Son Of Omicron

“A rose is a rose is a rose.” –Gertrude Stein

Omicron is Omicron is Omicron (except when it becomes something different).

Two-plus years into the pandemic, many Americans are ready to declare the COVID crisis over. But, we have been at this juncture before—at the end of the very first surge (remember “flattening the curve?”), and again as Delta faded. Each time, a new virus variant came roaring back. Why should it be different now?

There are reports of two new sons of Omicron circulating in the world. The original Omicron, or BA.1 has spawned BA.2 and BA.3. While little is known about BA.3 at this time, very early indications are that BA.2 represents an even more infectious variant of Omicron, and it is spreading around the world and the US. This variant of a variant seems to be about 30% more infectious than Omicron BA.1. It quickly overtook BA.1 in South Africa and other countries and has caused a second Omicron surge in Denmark. BA.2 has been detected in 74 countries, and has become dominant in at least 10 of them: Bangladesh, Brunei, China, Denmark, Guam, India, Montenegro, Nepal, Pakistan and the Philippines, according to the World Health Organization's weekly epidemiological report.

In the US, BA.2 has been reported in 47 states and accounts for ~4% of all new infections according to the CDC, and it appears to be doubling fast. Samuel Scarpino, director of pathogen surveillance at the Rockefeller Foundation says that if infections double again to 8%, we will be in another exponential growth phase, or the fifth wave of the pandemic. In other words, BA.2 seems to be quickly backfilling the vacuum left as BA.1 peters out.

While BA.2 clearly arose from BA.1, it carries dozens of additional gene changes, making BA.2 as distinct from BA.1 as the Alpha, Beta, Gamma and Delta variants were from each other. This suggests that BA.2 might soon be given its own unique Greek letter designation.

What does BA.2 augur? While vaccination and prior infection still appear to protect fairly well against BA.2, this variant still seems more adept at skirting the immune system then the original Omicron. An early report also shows that vaccine induced antibodies often fail to neutralize BA.2 in tissue culture, and that the virus better replicates than BA.1 in nasal epithelial cell cultures. Nevertheless, those who have been vaccinated and boosted are 74% less likely to become ill from BA.2.

Hopefully, this reduced immunity will still be enough to provide an immunological redoubt against extensive spread of BA.2. The best thing that could happen is that as we become increasingly immunized by vaccine and infection, it might be enough to continue the drop in BA.1 Omicron infections, and check any surge from the new BA.2 variant. This is speculation at this point, and one thing we have learned over the last 2+ years is that the virus does not often respond as expected.

Then there is this: Very preliminary laboratory data hint that BA.2 might cause more severe disease than BA.1, and it appears capable of foiling some of the key weapons we have against COVID-19. In initial lab studies, a Japanese team reported that BA.2 has structural features that might make it as virulent as Delta was. This prediction of increased virulence was supported by hamster infection experiments, but this has yet to be confirmed or refuted in real-life epidemiological studies. Rest assured, those studies are underway, so we will see.

BA.2 also is almost completely resistant to some COVID treatments, such as sotrovimab, a monoclonal antibody therapy that is currently used against Omicron.

Bottom line: During the Spanish flu, as people wearied of the social restrictions designed to prevent the spread of the virus (there were no vaccines or drugs for flu then), many pushed back against the restrictions, which led to premature relaxation of the mandates. Cities like Denver and Philadelphia, which lifted their mandates early paid a hefty price. Other cities like St. Louis, which took a more cautious approach were relatively unscathed. Let’s hope that we are not relaxing and entering a “control phase” too quickly.

What’s ahead of us is not COVID’s end, but might be the start of a phase in which we continue to invest in measures to continue to shrink the virus’s burden. Success in this is not entirely up to us. The virus will have a say too. Our future will depend both on the virus’s continued and unpredictable evolution and on our responses, both immunological and social. The goal is to get ahead of any new variants with wide spread immunity and a growing formulary of antibody and drug treatments, and, yes, this might also require renewed mandates.

