Coronavirus news & views

Part 2: Gain-Of-Function Research At The Wuhan Lab—What Exactly Was The Wuhan Lab Doing With Coronaviruses?

“I’m just a soul whose intentions are good; Oh Lord, please don’t let me be misunderstood.”  —The Animals

In the first part of this two-part blog series, I described what gain-of-function research entails in order to set the stage for this blog post which describes the coronavirus research that went on in the Wuhan labs. So, was it dangerous and risky? Did it likely lead to the release of SARS-CoV-2 that caused COVID? Let me try to clarify all that now.

Coronavirus research at the Wuhan lab: After the first SARS epidemic in China in 2002, the Wuhan Institute of Virology (WIV) had established itself as a world class coronavirus research lab. It was from their diligent work that the world learned that the first SARS virus came from a horseshoe bat via other animals such as civets and raccoon dogs. That was the result of years of arduous research trudging through bat guano muck in hundreds of caves throughout China to collect samples from thousands of bats. They reported their finding 14 years after SARS appeared and shortly after another strange, lethal flu popped up in the Middle East that was soon attributed to yet another bat-borne coronavirus that came via camel intermediate hosts—MERS.

Before these two coronaviruses that jumped from animals to cause significant disease in humans, the viruses were only known to cause mild human maladies; basically, the common cold. Therefore, when it was learned that the deadly SARS and MERS diseases were caused by coronaviruses, it rattled the cages of health experts around the world. This was brand new!

Hence, even before COVID struck, bat-born coronaviruses were hot on the radars of infectious disease nerds and public health worrywarts. The WIV, as one of the world’s preeminent labs for identifying novel coronaviruses was given international funds to continue their efforts to identify and catalog bat coronaviruses. As they did years earlier when they identified the origin of the SARS virus in horseshoe bats, WIV scientists traveled to far-flung Chinese caves to collect bat guano and biological samples (blood, saliva, fecal) from captured bats. The samples were brought back to the lab in Wuhan for analysis.

Since it is exceedingly difficult and potentially very dangerous to grow wild viruses from such samples (failure is the norm even when many viruses are present in the samples) the lab resorted to their previous tried and true methods of searching the samples for viral genome sequences. They found a LOT of new ones!

Their first and primary order of business in this research was the very mundane task to sequence and catalog all the different coronaviruses they found. They then colligated these genomes into trees of different virus families and posted all the data in a vast database for world scientists to use. They were coronavirus genealogists.

The database is an enormously useful research tool for scientists around the world studying the origins and evolution of coronaviruses in animals and humans. (Coronaviruses also cause significant animal disease, so they also are of great agricultural interest around the world.)

The Wuhan lab also was charged with predicting which of the new virus sequences they found might pose future health threats to humans.

This is where all the controversy begins.

Remember that the Wuhan scientists actually did not have these viruses on hand, just their genome sequences. So, without the actual virus, how could they evaluate the ability of new coronaviruses to infect humans? To do this WIV scientist, Zhengli Shi, used a genetic engineering technique first published in 2015 by Univ. of North Carolina Scientist Ralph Baric to study coronaviruses from their genome sequences (she was a collaborator on Baric’s 2015 paper, so was quite familiar with the approach). It was a technique that also was in use at the time by several labs around the world. It is notable that NIH funded this coronavirus research conducted by Baric at UNC well before COVID appeared and didn’t consider it to be GoF research then.

Using Baric’s genetic engineering technique, Shi’s lab at the WIV used as a tool, a benign coronavirus that they could grow in the lab that was only distantly related to the first SARS virus, but was not known to cause human disease. Its genome sequence was not at all related to SARS-CoV-2 that caused COVID, and which had not yet appeared.

Shi’s lab removed the spike protein gene sequence from the genome of this benign lab virus tool and methodically replaced it with spike protein sequences from each new virus they sequenced. They then grew the lab virus tool carrying the new spike protein and tested its ability to infect human cells in tissue culture.

It is the spike protein that determines whether a coronavirus can infect human cells. Therefore, if the chimeric lab virus carrying the new spike gene infected human cells, it would indicate that the virus the spike protein sequence came from was a likely human pathogen and that virus sequence was then listed on the database as a potential human risk. However, if the chimeric test virus failed to infect the human tissue culture cells, that meant that the spike protein from the new virus genome would not support infection of human cells and the new virus sequence was not categorized as a concern for human infection.

This is how newly identified coronavirus sequences were categorized as potential human health threats without ever having to grow or isolate each virus itself.

In other words, this test simply expressed the spike protein of each novel coronavirus on the backbone of the safe lab virus genome in order to see if it could infect human cells. This completely negated the need to grow and handle the potentially much more dangerous wild-type virus.

It is important to notice that this strategy eliminated all risk of a lab leak of any dangerous virus since it was not necessary to grow or handle potentially dangerous wild-type viruses using this technique.

