Category Archives: Treatments

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 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 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

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 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.

_____________________________________
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.
_____________________________________
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.
_____________________________________

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

Case Update: November 23rd, 2021; Is Vaccine Effectiveness Going Down?

This is a case update.  I’ll also discuss data suggesting that the v@¢¢¡nes are having a mixed effect.

For the US, new case numbers have begun to creep back up.  Several states like Vermont, Minnesota, Colorado, and West Virginia are experiencing increased cases right now.  This is likely at least partly because colder weather is forcing more people inside. Several states are still enjoying decreasing case numbers after the Summer Delta wave, like Oregon, Washington, Alaska, and the Southern states.

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 21st, 2021
Endcoronavirus State Level Map, November 22nd, 2021

Last year’s Fall wave started in October, so it’s good news that a new wave may just be starting now, but keep in mind that new case numbers are just as high now as they were at the peak of last Summer’s wave.

In California and San Diego County, new case numbers are persistent, at around 5000 and 500 new daily cases respectively.  The higher persistent number likely reflects the higher infectiousness of the Delta variant.

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.

Internationally, several European countries like Germany, the Netherlands, Hungary, and Czechia are experiencing increasing numbers of cases right now.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
Daily new cases from Germany, November 23rd, 2021.
Daily new cases from the Netherlands, November 23rd, 2021.
Daily new cases from Czechia, November 23rd, 2021.

V@¢¢¡ne effectiveness:  A pile of new papers have come out regarding v@¢¢¡ne effectiveness.  A few weeks ago, I discussed Subramanian et al which claimed that v@¢¢¡nation rates are not correlated to case numbers internationally.  New papers from Britain, Germany, and even a story on msn.com are claiming that v@¢¢¡ne effectiveness is becoming reduced. 

The British paper states something I’ve suspected for a long time, that most SARS-2 transmission takes place in households, explaining why lockdowns are not an effective means of controlling COVID. They also claim that v@¢¢¡nation status is nearly irrelevant in a household setting, because of long term exposure to family members.

A Swedish paper (Nordström et al) suggested that v@¢¢¡ne effectiveness is reduced over time, especially for elderly men and those with co-morbidities. Effectiveness against severe symptoms begin to be reduced after about 9 months.

From Chris Martenson, using data from Nordström et al.

Disturbingly, some have suggested that v@¢¢¡nation is doing more harm than good.  A set of British data claims that v@¢¢¡nated individuals are dying at twice the rate of the unv@¢¢¡nated.

A German analysis of national data comparing German states is claiming similarly that excess mortality is actually due to v@¢¢¡nation.

Meanwhile, in the US, the CDC is claiming that v@¢¢¡nation greatly reduces the chances of hospitalization and death, although not to zero.  The agency currently claims that the unv@¢¢¡nated are 5.8 times more likely to become infected and 14 times more likely to die than v@¢¢¡nated individuals.

What are we to make of all this?  Is the v@¢¢¡ne really making people sicker?  Are things different in the US and Europe?  It’s hard to know right now.  We are in a period when v@¢¢¡ne effectiveness may be going down right now, so we may be getting mixed signals because we’re seeing this in real time.  The Delta variant is certainly exacerbating the issue, eluding antibodies developed against the Wuhan strain. We also have to consider that we may be seeing the effect of Antibody Dependent Enhancement (ADE), which may cause greater symptoms in those already infected with a related strain.

The present confusing situation is a great example of why it’s so crucial to accumulate as much data as we can, and to be as objective as possible about the results.  US agencies are still openly admitting that they have as a goal to promote vaccination (see slide 2),

From CDC powerpoint, July 29, 2021, slide 2. Red oval is mine.

and even to suppress information that works against this goal (see “Are adverse reactions …”). 

Screenshot from OSHA FAQ on vaccines. Accessed November 23rd, 2021

I cannot stress strenuously enough that if we work from incomplete or faulty data, we have no hope but to come to faulty conclusions and bad solutions.  If you have a hole in your gas tank, it doesn’t matter how much gas you put in it.  You will still have no gas.  You have to deal with the real problem first. 

The CDC has one and only one job.  To produce data and guidance on how to fight disease. But the very sad fact is that I don’t trust the CDC to produce truthful and/or complete data.  This is why we are relying on papers from foreign sources like Britain, Israel, and Japan to inform us on how to approach COVID.  With all the cases here, and 53 different approaches to the virus, we should have the best and most complete data set for figuring out what to do.  But politics continues to make this impossible. I hope this will change.

