Category Archives: Omicron

Case Update, August 12, 2022, Monkeypox Update.

This is a case update. I’ll also have an update on the Monkeypox epidemic.

Not much has changed in the last 2 and a half weeks. Cases are still at a moderate level, at least according to official case numbers in the US, California and San Diego County. However, deaths in all 3 regions are still relatively low. This situation has persisted since early May. Even the more dangerous BA.5 has not really produced a large increase in official cases.

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 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. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.

Most people are not getting tested in a medical setting right now, preferring to test themselves with over the counter antigen tests. As I posted a few weeks ago, these tests are producing a lot of false negatives right now, so many with COVID think they just have a cold. I believe I had COVID in mid July, but I tested negative twice, and never tested positive.

A better measure of case load is hospitalizations. In the US, hospitalizations likely peaked just a few weeks ago, and are now headed down. In San Diego County, hospitalizations likely peaked on around July 10th.

Hospitalizations, from the CDC website.
Hospitalizations in SD County, May 1st to July 30th, 2022. Gray area represents time-frame in which data is still being collected.

Right now, 89% if the COVID in the US is of the BA.5 variant. This variant is theoretically more dangerous than previous Omicron variants, but has not had a large impact, likely because of a lot of immunity in the population, either vaccine or naturally acquired. As for me, my case in January was much more severe than my case in July, despite my case in July being a more “dangerous” variant.

From the CDC page on Variant Proportions. Updated on August 13rd.

Most in the public are acting as if the pandemic is basically over. For the vast majority, there is really no longer a danger of severe disease or death. If you have not yet had COVID, you may still want to take precautions to prevent infection. Wear a medical respirator (N95, KN95, or KF94) when indoors in public.

Monkeypox Update: Despite being only moderately infectious, Monkeypox has continued to spread in many countries. There are now 11,000 confirmed cases in the US. The disease is similar to Smallpox, but is much less severe. It is spread primarily by skin to skin contact. With medical attention, Monkeypox is very rarely fatal, with currently only 3 fatalities in Europe. Monkeypox is endemic in central Africa, and occasionally produces outbreaks.

From the CDC website on Monkeypox cases, accessed August 12th, 2022.
From a UK government website on Monkeypox accessed August 12, 2022.

Monkeypox virus has been found on surfaces and in airborne droplets, so it is theoretically possible to contract it via these routes. However, there have been no confirmed cases of airborne transmission in the UK, according to a UK government document.

Some people living with infected persons have also contracted Monkeypox, so it appears that prolonged indirect contact can also spread this disease.

At the moment, 95.3% of cases in the UK are in a category called “men who have sex with men” (MSM), and this rate is likely similar in the US, but if cases continue to go up in the US, we will likely see more cases in the broader community. The good news is, new daily cases in the UK peaked in early July and are coming down now, so the US will likely start seeing a reduction in cases soon. Hopefully, the Monkeypox epidemic will be short lived.

A note on symptoms. Most of the public and even physicians assume that Monkeypox produces boils similar to smallpox or chickenpox. While it often does, it commonly seems to produce small rashes instead, leading to misdiagnosis. So if you or someone you know has small rashes, they should assume Monkeypox, isolate themselves, and seek medical attention. Smallpox vaccine appears to be effective against Monkeypox, so a vaccine is already available, but it is in short supply right now.

Monkeypox rashes, from Wall Street Journal video, Why Monkeypox is a Global Health Threat.

Don’t fear, but be smart,
Erik

Do the Antigen Tests Work for BA.5?

This post is about the over the counter Antigen tests that a lot of us have used in the last few months, and whether they really work.

As we’ve discussed, BA.5 is re-infecting lots of people, even those who’ve had Omicron just a few months ago. Those with recent cases generally have a mild case the second time around, even with BA.5

I just got back from summer camp with a bunch of high school students. I knew I could get COVID again, but since I had Omicron in January, I figured I’d be OK, even if I got BA.5. One of our counselors got sick while we were there, and tested negative for COVID, with an antigen test. I got sick on Sunday morning, after we were back, and also tested negative for COVID using an antigen test. On Sunday I just had a sore throat, Monday and Tuesday morning I had fatigue, sore throat, and just a little coughing. My sore throat felt very similar to the one I had in January, kind of like a weird heart burn, so I tested myself again on Monday. Still negative.