Is this gain-of-function-research? Strictly speaking, no. Remember, this sort of coronavirus engineering research had been done years earlier in Baric’s UNC lab, and was being done in other labs around the world, and it was never regarded as GoF research then by NIH.

NIH considers GoF research on pathogens to be research that either: 1) increases the pathogenicity of a microbe (that is, makes its disease worse), 2) improves its transmissibility or its ability to infect hosts, or 3) alters the host range of a pathogen. Therefore, in the WIV experiments to assess the ability of novel virus genome sequences to infect human cells, the chimeric test viruses that simply expressed new spike proteins on a laboratory virus backbone either retained the ability of the original lab virus to infect human cells, or they lost the ability to infect human cells.

Therefore, the chimeric viruses gained no new function that was tested. They either retained or lost the ability to infect human cells. The experiments were not at all designed to give the test virus any new functions. Furthermore, these experiments could not have led to the development of SARS-CoV-2 that caused the COVID pandemic, even by accident, since the laboratory test virus used to create the chimeric viruses in the experiments was not at all related to the SARS-CoV-2 virus.

There is a devil in the details: But. Notice that one of the the NIH definitions of GoF research is research that alters a pathogen’s host range. For example, take a flu virus that only passes between birds; avian flu. If you make changes in its genome so that the birds can also pass it to humans that mutation alters its host range and is a GoF change.

In the WIV lab, viruses with new spike protein gene sequences were only tested for their ability to infect human cells in a petri dish. The ability of these chimeric viruses with new spike proteins to also infect other animals was not tested. Theoretically, the chimeric test viruses could feasibly also infect, say a water buffalo, or a wart hog, or some other animal that the original lab virus might not have been able to. That would be a technical gain-of-function. But, that begs the question; in such an experiment, how would you know whether or not the host range of the chimeric virus had changed until you possibly had tested its ability to infect every known animal? A logistical impossibility.

Therefore, based on this theoretical point, it cannot be definitely stated that the experiments were not GoF experiments. In fact, chances are pretty good that some of the novel spike protein sequences attached to the lab test virus in fact altered its host range and, thus, the experiments would technically be GoF research.

Bottom line: Technically speaking, therefore, these experiments carried out at the WIV probably could be called GoF experiments. By a lawyer. Not by a scientist. That picks the proverbial nit and splits a very fine frog hair, to mix metaphors. The same research had been done ten years earlier in Ralph Baric’s UNC lab and was not considered GoF then. What is important is that the research at the UNC or the WIV never set out to create viruses with enhanced virulence, transmissibility, or altered host range. That was never the intent. The aim of the WIV research was solely to predict the human risk posed by novel coronaviruses without actually having to directly work with the potentially dangerous pathogens. Actually working with the dangerous viruses would have posed a very real risk.

Bottom, bottom line: The research conducted at the WIV was the most safe and responsible way to identify new coronaviruses that could potentially pose future human health risks. It is to the detriment of human health that this research has come under heavy criticism and that such future research has been hampered by criticism from people who fail to understand what the research is about and have, therefore, demonized it and want to prevent it.

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Is Intentional COVID Vax Disinformation Criminal?

Note: Disinformation is different from misinformation. Disinformation is false information which is deliberately intended to mislead. Misinformation is wrong information spread without malicious intent.

 

“We have met the enemy and he is us.”

--Pogo Possum

Your humble blogger first wrote about vaccine disinformation way back on March 31, 2021, just over two years ago. That was not long after the vaccines, as well as the lies about them began rolling out. Unfortunately, the fiction continues and it is now necessary to provide an update.

In the first quarter of the Monday Night Football game on January 2, 2023, 24 year old NFL player, Damar Hamlin, made a tackle, got up from the play, took a couple of steps, then fell over backward and didn’t rise. He suffered a cardiac arrest and needed to be resuscitated on the field with a defibrillator.

Almost immediately social media came alive with speculation and even outright claims that Hamlin’s collapse was due to the COVID vaccine. Without knowing whether he had even been vaccinated, conspiracy quacks immediately linked old reports of rare post-vax events of cardiomyopathy in young adults and occasional problems with blood clots with Hamlin’s sudden cardiac arrest. They completely ignored other explanations such as how the blow to Hamlin’s chest during the tackle could have caused his heart to fibrillate.

Your still humble blogger attests that this can be a concern to blows to the chest during sporting events. As a 13 year-old, playing first base in a summer league, I was knocked off balance by a runner scrambling to return to the base as the second baseman zinged a fastball to me to pick off the errant opponent after snaring a line drive. The ball hit me square in the chest over my heart and dropped me to ground. I don't remember anything for a few moments, and I was whisked by ambulance to an ER where my heart function was carefully monitored for a few hours before I was released. It was suspected, but not proven, that I had a brief cardiac event but quickly recovered on my own and I was no worse for the wear. It happens.

