COVID Transmissions for 3-15-2022
Rising global COVID-19 signals; debunking some vaccine misinfo
Greetings from an undisclosed location in my apartment. Welcome to COVID Transmissions.
It has been 819 days since the first documented human case of COVID-19. As of last week, we are now in the third year since the WHO declared COVID-19 a pandemic.
In 819, a conflict between the Frankish Empire and the Slavs of Lower Pannonia was raging, and I think that is representative of an early moment in the divide between Eastern and Western Europe that continues to have geopolitical impacts to this day.
I’ll stay off the geopolitics for now, though, and instead today we will discuss rising COVID-19 signals in the US, UK, and Europe as well as a very bad paper that is being used to justify incorrect antivaccine messages.
Today has a paid section, “Other Viruses,” that covers the viral origins of the placenta.
Also, as a reminder, we are on a new schedule. COVID Transmissions will appear on Tuesdays and Thursdays until further notice unless major developments demand a more frequent schedule.
You may have noticed I missed the Friday issue last week—that wasn’t because of the schedule change. Instead, for the first time since I started writing this newsletter, my Internet access went down during the time I would normally have been finishing up. Hopefully that won’t happen again.
Bolded terms are linked to the running newsletter glossary.
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Now, let’s talk COVID.
Concerning COVID-19 signals around the world
COVID-19 is on the rise in Europe, and that usually signals that the US isn’t far behind either:
That tweet from Dr. Eric Topol shows that once again, we are seeing increases in Europe and the UK—and that historically, when there has been a wave in those two places, the US has experienced a wave too.
And, it’s possible that we are starting to see it in the US too—take a look at these wastewater surveillance data:
In that map of the US, again tweeted by Dr. Topol, we see lots of red and orange dots, where wastewater signal of SARS-CoV-2 mRNA has gone up by between 100% and 1000% in the last two weeks.
Wastewater spikes tend to predict COVID-19 case waves, at least historically. Unfortunately, the surveillance coverage is sparse, as the map also shows, so it is hard to make national predictions. But the signs are worrying.
While the CDC may have told you that you can go without your mask for now, I think you should consider this information before choosing to take it off. There could be another wave on the way, and it may be prudent to make sure you are as protected as possible. That means masking, getting boosted, and evaluating whether travel or being in large groups is really the right decision for you. I can’t make that choice for you, and being both boosted as well as having relatively recently recovered from the predominant variant of SARS-CoV-2, I do feel a little more secure than most people might. Still, I think my masking practices may get a little more restrictive again. Prevention is a decision best made before things get bad.
But that is my unique situation. Your unique situation should be considered, too, and I would not take these signals lightly. If nothing comes of them and you wore a mask for a week or two, I think we can actually call that a win. Any situation where you don’t have to get COVID-19 is a win.
Bad paper being used by bad actors to mislead on mRNA vaccines
There is a (sadly, peer-reviewed) paper making the rounds that claims that mRNA from mRNA vaccines is rapidly converted to DNA (in a matter of hours) and then integrated into host genomes.
I am reluctant to even link this paper because it is completely and utterly wrong to suggest that this happens in living people. But, of course, it is being used by bad actors as evidence that this is definitely something that happens when the vaccine is given to people. It does not.
The paper itself contains experiments that I believe generated the reported results, but the authors overstate and speculate that this may be relevant in humans. What I’m here to tell you today is how it can be true that an experiment is accurately performed and reported, but doesn’t have applicability to real, live humans.
This particular paper was conducted in a cell line called Huh7 cells. These are a very common laboratory model cell line. So common that there is a website specifically dedicated to them:
https://huh7.com/#:~:text=Huh%2D7%20is%20an%20immortal,typically%20grow%20as%202D%20monolayers.
I have to take a minute here to talk to you about cell lines. The cells in your body are very different from the cell lines, even the human-derived ones, that are used in laboratories for experiments. Here’s how:
The cells in your body are “terminally differentiated”; in other words, your skin cells are programmed to be skin cells and won’t become muscle cells or bone cells without something going seriously wrong. They divide infrequently (except for some types that need to be frequently replaced), with some cells in the body dividing only 4 or 5 times in adult life. They copy their DNA infrequently because of how rarely they divide. Evolutionarily, they are built to be inside your body—they are optimized to live in their specific tissues, and not to be exposed to the open air. It may sound weird, but most of your cells prefer to be in a relatively oxygen-deprived environment. They take in oxygen from your blood for metabolic work, at a relatively fixed rate. Most cells are not bathing in a 20% oxygen atmosphere like the one that exists at the surface of your body.