A detailed report  looking at past suspected coronavirus pandemics (e.g., the Russian “flu”of 1889, which was probably a coronavirus) published last August in the journal Microbial Biotechnology, suggested plausible scenarios in which elevated levels of COVID-19 deaths could last another five years or longer. This of course depends on what happens to and after BA.2.

It probably is not quite time to relax all mask mandates or let up on the push to vaccinate.

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COVID And Heart Disease—It’s All Relative

A new COVID study recently reported in Nature got the attention of your aging scrivener. It reported that COVID-19 increases risk for cardiovascular disease for at least a year after infection.  This was a large study of US veterans that found that the risk of having a heart attack, stroke or several other cardiovascular events was higher for those who had COVID-19 the year prior compared to those who weren’t infected. The risk was highest for those who had been hospitalized but was still elevated for those not admitted.

But when you read about elevated risk in the news or especially on social media, what does it mean? Hint: the media usually will not tell you this.

In order to understand the significance of such risk, we need to know both the relative and absolute risks. Relative risk is what we often see reported in alarming headlines—for example in this case, the risk of a heart attack was reported to be 63% higher in those who had had COVID-19. That is relative risk and it sounds pretty bad, right? Relative risk tells us that a risk is higher in one group than in another, but it doesn’t tell us the whole story. To put relative risk in perspective, we also need to know the absolute risk of the bad thing happening.

For example: let’s say that in a group of 100,000 “normal” people, one is expected to develop a rare cancer. But in people who were recently x-rayed, two people in 100,000 develop the cancer. The headlines would scream that x-rays caused a 100% increase of the cancer. The risk doubled after being x-rayed. Pretty chilling. Yet, the absolute risk in this example is extremely small—only one extra person out of 100,000 who are x-rayed gets the cancer.

Compare that to a situation where 10,000 out of 100,000 typically develop this cancer and x-rays again double the risk. That means 20,000 out of 100,000 people getting x-rays will get the cancer. In the two scenarios, the relative risk is identical—x-rays are associated with a doubling of cancer cases—a 100% increase in cancer risk. But in the second example, the absolute risk is much, much greater. Instead of causing cancer in only one out of 100,000 people (0.001%) as in the first example, the second example has x-rays causing cancer in 10,000 of every 100,000 people, or 10%.

Going back to the study in Nature, remember having COVID led to a 63% increased chance of having a heart attack. The data showed that the absolute risk of heart attack was 4.67/1000 for uninfected people compared to 7.59/1000 for those who had COVID-19 in the previous year. So, in absolute risk terms, an extra 3 people out of 1000 had a heart attack after having COVID-19. That puts the 63% increased relative risk in perspective.

Now that relative vs absolute risk have been explained, we are still left with the question of whether these extra three heart attacks are concerning. Like many other things, it depends how you look at it.

With tens of millions of people getting infected with COVID-19, an increase of three heart attacks for every thousand people can add up fast. Looking at the population level, this could lead to a noticeable rise in cardiovascular disease burden and lead health experts to begin planning for a wave of heart attacks. But, looking at the individual level, most COVID infected peoples’ risk of having a heart attack in the next year is pretty low. So, if you have COVID, you do not need to begin planning your funeral.

Bottom line: These alarming headlines need to be understood in terms of relative vs absolute risk and then looked at in terms of the effect on the population vs on the individual. Way too often during this pandemic, I have seen folks abusing both. For example, how often do you hear people saying that COVID is overblown because <1% die from it. This totally ignores the absolute risk (how many deaths is that) and focuses only on the individual effect while totally ignoring the population level effect (1% of 100 million is a lot of people).

It is all relatively absolute and absolutely relative.