That conspiratorial chorus in the ether was soon followed by a similarly crazy cacophony of television and radio talking heads also intimating, again without facts, that Hamlin had suffered a vaccine-related cardiac side effect. These pundits included popular host Tucker Carlson who, on his Fox cable show just two days after the game, while Hamlin was still hospitalized in an induced coma, called medical experts “witch doctors” as if he knew more than they did. Dallas cardiologist and anti-vaccine podcaster, Peter McCullough announced on Carlson’s show that ‘vaccine induced myocarditis” likely caused Hamlin’s episode (I guess McCullough was not a “witch doctor” or a “medical expert” according to Tucker's criteria).

Even the very evening that Hamlin collapsed, Charlie Kirk, a radio talk show host, and COVID vax conspiracist claimed on Twitter that many athletes across the country are suddenly dropping like Hamlin did because of the vaccine. And the same evening there was an Instagram post from bodybuilder Louis Uridel showing a screenshot of a tweet stating that Hamlin's cardiac arrest was caused by the COVID vaccine. "24 year old elite athletes in the NFL don't just have a cardiac arrest in the middle of a prime time game," the tweet read. "This is squarely on the back of every single person who pushed that poison…", meaning the vaccine.  

An astonishing statistic is circulating throughout many social media circles claiming that more athletes died suddenly in the last year than have died in the last 38 years, implying that the vaccine is to blame. This originated with the same Peter McCullough who Carlson had on his show right after the football player collapsed. McCullough published a letter on Dec 2022 examining sudden cardiac deaths (SCD) in athletes. The problem, however, is that in his research he did not compare apples to apples. According to an epidemiologist who dug into McCullough’s data, he often compared cardiac events young athletes to events in old athletes(!), he mixed definitions of SCD indiscriminately, he included people who didn’t die of SCD or people who were not even athletes, and he even included people who did not die. But, the damage had been done; McCullough’s letter has spread far and wide and is now conspiracy gospel. Conspiracy buffs don’t really care about data, it is the headlines and talking points confirming their bias that grab and keep their attention. So, the false claim that the vaccine is causing excess deaths in athletes persists.

It is true that most conspiracies are often anchored in some fact, and on that foundation, the rest of the flimsy house of fantasy is constructed with fakery and fraud. Therefore, it is true that some COVID vaccines have been linked to very rare cases of myocarditis in young men. These cases were mostly very mild and were quickly resolved with no medical intervention needed. In fact, many cases were asymptomatic and were only detected because the sufferers participated in the clinical trials of the vaccines. Hence, trial participants were vaccinated and closely followed for adverse effects. This included regular blood draws which revealed that some vaccinated subjects with no physical symptoms at all still showed abnormal levels of a cardiac protein in their blood indicative of myocarditis, which quickly went away. These cases would have been missed completely if they had not been in the vaccine study. After now vaccinating hundreds of millions of people around the world, it is safely concluded that myocarditis following vaccination is very rare (~1 in 100,000) and not a serious problem. In fact, myocarditis following infection occurs seven-times more often than after vaccination, and is more severe. Therefore, it would have been more logical for Tucker Carlson, Charlie Kirk,  Peter McCoullugh, et al., to conclude that Hamlin’s problem resulted from a recent infection rather than a vaccination.

Then there is the blatantly dishonest video documentary, Died Suddenly, that is wildly popular in the anti-vax sector. It was made by Stew Peters and it asserts that people are dying in droves due to the vaccine, which itself was supposedly engineered by an elite cabal to depopulate the planet (seriously!). This video flashes through many alarming news headlines of people dying and shows videos of people collapsing, supposedly after receiving a vaccine. Whole essays have been written rebutting this video (you can read one here), but here are some quick take away points: 

• Google the news headlines shown in the video and you will learn that many incidents were not caused by the vaccine. In one headline, the person died in a car accident not from the vaccine. Another died before the vaccines were even available! Yet another collapsed during a basketball game, also before the vaccines, but never died. How inconvenient.
• The video alleges that mRNA vaccines are killing people via blood clots. As “evidence” it simply shows images of blood clots being removed from the blood vessels of cadavers. However, it fails to mention that blood normally clots after death! Ooops. No other evidence for vaccine-induced clots causing widespread death is offered.
• The video also showed images of a huge blood clot (a pulmonary embolism) being surgically removed from a lung vessel, letting viewers assume the clot was caused by the vaccine. However, the footage was from a 2019 medical education video, that was made, once again, before vaccines were available!

The Died Suddenly documentary is dishonest to say the least, yet it is regularly trotted out as prime evidence for the danger of the vaccines.

If the vaccines are so dangerous, one wonders why the evidence needs to be fabricated!