Meanwhile, the other counselor tested negative again when he got home, but then tested positive after that. His wife too. So he had 2 negative tests before testing positive.

So did I have COVID again? I still don’t know. I’m at the “just getting over a cold” stage right now and am feeling pretty normal. I had 2 negative tests and I’m not going to test myself again.

Doing a good scientific study is a slow process, and we’re probably unlikely to get good scientific articles on how well the antigen tests work for every new variant. The only articles I could find on BA.5 and antigen tests were from Slate and CNET. I usually don’t bother to read popular level articles on COVID since journalists often get things wrong, but that’s all we have. Both basically say that yes, they work, but you may need to take several tests. Well, that’s kind of like saying they don’t work very well.

How Antigen tests work: There are 2 kinds of tests that use antibodies for testing. One is an Antibody test. This kind of test looks for human antibodies against SARS-2 proteins. It actually determines whether you’ve been infected at some point in the past. IgM antibodies appear after a few days and persist for about a week. IgG antibodies appear after about a week and persist for weeks or months. So a positive SARS IgM tests says you basically have COVID right now, while a positive IgG test you have it now, or had it weeks or months ago. An IgG test is not useful if you want to know if you have COVID now.

An Antigen test detects actual SARS-2 proteins. They usually detect the Nucleocapsid protein (N), a protein on the inside of the virus which does not mutate rapidly. In theory, these tests should work well even if the Spike protein changes, which is by far the most common changes in new variants. They are not usually thoroughly tested with each new variant.

The Slate article suggests the tests may not be working as well because the BA.5 variant may not be as present in the nostrils as previous variants. Scientists know that a Nasopharyngeal (back of the nose/throat) site is better, but patients far prefer a nostril test. So this may be why the tests are not working as well for BA.5.

Antigen tests are less sensitive than a PCR test, but they are far cheaper, faster, and easier to use, which is why they are so common now. If you really need to know if you have COVID, a PCR test is the way to go. I frankly am pretty disappointed that a clearly symptomatic person can test negative for COVID right now with an Antigen test.

All this to say, if you have cold-like symptoms in the next few weeks, you’re better off staying at home and laying low for a few days, even if you have a negative Antigen test. You may actually have COVID.

Happily, if I indeed have COVID now, it’s a very mild case.

Don’t fear, but be smart,
Erik

Case Update: July 26th, 2022; Cause found for hepatitis in children.

This is a COVID update. I’ll also briefly discuss a mystery from a few months ago, a hepatitis in children of unknown cause.

It’s been almost 3 weeks since my last post. Since then, we’ve seen remarkably little change in either infections or deaths in the US, California, or 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 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. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.

Some scientists now argue that since so many who are newly infected test themselves with over the counter tests, hospitalization is really the new measure of how much COVID is in the population. In the US, BA.5 has caused hospital admissions to go from about 4000 to about 6000 per day.

Hospitalizations, from the CDC website.

BA.5 is more dangerous than previous Omicron versions because it replicates down deep in the lungs like the original Wuhan strain, Alpha, Beta, and Delta strains. Most Omicron strains were less dangerous because they replicate in the trachea, thus can’t cause pneumonia. BA.5 is now 80% of new infections in the US.

From the CDC page on Variant Proportions. Updated on July 23rd.

John Campbell has an interesting new video out about BA.5. He argues that while BA.5 reinfect those with previous infections, even Omicron, natural immunity does give substantial protection. Dr. Campbell is from the UK, so much of his data comes from the National Health Service, which as been doing a better job at publishing data than the CDC.

Campbell discussed a paper from Altarawneh et al that claims that only 15% of Britons have no previous infections. 55% of new BA.5 cases come from this 15%. That means that 45% of new BA.5 cases come form the other 85% of people who have no previous infections.

After doing all the math, the authors suggest that infection with a pre-Omicron variant is 28% effective at preventing infection with BA.5, and infection with a previous Omicron version was 79.7% effective against reinfection with BA.5. All this to say, if you’ve had COVID before, you are less likely to get BA.5, and will likely have less symptoms as well.

