Making Sense of Medical Science (MSMS)

A medical scientist explains medical news for lay people

recent posts

about

Steve Clark, PhD is a retired university professor with a PhD in immunology and a past Special Fellow of the Leukemia Society of America. Clark has published dozens of papers based on his research and holds two drug patents. He taught medical and graduate students about cancer biology and genetics, and about research ethics. He also directed an NIH-funded PhD Graduate Program and chaired several executive-level faculty committees. Clark served on the University Chancellor’s Speaker’s Bureau. While retired, Clark has been blogging on the COVID pandemic, which is the subject of his next book.

  • COVID And Kids

    On May 27, 2025, RFK, Jr. continued his anti-vaccine crusade by announcing that the CDC would no longer recommend COVID vaccines for children and pregnant women. The announcement was a complete surprise to medical scientists, physicians, and other healthcare professionals. It also was a huge surprise to the CDC, which was completely blindsided by the abrupt change in its vaccination recommendations. This misguided announcement also goes against the most recent data showing who is getting hospitalized and who is dying from COVID that Kennedy should be aware of but seems to be oblivious to.

    On April 15, 2025, just one month before RFK Jr.’s misguided announcement, Fiona Havers from the CDC presented the following data to the Advisory Committee on Immunization Practices (ACIP), the independent group of experts that advises the CDC on vaccines, and which Kennedy has purged and replaced with his hand-picked vaccine nay-sayers. Havers reported the following from the previous year in the US.

    • In just one year, 2024, about 165,000 people were hospitalized with COVID and 40,000 died from the virus. Of these, ~7100 COVID hospitalizations occurred in children and 150 of them died from the disease; more than who died from the flu. Most of the hospitalized were less than 4 years old and otherwise healthy (that is, had no co-morbid conditions to contribute the severity of their illness).
    • About 1 in 5 children hospitalized with COVID were admitted to the intensive care unit.
    • Significantly, >90 percent of these children who were hospitalized or died from COVID weren’t vaccinated.
    • A disproportionate number of children who died from COVID were <6 months old. Since newborns <6 months old have only rudimentary immune systems that need to mature over time, these children are initially protected from infectious diseases from their mothers’ antibodies that cross the placenta during fetal gestation. Thus, the only way these children could have been protected from COVID would have been if their mothers had been vaccinated during pregnancy as I explained earlier in these pages.

    Research data clearly have shown that vaccinating children and pregnant women is safe. Therefore, Kennedy’s change in the CDC vaccination recommendations, without feedback from the CDC, is reckless and will endanger the lives of thousands of children in years to come.

    Note: In order to have blog updates delivered to your email, see the simple Subscription Instructions here. Remember, you can easily unsubscribe when you want.

  • Are mRNA Vaccines Gene Therapy?

    "There are in fact two things, science and opinion; the former begets knowledge, the latter ignorance"

    -Hippocrates

    Note: In order to have blog updates delivered to your email, see the simple Subscription Instructions here. Remember, you can easily unsubscribe when you want.

    While this blog post is not directly about the COVID pandemic, it is about a related, unexpected outcome from that sad miasma that overwhelmed the world for a few years. The vaccine dissemblers have blithely and dishonestly equated the effective anti-COVID mRNA vaccinations with gene therapy. Derisively calling vaccines gene therapy, which is intended to tarnish both technologies, is the sort of ignorant, non-science opinion Hippocrates referred to above. There is no truth at all in that association, only ignorance. Vaccines are much different than gene therapy and mRNA cannot affect a cell’s genes at all. I explain all this below.

    Vaccines. We all have been lucky to live in an era where we have been able to get vaccinated for a plethora of infectious diseases that have “bugged” (pun-intended) humanity and even our animal friends from the beginning. Before vaccines, many of us often died or were greatly incapacitated from pathogenic bacteria, viruses, fungi and the nasty stuff they produced that poisoned us. It is no accident that human life expectancy has soared coincident with the appearance of vaccines to infectious diseases. Just go to a cemetery and count the number of childhood deaths of those born before 1950. Then count the deaths of kids born after 1960. The sharp drop in kids’ deaths is mostly due to vaccines.

    The first vaccine probably was nasty, unsanitary pus from a smallpox blister. The blister was popped and its unsavory contents were scratched into the skin of a recipient. This immunization was called variolation and was done in the 1700s (and it helped the Colonial army beat the Brits back then). This was a very crude, but pretty effective way to vaccinate against smallpox. Eventually vaccination moved on to other less risky and less yucky ways to confer immunity to smallpox and other pathogens—vaccinology science moved forward. These vaccines initially used whole viruses or bacteria that were grown in large vessels in the lab and either killed, inactivated, or otherwise treated so they could infect or otherwise stimulate an immune response like an infection, but not cause disease when injected. In other words, the bug, with its full genetic complement went into your arm to simulate disease. As a result, your arm often became sore and you sometimes felt crummy for a few days, sometimes running a low grade fever. On rare occasion, the reactions to the shots were worse, but your immune system was fully awake without you actually catching the disease.

    Basically with these types of vaccines, which were developed in the 1800-1900s, and iterations of which still are used today, we got the full immunological load of the pathogen without any of the virulence of the bug we were immunized against. In other words, our immune systems were tricked into thinking we were infected with a live germ by exposing them to a pseudo-infection that could not make us sick—a vaccine. Our immune systems went into full response mode, yet with the crippled pathogen, we did not get the disease it normally caused. Better yet, we did not even get sick, or get very sick at all when we did encounter the viable malevolent agent in person later in real life—we were protected. Vaccines were a brilliant preventive medical science discovery.

    Now, stop and think of all that DNA and RNA from all the vaccines that have been pumped into your arm over your lifetime. Also consider all the foreign DNA and RNA that has been pumped down your gullet with the food you have eaten—after all meat and plants we eat are organisms consisting of millions of cells, each of which contain DNA and mRNA. Then consider all the airborne germs and dirty bugs you have inhaled, licked, or scraped up over your lifetime. We have taken in a ton of foreign DNA and RNA from all sorts of microscopic things we cannot see ever since we were born. We are used to it. It usually is no big deal and our immune system does a pretty darn good job keeping us upright after this lifetime of continuous pathogen exposure.