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Another Unexpected Pandemic Consequence: Undiagnosed Cancer

In these pages, your humble bloggeur (that would be me) has written about several unusual consequences of the COVID-19 pandemic. Most of these were on the ironically funny side, such as farmed fish being too large for restaurant plates, rattlesnakes climbing in plane landing gears, and the ketchup packet shortage. But, not all of these odd aftermaths of the pandemic are humorous. The topic of this post is very unfunny.

Lungs

It seems that as healthcare providers were swamped with COVID cases, or were at reduced capacity because staff became ill, or because service slowed in order to prevent CoV-2 spread, many people have missed routine medical care for non-COVID problems. It is feared that this will create a crisis in coming years involving increased diagnosis of cancers that were caught later than usual. As we deal with the fourth wave of COVID-19 caused by the Omicron variant, we are learning that the pandemic dramatically disrupted routine health screenings for cancer and other chronic diseases. Some now predict that the next crisis that could overwhelm the US health system will be a surge in advanced chronic diseases like cancer that went undiagnosed and untreated for too long.

Screenings for several major cancers and new cancer diagnoses fell significantly during 2020, according to a study published in December 2021 in the journal Cancer. This was not because there was less cancer in the world. It was because fewer patients were seeing their doctors.

A co-author of the Cancer study, and who is a professor at the University of Maryland School of Medicine, said that we have never before seen screening rates drop so dramatically in such a short time.

In one case, a Hispanic man in his 40s first noticed rectal bleeding in early 2020 that his doctor said was probably due to hemorrhoids. The man was unable to get a timely colonoscopy to rule out cancer because the local hospitals were overwhelmed with COVID-19 patients, and he also feared catching COVID if he went to a hospital swamped with COVID patients. Eighteen months later, he finally got a colonoscopy, which revealed advanced rectal cancer. Those 18 months likely were the difference between being cured by a simple polyp removal vs dealing with a cancer that had metastasized throughout his body.

At this point, nobody knows how many cases like this are out there. We will find out.  

This patient, as thousands of others like him, had the misfortune to notice symptoms that needed followup amid the biggest disruption of medical care in US history. In 2020, while hospitals curtailed services in order to prepare for the COVID surge, the number of colonoscopies plummeted 93 percent. By the end of the year, there had been 133,231 fewer colonoscopies performed compared to 2019. There also were 62,793 fewer chest CT scans, 49,334 fewer fecal blood tests, and prostate biopsies dropped 25%.

This drop in screenings has created a huge backlog that will take months to clear. A gastroenterologist at a small community hospital in the Middle-of-No-Where, Kansas was recruited by a larger hospital in Kansas City to do nothing but colonoscopies from 7 in the morning to “whenever at night.” They had a backlog of 1000 patients—a certain percentage of whom have cancer already growing in their colons while waiting to be told they had colon cancer. And that backlog begets a fresh one of new patients who also need to be scoped because they just noticed something like rectal bleeding, but will have to wait for those who have already been waiting.

This backlog creates a subtle form of medical rationing. It forces doctors to make hard choices about which patients to prioritize. "Lucky" are the serious patients who are moved to the head of the line. Not so lucky are those whose colonoscopies or mammograms or biopsies are then further delayed.

I would rather deal with rattlesnakes in my plane's landing gear or forgo mustard on my brat (which would be pushing the limit) than delay a needed medical test or procedure. It seems that your humble bloggeur (me again) has been caught in the backlog. I am scheduled to have an enlarged parathyroid gland removed next week, but COVID can still derail that. I won’t be certain that the surgery will happen until the day before I am to be operated on and that depends, in part, on everyone, including me, being COVID-free, and the OR not being diverted for use as a COVID ICU. If it proceeds as scheduled, I will have waited several months since the initial diagnosis for the surgery. An additional routine diagnostic test I need in order to determine how the fractious organ might have affected my bone health was scheduled six months out. Six months for a routine scan?


Harry Became Severely Disabled After The Vaccine

Does the crowing of a rooster cause the sun to rise?