Hepatitis of unknown origin in children: A strange story came out earlier this year about dozens of children in a variety of countries that presented with hepatitis, or inflammation of the liver. The suddenness of onset and also the global nature suggested a widespread infectious disease. There was no correlation in cases with COVID or COVID vaccination. In some children, adenovirus was found. 18 children have died world wide from this hepatitis.

Adenovirus is a very, very common virus in humans. It’s so common in fact, that most of us catch when we are very young, and have no symptoms, which is why we don’t hear about it much. Some adenovirus infections can look like a common cold. Adenovirus does not cause hepatitis.

However, doctors recently discovered that all of the children tested were positive for an unusual virus called Adeno-associated virus-2. This weird virus can only replicate in a human that is already infected with an adenovirus. So this is an unusual case in which 2 simultaneous infections are required to cause disease. AAV2 appears to be the actual cause of hepatitis in children.

At this point, researchers believe that the lack of exposure to common pathogens during the lockdowns has lead to the result that many children do not have immunity to common viruses that they usually do. AAV2 hepatitis does not happen in adults because they already have immunity to Adenoviruses.

So what should you do if you have small children? Well at first, in my opinion, allowing a normal social schedule is likely a good idea at this point. Death rates from COVID are still low and have not really increased due to BA.5, so the risk to others is likely low. You may want to limit their contact those who are at high risk for COVID.

Also, if your child experiences any of the following, especially in combination, seek medical attention immediately, at least a phone call to your doctor:

Nausea
Abdominal pain
Vomiting
Diarrhea
Jaundice (yellowing of the skin)

Don’t fear, but be smart,
Erik

Case Update: July 6th, 2022; BA.5 may be more dangerous than previous versions, and escapes immunity from Omicron infections

This is a case update. I’ll also discuss important new data in regards to BA.4 and BA.5 variants which you may want to take into account as you move around in our “post-COVID” world. You should especially read this if you’re one of the few who have never had COVID. I’ll also suggest a range of strategies that you may employ to keep yourself safe.

The update is actually not much different in the US from last week. Cases are medium-high but flat right now, and we have happily not yet seen increased deaths due to Omicron BA.2.12.1, BA.4, and BA.5 variants.

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.
Endcoronavirus County Level Map, July 6th, 2022
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. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

BA.4 and BA.5 now predominate in the US, being 17% and 54% of cases respectively. Together, they are 70% of new cases. Hospitalizations are up slightly, but not nearly so high as in January, at the height of the Omicron wave.

From the CDC page on Variant Proportions. Updated on July 2nd.
Hospitalizations, from the CDC website.

Keep in mind that many and perhaps most people who have COVID right now are not getting tested by a health care provider, and are not being treated, so they are not a “case” and do not appear in current statistics. While it’s great news that we haven’t yet seen increased deaths in the US, there is sobering news which may cause a change in this in the next few weeks.

BA.5 reinfecting Omicron patients: A few weeks ago, an urgent care doctor friend of mine said that he had seen some patients who have had Omicron twice. Just this week, some friends of mine who had Omicron in January, just like me, came down with it again. They have COVID right now. Like me, they were pretty miserable in January for a full 2 weeks. Happily, their symptoms are moderate now, like a bad cold, just for 2 or 3 days.

Just yesterday, John Campbell released a video regarding BA.4 and BA.5. While he has a pretty bland delivery and focuses on the UK, he’s honest, balanced, and one of the only pundits still covering COVID in any detail.

Dr. Campbell’s newest video has some sobering information about BA.4 and BA.5 variants. As you can see from the data above, BA.5 is more infectious than BA.2 and BA.4, and will probably become dominant in the US in the next few weeks.

While still being called an Omicron variant, I wouldn’t be surprised if BA.5 gets it’s own Greek letter. Maybe Pi or Rho.

Unfortunately, Dr. Campbell claims that BA.5 is different enough from earlier Omicrons that they do not provide robust protection against BA.5 infection. He says Omicron is “poorly immunogenic”, but later clarifies in the video that this is likely because SARS-2 variants are changing very rapidly right now. The current COVID vaccines are having little impact, and the virus is changing so rapidly that updated vaccines are not practical to produce, meaning that the age of COVID vaccines is really already over.

For some good news, reinfections are usually milder than previous cases. So if you’ve already had COVID, BA.5 is likely nothing to be worried about.