    Most things in life tend to progress and improve over time, from housing, travel, communications, sanitation, and so on. So does medical science including the science of vaccines. In fact, the mRNA technology, which took decades to develop as I described here previously, and that gave us the COVID vaccines, is such a modern advance in medical science. The technology won the medical science Nobel Prize in 2024 and is fast at work making many new, previously impossible vaccines to HIV, malaria, cancer and other things. Other mRNA-based technologies beyond vaccines also are in development. We are in the midst of a medical revolution that many people with strange, strong objections to the science automatically reject. They are like the folks who were so comfortable with their horse and perfectly fine buggy that they automatically rejected the new-fangled automobile when a few visionaries like Henry Ford who could see as far as the future came out with the new transportation technology. Today’s anti-vaxers are like yesterday’s Luddites who rejected the auto in order to retain the old standard horse and buggy. Well, science won and opinion lost. You don’t see too many horse and buggies these days.

    Never once did anyone ever called the enormous amount of whole microbial genomes we have taken into our bodies since birth via vaccination and other various routes gene therapy. Then suddenly, about 2021, a vaccine that contains just a fragment of one viral gene, excluding all the rest of the viral genome and the rest of the virus itself is suddenly pejoratively labeled “gene therapy.” If the full virus with its entire genome was given as a vaccine, it would not have been sinisterly labeled gene therapy. What changed in people’s minds where a genetic fragment was suddenly considered a genetic poison when the entire genome was not?

    As immunologists have learned that we don’t need the entire pathogen’s genome to develop a protective immune response. We can narrow what the immune system needs to be teased with in order to think its turf is being invaded. Then using the modern bio-science I earlier dubbed BioX, all we now need to do, rather than grow dangerous bugs in vast vats, inactivate and purify away the contaminates, we can just sequence a very small part of their genetic goodies, stick it in a lipid micro-bubble and provide the same kind of immunity to millions of people. With this, we eliminate most of the risk of having to handle and grow and inject dangerous pathogens. And we can do all this in weeks instead of years. That is what the mRNA vaccines did. That is the new medical science. We are now in the world of modern science and that wins over stale opinion.

    Gene therapy. Notice that when folks are opposed to something like a new vaccine, but don’t really understand that thing, they typically don’t debate it using specific well-reasoned science arguments. Rather they use vague innuendo or unsupported allegations that try to associate the thing with something else that is risky, unsound, or otherwise unfavorable in order to sway public opinion against it. This way, they don’t actually have to directly argue against vaccines, just associate them with something else that is sinister. When you recognize this tactic, you should ask these questions; “exactly what is the associated technology in question, is it being portrayed accurately, and is it really linked to the central technology at hand?” So let’s bring all this back to the COVID vaccines and ask those questions now: What is gene therapy? Is it really as sinister as anti-vaxers imply it is? And is gene therapy at all relevant to the COVID mRNA vaccines? I address each of these questions below.

    What is gene therapy? The formal definition of gene therapy is any treatment that intentionally and permanently modifies a cell's genome. Does the mRNA vaccine do that? We examined the basics of vaccines earlier in this article; now let’s explore gene therapy a bit.

    While the idea of gene therapy was first conceived in the 1960s, it didn’t come into much use until the 21st century. It is now successfully used in a few relatively rare inherited genetic diseases caused by single-gene defects such as certain muscular dystrophies, cystic fibroses, sickle cell anemia, some cases of blindness, hearing loss, etc.  

    Getting to a gene therapy cure for such a disease is arduous using classical molecular biology. In each case where it is used, the disease-causing defective DNA sequence first must be identified, which can involve many years of old-fashioned gene cloning and molecular biology lab research (boy, it breaks my heart to call that research “old-fashioned).” Then the “normal,” or corrective gene sequence also must be isolated and cloned into a “gene vector” or carrier via several DNA cloning steps, which also can take significant amount of time. The carrier with its corrective genetic sequence is then administered to the diseased cells. This is done either in the lab in isolated diseased cells, or sometimes directly in the patient. If the gene is introduced into cells in the lab, then the cells are given back to the patient.

    Is gene therapy a type of sinister Frankenscience? Above is a very basic explanation of the very complicated technologies and multiple steps involved in current gene therapy; a technique which already is becoming obsolete. It has taken decades to figure out how to do this for a relative few genetic problems in single genes. Now, however, we are in the modern era of biological science where we can now treat even more difficult genetic disease problems without even having to go through all the arduous steps of replacing problem gene sequences. Instead, we actually can now correct the genetic defect right on the chromosome. This is a type of modern, personalized gene therapy called gene editing. In a way, it is like correcting a misspelling in a document on your computer, only a bit harder. It is now being used and developed for treating individual genetic diseases, viral diseases and certain cancers. How can any of this be taken as something sinister?

    Can mRNA vaccines affect genes? Note that the mRNA vaccine does none of the above. In fact it is not possible for mRNA to affect your genetic DNA at all. Here is a simple description of how gene expression works: When each of your cells wants to express a gene, a copy of the gene is first made into messenger RNA or mRNA. That messenger is how the gene information gets from the chromosomes in the nucleus into the cytoplasm of the cell (hence the name “messenger). In the cytoplasm, proteins are made from the mRNA copy and these proteins are what makes a liver cell a liver cell, an eye cell an eye cell, and so on. After the mRNA gene sequence is translated into a protein, it is pretty quickly chewed up and the pieces recycled. mRNA is quite short-lived. It cannot and does not go back into the nucleus where your genes reside, so it cannot affect the genes on the chromosomes in the nuclei. That is biologically impossible. RNA and DNA, while related, are chemically different molecules, which is critical for their very different functions.

    It is biologically impossible for an mRNA vaccine to affect your cell DNA in any way. Think about it—it if could, then all of your cellular mRNA from normal genes being expressed, and the mRNA you eat, breath get from other vaccines, wounds, etc. could do the same. But it does not.

