Category Archives: Omicron

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

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

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

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

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus County Level Map, December 15th, 2021
Endcoronavirus County Level Map, December 15th, 2021
Endcoronavirus State Level Map, December 15th, 2021

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

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

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

Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a linear format.

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

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

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

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

From Statens Serum Institut, part of Denmark public health.

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

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

From the CDC page on Variant Proportions.

Will Omicron be a blessing?: Several commentators like John Campbell, Chris Martenson, and Mobeen Syad are feeling optimistic that Omicron really may represent the end of the pandemic. Here’s what needs to be in place for this to be a reality, and how the data stands right now. As a reminder, I am not an epidemiologist, I’m a molecular biologist.  This is my informed but not expert opinion.

  1. Omicron must not use the ADE pathway to produce more severe cases:  Looking at the available data so far, while Omicron may preferentially infect those who have been previously infected, cases are still mild, and fatality rates very low. So for now, this criteria is met.
  2. Low fatality in older populations:  South Africa has a relatively young population, so reports of mild symptoms may not carry over to countries with older populations. At this point, it appears preliminarily in the UK that fatality rates are lower than with Delta, so I’m going to say this criteria is met with some caution.

    The next 3 are related, but not exactly the same.
  3. Displace Delta: Delta is currently the most common strain in the world, and almost 100% of COVID in the US right now.  Omicron must displace Delta as the dominant strain.  Binding of a more infectious SARS-2 strain to cells will prevent others from binding instead, so this criteria will likely be met.
  4. Omicron must not circulate independently from Delta: Related to the above, if Omicron is very different from Delta, it may act as a completely different virus.  There’s a chance that Omicron may displace Delta on the short term but still allow Delta to persist.  Right now, most guess that Omicron will not be independent from Delta, but we’re not sure yet.
  5. Omicron infection must immunize against future SARS-2:  Since Omicron appears to infect those with immunity to Delta, it may be that it is different enough that it will not provide immunity to Delta or other SARS-2 strains.  This criteria is not strictly necessary if Omicron completely displaces other SARS-2 strains (see 3 above), but it would be really nice to have some protection against future strains.
These are my criteria for whether Omicron is likely to end the pandemic. If all criteria are met, we may see a large reduction in COVID cases world wide in the coming months. I am not an epidemiologist, I am a molecular biologist. This is my informed but not expert opinion.

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

Don’t fear, but be smart,
Erik

Case Update, December 8th, 2021; Omicron may be more infectious for previously infected, Monoclonal antibodies

This is a case update. I’ll also discuss the first pre-print paper on Omicron, from a lab in South Africa.

Cases are rising in the US and cases in the Northeast are rising sharply at the moment. While the Omicron variant is now present in 19 states, most new cases are still from the Delta variant, and Omicron cases in the US are still very low.

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 6th, 2021
Endcoronavirus State Level Map, December 8th, 2021

California is still not showing an increase in cases due to the Winter season, although the persistent number of cases after the Delta wave is still quite high, almost as high as last Summer’s wave.

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

In San Diego County, last week had a surge in new cases. We’ll have to see if this is the beginning of a new wave, or just temporary.

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 causes increased co-infection: A pre-print paper has been released from a lab in South Africa, Pulliam et al. The paper looks at Omicron infections and also previous history with other SARS-2 variants. Since vaccination is relatively low in South Africa, the ability of vaccination to prevent infection by Omicron is not accessed.

The big take away from the paper is that while previous infection with a Wuhan strain prevented infection with Beta or Delta variants, it does not prevent infection with Omicron, at least according to this study! In fact, Omicron may be using the ADE pathway to reinfect patients, as risk of infection with Omicron appears to go up if a person has had a previous version.

The paper does not directly address whether vaccination will prevent infection with Omicron, but at this point, it seems unlikely. Unfortunately, the paper also does not discuss case severity in Omicron patients. A previous report from Dr Angelique Coetzee suggested that symptoms from Omicron are mild.

This data suggests that getting one of the current vaccinations will NOT help to prevent infection with Omicron. If you have not been vaccinated at this point, I suggest you NOT get vaccinated now, but instead take precautions until we find out how severe infection with Omicron will be. Of course, I am a molecular biologist, not a physician. Consult with your physician when making medical decisions.

From Pulliam et al, the new South Africa paper. Case numbers from the initial wave, and Beta, Delta and new Omicron waves are shown in figure 1A. The Omicron wave is on the far right and does not have a highlight color band. In figure 1C, reinfections are shown. Notice the reinfections are very high for Omicron in proportion to infection numbers.

If you’re interested, see this detailed analysis from John Campbell.

Monoclonal antibodies: Monoclonal antibodies are a common and effective treatment against SARS-2. They work similar to your own antibodies, but are often used early in disease before a person’s own immune system has yet been able to produce an immune response.