Portugal had a lot of BA.4 and BA.5 in May and June, and they experienced more hospitalizations and deaths. Some worry that BA.5 may produce more severe cases in “naive” people, those with neither natural nor vaccine mediated immunity. Drs. Kei Sato and Stephen Griffin claim that BA.5 is growing deep in the lungs, like pre-Omicron versions, which makes it more likely to produce pneumonia. Most Omicron variants grow primarily in the trachea, which is why they are less likely to produce severe disease.

Last, Dr. Campbell argues from a letter by Hachmann et al, that prior infection plus vaccination offers better protection than either alone, but that BA.5 is still escaping neutralization. In my personal view, vaccination carries risks of it’s own, so if you are still not vaccinated, I would suggest taking increased precautions rather than vaccination at this point.

Cases in the UK are rising quickly right now, and often is a few weeks ahead of the US in any recent COVID trend. If data from Portugal and the UK hold true in the US, we may expect increasing cases in the US and perhaps more deaths as well.

Viruses have a tendency to become more infectious and less pathogenic over time. While this has been shown to be true many times in the last century, this is only a tendency and does not always hold true. While BA.5 is more infectious than previous versions, it’s tendency to grow in the lungs may make it more dangerous, so BA.5 is bucking the trend.

Strategies: Of course, it can be very hard to predict what will happen next. We also have a lot of different COVID experiences in the US in terms of whether someone has had COVID, what variant they had, whether they were vaccinated, etc. So any suggestions I make may not pertain to you.

Since I had COVID in January, I’ve been behaving in public as if I’m totally protected against a new infection. This may have been warranted, since I haven’t been infected again. I’ve even visited people with COVID at their house, treating it as an opportunity for a free booster. But this new information gives me pause. I may be more vulnerable to BA.5 than I had hoped.

On the other hand, even BA.5 is mild in those with previous infections, so I will likely be OK if I get BA.5. I am still not vaccinated and don’t intend to be. So going forward, I am going to continue to behave as normal, without masking in public at this point.

My main reason for being so careful before I got infected was the Antibody Dependent Enhancement (ADE) issue. Now that I’ve been infected, it’s not useful for me to continue with my previous caution. In fact, the “free booster” method may now help me with future versions more than avoiding infection would.

If you have never had COVID, you may choose to take increased precautions to prevent infection. Wear an N95, KN95, or KF94 mask when indoors in public. Don’t wear a cloth or blue surgical mask. These masks will not protect you from BA.5. Vaccination alone is not likely to be of much protection from BA.5.

If you do end up being infected with BA.5, regardless of the severity of your symptoms, stay home until you’re COVID negative to protect those around you who may be vulnerable.

Will COVID be endemic? A client of mine was kind enough to recommend my posts to his board, saying that my COVID predictions always come true! I would love this to be that case, but I can’t claim that kind of record. I have certainly been wrong during the pandemic. In particular, I’ve said that Omicron will end the pandemic, and that it will won’t likely have a new dangerous variant. BA.5 may end up proving me wrong on both counts. The lightning speed that new variants are developing also challenges my previous statements. I can’t claim to always be right, but I will tell you as soon as possible if I’ve been wrong.

So will COVID last forever? In spite of BA.5, I still say no. While it has exceptions, the tendency for new viruses to be less pathogenic still holds true. I still expect new variants to generally be less dangerous than older ones. In fact, BA.5 will likely still have less impact than previous versions simply because so may people have previous infections.

Don’t fear, but be smart,

Erik

Fauci’s time with COVID and Paxlovid

This is a post about Tony Fauci’s time with COVID and the drug Paxlovid, which I have discussed in the past.

On June 15th, a story came out about Tony Fauci having contracted COVID, despite having been fully vaccinated and boosted. I didn’t cover this before since I’d already discussed the fact that the vaccines don’t prevent infection by Omicron variants.

However, something else very interesting happened. Dr. Fauci took Paxlovid, which I’ve discussed briefly before, and became COVID negative. But after his 5 day course, he became positive again with worse symptoms. This means that a standard 5 day course of Paxlovid will not necessarily reduce your viral load to zero, and patients may experience “Paxlovid rebound”. Fauci even claims that this kind of rebound with Paxlovid is starting to be seen as “typical” as more patients use it.