    Bottom line. Science revisionists who prefer to remain in the scientific horse and buggy days like to mention the COVID vaccine and call it “gene therapy” in an attempt to associate it with a supposedly malevolent technology—a kind of Frankenscience. That is because they cannot debate it on any real scientific point. It is notable that the mRNA technology, which languished in obscurity for many years, and almost disappeared due to lack of funding and general interest, finally exploded on the scene. This was based on a single, seminal finding that made the promise of mRNA, which, like many science breakthroughs at first only could only be seen by a couple of visionaries, finally became visible to the rest of science world. The technology then exploded and won a Nobel Prize in 2024 for being able to rapidly respond to a brand new infectious disease (COVID) and save millions of lives. It is a stirring story how all this transpired and two scientists, Katalin Karikó and Drew Weissman, perservered against daunting odds that threatened their careers. And consider how the idea of “gene therapy” in this narrative is supposed to be something sinister when it is linked to the mRNA vaccines. Gene therapy has only been used to correct terrible genetic diseases that heretofore have been incurable and have perplexed humans for centuries. What could be more dishonorable than using blatant lies and disinformation to discredit two new, cutting edge technologies that are now saving lives?

    Folks who live in the anti-vaccine horse and buggy world, it is time to join the modern world. Upgrade your buggies and roll up your sleeves. The times are passing you by!

  • Vaccinating Pregnant Women And Kids Against COVID: Suspicion vs Science

    Note: In order to have blog updates delivered to your email, see the very simple Subscription Instructions here. Remember, you can easily unsubscribe when you want.

     

    “There are in fact two things, science and opinion; the former begets knowledge, the latter ignorance.”

    -Hippocrates

    Background. The announcement in May on X by Health Secretary RFK, Jr. that the CDC will no longer recommend COVID vaccinations for children over 6 months and pregnant women took the entire CDC by surprise. Kennedy’s decree represents a profound policy shift as well as a major assault on science-based medicine. It completely abandons established procedures for vaccine policy development. Normally, recommendations for vaccines are made by the CDC director based on votes by the National Center for Immunization and Respiratory Diseases (NCIRD), and the Advisory Committee on Immunization Practices (ACIP), which meet in public with independent experts who review the evidence for vaccine safety and efficacy in order to make appropriate recommendations on their use. This review process was entirely bypassed. Kennedy made a solo decision without this sort of expert advice, public input, or peer review, which have long guided vaccine policy. This unvetted policy shift endangers vulnerable people, namely soon to be moms and their newborns who do not have a fully formed immune system, and young children. This surprise policy shift reflects Kennedy’s long-standing antipathy toward any vaccine. He is on record for claiming that there are no safe or effective vaccines. None.

    Then, just days after Kennedy’s unilateral policy shift, the CDC came out with its own announcement that countermanded part of RFK, Jr’s. anti-vaccine mandate. The agency kept COVID shots on its schedule for kids 6 months to 17 years old, but did not change the vaccine denial for pregnant women even though the FDA has just cited pregnancy as a high-risk condition for severe COVID disease, and the CDC website continues to encourage pregnant women to get the vaccine. At this point, it is not clear which policy, Kennedy’s or the partial pushback policy from the CDC will rule.

    Is Kennedy’s solo policy wise?

    The evidence for vaccinating pregnant women. The scientific foundation supporting COVID-19 vaccination in pregnancy is overwhelming and unambiguous despite Kennedy’s notions. Consider the comprehensive systematic review of vaccinating over 17 million pregnant women, which found no safety concerns for COVID vaccination during pregnancy. Nada. This massive body of evidence, gathered across multiple countries and healthcare systems, demonstrates consistent COVID vax safety through all trimesters of pregnancy, with no increased risk for stillbirth, preterm birth, congenital malformations, or pre-eclampsia. This conclusion is further bolstered by numerous other studies, too. What is missing is any scientific evidence that the vaccine is dangerous for pregnant women or their fetuses. On the other hand, in contrast to the vaccine, COVID itself increases a pregnant woman’s chance for stillbirth, preterm birth, hospitalization, and death. This is because the pregnant woman is relatively immunosuppressed and more susceptible to various respiratory diseases including COVID. All countries, except the US now, believe that pregnancy is a risk factor for COVID. The American College of Obstetricians and Gynecologists (ACOG) agrees with the FDA that pregnancy is one of the significant risk factors for serious COVID outcomes. For this reason, they too strongly recommend that pregnant women receive a COVID vaccine.

    Furthermore, maternal vaccination is doubly effective: it not only protects the mother from high-risk COVID complications, it also provides crucial protection over her newborn’s first six months via antibodies that are transferred from the mother to the fetus across the placenta. These antibodies from COVID-immunized women protect the newborn while it develops its own immune system so it can make its own antibodies. Specifically, ACOG released the following statement in response to Kennedy’s zealous policy manifesto:

    “ACOG is concerned about and extremely disappointed by the announcement that HHS will no longer recommend COVID-19 vaccination during pregnancy. As ob-gyns who treat patients every day, we have seen firsthand how dangerous COVID-19 infection can be during pregnancy and for newborns who depend on maternal antibodies from the vaccine for protection. We also understand that despite the change in recommendations from HHS, the science has not changed. It is very clear that COVID-19 infection during pregnancy can be catastrophic and lead to major disability, and…. (t)he COVID-19 vaccine is safe during pregnancy, and…can protect our patients and their infants after birth.”

    Thus, all the science shows that vaccination of pregnant women is a very good idea. Kennedy’s anti-science policy is not.

    What about newborns who can’t be vaccinated because their immune systems are not developed? Kennedy’s policy change excluding soon-to-be mothers from vaccination creates an especially dangerous gap in protection for infants younger than 6 months old, who were previously protected by maternal vaccination during pregnancy. These babies, too young to be vaccinated themselves, relied entirely on antibodies transferred from vaccinated mothers for protection during their most vulnerable early months of life. By removing recommendations for maternal vaccination, the policy eliminates this critical shield for newborns who lack an immune system, leaving them exposed to a disease that can cause severe respiratory illness, multisystem inflammatory syndrome, and other serious complications. These newborns will have to wait until they develop their own immune systems in order to be able to fight off infections like that which causes COVID.

    The evidence for vaccinating kids older than 6 months. Kennedy’s policy reversal against COVID vaccination in older children poses particularly grave risks for kids from the COVID complications described below.