In the end, COVID vaccines prevented 18.5 million additional hospitalizations and 3.2 million additional deaths in the US. Prevented not caused. 

Spreading vaccine disinformation can be very lucrative. It can bring in advertising revenue, attract subscribers, and help sell supplements and nostrums.

Twelve people are responsible for 65% of the vaccine disinformation on social media in the US, and they do so for profit. Their impact is mostly seen on Facebook, but there is plenty of vaccine disinformation on Instagram and Twitter as well.  Here are some notable examples.

• A scientific study published in the science journal, Nature, reported that by far most (25%) of the COVID vaccine disinformation posts come from the organization, Children’s Health Defense, an anti-vaccine organization owned by Robert F. Kennedy, Jr, the 69 year old son of the late Senator, and recently declared Democratic candidate for US president. RFK, Jr., is a long-time opponent of vaccines. Any vaccine. He gained more than 1 million new paying subscribers in 2020 and traffic to his website rose sharply in March 2021 with 2.35 new million visits in response to his anti-COVID vaccine efforts.
• Joseph Mercola, DO actually claims in hundreds of Facebook articles that the vaccines will alter your DNA and turn you into a viral protein factory. He does this in order to promote the sale of supplements, books, and health food. During the height of the pandemic, he promoted a new website designed to prevent or treat COVID with his alternative remedies. His business has a net worth of $100 million! As I explained earlier in these pages, it is biologically impossible for the mRNA vaccines to affect your cellular DNA in any way. Mercola is selling a flat lie for profit.
• Steve Hotze, MD a Houston based doctor who used social media to unabashedly tell people to not vaccinate, but rather buy his vitamin and mineral concoctions, which, he claims was all one needed to fight the virus and many other diseases. In his case, the FDA found the products and marketing to be misleading and issued a cease and desist order.

Bottom line. The insidiousness of these charlatans is that while they claim to be saving peoples’ lives, they are causing deaths. The Kaiser Family Foundation found that between June 2021 and March 2022, 234,000 deaths could have been prevented in the US with COVID vaccinations. Vaccine disinformation that convinces people to avoid being immunized against the virus that causes COVID, undoubtedly caused many of these deaths.

How is a death caused by these deceitful claims about vaccines different from a death caused by criminally refusing to give insulin to a diabetic in crises?

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The Virus Came From Wuhan Lab DOE Now Says…..Sort Of

 “Where’s the beef?” Clara Peller in a 1984 Wendy’s commercial

So, the world has been abuzz since the Department of Energy recently reported that it decided, albeit with low confidence, that the SARS-CoV-2 virus might have leaked by accident from the virology lab in Wuhan. Across cable television and the internet, including sources such as Fox, Breitbart, Joe Rogan, gossip lines, et al., are full of “I knew it all along,” and “I told you so’s.” Never have so many virology experts suddenly been spawned on Facebook. And most of them could not tell you whether a coronavirus is an RNA or DNA virus, let alone the difference between RNA and DNA.

But let’s slow down a bit. Have you even wondered why the Department of Energy is releasing an assessment about a virus? And did you wonder what data they based their assessment on? I did and I explain it here. What I learned tells a much more complete, and less compelling story than what most of the priests of the press, Junior virologists, and other rumor mongers have reported. What has been reported has been woefully inadequate and vastly misleading.

The DOE report was based on intelligence data that remains classified, and is not a science report. Apparently intel spooks weigh science information much differently than scientists do, and often put less credibility in published science because the information usually does not come from “trusted” sources that an spook has history with (their version of "peer review" I guess). The US intelligence community is distributed between 18 agencies, including Energy, State, Treasury, and others including, of course, the CIA, FBI, and DOD. Eight of these entities have been involved in reviewing the COVID-origins issue.

In 2121, the Energy Department, which oversees 17 national laboratories, several of which study SARS-CoV-2 and its origins, reported it was undecided on how the virus emerged. What caused DOE to recently change their assessment is not known. They are not releasing the classified data. Therefore, their information appears not to be scientific data, which is usually published. Four other unnamed agencies, along with a national intelligence panel, still judge that the virus was likely the result of a natural transmission from an animal to humans, and two other agencies are undecided. Only the FBI agrees with DOE in thinking that the virus leaked from the lab. Notably, the CIA also remains undecided. In other words, the DOE’s opinion is a minority opinion of low confidence in the intel community. It is hardly worth all the breathless excitement it elicited from Tucker Carlson and other bloviators who now dishonestly insinuate that it has now been proven the virus came from the lab. That is far from decided.  

The intel community’s definition of low confidence intelligence is “that the information’s credibility and/or plausibility is uncertain, that the information is too fragmented or poorly corroborated to make solid analytical inferences, or that reliability of the sources is questionable.”  Someone should send that to Tucker.

