All posts by Erik P. Johnson

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

Case Update, September 8th, 2021

This is a brief case update. Last week may represent a lowering of cases in the US, and we may finally have reached the peak of the Delta Wave in the US. Deaths continue to increase but they are proportionally lower than for previous waves. Endcoronavirus shows many counties and states in the country finally recovering from Wave 5.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format. Wave names are mine, not necessarily endorsed by healthcare officials.
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 8th, 2021.
Endcoronavirus State Level Map, September 8th, 2021

A word of caution on interpreting some case graphs that you may see. As you can see on my graphs, there is usually a disproportionately higher number of cases reported on Friday and Monday, and a lower number reported on Sunday. Some maps will report very high cases for an area (see Endcoronavirus state map for Louisiana) but zooming in on the map shows that the very high peak just shows cases for Fridays. So look for this when interpreting some data you might see.

Endcoronavirus State Level Map, September 8th, 2021. Delta wave in this view appears to be higher than the Fall/Winter wave.
Endcoronavirus State Level Map, September 8th, 2021. Clicking on the Louisiana graph on the Endcoronavirus state map gives you this graph. Note that the average case number is not nearly as high as is suggested by the higher days. This is not true for every state, so check your own state’s information.

California and San Diego County both continue their downward trend in new confirmed cases. It’s still to early to say, but deaths in San Diego County may have already peaked for the Delta peak. If this is the case, then deaths due to Delta have been very low. Hospitalizations have been proportionally as high as the Winter peak during the Delta Wave, however, at least in San Diego County.

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 by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Weekly update, San Diego County, 9/1/21
Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.

Many have been interested in the Israel data on vaccination. The paper associated with that data has finally been pre-printed. I haven’t had a chance to read it myself yet, but I’m providing the link in case you’re interested in it.

Don’t fear, but be smart,
Erik

Case Update, September 1st, 2021; FDA approval for Pfizer vaccine, 2 shots of vaccine, or 1 after COVID infection improve protection from Delta.

This is a case update. I’ll also discuss the potential for a Fall peak, new branding for the approved Pfizer vaccine, and whether you should get a vaccine shot if you’ve had COVID.

In the US, cases continue to rise, but the rise is slowing. Numbers from this last weekend suggest we may be seeing a peak in cases, but it’s too early to say. Deaths from the Delta peak are increasing also, but are proportionately less than for previous peaks.

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.

We are starting to see fewer cases in the South. Last year, the Summer peak was centered in the warmer states, California to Florida, and then we had a very large wave starting in the North starting in October. With cases still high at the start of September, we may see another large surge of cases in the North as we head into Fall.

Endcoronavirus County Level Map, August 31st, 2021. New cases slowly receding in the South and growing in the North. Michigan, Missouri, Nebraska still appear to not have strong outbreaks as of now, likely because of large case numbers during the UK variant wave in the Spring of 2021.
Endcoronavirus State Level Map, August 31st, 2021

New cases continue to fall in California and San Diego. Tentatively, it even looks like deaths are falling as well.

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 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.

The Pfizer vaccine recently received FDA approval. The confusing part, is that legally speaking, the approved vaccine is not the same legal entity as the Emergency Authorized vaccine. The Pfizer vaccine we’re used to is called “Pfizer-BioNTech COVID‑19 Vaccine”. The FDA approved one is called “COMIRNATY (COVID-19 Vaccine, mRNA)”. I’m not a legal expert at all, but my understanding from watching some legal analysis is that the original vaccine is still only EUA authorized, and has some liability protection for Pfizer. However, Pfizer does not have liability protection for the COMIRNATY vaccine. According to the approval letter from the FDA, the formulations of the 2 vaccines are the “same formulation” and “can be used interchangeably”.

So why the name change? An analyst I watched said that Pfizer would like to continue to use the original vaccine under the new approval, but avoid liability. So those getting the vaccine now would still be getting the vaccine with liability protection for Pfizer. If you want to get a 3rd shot, you may want to wait until the legally approved COMIRNATY vaccine is available. Again, I am not a legal expert, so my analysis may be wrong on this.