    The rational for not vaccinating kids is that since children are at less risk than seniors from significant COVID health problems, they don’t need vaccination against the CoV-2 virus, which causes the disease. However, data show that this benign notion is flawed. As of 2022, at least 1,800 children have died of COVID in the United States (that is the equivalent of six jumbo jet crashes). In other words, about 600 kids died each year from COVID, while the flu death rate in children only ranged from 39-199 per year since 2004. Thus COVID is much more lethal than influenza in children. Beyond these fully preventable COVID deaths, many more kids required hospitalization, including intensive care. In 2023, one million kids, or about 1.4% of children, came down with long COVID, the chronic problem that bedevils many COVID sufferers well after contracting the disease. In kids, long COVID problems include headache, fatigue, loss of IQ points, a variety of GI issues, and memory and other neurological problems. Neuroscience research has shown that young people who have recovered from COVID often show distinct changes in their brain activity as measured by scans while performing cognitive tasks.

    Furthermore, kids can also develop a nasty multi-organ pathology known as Multisystem Inflammatory Syndrome, or MIS. MIS occurs post-infection and can lead to organ failure and other long-term health problems. The condition is reminiscent of toxic shock syndrome where different organs, including the heart, brain, lungs, kidneys, skin, eyes and GI system can become inflamed and/or fail. More than half of COVID MIS cases are under nine years old.

    All together, these facts provide sobering reminders that this disease is not benign in pediatric populations. Vaccination protects kids against serious COVID disease and death as well as against these complications of long COVID and MIS.

     Despite these substantial problems kids can face from COVID, I keep encountering people who totally dismiss the disease in children simply because its effects are more devastating on older people with other co-morbidities. But, it really is a very poor reason to brush aside the effect of the disease in children simply because another demographic fares worse. It is even worse to use this argument to say that kids need not be vaccinated as Kennedy just did. In children, the mRNA vaccines are about 90% effective in preventing the disease and its complications, and this protection is durable. Other studies show that keeping kids up to date on COVID vaccines helps reduce illnesses, doctor visits, missed school, and complications from long COVID and MIS. Unvaccinated children were up to 20-times more likely to develop long COVID than those who were vaxed.

    Bottom line. People who think that it is unnecessary to vaccinate pregnant women and young kids totally ignore well established science. As an immunology student, I remember learning some 50 years ago that maternal immunization provides important passive immunity for newborns from their mothers, giving babies time to develop their own immune systems. Furthermore, there is absolutely no credible evidence that such maternal vaccination harms the mother or the fetus. It also is abundantly clear that children over 6 months of age benefit in very important ways from COVID vaccination. Sure they seldom die from the virus, but all these deaths are preventable. Also, many more kids can and do succumb to serious complications from COVID that vaccination protects them from.

    What rational person could be against protecting kids from a preventable disease?

  • New Data On COVID Vaccine Deaths

    Note: In order to have blog updates delivered to your email, see the simple Subscription Instructions here.

    “There are two ways to be fooled. One is to believe what isn’t true; the other is to refuse to believe what is true.”  – Soren Kierkegaard

    Two years ago, a Kaiser Family Foundation poll showed that 34% of Americans believe that the COVID vaccines have caused thousands of sudden deaths. As a result, some health departments have been forbidden from promoting the shots or have had to even ban them. Furthermore, despite clinical evidence to the contrary, 27% of people believe that the vax itself causes infertility-it does not, and 31% still believe that the anti-parasite drug, ivermectin, effectively treats COVID-it has been proven not to.

    The rumor of “thousands of deaths” was partly driven by viral videos of young, healthy athletes collapsing on the field, alleging COVID vaccines were to blame. One of the most promoted of the videos, Sudden Death, has been exposed in these pages and by others as fabricated and blatantly dishonest. In many of the examples shown in the video, it has been proven that the collapsing athletes hadn't received a COVID shot, and deaths that did occur happened well before COVID vaccines were even available! Absolutely no evidence for a vaccine-related death can be found in that video.

    After the real on-field cardiac arrest of the Buffalo Bill's Damar Hamlin in 2023, another unsubstantiated rumor by Peter McCullough, an MD darling of the anti-vax crowd, reported that sudden deaths in athletes had increased dramatically after the vax rollout. But, an epidemiologist who dug into McCullough’s data, found that his numbers were inaccurate and inflated–for example, some of the "young athlete deaths" were not actually healthy athletes who died suddenly on the field, but instead were random news reports of people of all ages dying from many different causes, including an elderly woman who died at home! McCullough is now hyping a non-existing health problem in the US so he can sell people his nostrum he claims mitigates the problem. Go figure.

    Cardiac arrest. In contrast to all this disinformation, a new study published in the Journal of the American Medical Association last February specifically looked into vaccine-associated deaths. It examined whether there was any increase in sudden cardiac arrest (SCA) (where the heart suddenly stops, but the person survives), or in sudden cardiac death (SCD) in young US athletes after either the appearance of COVID (2020) or the introduction of COVID vaccines in 2021.

    The study found no association between the vaccine and cardiac problems. The highest year for both sudden cardiac arrest and death in the study was 2017, well before both the virus and vaccines were on the scene. Furthermore, the incidence of cardiac-related deaths did not change much from year to year, even AFTER the appearance of the virus or the vaccine! This is shown by the figure below (also notice how small the actual numbers are).

    FigureAstley et al, JAMA, 2025

    This finding is further supported by other studies that also have shown no increase in cardiac arrest in young people in general (ages 5-50) during the COVID vaccine rollout in Australia, and an overall decreasing rate of rare sudden cardiac deaths in NCAA athletes during the COVID vaccine roll out in the US.

    Myocarditis. Many conspiracy theories are rooted in partial truths that are overinflated and vaccine-induced myocarditis is no exception. There are real, but very rare, documented incidences of myocarditis (inflammation of the heart) after getting a COVID vaccine. Research from the Yale School of Medicine indicates that myocarditis happens in 0.036% of males age 12-17 after an mRNA vaccine. In contrast, this same age unvaccinated group experiences myocarditis twice that rate after COVID infection; thus the vaccine actually protects against the inflammation. Furthermore, vaccine-associated myocarditis is milder than other forms of myocarditis and patients quickly recover.

    Bottom line. In reality, serious adverse events were very rare in large, randomized mRNA vaccine trials and occurred at a similar rate among people who got the vaccines and those who got the placebos. Finally, if the vaccines are so dangerous, why does the evidence proving that need to be fabricated?

  • Tracking The Origin Of Coronaviruses Via Viral Genome Sequence Analysis

    Note: In order to have blog updates delivered to your email, see the simple Subscription Instructions here. Remember, you can easily unsubscribe when you want.

     

    “You are welcome to my opinion.” 