As discussed in the paper by Liu et al, boosters against the Wuhan strain will likely not offer long term protection against the Delta strain.  Instead, those who have been v@¢¢¡nated should get a v@¢¢¡ne against the Delta strain as soon as it is available.

Most people with severe symptoms are Vitamin D deficient. If you aren’t already, remember to be supplementing with Vitamin D, Vitamin C, and Zinc in order to reduce symptoms and viral load if you should be infected. Most Americans, especially those with darker skin, are Vitamin D deficient, since we spend so much time in doors. Alternatively, make your own by spending 30 minutes outside per day in shorts and a T-shirt!

Don’t fear, but be smart,
Erik

Indefinite stay on Vaccine Mandate issued by the 5th Circuit.

No COVID case update this week. Like last week, new cases are persistent in the US, California, and San Diego County. 

However, just wanted to note that the 5th circuit has placed a second stay on the OSHA vaccine mandate until further notice.  OSHA has suspended efforts to enforce the mandate. Text on the OSHA website reads:

“On November 12, 2021, the U.S. Court of Appeals for the Fifth Circuit granted a motion to stay OSHA’s COVID-19 Vaccination and Testing Emergency Temporary Standard, published on November 5, 2021 (86 Fed. Reg. 61402) (“ETS”). The court ordered that OSHA “take no steps to implement or enforce” the ETS “until further court order.” While OSHA remains confident in its authority to protect workers in emergencies, OSHA has suspended activities related to the implementation and enforcement of the ETS pending future developments in the litigation.”

Don’t fear, but be smart,
Erik

Case Update, November 5, 2021; Vaccine mandate details released, Should you get a booster, do vaccines cause new variants?

This is a case update. I’ll also talk about the newly release v@¢¢¡ne mandate from OSHA, whether you should get a booster, and the question of whether v@¢¢¡nes lead to new SARS variants.

New cases in the US, California, and San Diego County are all fluctuating right now.  It’s hard to say if this represents the beginning of a new wave.  Most of us are feeling like the pandemic is basically over, but I will point out that in the post-Delta trough, we still have as many new cases per day as we did at the peak of last Summer’s wave.  Minnesota, Colorado, New Mexico, and Arizona are all experiencing increases in cases 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, November 3rd, 2021
Endcoronavirus State Level Map, November 5th, 2021
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.

V@¢¢!ne mandate finally drops: In September, the President said he wanted government agencies to produce a mandate for v@¢¢¡nation.  Just this week, OSHA issued an Emergency Temporary Standard. This is official form of the v@¢¢¡ne mandate we’ve been waiting for.  The mandate conforms to the news you’ve heard, all employers with more than 100 employees must get v@¢¢¡nation status from all employees, and those who are not v@¢¢¡nated must be tested weekly.  The testing option means that the standard does NOT require that everyone be v@¢¢¡nated. Enforcement will begin January 4th, 2022.

Full length OSHA Emergency Temporary Standard.

As we saw last week, the CDC has known since July that a significant number of hospitalizations and deaths have occurred in fully v@¢¢¡nated individuals.  In addition to this, a recent Lancet paper from Singanayagam et al suggests that the transmission of Delta is less from v@¢¢inated individuals, but is still very significant. In light of this, I think all employees, regardless of v@¢¢¡nation status, should be tested regularly, although it would be impossible to test everyone every week. Ignoring the transmission threat from v@¢¢inated individuals is likely to lead to trouble. Everyone exposed to someone who tested positive for COVID should also be tested.

I saw a truly amazing thing on an OSHA FAQ page regarding v@¢¢ination. I checked it again just now to make sure it was still there.  Under the item “Are adverse reactions to the COVID-19 v@¢¢¡ne recordable on the OSHA recordkeeping log?” The answer reads:

DOL and OSHA, as well as other federal agencies, are working diligently to encourage COVID-19 vaccinations. OSHA does not wish to have any appearance of discouraging workers from receiving COVID-19 vaccination, and also does not wish to disincentivize employers’ vaccination efforts. As a result, OSHA will not enforce 29 CFR 1904’s recording requirements to require any employers to record worker side effects from COVID-19 vaccination at least through May 2022. We will reevaluate the agency’s position at that time to determine the best course of action moving forward.