The CDC actually issued a warning about Paxlovid Rebound in May, but it was not widely reported.

With so many rebound cases, it’s likely that 5 days is not adequate to eliminate all viruses from the system, allowing rebound. However, Paxlovid does have side-effects, so don’t take it for more than 5 days without consulting your doctor! Hospitals are now only prescribing Paxlovid to high risk patients.

Whenever taking anti-viral or anti-bacterial medications, always take the full course of treatment. If any virus or bacteria survive treatment, they may give rise to a more resistant strain. Don’t just stop your treatment when you feel better. I take anti-biotics as a last report, but when I do, I take the full course. I even made a doctor give me the full 10 day course when she just wanted to give me a half course!

Just to repeat the point on the vaccines, I still hear ads on the radio encouraging vaccination. At this point, the vaccines are really not doing anything against the current COVID variants. There is really no benefit to getting a vaccine or a booster. If you haven’t had COVID yet, I would simply recommend preventative measures. Wear an N95, KN95, or KF94 mask when indoors in public. Cloth and surgical masks will not prevent infection.

Don’t fear, but be smart!
Erik

Kim Iversen’s more in-depth discussion of Dr. Fauci’s rebound.

Case Update, June 28th, 2022

This is a brief COVID update. Cases have been flat in the US, California, and San Diego County, neither rising or falling. This may be partially because of the introduction of 2 new variants, BA.4 and BA.5. These new variants are both of the Omicron vintage. The good news is that deaths have not risen for many weeks even after cases rose due to the BA.2 variants.

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.
Endcoronavirus County Level Map, June 28th, 2022
Hospitalizations, from the CDC website.
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. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

My guess is that BA.4 and BA.5 will continue to drive new cases for a few more weeks before we start seeing cases come down. It appears that the fatality rate for these new variants is also very low when compared to other COVID variants.

The contribution BA.4 and BA.5 variants in the US is growing, as they new represent approximately 50% of the total SARS-2 viruses in the country.

From the CDC page on Variant Proportions. Updated on June 30th.

Don’t fear, but be smart,
Erik

COVID Update, June 14, 2022; BA.4 and BA.5 Emerge in the US.

This is a COVID update, and I’ll discuss the emergence of BA.4 and BA.5 in the US.

New daily cases have peaked in the US, California, and San Diego. We have yet to see a sustained increase in deaths due to the new BA.2 variant in any of these regions. While new cases have not really started to decrease, the numbers have definitely peaked.

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.
Endcoronavirus County Level Map, June 14th, 2022
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. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

BA.4 and BA.5 in the US: I commented on May 24th about the new BA.4 and BA.5 variants. At that time, the CDC was not reporting these variants in the US. The new CDC bar graph of variants now shows that approximately 20% of the SARS-2 virus in the US now from BA.4 and BA.5.

From the CDC page on Variant Proportions. Note that when I posted on June 3rd, the CDC did not report BA.4 and BA.5 in the US.

Will we have another peak? Maybe. These variants may have arisen in South Africa, and the BA.4 and BA.5 peak has already come and gone there. The peak was much smaller than the original Omicron peak, and generated even fewer deaths. South Africa did not experience a BA.2 wave of Omicron cases.

From Worldometer. The wave starting in December 2021 is the B.1 Omicron wave, the wave starting in April 2022 is the BA.4/BA.5 wave.
From Worldometer. The wave starting in December 2021 is the B.1 Omicron wave, the wave starting in April 2022 is the BA.4/BA.5 wave.

These new variants appear to follow the tendency for new viruses to be more infectious and less pathogenic (disease causing) than earlier ones. So we may see a shoulder to our current peak, but we won’t likely see significantly more deaths. Obviously, I’m using “significantly” in a cold, statistical sense here.

A negative trait of the BA.4 and BA.5 are that they are even less responsive to vaccination than previous Omicron variants. So vaccination is not likely to help much against infection. Reinfection after previous infections with Delta and earlier versions appears to be more likely.

I haven’t seen much in our popular media about these new variants. The only commentator who has discussed these new variants significantly is John Campbell.

If SARS-2 continues to become more infectious and less pathogenic, it may become part of the background, like a cold. I still don’t think it will last forever. I think it will eventually burn itself out.