The origin of the virus has been actively investigated over the last couple of years and your sometimes humble correspondent has reported previously on those investigations in these pages (it is worth reading for background). These blog posts have favored the natural origin of the virus, because that is what the preponderance of data have suggested. There have been no published data supporting a lab leak hypothesis. None. Also, recent science reports in top-flight science journals continue to conclude that the virus had a natural origin. A paper just published in 2023 in Cell reported that SARS-CoV-2 is the ninth known coronavirus to have jumped from an animal into humans. Two earlier reports in Science, and also summarized in these pages last March, agreed that the virus originated in the Wuhan wet market not just once, but twice. These studies included genetic evidence and epidemiological tracing showing that the early cases of COVID all centered around the Wuhan wet market and not around the lab eight miles away.

Furthermore, back in 2020, I also wrote a summary of how the earliest events of the pandemic unfolded. Here is a synopsis of the first few days: On December 31, 2019, Chinese officials informed the WHO about a cluster of 41 patients with a mysterious pneumonia in the city of Wuhan associated with a new coronavirus. Then, in the middle of that night a Chinese CDC team from Beijing arrived and collected 585 “environment” samples from a garbage truck, drains and sewers in the wet market. Thirty-three of the samples tested positive for the new coronavirus. Fourteen of the positive samples were from the area of the market where wildlife was traded. At the same time, Wuhan officials quietly began disinfecting the market, and it was closed.

It is interesting that the immediate focus was on the market and not the lab.

Keep in mind that we have very many examples of viruses, including several other coronaviruses similar to SARS-CoV-2, spontaneously passing from animals to cause disease in humans. This includes the first example of SARS-CoV-1 that came from a food market in China in 2002, and then MERS, which passed from a camel to humans. It was natural for medical scientists to first think that SARS-CoV-2 arose similarly. So far, the evidence is not convincing that it did not. The fact that we have not yet convincingly identified an animal source for the virus is not surprising. It took 30 years to establish the source of the HIV virus, and we still do not know the source of the Ebola virus.

So far, despite the very weak statement from the DOE, the preponderance of data still favors a natural origin of the virus, not a lab origin. But, that still is far from definitive. That “preponderance” of evidence, can change in a hurry with new data. Therefore, it remains worth further investigation. But until the Chinese government allows outside scientists to review lab data books and interview scientists from the Wuhan labs, the investigation will proceed with one hand tied behind its back. It remains remotely possible that an animal carrying the ancestral coronavirus will be caught confirming that it did come from an animal. Yet, even if we did find an animal source for the virus, it may not tell us about the path it took to get into humans. We might never know that to the delight of the conspiracy nuts and fabulists out there who have never weaned off the teat of fantasy.

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Pandemic History: Long COVID

"We learn from history that we learn nothing from history."
--George Bernard Shaw

Let’s hope GBS is wrong about what we learn from the recent pandemic. As it recedes in our rear view mirrors, scientists are looking to all the data and information collected to retrospectively see what we learned about this new virus and disease. This is especially true for that totally unexpected disease phenomenon called “long-COVID.” As we became aware that some COVID survivors continued to suffer from a strange constellation of symptoms, referred to as long COVID, I wrote in these pages about what that affliction entailed, and what we were seeing and discovering about it. You can find several other blog posts on that topic by looking under “long COVID” in the "Categories" listed to the side of this post.

Long COVID was particularly difficult to study since, by definition, it lasts months, maybe even years in some people. That means that discerning how it manifests itself, and how to effectively treat it would take months to flesh out. We have gleaned a bit about that and also have identified areas we need to look at more closely in order to fully understand this part of the disease.

A Scottish study of about 100,000 participants began while the pandemic fulminated, and the results of that study are just being released. The study helps clarify how to diagnose long COVID, which earlier had vexed physicians who had no idea what they were looking at. Long COVID presented doctors with a hodge-podge of seemingly unrelated symptoms—was it a single disease? Different disease manifestations? Psychosomatic? What it then was was a head scratcher. The Scottish study helps confirm that it is a real COVID-associated problem, and the most common symptoms include breathlessness, palpitations, chest pain and “brain fog” or reduced mental acuity. We also learn from the study that the risks of acquiring long COVID is greater in women, older people and economically disadvantaged people. Also, people already dealing with other physical and mental health problems, such as respiratory problems or, surprisingly, depression, are more prone to long COVID. Why is that? The study also found that 1 in 20 people had not recovered up to 18 months after coming down with COVID. It also reported that people with asymptomatic infections were unlikely to suffer long-term effects, which helped confirm what we expected, that it probably is not the virus that causes long COVID, but the culprit is some people’s immune response to the virus. Who are those people susceptible to long COVID, and what is different about their immune response? It also seems that vaccination protects a bit against long COVID, but not as much as previously thought. But, this observation complicates things. The vaccine is designed to stimulate an anti-virus immune response without the risk attendant to an infection. Why doesn't this immune response cause long COVID symptoms like the immune response to the actual infection? Basically, how it all works still is not well known, but that bit of new information scientists are gleaming from the data moves us gradually closer to finding out.