If all this is true, you may regard this as a dirty trick by Pfizer. I try not to be cynical about things that I have only a vague understanding of, but if you thought that, I couldn’t disagree with you.

2nd shot improves protection against Delta, even for those with natural immunity. In a video by Dr. Roger Seheult, he argues that another shot greatly improves the immune response to the Delta variant. This follows both for those with only a single shot of the Pfizer vaccine, or with natural immunity. All this to say, if you’ve had COVID, 1 shot of a vaccine will help protect you from a breakthrough infection from the Delta Variant.

From Planas et al, 2021. Data suggests boosted binding of antibodies to Delta Variant after natural immunity (COVID infection) and 1 shot of the Astra Zeneca or Pfizer vaccine.
From Planas et al, 2021. Data suggests boosted binding of antibodies to Delta Variant after 2 shots of Pfizer vaccine.

Don’t fear, but be smart,
Erik

Possible low efficacy of current vaccines against Delta, possible Delta enhancement in the future.

This post is detailed, but adds an important new set of facts regarding the Delta Variant, the current vaccines, and prospects for a new booster shot.

You may have heard commentators in the last few days talking about the reduced efficacy of the current set of vaccines. There has also been a lot of discussion about a study from Israel about relatively high numbers of Delta COVID cases among vaccinated individuals.

First a little background on antibodies. Your immune system is making a random set of new antibodies all the time. In an ingenious mechanism, your immune cells “mix and match” pieces of a gene in your immune cells, producing the ability to make a zillion (scientific language for a whole lot) of different antibodies. Your body is basically making different “keys” that can fit into the “lock” of some new protein.

When you get an infection, several different antibodies may bind to the invading agent, on different regions, so you may be protected by several different “keys”. When this happens, a bunch of different things happen, including the manufacture of Memory B cells which makes just the antibody that binds to a particular protein. These cells get activated if you get re-invaded by something with that protein. All this to say, if you’ve had COVID, or been vaccinated, your body will have B cells with antibodies on them that bind to different parts of the Spike protein.

Before I say anything else, I want to repeat that I have not been vaccinated, but have recommended that high risk individuals get vaccinated! I’ve also pointed out many times in the past few weeks that countries with large vaccination programs have lower death rates due to Delta than other countries!

Literally 30 minutes after Thursday’s post on vaccine myths, a doctor friend of mine sent me a pre-print paper from a lab in Japan. Please note, this is a pre-print paper and has not yet finished peer review! The paper describes experiments using antibodies derived from patients infected with the Wuhan strain, as well as with the Delta Variant. They then studied binding of these antibodies to artificial viruses. The paper argues that Delta variant viruses are less neutralized by vaccines against “wild-type” or Wuhan strain vaccines. While the “wild-type” antibodies against Wuhan can neutralize a region of the Delta Spike protein called the Receptor Binding Domain (RBD) (Figure 1C), other antibodies binding to another region of Delta Spike protein actually enhance infectivity. Figure 1D from the paper shows negative levels of “neutralization” for antibodies that bind the N-terminal domain of the Spike protein. The paper calls this “enhanced”. Yes, this is the ADE I’ve been talking about.

Figure 1 from Liu et al 2021.

They suggest that with rapid changes in COVID variants, a new version of Delta is going to be able to use the ADE pathway in the near future, when Wuhan era antibodies will no longer be able to neutralize a mutated Delta strain.

To sum that all up in simpler language, it basically says that Delta is more infectious because it is partially using the ADE method of infection. Future versions may be less prone to be neutralized by Wuhan antibodies, making them fully enhanced. If this happens, we may have more severe disease in those who get infected with this new enhanced Delta.

They conclude by saying a booster against the Wuhan strain will not be effective in improving protection from Delta, and that a new vaccine against Delta will be required.

The material in the paper may help to explain why we have been seeing lowering levels of vaccine effectiveness in some countries.

Just to be very clear, they are not saying that this new enhanced Delta exists now, just that it may exist in the future.

I will pay close attention to this issue. If you have already been vaccinated or had COVID, a new Delta vaccine will be your best defense against possible ADE arising from a possible enhanced Delta.