In effect, an official government page is saying, we are asking you to ignore health information in order to get people to do what we want.  Some of you may be wondering why so many people are willing to ignore official calls to get v@¢¢¡nated, or are suspicious of government in general.  This is why. This also answers the question as to why it is so difficult to get clear information on adverse events. The government appears to have an official policy of ignoring these events.

Screenshot from OSHA FAQ on vaccines. November 5th, 2021

I’ll say again what I’ve said many times, I am not anti-v@¢¢¡ne.  I think many people with risk factors including age, obesity, respiratory or cardiac issues, those who work closely with the public, etc. should get v@¢¢¡nated. However, I am against a v@¢¢¡ne mandate.  I am not v@¢¢¡nated, mostly because of the ADE issue, and because I think I can avoid being infected.

I will also state what is obvious to many, but not to some that are making policy.  Lying or hiding information from the public will make people mistrust you.  You can sometimes force people to comply, but you cannot, even in principle, force people to trust you.  Trust must be earned. Once you lose it, it is very difficult to get back. 

This rule can be applied to any area of life.  Remember this if you’re a husband, wife, parent, child, pastor, politician, consultant, leader of a company, employee, or anything else where trust is required.  Trust is earned, and once broken, is very hard to get back. 

Should you get a booster?: Several people in the past few weeks have asked me if they should get a booster.  Right now, unfortunately, my best answer is “I don’t know”.  A booster may improve your immune response to the originally Wuhan strain of the SARS-2 virus, but the Spike protein from the v@¢¢¡ne is likely toxic on it’s own. In addition, the paper from Japan I wrote about some time ago suggests that another booster of the current variety is unlikely to provide complete protection against Delta.  Instead they recommend a Delta derived booster. 

Anyone who has had COVID or has been v@¢¢¡nated should get a Delta v@¢¢¡ne as soon as it is available to protect from any ADE related effects. Several companies are currently working on v@¢¢¡nes against Delta.

Does the v@¢¢¡ne create variants?: A nobel prize winning scientist is claiming that v@¢¢¡nation creates SARS variants.  I absolutely agree that v@¢¢¡nation creates selection pressures that can force viruses to gain new forms to avoid neutralization.  However, the very same can be said for natural immunity.  Both natural immunity and v@¢¢¡nation create selection pressures that can lead to new viral variants.  This is true of all viruses and other invading agents. In spite of this, our bodies are designed to use the immune system to fight off infection, and immunity has had a tremendous benefit, despite the selection pressure it poses. ADE is a rare exception to this rule. Our immune systems work much more quickly than viruses can adapt to them, which is why they are so effective at preventing infectious disease.

____________________________________
Updated November 23rd, 2021:

No COVID case update this week. Like last week, new cases are persistent in the US, California, and San Diego County. 

However, just wanted to note that the 5th circuit has placed a second stay on the OSHA vaccine mandate until further notice.  OSHA has suspended efforts to enforce the mandate. Text on the OSHA website reads:

“On November 12, 2021, the U.S. Court of Appeals for the Fifth Circuit granted a motion to stay OSHA’s COVID-19 Vaccination and Testing Emergency Temporary Standard, published on November 5, 2021 (86 Fed. Reg. 61402) (“ETS”). The court ordered that OSHA “take no steps to implement or enforce” the ETS “until further court order.” While OSHA remains confident in its authority to protect workers in emergencies, OSHA has suspended activities related to the implementation and enforcement of the ETS pending future developments in the litigation.”
_______________________________________

Don’t fear, but be smart!
Erik

Case update, October 25th, 2021; Vaccination vs Cases, Do Vaccine Mandates Exist?

This is a case update.  I’ll also discuss a new paper regarding v@¢¢!nation and new cases, as well as v@¢¢!ne mandates.

New cases for the US continue to go 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, October 23rd, 2021
Endcoronavirus State Level Map, October 25th, 2021

For California and San Diego County, however, there is a persistent higher case number, and the numbers for last week may even reflect a very slight increase in new 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.
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.

The very large wave from last Fall and Winter started in October.  We may be seeing the very beginnings of a Fall wave.  Hopefully our Summer Delta wave will have provided some extra immunity.

V@¢¢!nation and new cases:  A paper came out in September regarding the correlation between v@¢¢!nation rates and new cases.  The study compares data in 68 countries and 2947 US counties that had 2nd v@¢¢!ne doses available. 

The most interesting figure features a piece of data called a “linear regression”. This kind of data compares 2 variables and shows visually if they are related.  In the below hypothetical example, the 2 variables, the number of tests in a day and the number of confirmed cases in a day, shows a high correlation between these 2 things. Notice that the line plotting the relationship between data points goes from bottom left of top right as the values of each variable increase.