The cells in a lab are growing on plastic, covered in nutrient fluid, in a 20% oxygen, 5% carbon dioxide environment. The carbon dioxide is added artificially to help maintain pH balance in the nutrient fluid. Cell lines in particular have been subjected to a process called “immortalization” and have been “transformed.” These two terms come to us from the worlds of cancer biology, because cancers are regular human cells that have been transformed until they are immortal. Many cell lines used in the lab started out as human cancers, in fact. But they’ve adapted even further, because again, tumors don’t naturally live out in the open air.
The cells in the lab are seriously messed up. They don’t have the same number of chromosomes as a cell in your body, in many cases. Major chunks of their chromosomes have often broken off into new chunks. They modify and mutate their DNA far more frequently than any body cell in a human does. And they divide extremely frequently. A very large amount of protein and RNA machinery related to DNA is turned on in laboratory cell lines all the time, whereas in a body cell in a person this machinery is infrequently made, let alone activated.
There was a time when I contemplated using this difference as the seed for a science fiction story. That time has not passed, for what it’s worth.
But, I digress. If I have now convinced you that body cells and laboratory cell lines are very, very different, you may be asking yourself why we use them at all. For that, I return you to a premise I’ve shared here before: all models are wrong, but some models are useful. Scientists recognize that our laboratory cell models are not accurate representations of an entire organism, and they’re not supposed to be. They are powerful tools for us to set up systems that are analogous to living organisms, but we recognize that they are not really the same thing.
However, they are a lot cheaper and faster to work with than mice, ferrets, guinea pigs, cats, dogs, monkeys, or people. There are a few animal systems that compare well with cell lines in terms of costs and speed, but they’re not mammals—they’re generally worms or flies. Cells are the fastest, cheapest way to test hypotheses in a mammal-derived system. They can offer great insights to rule out impossible things before wasting years trying to get it to work in a more expensive model.
Back to our paper, though. Huh7 cells are a hepatocarcinoma-derived cell line; they came from a liver cancer originally. They have been “passaged,” which is to say maintained by growing them in tissue culture dishes until they fill the dish, then detaching, diluting them, and transferring them to new dishes, for 40 years. Passaging is done every few days. Every passage has a selective effect on cell lines, encouraging mutation and adaptation. So, suffice it to say, Huh7 cells are very different than they were 4 decades ago when they were a a liver cancer.
One way in which we know they are different is that they process DNA and RNA differently from human body cells. this is, in fact, acknowledged explicitly in the paper I am deliberately not linking here.
In that paper, the introduction of mRNA from the Pfizer vaccine led to rapid “reverse transcription” of that mRNA, within about 6 hours. Reverse transcription is the copying of mRNA to DNA. In most human cells, reverse transcription is extremely rare because the enzymes that do it are not found at high levels. In Huh7 cells, they are apparently substantially more common and can be activated when the cells are stimulated. Already, we are seeing a phenomenon in that paper which is not going to be happening in human body cells—but I will expand on that in a moment.
First, I want to mention that simply detecting DNA does not mean that DNA has become part of the genome. Plenty of viruses with DNA genomes produce DNA in infected cells, as an example, but do not integrate that DNA into the host genome. The work done in this paper I am discussing does not effectively demonstrate anything other than the presence of DNA based on the Pfizer vaccine in their experiment—it does not suggest that this DNA became a part of the Huh7 cell genomes. Since assessing that would be a pretty obvious experiment to do, the fact that the authors didn’t publish it tells me that there is something missing here.
That having been said, I do not doubt that the authors here honestly depicted the work that they did, and this paper’s experiments have to be treated as accurate. However, the authors go on to make several unsupported statements suggesting that we might see genome integration of DNA derived from the Pfizer vaccine in actual vaccinated humans.
Their data do not even tell us that we would see this in Huh7 cells, let alone actual people. In fact, other work has demonstrated that even if SARS-CoV-2 RNA is reverse transcribed in various cell lines, it does not readily integrate into the genome: https://www.pnas.org/doi/10.1073/pnas.2109066118
In fact, I think it is pretty evident at this point that we do not see this phenomenon in humans with any regularity. It would be incredibly obvious by now, and in fact, it would have been happening before these vaccines were invented.