If an enhanced Delta arises, and you have had Wuhan COVID or a Wuhan vaccine, and you haven’t had Delta, then you may be at greater risk for severe disease.

If you have had COVID since July 2021, you are likely already immune to the Delta variant, and this will not be an issue for you.

I am fully aware this complicated. Also, the CDC has rarely if ever discussed this possibility, so unfortunately, most of the people you talk to about this will not believe it. I am sharing this with you so you can make wise decisions for you and your family.

Some companies are already working on Delta versions of the vaccine. If you have had the current vaccines, or had COVID, you should get the Delta vaccines as soon as they are available.

Of course, discuss your medical history with your doctor before making medical decisions.

Another note on misinformation: My post from last Thursday generated a lot of discussion regarding censorship and misinformation. I argued strongly that the dangers of misinformation do not outweigh the benefits of free speech. Many of you are pro-vaccine and others are suspicious of the vaccine. I would simply urge this:

1) If you use the words “misinformation” and “disinformation” in a post or in a discussion, please come ready with evidence to support whatever claim your making! Don’t just throw out this word, support it!

I recently saw a video with a pro-vaccine medical person saying “we just need to keep pounding this information into people”. That is the wrong approach. With someone who is not yet convinced to get a vaccine, “pounding” away on them is just going to raise their defenses and exasperate you. Instead, gently show them your reasons for believing what you do! Explain to them what the data means. You may not convince them, but you may move them toward being more open to your view.

2) If someone makes a claim that sounds unfounded or that you don’t trust, don’t just tell them they’re wrong or make a counter claim, ask them to provide evidence, or where they got their information. You don’t have to do their homework for them! If they can’t produce any evidence, you are under no obligation to counter it. I’ve saved myself A LOT of work with this approach. It’s OK that they just heard it somewhere IF their source is reliable and has evidence themselves. You can still ask them to provide you with a link or something to that person’s statement. However, “I just heard it somewhere” is not evidence.

Part of the reason I’m not so worried about “misinformation” for myself is because of my regular use of suggestion #2.

Don’t fear, but be smart!
Erik

Video: “Top 3 vaccine Myths” and Tech Censorship

In the interest of openness and full disclosure, I need to share a video with you that I just watched. Dr. Zubin Damania is a Youtube commentator that I actually listen to a lot, and I find him more reliable than many. He just posted a video “Top 3 COVID Vaccine Myths“. Two of his myths are:

2) The Spike protein is toxic.
3) Antibody Dependent Enhancement may cause vaccinated individuals to experience more severe disease if infected with SARS-2.

If you have been reading my posts, then you know I have been concerned about both these issues. So am I spreading myths?

2). My concerns about Spike protein toxicity are based on persistent rumors of people having moderate severe reactions to the vaccines. For awhile, I dismissed these as just the standard reaction that some have had to any vaccine, including those for flu. But more and more rumors piled up and made me wonder if something else was going on. Then I saw the video by Bret Weinstein and Robert Malone. Dr. Malone is the inventor of the mRNA vaccine technology. The video argues that the Spike protein itself is toxic. Dr. Malone’s credentials are at least as good as Dr. Damania’s on this matter, likely better, so I can’t dismiss his view.

Unfortunately, I haven’t yet been able to find enough reliable information on adverse events to form my own opinions based on the data, so I’ve been relying on others to inform me. Frankly, because of the politicized nature of the vaccine issue, I don’t feel at all confident that I can get reliable information. So I may never be able to develop an informed opinion on this matter.

Dr. Damamia claims that convincing evidence exists that demonstrates that Spike protein is not toxic, but he doesn’t give it in this video. This of course is very common.

3) I’ve talked a lot about the ADE issue. In this video, Dr. Damania claims that ADE has not been an issue in the vaccine roll out, and the new variants have not caused more severe symptoms. I agree with both of these points. I point these out in my November 2020, December 2020, and April 2021 updates to my ADE post. I am still concerned about that new variants may someday arise that can use the ADE pathway, or that a new SARS strain, a hypothetical “SARS-3” will arise that will be different enough to trigger ADE. So while I agree with Dr. Damania’s point on ADE, it’s not quite the point that I’m still concerned with.