A linear regression plot with hypothetical data. Good correlation gives an R squared value between 0.95 and 1. If the variables are negatively correlated, the R squared value will be between -0.95 and -1.

The paper shows a linear regression plot with the percent of the population that is fully v@¢¢!nated on the x-axis, and the per capita confirmed case rate on the y-axis. If v@¢¢!nation strongly protects individuals from infection, new cases would go down as v@¢¢!nation went up.  In this case, the plot line would go from top left to bottom right (the green line).  Instead, it appears that there is little correlation between percent v@¢¢!nation and cases, producing the black line.

V@¢¢!nation vs cases produces black line, showing little correlation between the 2 variables. The green line was added by me and shows hypothetical data that would show strong correlation. From Subramanian et al.

They also have a box plot with US counties showing the new per capita case loads arising from counties with various levels of v@¢¢!nation. While counties with high v@¢¢¡nation rates do have fewer cases, the impact is not as profound as might be expected, and the difference between counties above 50% v@¢¢!nation rate is likely not statistically significant.

Box plots showing v@¢¢¡nation vs per capita cases in US counties. V@¢¢¡nation rates are groups in blocks for this view. Notice that very little difference exists between counties above 50%. From Subramanian et al.

It should be noted that this study was performed in September with data mostly from August.  This is during the Delta wave in the US and many Western countries.  The Delta variant may be different enough from the original Wuhan strain to enable the Delta virus to avoid neutralization by Wuhan induced immunization.

It has long been rumored that v@¢¢!nation does not prevent infection, and this paper seems to support this view. In spite of this, most scientists, including me, still hold that v@¢¢!nation does reduce the chance of hospitalization and death in infected patients.  This is still true.  However, a power point published by the CDC shows that this protection is diminishing as well.  In January, hospitalization and death among v@¢¢!nated individuals was essentially 0%, but now 9% of hospitalizations are among v@¢¢!nated people, and 15% of deaths.

From CDC powerpoint.

Why is this happening?  There are likely multiple factors. Certainly, the Delta variant is not the same virus as the Wuhan strain.  The different Spike protein makes it more infectious, and may not be recognized by an antibody against, the Wuhan strain.  It may even be triggering the Antibody Dependent Enhancement (ADE) pathway in some patients.  Also, it is becoming clear that v@¢¢!ne mediated immunity has been going down over time, necessitating a booster.  The paper from Liu et al argued that given the differences in Delta, a booster against Delta would be much more effective than another booster against the Wuhan strain.

V@¢¢!ne mandates: I still believe that v@¢¢!nation is a good choice for some with risk factors like age, obesity, diabetes, or respiratory problems.  However, I remain against v@¢¢!ne mandates because they do not take into account the medical history of individuals, the data that natural immunity is significantly better than v@¢¢!ne mediated immunity, and also the potential danger of ADE.  In addition to these scientific reasons, I have also felt an increasing orneriness on my own part.  Orneriness is not a good reason to make scientific or medical decisions, but policy makers should realize that it is a powerful reason for many.

For myself, I have chosen to not be v@¢¢!nated, but to remain careful to not be infected.  I continue to wear a mask indoors when there is poor ventilation. 

President Biden mandated v@¢¢!nation for federal agencies soon after taking office.  He announced in September that he would seek v@¢¢!nation mandates for private companies with more than 100 employees.  While many assume that a mandate for private companies is in effect now, as of this writing, no such mandate for private companies actually exists, either by law or by executive order. Companies that have enacted v@¢¢!ne mandates as of now have done so voluntarily.

________________________________________________
Update: November 5th, 2021

The official vaccine mandate was released on November 4th 2021 and is scheduled to be enforced starting on January 4th 2022. Details are on my November 5th post.
________________________________________________

Updated November 23rd, 2021:

No COVID case update this week. Like last week, new cases are persistent in the US, California, and San Diego County. 