    -William F. Buckley

    Background. In early 2020, during the first weeks of the COVID pandemic, an unsubstantiated rumor circulated (and is still around) that the CoV-2 virus that caused the pandemic was a biological weapon created by the Chinese Army. However, a group of scientists analyzed the genome sequence of the spanking new CoV-2 virus and rejected that idea saying there was no molecular evidence that the virus was man-made. Although they couldn’t rule out an accidental lab leak, they favored a natural origin of the CoV-2 virus at the time. Fast forward several years and the science still predominately favors the notion that the virus arose from a wild animal found at the Wuhan live market.

    Eight of 18 US intelligence agencies have also examined the origin of the CoV-2 virus with mixed conclusions. Despite what scientists believe, the FBI, and more recently the CIA have come out in favor of an escape from the Wuhan Institute of Virology, although that conclusion is made with only the lowest of confidence. The Department of Energy intelligence folks also concluded with low confidence that the virus escaped from a different lab in Wuhan. Note that 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.” Meanwhile, the remaining five intelligence agencies do not favor a lab origin scenario.

    Importantly, the three agencies that favor a lab origin for the virus have not made their evidence public, so scientists cannot evaluate the bases for their conclusions. In contrast, several peer-reviewed science papers have been published on the topic and all conclude that the virus came from wild animals. Their prevailing understanding is that the virus then entered humans at the Huanan Seafood Market in Wuhan.

    One of the most common arguments for the lab origin of CoV-2 is that the virus first infected humans in a city that was hundreds of miles away from where bat coronaviruses are endemic. Proponents of lab-leak theories have pointed to the long distance between Wuhan and the locations where the closest relatives of CoV-2 have been found as evidence for a lab leak. They believe that Wuhan is too far from where coronavirus-infected bats roamed for bats to be the source of human-infecting CoV-2. Furthermore, Wuhan has a coronavirus research lab (the Wuhan Institute of Virology or WIV). If Wuhan was too far for bats to fly and then infect wild mammals, some people assumed that scientists at the WIV must have developed the virus in a lab from which it either escaped or was released.

    However, it is very relevant to note that in 2002 the first coronavirus, CoV-1, began infecting humans in Guangdong Province, China, which also was hundreds of miles from where bat coronaviruses are found. Notably, no lab in Guangdong Province studied coronaviruses. It was determined that a CoV-1-related coronavirus circulating in horseshoe bats jumped into raccoon dogs and other wild mammals in southwestern China. Some of those animals were caught and transported by humans for sale in markets in Guangdong where the coronavirus jumped again, into humans. The result was the first SARS pandemic, which spread to 33 countries and claimed 774 lives before non-pharmacological measure (read social isolation and masks) convinced it to quickly peter out in 2004 before any vaccine or medicine to treat it was developed. A few months into the first pandemic, scientists discovered the CoV-1 coronavirus that caused human disease (SARS) in mammals known as palm civets, which were sold in a market at the center of the outbreak hundreds of miles from where the virus was endemic. That was the smoking gun. It was concluded that the virus arrived there not by bat migration, but was carried there in infected animals by traders who sold the animals in the market. Wildlife animal traders were responsible for the fast appearance of the CoV-1 virus so far away.

    The Recent Study. Seventeen years after the first SARS pandemic began in 2002, another coronavirus, CoV-2, suddenly appeared and infected people in Wuhan, China launching the COVID pandemic that ravaged the world and is still with us. Like CoV-1, CoV-2, also first appeared several hundred miles from where coronavirus-infected bats are found. How did the virus get to Wuhan? Was it carried by bats whose average home range is about ½ mile and are not migratory (unlikely)? Was it created and released from the lab in Wuhan that did research on coronaviruses, or, like CoV-1, did it arrive with animals brought to the city by animal traders? New research published in the May 2025 edition of the journal Cell indicate that animal traders brought the CoV-2 virus with them along with the animals they sold in the live market.

    In the study, an international team of researchers mapped the evolutionary and geographic history of coronaviruses by first sequencing the genomes of 248 coronaviruses from bats. They then compared the genetic similarities and difference between all the different viral genomes to the known genome sequences of CoV-1 and CoV-2. From these data, they were able to use evolutionary modeling techniques to reconstruct relationship trees and dissect the evolutionary history of the coronaviruses that cause both SARS and COVID. The researchers then showed that the spread of the CoV-2 virus doesn’t support natural dispersal by the native horseshoe bat host, or its creation in a lab. They instead found that CoV-2 dispersion mimicked that taken by CoV-1.

    As coronaviruses infect animals, different types of the virus sometimes ended up inside the same cell. When the cell makes new viruses, it can accidentally create viral hybrids that carry genetic material from both of the different coronaviruses. This mixing of the genetic information is called recombination. Flu and other viruses are very capable at recombining and forming novel mosaic viruses. It turns out, coronaviruses are pretty adept at recombination too and they use the same genetic regions to repeatedly recombine over eons of time. Therefore, in order to examine the relatedness of the different bat coronaviruses, the researchers focused on regions of the genome that were not involved in such recombination in order to more closely follow the same evolutionary history of each genome and compare that to the non-recombinant regions (NRR) of CoV-1 and CoV-2. The sequences of all so-called “non-recombinant regions” or NRRs were compared and from the mutations identified in each region, a “molecular clock” was determined in order to date the emergence of each viral variant.

    The data showed that ancestors of both human coronaviruses circulated in bats across much of Southeast Asia for thousands of years. The horseshoe bat species that hosts the coronaviruses has been around for over 13 million years. So the virus had a constant host in which to mix and mutate.

    In 2001, just a year before the SARS pandemic started in Guangdong, the Cell paper reports that CoV-1 underwent its last genetic mixing in bats. And since Guangdong is several hundred miles from the ancestral region of CoV-1, infected bats would not have been able to bring the virus to the region in just a year. Instead, researchers generally agree that this CoV-1-similar virus from bats infected wild mammals that were later transported to Guangdong for sale in the city’s live animal markets. A few months after the start of the SARS pandemic, researchers discovered CoV-1 in palm civets and other wild mammals for sale in those markets.