As I’ve stated many times, the vaccines are likely to help you if you have a risk factor and I have several friends and family members that I have recommended get the vaccine. So I am not anti-vax per se. But I don’t think it’s the obvious choice for everyone, and I’m staunchly for personal medical freedom in regards to COVID vaccines.

So what do I do now? What should a thinking person do when confronted with new information from a trusted source that you’re not sure about? These things are all true when dealing with complicated issues:

People you generally agree with may say something you don’t agree with.
People you generally disagree with may say something you agree with or makes you think about an issue in a new way.

Both of these are normal. When dealing with a complicated issue like COVID, race relations, worldview, politics in general, it is critical to keep an open but critical mind. You have to read widely from both your side and others to hope to get a clear view of the issues involved.

I respect Dr. Damamia. He might be right! I’ll have to think about his points, do some more homework, and reassess my opinion. There are 3 possibilities.

I will abandon my position and accept his.
I will learn new things that will reinforce my position.
I will do a bunch of research, but will not find conclusive information that will allow me to form a new opinion either way.

If I can arrive at a place closer to the truth, then the exercise will be a good one. If I decide I think Dr. Damania is wrong on these points I’ll likely still watch his videos, since I think he is right more often than he is wrong, and he’s more open minded than most, so I think he is at least being honest about what he believes, which is a very valuable trait! Dr. Damania is both for COVID vaccination and against vaccine mandates.

I started out posting on COVID because as a scientist I felt a responsibility to help my non-scientific friends and family members make some sense of the pandemic, especially when scientific communication is so often poor. I hope I have done that. I can’t claim to always be right, and have changed by view several times. But I have given you the truth as best as I can find it, and supported it with evidence.

A word on tech censorship: The WHO said 2 false things early on:

SARS-2 is not human to human transmissible
SARS-2 is not transmissible as an aerosol.

Both of these things were demonstrably false, and perhaps politically motivated, even at time the WHO stated them. In in spite of this, the social media platforms came to hold the WHO as the gold standard for the truth on COVID matters. To this day, F@¢3b00k may place a tag on the end of this post claiming the WHO as the authority on COVID matters. Most platforms would delete or restrict anything that ran against the WHO. Yes, computer programmers in Silicon Valley are still pulling down information posted by medical doctors and scientists. Even Dr. Damania has had videos censored!

One of the worst results of the pandemic in the US is censorship of divergent opinions. Freedom of speech allows 3 things:

All opinions to be held up to public scrutiny.
True things to rise to the surface.
False things to be discredited.

When freedom of speech is restricted, none of these can happen. If a wrong thing becomes the “orthodox” view, and no other views are permitted, then the orthodox view will always be wrong, and we will end up solving all of the wrong problems. If there is a hole in your gas tank, it doesn’t matter how many times you put gas in it. It will always be empty. Fix the real problem first.

This is why all the claims of misinformation, from all sides, are so insidious. When you claim misinformation, you are claiming to have the whole truth on an issue. Sure, we can and should argue against views we think are false. But we must also protect the right to air all views! Or we are doomed only to have the first view that becomes dominant, and we are less likely to find the truth!

I also found an article on why some are still vaccine hesitant. For those of you who are wondering, you should read it.

As always, Don’t fear, but be smart!
Erik

Case Update, August 25th, 2021

This is a brief case update. The US is still increasing in new cases, but the number of new cases is slowing. Several states appear to be past the peak new cases are now headed down, including Louisiana, Texas and Vermont. New COVID deaths in the US are on the rise, but are still far lower then during last wave. It will take several weeks to know how many new deaths we’ll see, since new deaths trail new cases by between 1 and 4 weeks.

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, August 25th, 2021


Endcoronavirus State Level Map, August 25th, 2021

New cases in California and San Diego continue to go down for the second week. New deaths are starting to creep up for both regions, but remain relatively low.

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

Don’t fear, but be smart,
Erik

PCR and the Ct Value

In the past few weeks in San Diego, I’ve heard several stories that discuss Ct values in regards to COVID testing. Since this is my field, I thought I’d talk about what a Ct value is and it’s relation to your results. This post is going to be pretty in the weeds, so if your not interested in the detail, you can skip this one.

