Category Archives: All Articles

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

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

Cases in the US, California, and San Diego County are all still going down sharply. Cases are now at the same level as in mid-December. According to Endcoronavirus, most states have decreasing cases.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, February 14th, 2022
Endcoronavirus State Level Map, February 14th, 2022
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Hospitalizations, from the CDC website.

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

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

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

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

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

Don’t fear, but be smart,
Erik

Case Update, February 8th, 2022.

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

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

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, February 8th, 2022
Endcoronavirus State Level Map, February 8th, 2022
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

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

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

2) Have you been vaccinated? When?

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

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

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

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

Don’t fear, but be smart,
Erik

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

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

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

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, January 25th, 2022
Endcoronavirus State Level Map, January 29th, 2022
Endcoronavirus State Level Map, January 29th, 2022
Endcoronavirus State Level Map, January 29th, 2022
Endcoronavirus State Level Map, January 29th, 2022
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.

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

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

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

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

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

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

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

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

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

Don’t fear, but be smart,
Erik

Aspiration during Vaccination.

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

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

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

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

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

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

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

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

Don’t fear, but be smart,
Erik

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

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

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

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, January 17th, 2022
Endcoronavirus State Level Map, January 18th, 2022
Hospitalizations, from the CDC website.
Endcoronavirus State Level Map, January 18th, 2022
Endcoronavirus State Level Map, January 18th, 2022

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

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

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

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

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

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

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

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

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

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

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

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

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

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

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

Don’t fear, but be smart,
Erik

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

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

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, January 12th, 2022
Endcoronavirus State Level Map, January 12th, 2022

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

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

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

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

From Worldometer.
From Worldometer.

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

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

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

Hospitalizations, from the CDC website.

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

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

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

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

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

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

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

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

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

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

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

Don’t fear, but be smart!
Erik

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 28th, 2021; Omicron Update, Omicron Proportion Downgraded to 58%.

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, 2021
Endcoronavirus County Level Map, December 27th, 2021
Endcoronavirus State Level Map, December 28th, 2021
Graph 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.

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.

In San Diego County, new cases were extremely high Monday, almost reaching peak numbers from last years Fall/Winter wave.

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.

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.

From the CDC page on Variant Proportions. Accessed December 28th, 2021.
From the CDC page on Variant Proportions. Accessed December 28th, 2021.

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.

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

Omicron gives Delta an Atomic Wedgie!

“Omicron” may sound like a killer robot, but it turns out, it’s OUR killer robot!

You’ll have to forgive my imprecise language this evening, but we have some potentially VERY good news, and I’m a little giddy. Last week I reported that 3% of the COVID cases in the US were because of the super infectious but mild disease causing Omicron variant. On Monday afternoon, the CDC updated their numbers from last week stating that 12% of the COVID was from Omicron. Today, they are reporting that for this week ending Sunday, a full 73% percent of COVID cases were from the Omicron variant! With only a doubling of cases in the last few days, that means at least 50% of Delta variant cases have been displaced by Omicron cases. This means that Omicron is displacing Delta. At the current rate of expansion, by Christmas, at least 95% of COVID in the US will be from Omicron, and nearly 100% by New Years! If we can keep Delta suppressed for at least 2 weeks, it will be eradicated from the US. This is so great!

From the CDC page on Variant Proportions. Currently, 73% of COVID cases are from Omicron.
From the CDC page on Variant Proportions. Currently, 60% of COVID cases in the Southwest are from Omicron.
Daily new cases in New York State. Note the doubling of cases in the few days. But 90% of these cases are from Omicron, so Delta cases are roughly 25% of what they were a week ago, having been displaced by Omicron.

I have often been overly optimistic, but literally, if things go they way they’re going now, the Pandemic could virtually be over by New Years!

You know that cop at the beginning of all those movies who is about to retire and then gets killed in the first 10 minutes? Don’t be that guy. We’re almost out of the woods. Don’t go crazy and get COVID now. Keep it together for another few weeks, for crying out loud.

After I’ve settled down a but, I’ll be adding more information, links to my blog post, and a more sober assessment on this topic tomorrow, so check again then. For now, crack open a Diet Coke, in the seclusion of your own home or sensible outdoor gathering and celebrate!

Don’t fear, but party on… sensibly of course,
EPJ