Harry: A follower of this blog, recently wrote to me about the experience of his senior friend, Harry. With permission, I relay the story here and add some thoughts.

Harry was 80 years old and living a healthy, robust life. He did his own home improvement projects, he was mobile and drove everywhere--he lived an active life. His only health concern was a bit of a problem with high blood pressure (who doesn’t at his age?) that was well controlled with a statin drug.

But, soon after his third shot (booster), his shoulder in the non-injection arm began stiffening. After that, one side of his groin became very painful and the pain migrated to the other side and then began shooting into his legs. Within weeks, he was unable to walk, relying on a walker or wheelchair. He became home-bound. His painful arm is now useless—he needs to hoist it with his other hand to get dressed. Same with both legs. Harry gets by each day on pain meds, but he is reluctant to take a higher dosage to fully control the pain as it makes him too groggy, so he only sleeps an hour or two at night due to the pain, then catnaps in his recliner throughout the day.

This sudden and quick decline began about a month after his booster shot so he was convinced his new maladies were a consequence of the vaccine.

VAERS: Harry’s case is the sort of case that is reported to the CDC’s Vaccine Adverse Effects Reporting Site or VAERS. When someone begins experiencing untoward health problems soon after vaccination they or their doc can easily report it on the VAERS site, which has served as an early warning system for identifying rare side effects of vaccines since 1990. Thousands of people have reported post-vaccination symptoms, and the site is accessible to anyone. Hence, there is a CDC database listing thousands of reports of health problems following COVID vaccination that you can pull up after a few clicks.

The CDC uses this uncorroborated raw anecdotal information to look for patterns that could point to previously unknown side effects of vaccines. This is common practice for all medicines after they have been approved for use. Data from clinical trials that form the basis for approval or rejection of a new medicine or vaccine only include results from ~40,000 test subjects. That is enough to discover very significant and fairly common side effects. But, after the medicine gets on the market, patient data still are collected in order to see if there are serious side effects that only appear in, say, one out of 250,000 people and that would not be found during the clinical trial on just 40,000 subjects. Remember the COX-2 anti-inflammatory drugs that were widely used in the 90s but were pulled because they were found to cause rare, but serious cardiovascular problems? This was found by collecting post-approval data from a few million people who had taken the drugs. Evaluating data collected after a medicine is on the market is referred to as post-market or Phase IV research. This is what the CDC uses the VAERS database for.

The CDC then digs into the raw VAERS reports to make sense of them. They first confirm the reports and then to see if they are just correlations or causative. Scientists look at further health data on the patients, and look for similar recurring problems in other patients. This also means that the raw data reported on the VAERS site are just that—raw. The raw data you can see on the site have not been confirmed or determined to have actually arisen from a vaccine side effect. In fact, the VAERS web site carries this clear disclaimer:

“VAERS reports alone cannot be used to determine if a vaccine caused or contributed to an adverse event or illness. The reports may contain information that is incomplete, inaccurate, coincidental, or unverifiable. In large part, reports to VAERS are voluntary, which means they are subject to biases. This creates specific limitations on how the data can be used scientifically. Data from VAERS reports should always be interpreted with these limitations in mind.”

The task for the CDC then is to separate health complaints that are just coincidental (i.e., that would have happened anyway without the vaccine) from those that are causal (i.e., that were caused by the vaccine). The fact alone that someone vomited a day after being vaccinated cannot be taken as proof that the vaccine caused the vomiting. There is a big difference between correlation, i.e., when two unrelated things happen together, vs causation when one thing leads to the other thing.

But, this is what the vaccine naysayers are doing—they look at the VAERS site and believe that all those raw reports are causative reports showing that the vaccines harm people. In other words, they completely ignore (or do not even read) the CDC disclaimer that the VAERS data are very incomplete and require further investigation before any conclusions can be drawn. When you hear someone on social media, TV, or the radio claim that tens of thousands of people have been seriously hurt by the vaccines, they are basing that claim on an incompetent (and possibly dishonest) use of the raw, uncorroborated VAERS data. I know this because every time I ask someone to back up their claim that the vaccines have injured tens of thousands of people, they eventually cite the VAERS database. When I quiz them further, most clearly have not even looked at the complicated VAERS web site, but are reporting second hand what they have heard elsewhere.