PCR: The Polymerase Chain Reaction (PCR) was invented in 1983, and by the 90s, it has become a commonly used technique foundational to several molecular biology techniques, including DNA sequencing, DNA manipulation, sequence detection, and many more. Basically, the technique is used to make many many copies of a small amount a DNA. The DNA molecule is double stranded, the 2 strands are reverse copies of each other, binding to each other with weak interactions.

Heat is used to separate the 2 strands, and small pieces of DNA called “primers” bind to the DNA copies at a lower temperature.

The primers are designed to perfectly match sequences in the template strands. This is why PCR reactions can be very specific to a particular target, like SARS-2.

Next, the template strands are copied by a protein called “DNA Polymerase”.

After this, the reaction is heated up again, and the process is repeated. For a PCR reaction used for detection, this is repeated 40 – 45 times. With every repetition of this process, the numbers of molecules doubles, so from every 1 molecule of starting DNA, you could theoretically end up with almost a trillion copies!

Real-time PCR: Lots of copies of DNA aren’t enough to detect it. You also need something else. Medical detection uses a process called “real-time PCR”. In this process, a third piece of DNA called a “probe” is also added. The probe has a fluorescent molecule called a “reporter” on the front end, and a molecule called a “quencher” on the back. The reporter gives off light during the reaction. The quencher is a molecule that absorbs light and coverts it to heat, effectively dimming the light coming from the reporter.

As the real-time PCR reaction progresses, the DNA Polymerase chops up the probe as well. When this happens, the quencher is separated from the reporter, and the reporter appears to give off more light! The medical instrument detects this extra light which leads to the result.

Ct values: You may have heard the term “Ct value” thrown around. As I mentioned before, with every cycle of PCR, the number of DNA copies doubles. At the same time, the reporter molecules start to give off more light. Even with all the reporter molecules around, the instrument can’t detect it until at least cycle 15. When it does, a graph of fluorescence coming from the reaction will start to show an increase.

Real-time PCR Results. This is from an ABI 7500 running version 2.3 software. The results for 5 patient samples. 3 would be reported as being positive, 1 negative. The sample giving the green line is over 40 Ct and may be repeated, or a new sample may be collected from the patient.

The more starting DNA you have in the reaction, the sooner the instrument will detect a rise in light. Scientists designing the test set a Cycle Threshold (the yellow line in “Real-time PCR Results”). This line is somewhat arbitrary at first, but when the test is validated, it is “set in stone” before being submitted to the FDA for approval. After the threshold line is set, the cycle at which the line of fluorescence for sample crosses the threshold line is called the “Ct value”. As you can see in the graph, the more starting DNA you have, the lower the Ct value is. The lower the starting DNA you have, the later the line will cross the Threshold, and the higher the Ct value.

A patient with a lot of SARS-2 in their sample will give a very low Ct value, almost never lower than 15-19. In the example above, the orange line represents a patient with a lot of virus. The higher the Ct value, the less virus a patient has in their sample. A sample that gives Ct value in the high 30s has very little virus, and is most likely not symptomatic. In fact, some scientists have even said that a Ct value of higher than 35 means the test is really just detecting viral debris after the virus has been cleared and the infection is basically over. A good test can detect as few as 50 virus molecules in a sample.

Most labs don’t even bother to report any result with Ct over 40. I’ve never heard of a lab reporting a result with a Ct over 45. Results like this are generally considered un-reliable, since PCR can give false positive results at very high cycle numbers. Most labs eliminate this possibility by just not reporting Cts over 40. A few weeks ago, a person at a San Diego County meeting claimed that many labs are reporting Cts over 45, and thus giving false positive results. I happen to know this man personally. We disagree on the proper approach to COVID, but he’s a good guy, and I like him personally. He is not a scientist. Anyway, I contacted him to ask him for evidence that labs are reporting Cts over 45, and I have not heard back. As I said before, I’ve never heard of a lab reporting a positive result for a real-time PCR test with a Ct over 45. So I’d be surprised if this was happening. If you have evidence of this, please let me know!