    The researchers also found a similar evolutionary and dispersal pattern when they examined CoV-2 and its related coronavirus sequences. The last recombination in bats took place between 2012 and 2014, just five to seven years before the COVID pandemic began in Wuhan several hundred miles to the Northeast. Researchers believe that, as with CoV-1, a predecessor to the CoV-2 virus entered and circulated in wildlife, which were then transported by traders to Wuhan for sale in its live markets. This explains how the virus could travel such long distances in a short time. This evolutionary pathway is wholly inconsistent with a lab origin for the CoV-2 virus.

    The researchers argue that these new research findings agree with earlier studies that they published in 2022 and which were described in these pages. Those studies provided evidence that the Huanan Seafood Market, one of four live markets in Wuhan, was where the COVID pandemic began. Wild mammals were sold there and all the earliest cases of COVID were centered around that market and not around the other markets or around the lab, which is seven miles away from the market. Chinese researchers also collected related strains of CoV-2 carrying a few distinct mutations from the market stalls and wastewater. In fact, the researchers concluded that the pattern of these mutations showed that the virus had twice spilled over to humans from wild mammals at the market.

    However, at the end of 2019 when it was first suspected that the market might be the source of a novel pneumonia, wildlife vendors at the Huanan market quickly removed their animals from the stalls before scientists could study them. And once China put a stop to wildlife sales, traders and farmers culled their animals so they could not be tested for the virus. That is part of the reason why the CoV-2 smoking gun (i.e., an animal infected with CoV-2) has been so hard to find.

    Bottom line. While this recent evidence is consistent with an animal origin of the CoV-2 virus, it still is not definitive proof. But, this research adds to the growing circumstantial argument that the virus migrated from a bat into wildlife that was sold at the Wuhan market. A “smoking gun” remains to be found to prove with certainty an animal vs lab origin for the virus. Note that it took 30-some years to find the source of the HIV virus, and we still do not know where the Ebola virus came from. So, we keep looking for unequivocal evidence to prove the origin of CoV-2 while realizing we might never find a smoking gun and will have to rely on the preponderance of evidence, which so far favors the animal origin of CoV-2.

  • COVID: Don’t Touch My Junk

    "It's not hard, (it's not hard)"

    –from the song, Piano, by Ariana Grande

     

    COVID is very strange. Earlier I reported that the SARS-CoV-2 virus, which causes COVID-19, a mostly respiratory disease, also messes with one’s gut health. Elsewhere in these pages, I have also discussed the relationship between COVID and new-onset diabetes type 1, Parkinson’s disease, cancer, dementia, and cardiovascular problems. That is quite a panoply of symptoms unrelated to respiratory disease. We now can also add to that complex array of health problems caused by a respiratory virus, broad effects on the male reproductive system. Ouch!!

    Several reports (here, here and here) together report that COVID-infected men often complain of the following several symptoms related to male genitalia:

    • Testicular pain
    • Erectile dysfunction (ED)
    • Reduced sperm count
    • Decreased fertility
    • Smaller penis size
    • Decreased sexual drive
    • Swelling
    • Prolonged erection

    How in the world does a respiratory virus affect all this in the male reproductive system to cause what is sometimes referred to as “COVID penis?” 

    Well, we now know that the organs of the male reproductive system, including the prostate, testicles, and penis actually can be infected by the COVID virus and, thus, have their functions compromised. This can lead to erectile dysfunction, decreased testosterone, and reduced sperm levels in 60-75% of infected patients (see here, here)

    The fact that a respiratory virus can widely infect men’s junk recently was shown by research from Northwestern University. The study used body scanning technology to surprisingly show that the CoV-2 virus had infiltrated the entire male genital tract of infected monkeys (including the prostate, persimmons, and tallywhacker). From these results, the investigators concluded that the manifold reproductive problems linked to COVID-19 are not secondary effects of fever or inflammation but rather a direct result of the virus infecting cells throughout the male reproductive system. It is believed that CoV-2 infection of reproductive tissues can make the organ’s small blood vessel linings not function properly, which then causes reduced blood supply leading to ED, maybe shrinkage, and the other consequences.

    Medical researchers at the University of Florida Health found that men with COVID-19 were more than three times more likely to be diagnosed with erectile dysfunction than those who didn’t have COVID.

    A July 2024 review of 16 articles involving 1250 men with active or recent COVID infection  and 1232 healthy controls confirmed that sperm count and motility are significantly reduced in infected men. The results also showed reduced testosterone levels and abnormalities in other hormones affecting sexual function. The fact that COVID has such broad effects on the male reproductive system raises a concern that the disease could be sexually transmitted. Fortunately, no COVID mRNA was found in the semen of any of the infected men, which suggests a low possibility of sexual transmission of the virus.

    Another question all of this raises is how long do these effects on men’s reproductive health last. The good news is that two studies published in 2023 and 2024 showed that the reduction in sperm count caused by COVID was transient. Sperm returned to normal levels and motility 3-6 months after infection. How long other problems persist is less  at this time.

    All of this information provides yet another good reason to make every effort to stay current with the COVID vaccinations.

    It is not hard.

  • This Post Is For The Anti-Vaxers…

    If you think vaccines are more dangerous than the illness the viruses cause, then feel free to avoid them. But read this testimony from Judith Pantages first….

    When I was a respiratory-therapy student, we had an iron lung in our lab as a vestige of our field’s history. I thought at the time: I have to get into it to feel what it was like. So I did. It was the scariest moment of my life. I couldn’t ask for help as the mighty negative pressure overtook my feeble effort to breathe. Then there was the claustrophobic effect of being enclosed up to my neck in a steel tube. It probably wasn’t the smartest thing for a student to do, but it gave me deep appreciation for my patients who were polio survivors.

    Today negative pressure ventilators have given way to positive pressure ventilators and other noninvasive methods. Still, being on such a thing is no picnic. I wish all those skeptical of vaccines would spend a few moments in an iron lung. Perhaps that would be enough to give them pause.

    In other words, get your shot….

     

  • ALERT!

    Hi folks,

    Thanks very much for following this blog on the COVID pandemic. I have a couple of topics in production that will soon be posted. I also have been distracted by writing two books, one of which should come out in a few weeks, and the second one based on this blog.