A note on BA.2: The BA.2 variant is significantly different from the BA.1 variants. Some scientists are now saying that the BA.2 variants should not have been considered an Omicron variant, and should have gotten their own Greek letter designation. The next letter is Pi. Maybe they would have skipped this one to avoid confusion at Marie Calendars!

“No, I would not like some Pi.”

Don’t fear, but be smart,
Erik

COVID Update: June 3rd, 2022

This is a COVID update. I’ve been posting only every 2 weeks for a while, but this has been an interesting week, so I’m posting a little early.

New case numbers for the US, California, and San Diego County show that the second Omicron wave, I’ll call it the BA.2 wave, has peaked, and numbers are now dropping sharply.

For some reason, my numbers are a little erratic for the last week for the US. This is likely because of irregular reporting by places that Johns Hopkins gets information from, so I’ll also show the US data from Worldometer.

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.
From Worldometer, Daily New Cases, United States.
From Worldometer, Daily New Cases, United States.
Endcoronavirus County Level Map, June 2nd, 2022
Endcoronavirus State Level Map, June 3rd, 2022
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. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
From the CDC page on Variant Proportions.
Hospitalizations, from the CDC website.

Anyway, new case numbers for all three regions are coming down now, and deaths have still not started to come up, despite us being 6 weeks into the BA.2 peak. John Campbell has also pointed out that new deaths have not tracked with new cases, so the BA.2 Omicrons seems to be less pathogenic than previous versions.

And yes, since cases are less severe and over-the-counter testing is available, infections are likely much higher than official reporting suggests.

Still not quite over: Since I had Omicron in January, and current strains are still in the Omicron family, I am not concerned about getting COVID again right now. So the Pandemic is essentially over for me, but people are still getting COVID.

I was with a buddy this week who was very fatigued and miserable, just like I was, but he didn’t have any life threatening symptoms, just like me. So just a word of encouragement for those who have COVID now or will get it in the coming weeks. You can be really miserable and not be dying! You generally only need to go to the hospital if your blood oxygen is low. Different sources have a different definition of “low”, some say below 90 and some say below 95. Feel free to chime in on this if you’re a health care worker! Get yourself a high quality pulse oximeter so you can reassure yourself if your oxygen is normal! Some medical networks also have a messaging system where you can ask your doctor COVID questions without going in.

Also, if you haven’t had COVID recently, supplement with Vitamin C, Vitamin D, and Zinc. A physician friend of mine says he has had patients who’ve had both Delta and Omicron, so “recently” means since December.

Don’t fear, but be smart!
Erik

_________________________
June 5th, 2022
Post Script:
Mark Foreman sent me a paper he found describing 47 cases in Denmark in which people who had been infected with Omicron BA.1 were also infected with BA.2 just a few months later. The cases were all in young, unvaccinated people who had had mild symptoms from their BA.1 infections.

Since BA.1 and BA.2 are so similar, I find this a little baffling, but my being baffled doesn’t discount the data. The data must speak for itself. One possibility suggested by the mild symptoms is that the patients had a low dose exposure to BA.1, so had mild symptoms, and perhaps only mounted a medium immune response to BA.1, allowing infection by BA.2. This is just a guess of course.

In all cases, the BA.2 infections in this group produced mild symptoms.

A very interesting paper that will perhaps give more insight into how our immune systems interact with this disease!

Case Update, May 24th, 2022; Omicron variants BA.4 and BA.5, Monkeypox, and Hepatitis in Children of Unknown Cause

This is a case update.  I’ll also talk briefly about new Omicron variants, BA.4 and BA.5, and also the new Monkeypox virus, and several cases of hepatitis in children.

New confirmed cases are still increasing due to the new Omicron BA.2 and BA.2.12.1 variants, which are now nearly 100% of cases in the US.  Hospitalizations are also up in the US.  However, new daily deaths are still not rising in the US or California, with only a temporary blip in San Diego County.  I have often cautioned that deaths trail cases by 2-5 weeks, but for the first Omicron wave in December and January, deaths trailed cases by just 1 week. Since we still aren’t seeing an increase in deaths after 6 weeks, this suggests that the BA.2 variants are not as deadly as even the BA.1 Omicron variants.