Medically useful antibodies can be obtained from a variety of sources, even purified from another person who has already had a disease. Monoclonal antibodies are made by first purifying immune B-cells from an infected animal or person, growing many copies of this cell in a lab, then purifying out the desired antibodies. These antibodies can then be injected into a patient to give them a boost in immune response.

And no, getting antibodies created from animal cells will not make you grow a tail or get beady little eyes.

If you get COVID, don’t hesitate to accept monoclonal antibodies if they are offered to you. They do not contain any vaccine components, nor do they involve any of the questionable ethical issues surrounding vaccines that are of concern to some.

Don’t fear, but be smart,
Erik

Case Update, December 1st, 2021; Vaccine against Omicron, Is COVID Endemic?

This is a case update. I’ll also briefly discuss the Omicron variant, the possibility of a vaccine against Omicron, and whether COVID is now endemic.

Cases in the US continue increase, with cases rising particularly in the Northeast, in states like New York, Pennsylvania, Vermont, and Michigan.

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, November 28th, 2021
Endcoronavirus State Level Map, December 1st, 2021

In California and San Diego County, cases are still stable, at a rate about as high as last Summer, but lower than the peak of Delta. Just hours ago, California Public Health and the CDC have announced that a patient with the Omicron variant has been detected in California. They had returned from South African on the 22nd, and the case was detected on the 29th.

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UPDATE: December 1st, 1:00 pm
Just hours ago, California Public Health and the CDC have announced that a patient with the Omicron variant has been detected in California. They had returned from South African on the 22nd, and the case was detected on the 29th.
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UPDATE: December 2nd, 2021
2 more cases of Omicron have been detected, in Minnesota and Colorado. The case in California and Colorado were in individuals who were fully vaccinated. All individuals have had mild symptoms so far.

Hours after reporting the above, another 5 cases of Omicron were reported in New York City. Suffice it to say, it’s now clear that Omicron is in the US and is already nation wide. I’m sure a lot more cases will be reported soon.

Most new cases of a new strain can only be reported after expensive and time consuming sequencing testing has been performed, so these results will come out more slowly than just a COVID detection.

I’m going to stop reporting individual new cases, since the point has been made that Omicron is in the US.
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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.

World wide, cases are climbing at the moment, with big increases in several European countries. Several countries have reported the detection of the Omicron variant, but so far only a few cases in each country are due to Omicron, so the big increase in cases may be due to Delta and the onset of Winter.

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

Vaccine against Omicron: So far, Delta is still the majority of cases world wide. Even in South Africa, only about 20% of the COVID cases are suspected to be due to the Omicron variant as of this writing. But because of the large number of mutations in the Omicron variant, scientists are concerned that the current batch of vaccines will not work against Omicron.

I saw an interview with Albert Bourla, the CEO of Pfizer. He stated that Pfizer could have a vaccine against Omicron ready for distribution in 100 days. Interestingly, Bourla also said in the interview that they had designed a vaccine against Delta, but they hadn’t released it because the original vaccine worked well against Delta. I was very discouraged by this comment. Many countries, including Israel, have been reporting that the vaccines have only been about 40-50% effective against Delta, and even the CDC admitted in July that 15% of COVID deaths have been in vaccinated individuals. I seems the me that the vaccines against the Wuhan strain have not worked well against Delta, and that vaccines against Delta should have been released. The comment seems to be evidence that Pfizer is not fully absorbing data on vaccine effectiveness from around the world.

Is COVID endemic?: I had hoped that once the vaccines came out, we would be able to generate enough immunity (natural and vaccine related) against COVID that it would go away. With 2 major variants that can evade the vaccine already out (Delta and Omicron), I’m becoming more convinced that COVID is indeed endemic at this point, meaning that it will continue to mutate, circulate, and be part of the fabric of life from here on out.

My personal strategy has been to avoid infection and vaccination until it all blows over. I’m becoming convinced that this will not work. So should I get vaccinated now? I’m concerned that Omicron might trigger the ADE pathway and cause worse symptoms for those with immunity to SARS-2. For this reason, I’m going to continue to keep myself SARS-2 free until more is known. Regardless of vaccination status, I encourage you to take some extra precautions until more is known about Omicron. Concern is good, panic is bad.

A glimmer of hope: As stated in Monday’s post, South African Doctor Angelique Coetzee has stated that her COVID patients have had very mild COVID symptoms. Her patients are mostly young people. If symptoms from Omicron are mild in older patients, and the new variant is very infectious, that there is a small chance that it will present a safe and effective way to provide immunity to lots of people. Of course, we will need to wait a few weeks to see.

Don’t fear, but be smart!
Erik

New Variant: Omicron

I hope you all had a wonderful Thanksgiving!

Unfortunately, I have some concerning news on the COVID front. The WHO has identified a new variant, currently called B.1.1.529. The variant likely first arose in South Africa, but has already spread to several countries in Southern Africa as well as at least Hong Kong and Israel. It has an estimated 32 mutations in the Spike protein alone. The new variant has been assigned the Greek letter Omicron (O).