Looking at other data collected since the pandemic reared its ugly head, the WHO estimates that about 10-20% of COVID survivors have lasting symptoms that reduce their quality of life to varying degrees.

The Washington Post reports that somewhere between 7-23 million Americans currently suffer from long COVID. One million of these are unable to work. People are not dying from long COVID, but they often are considerably impaired and that makes them heavy consumers of expensive medical care, and often unable to work at full capacity, which adds to the personal and social costs of the chronic complication.

Anthony Fauci, in an interview with The Guardian, cautions that even though COVID deaths and hospitalizations are declining, it is premature to declare victory over COVID since we continue to deal with the insidious chronic sequelae of the disease. Furthermore, all indications suggest that COVID will be a recurring problem for the world and as it regularly sweeps across the globe, it will continue to create new cases of long COVID. This means that we still need to remain vigilant to avoid the virus when possible, and to make sure that vaccinations are effective and available to the population. Other therapies continue to be explored, but, unlike, antibiotics that fight bacteria, safe anti-viral drugs are very hard to develop because they often come with too extreme side effects.

Continued research into the virus and disease by medical scientists, and further examination of the pandemic history by epidemiologists hopefully will lead to a better understanding of the causes of long COVID, how to more definitively diagnose it, and ultimately how to effectively treat, or even prevent it. Toward these ends, Fauci’s National Institute of Allergy and Infectious Diseases recently launched a $1.15 billion initiative to achieve these goals. The CDC also recently began its own major study of the problem.

Stay tuned for changes in how we deal with the virus and with long COVID as we learn more about it. That is how science works.

COVID More Deadly Than Flu For Kids

In the US, nearly six times more kids and teens died from COVID in one year than did from the flu, according to a new analysis of pediatric mortality data. According to CDC data, childhood flu deaths have ranged from 39 to 199 per year since 2004. Meanwhile, in 2021 alone, more than 600 children died from Covid-19, according to an analysis done by researchers at the Harvard University Medical School and at Brigham and Women’s Hospital in Boston.  The analysis used data from the CDC to compare COVID deaths during the pandemic to flu deaths over the last decade (see figure below).

Of the known respiratory viruses, only CoV-2 has ever killed more than 100 US kids in a single month since the middle of the 20^th century. Much of that is because we have long had vaccines for other viruses that cause human respiratory disease, but have yet to widely vaccinate children against COVID-19. Hopefully, new vaccines will also render COVID less deadly for kids like vaccines have done for several other respiratory diseases.

Throughout the pandemic, some have argued that COVID poses little health risk to kids aside from a few days of sniffles. Though kids often experience less-severe symptoms than adults, COVID is still a very real risk. An estimated half a million kids now deal with long COVID, a number that experts say is likely an undercount because its myriad symptoms make it tricky to diagnose.

Masks Redux

"You’ve got to be very careful if you don’t know where you are going, because you might not get there."

—Yogi Berra

As cases of COVID-19 ascend in areas of the US, some schools are reverting to requiring masks. Of course this is accompanied by renewed claims that they are ineffective. In fact, Florida governor Ron DeSantis issued an executive order barring local school districts from requiring their students to wear masks, claiming that there was no evidence that masks prevent infection in schools. That claim has been levied over and over by many politicians, talking heads, pundits, and assorted Facebook “experts.” But, they are flat wrong. There are multiple lines of evidence from a variety of disciplines—including materials science, infectious diseases, pediatrics and epidemiology—showing that masks can help protect children and teachers from getting COVID in schools. Some of that evidence has already been presented in these pages, and I now add to that body of evidence, more  data recently summarized in Scientific American.

1. For starters, laboratory experiments show that masks block the respiratory droplets and aerosols that transmit SARS-CoV-2, the virus that causes COVID. In one test, an engineering team at the University of Wisconsin–Madison used a machine in a classroom setting to pump out particles the same size as those that carry the virus from an infected person. The researchers placed several CPR dummies with or without masks around the room and measured the degree to which the aerosols penetrated the masks. They reported that a surgical mask reduced the chances of penetration by 382 times when compared to the maskless mannequins.
2. Then, in the real world, not a laboratory setting, several epidemiological studies also concluded that masks in schools work. Researchers at the ABC Science Collaborative in North Carolina collected data from more than a million K–12 students and staff members from schools across that state, which mandated masking in schools from August 2020 until July 2021. The scientists reported little in-school transmission when the mask mandates were in place during the fall, winter or summer months. During this time, in-school transmission remained low as COVID cases fluctuated outside the schools. With mask mandates, rates of within-school spread were as low as one percent.
3. Masks, combined with other prevention efforts, also reduce the risk that students might bring home the virus to parents or other relatives. An online survey of 2.1 million Americans by researchers at Johns Hopkins University showed a 38 percent increased risk of COVID-related illness in households with a child attending school in person. That risk went down, however, as the number of school-based mitigation measures, including mask mandates went up.
4. Studies done in wider communities beyond schools give the strongest real-world evidence that masks stop COVID’s spread. An international team of researchers conducted a randomized controlled trial involving nearly 350,000 people across 600 villages in rural Bangladesh. Half of the villages got free cloth or surgical masks and a promotional campaign encouraging their use. The other half did not. The researchers found that the mask intervention significantly curbed coronavirus transmission.