You see, the mRNA in the Pfizer vaccine—and the Moderna one—is treated essentially the same within the body as regular RNA that cells make themselves. And cells make a lot of mRNA. They also make mRNA based on viruses that infect them. The creation of mRNA is a basic, central function of life. If you could not make mRNA molecules in their thousands in every cell of your body every hour, you would die gradually of something not unlike radiation poisoning.
If, indeed, mRNA is reverse transcribed into DNA in normal body cells, and then integrates into the genome, we would see new genes inserted into the human genome all the time. It would be tremendously disruptive to the genome, and would kill cells frequently. I am not sure we would be viable as a species. If this happened with mRNA produced by viruses, it would be nearly impossible for anyone to ever be cured of any virus.
I am not making this statement baselessly. There is a virus that integrates reverse-transcribed RNA into the human genome. It’s called HIV, and as a result of its ability to integrate into cell genomes, it is nearly impossible to cure.
In other words, if mRNA expressing the SARS-CoV-2 spike protein was readily reverse transcribed and integrated to the human genome, we’d know about it because a large number of people who got SARS-CoV-2 would have DNA in their bodies that codes for the spike protein. This has actually been assessed experimentally and it has been shown that in a large recovered patient population, the only times DNA coding for SARS-CoV-2 sequences appeared were cases of cross-contamination inside the testing laboratories. See that here: https://www.pnas.org/doi/10.1073/pnas.2113065118
If integration of SARS-CoV-2 mRNA or vaccine-derived mRNA were happening regularly, we would be seeing a population of people who test positive for a long time—not just for a few weeks or months, but years, maybe even forever—when they go to get PCR-evaluated for SARS-CoV-2. These people would not have been missed.
Admittedly, the vaccines contain slightly different molecules of mRNA than the virus does, but ultimately, we have years of study indicating that it is rare in adult humans for an mRNA molecule to be reverse transcribed and integrated into the genome. There is nothing particularly special about an mRNA molecule introduced to a cell that would make it different in this regard.
The Conversation has a good article that explains this, if I haven’t done the job well enough for you today: https://theconversation.com/can-the-pfizer-or-moderna-mrna-vaccines-affect-my-genetic-code-162590
I should note, of course, that because some viruses do integrate into genomes, sometimes—maybe once in twenty million years or longer—you get a permanent change that is passed down to the descendants of a virus-infected individual. This happens to be the suspected origin of the placenta that makes mammal births possible. We’ll discuss that in the Other Viruses section today.
I feel pretty comfortable that these sorts of events require very particular types of viruses to be involved, and that they happen so rarely that humanity may be extinct before it happens to us. Certainly against that backdrop, and knowing the available evidence, I’m not worried that an mRNA vaccine can change my genome. After all, I am very, very different from a 40 year-old tumor cell growing in a plastic dish.
Part of science is identifying and correcting errors. If you find a mistake, please tell me about it.
Though I can’t correct the emailed version after it has been sent, I do update the online post of the newsletter every time a mistake is brought to my attention.
No corrections since last issue.
What am I doing to cope with the pandemic? This:
Watching: Taskmaster
My wife has gotten me partway into a British show called Taskmaster where comedians are asked to compete by doing various ridiculous tasks that they need to creatively accomplish. It’s extremely silly, and I believe it’s available on YouTube for free in its entirety. If you think it sounds like fun to watch British comedians subjected to what the Geneva Convention might otherwise consider very light psychological torture for prizes, then this show may be for you.
But really, it’s a lot of fun. And pretty low-rent on the brain. I also believe the contestants are happy, healthy, and having a good time.
You might have some questions or comments! Join the conversation, and what you say will impact what I talk about in the next issue. You can also email me if you have a comment that you don’t want to share with the whole group, or if you are unable to comment due to a paywall.
If you liked today’s issue, please consider becoming a paid subscriber and/or sharing this newsletter with everyone you know.
For those who won’t be continuing beyond that into the rest of the paywalled section below—as well as everyone who will—please know that I deeply appreciate having you as readers, and I’m very glad we’re on this journey together.
Always,
JS
The viral origins of the placenta
As I have mentioned earlier on today, there is a class of viruses that can change the human genome, and that class of viruses—the retroviruses—is responsible for the existence of placental mammals as we know them today.
Without these viruses, we might all have hatched from platypus-like eggs. The world would be a very different place. Join me as I explain how this happened.