A local radio commentator in San Diego suggested on air that labs should report the Ct number. I’m all for this, but I know first hand that labs usually do not report the Ct number. In fact, many patients, and yes, even many physicians, don’t know what this number means and don’t actually want to see it in a report! Yes, that’s right, on one complicated test I built in which I included the Ct value in the report, doctors called to ask us to remove it! They said it was confusing the issue for them. This may have been because it was confusing their patients, but suffice it to say, many downstream users don’t want the Ct value and that’s why it’s not included. Generally, labs just report “COVID Positive” or “COVID Negative”. In some cases, “Detected” or “Not Detected” are used instead, to avoid confusion.

This is to avoid the issue of a patient saying “My result is positive! That’s great!” No, sir, it’s not that kind of positive.

I actually think the Ct number is very useful, and would love to see it included, but it probably won’t be.

Anyway, hope that was helpful. Your questions below will help me make this all clearer.

Don’t fear, but be smart!
Erik

Case Update, August 19th, 2021, Is COVID Endemic?, Mandatory Vaccination.

This is a case update. I’ll also briefly discuss the future of the pandemic.

Numbers continue to rise in the US, but are definitely slowing in their increase. New cases are most prominent in the West and Southeast. New deaths are rising, but much more slowly than for other waves.

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, August 19th, 2021
Endcoronavirus State Level Map, August 19th, 2021

For California and San Diego, it looks like we have crested the wave and new cases are starting to head down. In both of these regions, new deaths are not really increasing at all. This supports the pattern that in vaccinated areas, large numbers of new cases due to the Delta Variant are not followed by large numbers new deaths. I mentioned a few weeks ago that deaths can trail new cases by as much as 4 weeks, but we are now 6 weeks into the Delta Wave in California and San Diego without seeing a significant rise in new deaths.

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 by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.

Internationally, new cases appear to perhaps have peaked world wide, but it will take some time to see if cases start to go down. As stated above, countries with vaccination programs are experiencing almost no new deaths due to Delta Variant. Numbers for the Netherlands are striking, and other countries like the UK, Sweden, Japan, and South Korea show a similar pattern.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format.
New daily confirmed cases in the Netherlands, from Worldometers.
New daily deaths in the Netherlands, from Worldometers.

Several sources I listen to are now saying that SARS-2 is now or will be endemic. For some background, an epidemic is an outbreak of a disease in a small area or region. Avian influenza and the first SARS outbreaks were epidemics, since they didn’t leave Asia. A Pandemic is an outbreak in a large area including several continents. A disease becomes endemic when it becomes a constant feature of life in an area. I would include malaria, seasonal flu, and HIV in the list of endemic diseases. Interestingly, Wikipedia still considers HIV to be a pandemic.

I have resisted calling COVID endemic. I don’t think it fits the criteria at this point. While there have been several new variants that have caused additional waves of cases, they are all at least partially impacted by the available vaccines, and presumably by natural immunity as well. While this is the case, I still think it is possible that we can eradicate the virus from the world at some point.When might SARS-2 become endemic? For me, that would happen if either new variants arose that were not mitigated by natural or vaccine driven immunity, or if immunity in vaccinated or naturally immune people ceased to be effective in preventing new infection. Both of these would allow SARS-2 to continue to circulate indefinitely.

Some have argued that vaccine mediated immunity is not as long lived as hoped. This may be why there have been many “breakthrough” cases in the last few weeks. However, Youtuber Dr. Zubin Damania suggests that while protected from new infection wanes over months, vaccine protection against severe disease is persistent, at least against the Delta Variant. This may explain our current pattern of low deaths despite high cases in vaccinated regions.

So is COVID endemic? I still say no, and hope it can be eradicated. However, some municipalities, including Norway and the state of Iowa, have declared that is endemic and will be a permanent feature of the world. If I decide that the data shows that SARS-2 is endemic, then that is the day that I will get vaccinated. ‘Cuz I do want to go back to normal life someday, but I don’t want to actually get COVID. Obviously, many vaccinated and unvaccinated folks have decided to go back to living normally, despite official calls to maintain vigilance.