Bottom line:  The effectiveness of masks in schools is supported by many different studies and analyses that show similar results. There are more than a dozen studies beyond those cited here, that all point to the same conclusion:

Masks work.

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What Happened To The Flu And Other Respiratory Diseases?

A NYC based travel blogger who travels a lot used to get a respiratory infection whenever she flew. That stopped when the airline mask mandates went into effect. The mandates, of course, were designed to hinder the spread of the CoV-2 virus that causes COVID, but it makes sense that if masks and other physical (that is, non-medical) mandates worked to mitigate COVID, then we would see a decrease in other contagious respiratory diseases after the mandates were, well…mandated.

We did.

The mandates worked, despite persistent claims of some to the contrary. This particular blog subject was stimulated by a radio talk show where a couple of nonscientist talking heads announced that there was no scientific proof that the masks or other mandates prevented disease. I previously posted in these pages evidence that masks, in particular, do indeed work to retard the spread of disease (see here, here, here, and here). In this post, I present further data on how the mandates significantly reduced the incidence of other infectious respiratory diseases around the world. If the measures can reduce flu, then you can bet that they also reduced COVID-19.

Note, however, that this is not necessarily an endorsement for returning to the measures. Your humble scribe didn’t much like his glasses fogging up, or having to make two trips from the car to the store because he forgot his mask. But, let’s argue the issue based on its merits and not from false premises based on incorrect claims.

After South Korea implemented various hygiene and social distancing measures in response to COVID, they saw the 2019-20 flu season end an astounding 12 weeks earlier than the previous year. Epidemiological surveillance data bolstered by clinical diagnostic testing showed that infection from several different pathogenic respiratory viruses (including adenovirus, bocavirus, metapneumovirus, rhinovirus, flu, parainfluenza, and respiratory syncytial virus) dropped to nearly 0% just five weeks into 2020!

In the United States, the incidence of infection by influenza, respiratory adenovirus, rhinovirus, enterovirus, RSV, non-COVID coronaviruses, metapneumovirus, and parainfluenza viruses all decreased in March 2020, soon after implementation of mandates. Similar results were seen in Japan.

More dramatically, since pandemic mitigation measures were put in place, there has been a 99% global reduction of infections from both influenza types A and B compared to prior years. In particular, one of two flu B substrains has not been isolated in the world since August 2021 suggesting that this variant is now extinct. The overall genetic diversity of influenza viruses has also dramatically diminished indicating that other flu sub-types (or clades) have disappeared around the world since the pandemic mandates were put in place.

And this reduction of respiratory infectious disease does not only hold for those caused by viruses. Another study looked at surveillance data from 26 countries across 6 continents for several bacterial diseases caused by Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, which are typically transmitted via respiratory droplets. Numbers of weekly cases in 2020 were compared with corresponding data for 2018 and 2019. Data for disease due to Streptococcus agalactiae, a non-respiratory pathogen, were also collected from nine laboratories for comparison. All countries experienced a significant and sustained reduction in respiratory bacterial diseases in early 2020 (Jan 1 to May 31), coinciding with the introduction of non-medical COVID containment measures in each country. By contrast, the incidence of disease due to S agalactiae (which is not transmitted by the respiratory route) did not differ significantly from the 2 previous years.

Clearly, the mandates significantly reduced the incidence of respiratory infections by non-COVID viruses and bacteria. They worked. So, why did we still have COVID infections after the mandates went into place? The mandates reduced, not eliminated these diseases, so infections still happened. Since we did not have historical COVID infection data from previous years to compare with, the effects of the current mandates on the incidence of COVID are not as clear cut as they are with other diseases for which we do have historical data for comparison. But, as I wrote before (see above), it is clear that places in the US and around the world that used masks and other protective measures saw reduced incidence of COVID compared to similar places that did not.

Bottom line: The studies mentioned here regarding non-COVID infectious diseases fully support data previously posted in these pages that the mandates, including masks, are effective non-medical tools for controlling infectious respiratory diseases.

Don’t let anyone tell you differently.

