new cases, we will see some increase in deaths, just not nearly as many as we saw with Delta.
Omicron Update: The CDC posted a disappointing piece of data late last night. They republished the bar graph on variant proportions, but numbers were re-accessed for the weeks ending on December 11th and 18th. Now, the percentage of cases due to Omicron for the weeks of the 11th and 18th were just 7% and 22%, instead of the more optimistic 12% and 73%. The percent of Omicron for this week was listed as 58%. According to the new numbers, we are still seeing a rapid growth in Omicron, just not as much.
The numbers changed since last week, so the obvious question is “were they wrong then or wrong now?” Data on this chart includes what they call “Nowcast” data for the past 2 weeks. This includes “data” from computer models guessing as to the real percentage. According to this, data from 3 weeks ago (ending on the 11th) would be “real” data, while data from the last 2 weeks includes computer estimates. Whenever you see computer modeling in a set of data, know that computers only know what they are told. If the algorithm doesn’t model well, or bad data is fed into it, you will get inaccurate results. So always take computer modeled data with a big grain of salt. Variant proportions are collected by sequencing a sampling of patient samples, and sequencing is much more labor and cost intensive than just detection, so this data is always a little late. Sampling errors may also effect the results.
Do you have Omicron?: A LOT of people I know had a respiratory illness over the last week. Including us! We both had sore throats over the last week. Usually, this is just allergies, and it may have been, but I was also lightheaded for an hour on Saturday, so I may have had Omicron. I’ve never been lightheaded from allergies. If I did have Omicron, the symptoms were VERY mild, like a mild cold. We both tested negative for COVID by PCR.
A friend of mine, also in the testing field, had Omicron this week, along with her whole family. She is very careful to wear a KN95 mask indoors in public, and everyone in the house was fully vaccinated. She even had loss of taste and smell, rare for Omicron. Most interestingly, she tested negative for several days, only testing positive after several days of symptoms. This presents the disturbing possibility that some of the tests do not detect Omicron, or at least they aren’t as sensitive for Omicron as they were from previous versions. Most of the tests do not detect the Spike protein, which is the most mutated SARS-2 gene, but other genes do have mutations. This likely has lead to the loss of sensitivity. Of course this means that we likely have many more cases of Omicron than we think.
Omicron Symptoms: Omicron causes basic cold-like symptoms, including runny nose, sore throat, fatigue, headache, and cough. It doesn’t not necessarily include a fever, and rarely causes loss of taste and smell, inflammation and blood clotting. Omicron may be mistaken for a cold or simple allergies. Many will not seek treatment for Omicron, so many infections will not enter into the medical system and appear as cases.
Symptoms appear after an incubation period of just 2 days for Omicron, as opposed to the 5-14 for previous versions.
Omicron scorecard: Here’s my “scorecard” for this week. Because of the data revision from the CDC this week, some of these items will be in question, but I’m going to leave the score card unchanged for now, since the case and death numbers are still encouraging. 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. We are seeing a slight drop in deaths already.
3) Displace Delta: Delta has a much higher case fatality rate in the US than Omicron appears to have. For Omicron to end the pandemic, it must displace Delta from the COVID population of strains. With the super high infectiousness of Omicron, it might just do that.
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.
doubloondiagnostic.com 