Vaccination mandates: I have not been in favor of requiring vaccination in order to return to work, fly on commercial aircraft, or other activities. While I am all for precautions and continue to wear a KN95 indoors while in public, healthcare is a personal choice and should not be coerced. Some have even claimed that it is illegal to coerce a measure that does not have FDA clearance. While vaccination is a good choice for many, it does have liabilities that have made many resistant to vaccination. This should be honored.

I know several people in the healthcare industry who have not wanted to be vaccinated, and have quit or been fired from technical or nursing jobs. While an argument could be made that those working with patients should be vaccinated, it seems misguided to be letting go of nursing staff when there has been a long standing nursing shortage.

Don’t fear, but be smart,
Erik

How Mutation Leads to New SARS-2 Variants

This is a brief post on the issue of new COVID variants and their cause. There has been a lot of confusion as how new variants arise. For small biological organisms that evolve quickly (bacteria, viruses, parasites, some insects), new strains can arise relatively quickly. I say relatively because it can still take many years in some cases. This is because small changes in genetic material can lead to important changes in function.

Point Mutation: There are 3 kinds of mutations that can cause this. One is a point mutation, a change in a single nucleotide (the basic unit of genetics, like a letter of the alphabet). Depending on the point mutation, this can lead to no change at all, or an important change that can have an impact on drug resistance, protein binding to target, or other effect. This is particularly likely in viruses whose genome are made from RNA, because the proteins that make RNA strands in these viruses are particularly error prone. This is why HIV, the Flu, and Coronaviruses can change so quickly.

Genetic Re-assortment: Another kind of change common in some viruses like the flu, is a re-assortment of chromosomes, or “antigenic shift”. The Flu virus genome comes in 8 pieces. If 2 viruses infect the same animal and the same cell, then that cell can produce new viruses that have a combination of pieces from both infecting viruses. This often happens when a pig on a farm somewhere gets infected with 2 flu viruses, and produces a new, novel form of the flu. This is why new flus are often called a “Swine Flu”.

From the Wikipedia page on Influenza.

Conjugation: Bacteria can donate genetic material to other bacteria, even those of a different species, in a process called conjugation. Yes, it’s more like that than you might imagine. In this fashion, bacteria may acquire large amounts of new DNA. These new DNA fragments are kind of like software downloads, encoding whole new abilities like drug resistance, iron scavenging, and the ability to bind and invade new cell types. In fact, it could be argued that many or even all disease causing bacteria are this way because they’ve inherited DNA from other bacteria!

So how does this all relate to SARS-2? COVID changes using the point mutation route, which it does quickly because it has an RNA genome. The probability of a new variant arising is dependent on the speed of mutation, the number of viruses that exist, and time. This means that the more viruses that exist at any moment, the more likely that a new strain will arise. In our present moment, this means that the more people in the world that have COVID, the more likely a new variant will arise. This is a concern at a time when new infections are high.

The very good news is that the vaccines we have appear to work on all the existing variants, at least to some degree. So while we do need to try to keep the number of infected people down to avoid new variants, we are not defenseless against them. But there is a possibility that a new variant will arise that is not neutralized by the current vaccines, and this should be avoided of course.

Don’t fear, but be smart!
Erik

Case Update: August 13th, 2021

This is a case update. For the US, cases continue to rise, although the rise in cases may be slowing just slightly. New cases are being driven by a few states with rocketing new case numbers, in states in the South, as well as Washington, Oregon, and Hawaii. Only Hawaii is experiencing a decline in cases after a sharp 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 Johns Hopkins University COVID site. Graph is presented in a linear format.
Endcoronavirus State Level Map, August 13th, 2021

For California and San Diego, new cases are still rising, but more slowly all the time. COVID related deaths are still only creeping up for the US, and still haven’t risen at all for California and San Diego, 6 weeks into the Delta variant peak. At least for now, it continues to appear that the Delta variant is less virulent, at least in the US and some other heavily vaccinated countries.

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.

Incidentally, high infection rates in the South are likely caused by hotter weather causing folks to go inside for air conditioning. Just like last summer.

If the Delta wave isn’t over in the US by October, we are likely to see lots of cases in the North, just like last Fall.

Don’t fear, but be smart,
Erik