Omicron is currently estimated to be 500% (6x) more infectious than Delta. For reference, Delta was just 60% more infectious than Alpha. Because of the many mutations in the Spike protein, the new variant may evade current vaccinations.

Since Omicron is so new, there isn’t yet information on fatality rate. Historically, new viruses in a group tend to be more infectious and less pathogenic (disease causing) than previous versions.

Most outlets will never talk about Antibody Dependent Enhancement, but a new variant with a very different Spike protein has the potential to trigger the ADE pathway. I might recommend that you take more precautions until more is known.

The President has suggested that anyone who hasn’t been vaccinated should do so now. I disagree. Because of the possibility of ADE, vaccination may even be worse for you than not being vaccinated. Until we know more, take additional precautions regardless of vaccination status.

My precautions are:
1) Wear an N95, KN95, or KF94 mask indoors in public. These masks are rated to filter out 95% of viral particles. In my opinion, surgical masks and especially neck gators are nearly worthless in these settings.
2) Keep 6 ft away from others. (I basically ignore this one if other precautions are in place, especially on an airplane!)
3) Avoid indoor gatherings, especially ones in which singing or shouting is likely.
4) Outdoor gatherings are fine, even without masks, if everyone maintains a distance. I have hosted several outdoor gatherings.
5) While many restaurants are open for limited indoor seating, I personally am still not comfortable eating indoors at a restaurant. I enjoy eating outdoors at restaurants, however.
6) I never take my mask off on the plane, and find an isolate spot in the airport to eat or drink on layovers.
7) If you find you can’t do any of the above, try to produce as much ventilation for yourself as possible. Sit next an an open window, choose larger rather than smaller indoor areas, or use a number 10 Honeywell air filter in your home or office. You can even make a virus filter out of a box fan and a number 10 filter.

Because Omicron is new, and may trigger the Antibody Dependent Enhancement pathway, vaccination may be either worthless or even detrimental. We’ll just have to see. Even vaccinated people should be more careful until we know more.

This story is early and evolving, and will let you know when I have substantial information to share.

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Updated November 29th, 2021:

There is a little more news about the Omicron Variant. South African Doctor Angelique Coetzee was the first Doctor to alert health care authorities about the new variant. She says that symptoms are more mild than for previous versions, causing severe fatigue for a new days, but no cough and no loss of smell and taste. She cautions that most of her patients are relatively young and healthy, so she can’t yet say how symptoms will be for older patients.

Worse or Better?: With a huge number of mutations (34 in the Spike protein alone) the Omicron variant has the potential to be much worse than previous versions, because it may trigger the Antibody Dependent Pathway and make infections worse for those who have already had COVID. It is also likely to at least partially elude vaccination, putting us back to square one in terms of vaccination efforts. Omicron is also 6x more infectious than Delta.

The Omicron variant has 53 mutations relative to the original Wuhan strain. 34 of these are in the Spike protein. Delta has only 9 mutations in the Spike protein. Photo is from the Stanford University Variants Genome Viewer.

On the other hand, there is currently a chance that Omicron may be a blessing in disguise. IF symptoms are truly mild, and the fatality rate from Omicron is very low, the variant may spread very quickly and infect large populations with a mild disease, giving them safe immunity.

So at this point, there is a broad range of potential outcomes. I know many of you are “over it” and are living life normally at this point. However, I urge some increased caution at this moment, until we know more about the new variant. It will probably take a few weeks before we know how things will go.

At this point, I do not recommend strict lockdowns as practiced last year. Last years lockdowns did not prevent the spread of SARS-2, and had many more negative impacts. I recommend instead protecting your self from infections by taking the precautions listed above.

The United States and several other governments have put restrictions in place for travel to South Africa. The South African government is complaining that they are being punished for being transparent about the virus. I have mixed thinking about this. South Africa is to be greatly commended for being open and sharing information about Omicron, unlike the Chinese government when this all started. However, I do think it is warranted to be cautious regarding travel. We should take a pause while we access the situation.

I predict, however, that as countries sequence virus detected in patients, they will soon discover that Omicron is already wide spread. It may already be too late for travel restrictions to have a big impact. The new variant has already been detected in Israel, Hong Kong, the UK, the Netherlands, Portugal, and many other European countries. Given the extreme contagiousness of the new variant, it is likely already wide spread.
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UPDATE: December 1st, 1:00 pm
Just hours ago, California Public Health and the CDC have announced that a patient with the Omicron variant has been detected in California. They had returned from South African on the 22nd, and the case was detected on the 29th.
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UPDATE: December 2nd, 2021
2 more cases of Omicron have been detected, in Minnesota and Colorado. The case in California and Colorado were in individuals who were fully vaccinated. All individuals so far have had mild symptoms.
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Don’t fear, but be smart,
Erik