A Single Gene Doubles Risk Of COVID Death

“Nothing shocks me. I’m a scientist.” —Indiana Jones

British scientists recently identified an allele, or a version of a gene, that portends lung failure and death in COVID-19 patients. Research recently published in the journal Nature Genetics, found that a poorly studied gene expressed in lungs, designated LZTFL1, has a variant form that does not differ in its coding sequence. That is, the different alleles of the gene express the same protein sequence. They do differ, however, in their non-coding sequences that regulate expression of the gene. When expressed, the gene product prevents cells lining airways and the lungs from responding properly to the CoV-2 virus. The lining of the lung essentially transforms into less specialized cells which affects their normal function.

Previous work had identified a stretch of DNA on human chromosome 3 that doubled the risk of death from COVID. Using an artificial intelligence algorithm to analyze millions of genetic sequences from hundreds of cell types from all parts of the body, the Oxford University Howard Hughes research team honed in on the lung-specific genetic off-on switch. This is another example of what I previously labeled "BioX," the new frontier of bioscience, or post-molecular biology science.

Importantly, the variant allele that augurs a worse lung response to infection does not affect the immune system. Therefore, the it is probable that vaccination remains the best way to protect these at-risk patients. Finding this new allele could also lead to novel therapies to target the pathway affected by this genetic variant to provide targeted treatment for at-risk populations.

The troublesome variant is mostly found in people of South Asian ancestry—some 60% of whom carry the allele—which partly explains the severe devastation from COVID seen in the Indian subcontinent. In contrast, 15% of those with European ancestry and 2% of Afro-Caribbean people carry the risky allele.

It will be interesting to see if this lung-specific gene also affects the course of other respiratory infectious diseases.

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Lingering Post-COVID Vascular Risks

George Burns once opined that “the secret of a good sermon is to have a good beginning and a good ending; and to have the two as close together as possible.” The same might be said for blogs. If so, this is a pretty good blog post.

We have known for some time that patients with COVID-19 are at risk for dangerous blood clots (also called deep vein thrombosis, or DVT), pulmonary embolism, and bleeding. Findings reported this month in the British Medical Journal reveal that this risk continues several months after COVID recovery.

The study compared more than one million people in Sweden who had COVID-19 to a control group of more than 4 million people who did not. The overall risks for each problem were low, but still elevated for up to six months following COVID. According to the report, DVT occurred in 0.04% of patients who had had COVID and in just 0.01% of control patients during the same time. Pulmonary embolism occurred in 0.17% of post-COVID patients and in 0.004% of control patients. And bleeding events occurred in 0.10% of patients who had recovered from COVID, while only 0.04% of control patients had such a problem.

While the risks of blood clots and bleeding were highest in patients whose COVID had been more severe, those who had had mild COVID still showed an elevated risk.

Bottom line: You are not out of the woods after you recover from COVID. Significant problems can arise a few months later.

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Still More Evidence For An Animal Origin Of The Virus

Conspiracy buffs won’t like this, but compelling new evidence presented in three papers, which include photographic and DNA data, has pretty much nailed down the origin of the SARS-CoV-2 virus. It began in a wet market animal not in the lab eight miles away as the conspiracists have conjectured. This new data comes from an international team of scientists which concluded that the coronavirus twice jumped from  caged wild animals into people at the Huanan Seafood Wholesale Market in Wuhan. These data correlate nicely with previous geo-epidemiological data showing the market, not the lab, to be the infection nidus with later infections radiating out from there.

Despite the Chinese’s government denial that live animals were sold in the Wuhan market, the new studies provide photographic evidence of wild animals sitting in stacked cages in the market in late 2019, in or near stalls where scientists found SARS-CoV-2 virus on a number of surfaces, including on cages, carts and machines that process animals after they are slaughtered at the market. This, along with a new genetic analysis pinpoints a specific stall at the market where the virus passed from an animal into people. These data also estimate the time when not just one but two zoonotic spillovers occurred, once in late November or early December and then again few weeks later. This coincides almost exactly with the timing of the outbreak of disease at and around the market.

The two initial infection events involved slightly different versions of the SARS-CoV-2 virus. The fact that they were related is evidence that the virus had spread and mutated in animals in the market before it infected humans.

A leader of two of the studies was U of Arizona professor, Michael Worobey, a viral pandemic sleuth who has been at the forefront of the search for the origins of the bug responsible for the current pandemic. His lead in the research is significant since, back in May, 2021, Worobey, along with 17 other scientists, called for investigation into the lab-leak theory. His latest research overturned that conjecture. This new evidence adds to previous evidence for an animal/market origin of the virus presented earlier in these pages here and here.

Final thought. It is sobering to think how these two simple infection events that occurred in November and December of 2019 in a Chinese market triggered something that has now caused six million deaths and untold misery around the world. And it is not finished with us.

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