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.
Hospitalizations, from the CDC website.
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. Graph is presented in a logarithmic format to emphasize small numbers. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. San Diego County now only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

I’ll also point out that I continue to have friends who are getting COVID right now, meaning they are getting one of the BA.2 variants.  While some feel bad, none are going to the hospital, and none are becoming a “confirmed case” by getting tested in a medical setting.  If this is true on large scale, then we have lots of infections, maybe even most of them, that are not showing up in the “confirmed case” data.

BA.4 and BA.5:  I’ve heard some news about some more new Omicron variants BA.4 and BA.5.  So far, these variants have not come to the US and have not had a large impact on the pandemic.

Monkeypox virus:  There have been several clusters of Monkeypox cases in Europe, and just a few cases in Canada and the US, about 120 cases in total.  Monkeypox is a pox virus similar to Smallpox.  It is much less much deadly than Smallpox, but can cause death.  It is endemic (widespread and likely permanent) in Africa but does not usually cause serious outbreaks in non-African countries.  It is only moderately infectious, spread by contact and also by respiratory droplets.  It is not spread in aerosol form. Asymptomatic people do not generally transmit the disease.

Those vaccinated against smallpox will still have some immunity against monkeypox.  Pox viruses do not mutate quickly.

All this to say, most infectious disease experts do NOT think that Monkeypox poses a serious health risk to most people, and that it does NOT pose a potential pandemic risk.  Why am I covering this then? Because it’s in the news, and I wanted to clear up any anxiety about the virus.  It will mostly likely not become a big issue in the US.

As a side note, I do NOT intend to cover new infectious diseases forever when the pandemic is over, but may occasionally cover items of special concern.

Mystery hepatitis in children: The suffix “-itis” refers to swelling or inflammation in the body.  The term “hepatitis” refers to swelling or inflammation of the liver.  There are several Hepatitis viruses, (A, B, C, D, and E) but these viruses are not related to each other, and having hepatitis does not necessarily mean that you have one of these viruses.  It can be caused by other things.

A few weeks ago, hundreds of children in countries all over the world had sudden onset hepatitis.  So far, 11 children have died and medical care was necessary for many, including liver transplants.  None of the children had an infection of a Hepatitis virus.

Testing showed that many but not all patients were infected with an Adenovirus upon examination.  Adenovirus infections are very common, and usually have no symptoms, so are often not addressed medically.  Some adenoviruses can cause common cold like symptoms.

So far, 20 individuals tested have had a history of COVID infection, and most individuals were NOT vaccinated against COVID, so at this point, a connection to COVID or a COVID vaccine seems unlikely.

All this to say, the cause of these cases is still unknown, but many in the medical community are currently speculating that they are related to Adenovirus type 41.  At this point, there is no reason for general concern about hepatitis in children, but I will certainly let you know if this changes.

If you or your child experience any of the following, especially in combination, seek medical attention immediately, at least a phone call to your doctor:

Nausea
Abdominal pain
Vomiting
Diarrhea
Jaundice (yellowing of the skin)

Don’t fear, but be smart,
Erik

Case Update, May 6th, 2022; Yet Another Omicron Sub-Variant, New Drug Paxlovid.

This is a case update.  I’ll also give an update on new Omicron variants and briefly discuss a new anti-Coronavirus drug, Paxlovid.

In the US, cases continue to increase modestly, and may have peaked.  This increase in cases are likely due to Omicron sub-variants BA.2 and BA.2.12.1 (more on these later). However, new deaths are still decreasing.  I will caution that a rise in new deaths often trails new cases by 2-5 weeks. For the first Omicron wave, deaths followed cases by 2 weeks, and we are currently 4 weeks in to the BA.2 wave.

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, May 6th, 2022
Endcoronavirus State Level Map, May 6th, 2022

In California and San Diego County, cases are up modestly.  Again, new deaths have not yet begun to rise.

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. Graph is presented in a logarithmic format to emphasize small numbers. Starting on May 2nd, 2022, San Diego County only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from San Diego County Public Health. Graph is presented in a linear format. Starting on May 2nd, 2022, San Diego County only releases information Monday and Thursday each week. Data points shown are extrapolated using this information.
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

New Omicron sub-variants, BA.2 and BA.2.12.1: BA.2 has been well known for a few weeks.  I’ve stated before that BA.2 is very similar to the first Omicron variants, and predicted that it will not have a large impact.  A new variant BA.2.12.1 likely falls into the same category.  These variants now dominate the current cases with 98% of new cases being due to one of these variants. 