    Also, for those of you who follow me on Facebook, know that I have had problems with that account and had to set up a new one. I am trying to regain all my former friends. So, if you were a Facebook friend, or want to be, please send me a request to:

    https://www.facebook.com/profile.php?id=61573910458533

  • SARS-CoV-2, A Respiratory Virus That Messes With Your Gut

    The CoV-2 virus that causes COVID is a respiratory bug, right? They say we catch it, not from surfaces or food, like we do norovirus, but from airborne exposure—we breathe it in. That of course, means that it causes respiratory problems. Makes sense, right? Well, Sarah Carter, 36, from San Mateo, CA, caught the virus in late 2023. Her main symptom was not respiratory but relentless diarrhea that became so sever she had to take an ambulance to the ER. The runs caused her to become dehydrated, which in turn caused a spike in her blood pressure and heart rate. She urgently needed IV fluids to treat it all. After three more days of diarrhea she finally felt better. But, six months later the GI symptoms reappeared overnight without her being infected again. Nearly everything she ate set off diarrhea. She also had bloating and pain so severe that she said it felt like acid was running through her intestines. A gastroenterologist eventually diagnosed her with post-infectious irritable bowel syndrome (IBS).

    What in the world is a respiratory virus doing messing with her entrails, especially months after being infected? Did it make a wrong turn somewhere?

    We have gotten accustomed to testing for COVID when we feel crummy and run a temperature, have a sore throat, runny nose, loss of smell, cough, etc.—all symptoms of respiratory infection. But Dr Rohit Jain, an internal medicine doc at PennState Health told Time that when someone complains of problems affecting the exit at the other exit of the body: i.e., nausea, diarrhea, vomiting, etc., he always tests for COVID. Another doctor, Mark Rudd, chief of infectious diseases at the U of Nebraska Medical Center also weighed in saying that, “COVID-19 is really a GI-tract disease.”

    What??

    If it “really is a GI disease” why are we wearing masks, distancing, and worried about respiratory infection rather than hand washing and sanitizers??

    The SARS-CoV-2 virus and its disease, COVID, are very strange and threw the medical establishment for a loop after they first appeared on the scene at the end of 2019, and after COVID became a world-wide pandemic in early 2020. Docs dealt with myriad, seemingly unrelated symptoms in different patients; symptoms such as brain fog, loss of smell, severe pneumonia, hemorrhage issues that led to black toes and lungs that looked like they had filled with chocolate pudding, among many others; all from the same virus. Now add to that befuddling mix, GI problems to what was believed a respiratory virus,and COVID presents a conundrum. Docs have to now factor in the fact that many people experience no, or only mild gastrointestinal symptoms, while other patients experience significant digestive problems that can distract from the pulmonary problems which complicate diagnoses.

    As we have learned more about COVID over the last few years, it has become clear that infection symptoms can also include loss of appetite, nausea, vomiting, diarrhea, and stomach pain, according to Jain’s research. A 2023 study published in Nature Communications reported that 36% of COVID patients are likely to develop GI disorders such as ulcers, pancreatitis, IBS, and acid reflux. Another recent study in Clinical Gastroenterology and Hepatology found that 40% of adults hospitalized with COVID, had at least one GI relapse a year or more later. While both of these were small studies, they are in close agreement regarding the incidence of COVID GI problems. And like other symptoms of long COVID, the GI problems can last many weeks. That is quite concerning. Weeks of diarrhea, for example, is much more than an immense inconvenience and major mess, it is a serious medical issue. But not all patients experience these symptoms, just like not all patients lose their sense of smell, had black toes, or developed long COVID. Try to diagnose and understand COVID with this range of variable symptoms! How confusing.

    How can the same virus cause runs from both ends of the body; the nose and the other end?  Among the things we have learned over the last few years is that the CoV-2 virus infects cells that express the ACE-2 protein. While ACE-2 normally is important for certain cell functions, the virus decided to use it as a receptor on which to grab onto and then enter cells. The protein is found on many different types of cells throughout the body, but it is expressed in especially high levels in the lungs, which helps explain COVID’s respiratory symptoms. It turns out that ACE-2 is also highly expressed in cells of the GI tract. That explains the intestinal complications. Also, because it is found in the GI tract that could possibly make feces from infected animals, like bats, a great way to widely spread the virus to other animals, just like migrating birds spread the avian flu virus to poultry flocks and dairy herds. In fact, in 2012, six Chinese mine workers removing guano in a bat-filled cave where flying flittermice were found with COVID, developed severe respiratory symptoms. Three of them died. COVID infection from contaminated bat guano is suspected because the Wuhan lab eventually found evidence of an unknown coronavirus in the patient samples. But, this was years before the CoV-2 virus had been discovered, so the CoV-2 link to their disease comes with some uncertainty. Maybe the virus in ca-ca could be a way to spread it between people too, like norovirus is spread. To my knowledge, human-to-human spread this way has not been shown, but it makes sense to this scientist that it could. After all, since the virus is found in feces, wastewater surveillance has proven to a useful tool for tracking CoV-2 spread among human populations. It is routinely found in poop, and there is a good possibility that the Chinese workers caught it from the bat scat they were shoveling. Together, that makes it very likely that humans can spread it to other people via unsanitary practices. But, at this time, that is just the opinion of your sometimes humble correspondent. We will see.

    We also now know that the virus can hide in the nooks and crannies of the  bowel for months, or even years, according to Ziyad Al-Aly, MD, an epidemiologist at the Washington University School of Medicine in St. Louis, who co-authored the Nature Communications study on chronic post-COVID GI symptoms that was cited above. This might explain why gut-related symptoms can long outlast the initial acute infection. But other possibilities to explain long-COVID GI problems continue to be investigated. This is another “we shall see” issue.

    We also know that the virus can cause widespread and sometimes long-lasting inflammation, potentially affecting various organs throughout the body including the gut. GI inflammation can affect the gut microbiome, which is the collection of microbes that normally live in the GI tract and that are good for us. We have long known that changes in the gut microbiome can have manifold health effects affecting GI health, and even the well-being of the heart, kidneys and brain, including Alzheimer’s disease, which is a possible complication of COVID. Disruption of the GI microbiome also is related to obesity and diabetes and it is notable that COVID disease also is associated with new-onset diabetes. Inflammation in the gut can also damage the lining of the intestines, making them “leaky” so that nutritional goodies from foods you normally would absorb across your gut into the blood stream, instead escape into the abdomen, causing immune cells to mount an allergy-like response to foods. COVID-induced inflammation can also chew away at the nerves that control normal gut contractions (peristalsis) that move food along, and interfere with neurological signals in the gut causing pain. Not fun, ask Sarah Carter!