However, just wanted to note that the 5th circuit has placed a second stay on the OSHA vaccine mandate until further notice.  OSHA has suspended efforts to enforce the mandate. Text on the OSHA website reads:

“On November 12, 2021, the U.S. Court of Appeals for the Fifth Circuit granted a motion to stay OSHA’s COVID-19 Vaccination and Testing Emergency Temporary Standard, published on November 5, 2021 (86 Fed. Reg. 61402) (“ETS”). The court ordered that OSHA “take no steps to implement or enforce” the ETS “until further court order.” While OSHA remains confident in its authority to protect workers in emergencies, OSHA has suspended activities related to the implementation and enforcement of the ETS pending future developments in the litigation.”
_______________________________________

Don’t fear, but be smart,
Erik

Case Update, September 13th, 2021; Israel data, Mu variant

This is a case update. I’ll also discuss a hack for poorly ventilated areas, the paper from Israel everyone is talking about, as well as the new variant, the Mu variant.

For the US, it definitely looks like we’ve cleared the peak for the US. Cases in many states have started to go down. States in which case numbers are still rising include Utah, West Virginia, Maine, and Pennsylvania. A word of caution is that COVID spreads indoors in poorly ventilated areas. Last Summer, we had large case loads in the South, and the winter had even larger case loads starting in the North. Both phenomena were probably caused by the virus spreading indoors, where there was air-conditioning and heating respectively. As Summer ends, we may end up seeing a large number of cases starting from the Northern states and spreading south, just like we did last Fall. If this happens, it will likely begin in October.

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, September 13th, 2021
Endcoronavirus State Level Map, September 13th, 2021

Cases continue to fall for California and San Diego County.

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

Indoor virus filter: I recently heard a podcast from physician Mike Osterholm (Osterholm Update, Episode 66). He argued that indoor ventilation was actually much more protective than masks. For those who can’t ventilate a space well, he suggested making a large scale air filter (Corsi box) using a box fan and a MERV 13 air filter. This is equivalent to a number 10 Honeywell furnace filter like you’d get at Home Depot. If you have a space where people gather that you can’t ventilate, buy a filter roughly the same size as your fan and tape it firmly to the front of the fan. Make sure the filter supports are toward the fan blades. On a side note, he also argues as I do that loose fitting masks are nearly worthless, but N95, KN95, and KF94 respirators are very good.

Data from Israel: Lots of folks are talking about the pre-print paper from Israel (Gazit et al) on vaccination vs natural immunity (infection by COVID). The data was from a database of patient information. They compared breakthrough infections (a person who was vaccinated and later was infected with Delta) to reinfection (a person who was infected with a previous SARS-2 variant and was then infected with Delta). They did this as a whole and also in a time matched way, meaning that the date of likely infection was around the same as the date of the 2nd dose of vaccine. Note that the vaccines are against the original Wuhan strain, so the paper is also discussing the rate at which Delta infects those who had natural vs vaccine exposure to non-Delta strains.

The results show that naturally infected people were almost 6 times less likely to get infected by Delta than vaccinated people, and 7 times less likely to have symptoms. The results are even more striking for the time matched data. For these patients, naturally infected people were 15 times less likely to get infected, and 27 times less likely to be symptomatic. Over all, it looks like natural immunity is better than vaccination for resistance to the Delta Variant.

Protection from Delta infection from vaccination and natural immunity. Protection from vaccination is arbitrarily given a value of 1, while other categories are shown in fold increased protection.

They did another study comparing natural immunity to natural immunity plus 1 dose of vaccine. Those previous infected with COVID AND having 1 dose of vaccine were about half as likely to be infected with Delta. Or you could say that having 1 dose of vaccine made them almost twice as resistant to reinfection.

Protection from Delta infection from vaccination and natural immunity. Protection from natural immunity is arbitrarily given a value of 1. Natural immunity plus 1 dose of vaccine gives 1.88 fold increased protection.

Some cautions are in order. Countries are not responding to the Delta Variant in exactly the same way. As discussed before, countries with large vaccination programs are seeing much fewer deaths due to Delta than other countries. However, rates of infection in vaccinated people by Delta seem to be higher in Israel, suggesting a slightly different version of Delta is in that country. Some reports suggest the Pfizer vaccine is only 39% effective against Delta in Israel.

The Mu Variant: News is only starting to circulate regarding the Mu variant (pronounced “mew”). First detected in Colombia in January 2021, this variant is currently classified as a Variant of Interest, not a Variant of Concern, suggesting it does not have characteristics that are very different from other versions, and may not have a large impact. A recent paper from Italy suggests that currently available vaccines do neutralize Mu, although with less efficiency. On the other hand, a WHO press release suggested that it may be able to escape immune responses raised to other variants. Since there is some disagreement, more studies will need to be done.

Don’t fear, but be smart!
Erik