From the CDC page on Variant Proportions. Accessed May 6th, 2022.

These variants are more infectious than the first Omicron sub-variants, but it is still unknown if they are more or less pathogenic.  Viruses tend to become more infectious and less pathogenic over time.

Some Eastern states like New York were the first to see modest new waves due to BA.2.  New York has yet to see a significant increase in deaths.

From Worldometer, Daily New Cases, New York State.
From Worldometer, Daily New Deaths, New York State.

All this to say, for now, the BA.2 and BA.2.12.1 wave still appears to be somewhat insignificant.

If you had COVID from mid-December to now, you probably had Omicron.  Because BA.2 and BA.2.12.1 are very similar to Omicron, you should not be concerned about reinfection until a significantly new variant arises.  Some people who had Delta have also been infected with Omicron.

Omicron sub-variants get a lot of press, much more than previous sub-variants.  I’ll let you guess why that is. For now, don’t be alarmed about a new Omicron sub-variant.  They will probably all fall into the “don’t stress about it” category.

The pandemic isn’t quite over. If you don’t have immunity, you may want to continue to take precautions by wearing an N95, KN95, or KF94 when indoors in public. Cloth masks or blue surgical masks will not protect you from Omicron variant SARS-2 viruses.

Paxlovid:  2 friends of mine got COVID just this week.  They were both prescribed Paxlovid, a new anti-SARS medication.  The drug is a protease inhibitor, which prevents viruses from maturing as they are formed inside a human cell.  Protease inhibitors do not prevent infection, but they can significantly reduce viral load and improve symptoms.  Both of my friends are doing well now, one feeling significantly better within just 24 hours.  2 people is a very small sample size so this should not be taken as an endorsement. I’m just pointing out that there is a new therapeutic available.

I will point out that Paxlovid is a Pfizer product.  For some, this will cause concern because Pfizer has lost significant trust due to the vaccine mandates and the attending creepiness.

Don’t fear, but be smart,
Erik

______________________________________________
Important Update on Paxlovid, from July 2nd, 2022:

This is a post about Tony Fauci’s time with COVID and the drug Paxlovid, which I have discussed in the past.

On June 15th, a story came out about Tony Fauci having contracted COVID, despite having been fully vaccinated and boosted. I didn’t cover this before since I’d already discussed the fact that the vaccines don’t prevent infection by Omicron variants.

However, something else very interesting happened. Dr. Fauci took Paxlovid, which I’ve discussed briefly before, and became COVID negative. But after his 5 day course, he became positive again with worse symptoms. This means that a standard 5 day course of Paxlovid will not necessarily reduce your viral load to zero, and patients may experience “Paxlovid rebound”. Fauci even claims that this kind of rebound with Paxlovid is starting to be seen as “typical” as more patients use it.

The CDC actually issued a warning about Paxlovid Rebound in May, but it was not widely reported.

With so many rebound cases, it’s likely that 5 days is not adequate to eliminate all viruses from the system, allowing rebound. However, Paxlovid does have side-effects, so don’t take it for more than 5 days without consulting your doctor! Hospitals are now only prescribing Paxlovid to high risk patients.

Whenever taking anti-viral or anti-bacterial medications, always take the full course of treatment. If any virus or bacteria survive treatment, they may give rise to a more resistant strain. Don’t just stop your treatment when you feel better. I take anti-biotics as a last report, but when I do, I take the full course. I even made a doctor give me the full 10 day course when she just wanted to give me a half course!

Just to repeat the point on the vaccines, I still hear ads on the radio encouraging vaccination. At this point, the vaccines are really not doing anything against the current COVID variants. There is really no benefit to getting a vaccine or a booster. If you haven’t had COVID yet, I would simply recommend preventative measures. Wear an N95, KN95, or KF94 mask when indoors in public. Cloth and surgical masks will not prevent infection.

Don’t fear, but be smart!
Erik

Kim Iversen’s more in-depth discussion of Dr. Fauci’s rebound.