    Since the start of the pandemic in early 2020, GI docs have noticed an uptick in IBS in COVID patients. Medical scientists have long known that other gastrointestinal infections, like those from norovirus, giardia (a parasite), or salmonella (bacteria), can lead to IBS as well as functional dyspepsia, a type of chronic indigestion that causes frequent feelings of fullness and stomach pain or burning, like acid running through your innards. Does that sound familiar? Now we can add the respiratory virus, CoV-2, to the list of infectious agents that can cause IBS and other digestive problems.

    Bottom line: So, gut problems are added to the manifold issues associated with COVID disease. CoV-2 is a nasty bug that you don’t want to catch. Get vaccinated and spare yourself all these problems!

  • Over 400 Studies Show Face Masks Protect Against Respiratory Infection

    “Sometimes we need education in the obvious more than investigation of the obscure.”

    –Oliver Wendell Holmes

    In my meanderings across the blogosphere, opinion pages, talk radio, Facebook, and even chatting with friends and acquaintances, I continually encounter folks who assert that masking is ineffective for protection against respiratory infections. Of course they never provide evidence to support their claim beyond their confidence that they are correct. I often reply that they should invite their next surgeon to remove his mask during the operation. I have published in these pages a few articles showing how controlled trials and real-life empirical data show this to be wrong (see here, here and here).

    Now a new meta-analysis by University of Oxford researchers, or an analysis of some 400 published studies on facemasks, further confirms that if they are correctly and consistently worn masks effectively protect against respiratory infections, including COVID. The study also concludes that mask mandates are effective in reducing community transmission of respiratory pathogens. Note that health mandates have long passed Constitutional muster as I reported earlier. This new analysis was triggered by the controversial 2023 Cochrane review of non-pharmaceutical interventions for COVID, which several publications reported showed that masks were ineffective. However, Cochrane’s editor-in-chief later stated publicly that the review did not support such a conclusion and issued an apology for the confusion and a clarification. Several scholars also questioned the review’s methods and found flaws in its meta-analysis and criticized it for omitting a vast body of non-trial evidence. Hence the Oxford study was undertaken to learn the truth about the efficacy of face masks.

    Face masks, along with other non-pharmaceutical measures, such as social isolation, have long been used during infectious epidemics, especially when vaccines and antibiotics were not available. This goes back to the European bubonic plague in 1619, the Great Manchurian plague (1910), the 1918 Spanish flu, etc. When there is no vaccine or therapeutic intervention to treat an infectious disease, physical isolation measures, such as social distancing, quarantine, and masks are critical.

    The Oxford study. The study examined the relevant literature in a wide range of disciplines (public health, epidemiology, infectious diseases, biosecurity, fluid dynamics, materials science, modeling, data science, clinical trials, sociology, anthropology, psychology, and occupational hygiene). This included numerous randomly controlled trials as well as observational, or “real-world,” evidence. The results convincingly showed that cloth face coverings and disposable medical masks that are handed out at your doctor’s office can reduce infection risk, but the N95 respirators are much better.

    In the early COVID-19 pandemic, when randomly controlled trials of masks had not yet been done, the study’s authors found a systematic review and meta-analysis of observational studies reporting that respirators and masks decreased infection risk up to 85%. Further, in a school-based cohort study, the risk of COVID among the family members of students was reduced by 30% to 40% when teachers used masks.

    Other case-control and cohort studies in healthcare workers provided additional evidence of substantial reductions in COVID-19 risk associated with use of respirators. In 2020, one study found over 400-times lower odds of occupational acquisition of COVID among hospital staff using N95 respirators in respiratory, intensive care, and infectious diseases departments compared to those from other departments without continuous masking.

    While cloth face masks were proven to protect against airborne infection, N95 or FFP2 face-fitting respirators were most effective. The latter fit more closely to the face minimizing ambient air from leaking through the edges. They also work differently from cloth masks, which use multiple layers as a barrier to block pathogens. In contrast, respirators pass air through a specially designed filter that uses electrostatic charges to trap airborne particles, whether dust or bugs.

    The pore size in typical surgical masks and respirators is larger than many viruses, like Cov-2, but, viruses do not float around the air on their own. They are carried as passengers via respiratory aerosols, which are blocked by masks. Note that the International Standards Organization (ISO) provides standards for optimum filtration for respirators. This includes lab testing for filtration efficiency. This also includes personal testing while exercising in the face of a challenge contaminant. A respirator is considered to meet requirements when it achieves a 100-fold reduction in the challenge contaminate penetrating the barrier. Respirators outperform surgical masks by 8-12-fold. These results were further confirmed with animal Cov-2 infection experiments. Infected hamsters were separated from uninfected ones by a partition make of surgical mask material, which reduced Cov-2 transmission by 75%.

    Besides lab studies and randomly controlled trials of face mask use, the authors also conducted a systematic review of 44 observational studies involving SARS-1, MERS, and SARS-Cov-2. They concluded that masks and respirators reduced the risk of infection by 85%. Overall, respirators were 96% effective while surgical masks were 67% effective. This protection was “dose dependent,” meaning that protection increased with the frequency of use of masks. Masks were not only found to protect the wearer, but also were effective and preventing infection of non-mask wearers surrounding the masked person. But, the greatest protection was when both parties were masked.

    In addition, the study examined the effects of mask mandates in several different settings. The first such analysis found a progressive decline in epidemic growth rates after mandates were enacted when compared to time frames immediately before the mandates. Also, masking was an effective predictor of lower infection rates in the US. An analysis of masking in Boston schools, found a surge in CoV-2 infections after February 2022, when mandates were lifted. Similar evidence demonstrating the efficacy of mask mandates was reported in many other studies. Importantly, the meta-analysis did not find any evidence for significant harm to the health of mask wearers even during strenuous exercise. Specifically, they do not increase the carbon dioxide content of inhaled air. The biggest impediment to using them was discomfort and communication difficulty for deaf people who are unable to read the lips of a mask wearer.

    Study conclusions. The claim that masks do not reduce transmission of airborne pathogens is incorrect. They work. Furthermore, the level of protection increases as adherence to masking increases. Masks are a critical part of infection control during a respiratory infection epidemic.

    Note: In order to have blog updates delivered to your email, see the simple Subscription Instructions here. Remember, you can easily unsubscribe when you want.