The truth is that few of the VAERS reports have been confirmed to be related to vaccination. Furthermore, the side effects mostly are of the “sore arm” variety, while serious health effects are vanishingly rare. Only about 200 people have actually died from the vaccines. All this compares to the almost 900,000 deaths (and counting) from COVID, and the ~20 million (and counting) cases of long term debilitation from long COVID. Remember, both the deaths and long COVID are prevented by the vaccines.

Back to Harry: Harry developed his debilitating conditions shortly after his third shot and attributed his woes to the vaccine. That is a temporal correlation—the debilitation happened shortly after the vaccine. But, is there anything that proves the vaccine caused Harry’s debilitation?  Well, a deep dive into Harry’s medical condition, like the CDC does into the data in its VAERS data, proves the vaccine did not cause Harry’s condition.

Sadly, a couple of days ago my blog friend told me that recent scans showed a mass on Harry’s lung. He has end-stage lung cancer that has spread to his pelvic bones and shoulder causing severe bone lesions and the pain. He will soon die from untreatable advanced cancer. It seems that Harry has a 50+ history as a smoker. But, he, as well as folks who abuse the VAERS system, totally ignore that kind of history and jump on the less-likely correlation between vaccination and diminishing health as proving a cause and effect relationship between the two. In doing this, people must assume that there could be no other causative factor for any malady that appears shortly after vaccination. Harry himself, ignored his long history of smoking, which is, by far, the leading cause of lung cancer, while the vaccines have been associated with zero cases of cancer.

This is a sad example of the mental gymnastics anti-vaxers resort to in order to confirm their bias against the vaccine. Real data be damned once they see a simple correlation that fits their bias.

Bottom line: Just as the vaccine did not cause Harry’s cancer, the crowing of the rooster does not cause the sun to rise. Both are correlations of events only temporally, not causally related.

Do not buy into the claims that the VAERS shows that people are suffering by the thousands from the vaccines. It is not true.


File This Under ‘Weird Pandemic Effects’: Decreased Incidence Of Lightning

If lightning is the anger of the gods, then the gods are concerned mostly about trees.”

- Lao Tzu

Yup, since the pandemic began, it appears that trees are safer. Thanks to the lockdowns, there is less lightning to strike them.

A study presented at the fall meeting of the American Geophysical Union (AGU) analyzed atmospheric factors that may have contributed to lightning reductions of 10-20%. 

It seems that atmospheric aerosols produced by burning fossil fuels were reduced because of pandemic lockdowns. Particles in these aerosols enhance the collection of water vapor, which causes clouds to form. And the more these particles absorb water they also reduce rain and, therefore, the creation of small ice crystals that collide in the clouds and build electrostatic charges that create lightning. So, fewer aerosol particles, less bumping and rubbing, less static and fewer zaps.

I have previously noted other weird effects of the pandemic such as farmed fish being too large for restaurant plates, rattle snakes in plane landing gears, and a dearth of ketchup and mustard condiment packages to go along with less lightning. What crazy thing will happen next—the Cincinnati Bengals win a playoff game?

Oh….wait a minute……..

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The Long Haul, Part 4: The Cost of Long COVID In Terms Of Individual Health And Quality Of Life

Surviving COVID-19 is one thing, recovering is another.

My frustration with those who would minimize the impact of COVID-19 is reaching an apex. I constantly have to deal with their baseless rationalizations that “it is just a cold,” or “it only kills 0.01% of people” (actually the number is 2% around the world), etc. And I constantly reply to these iconoclasts that COVID has become, by far, the leading killer in the US. I also explain over and over that treating simple mortality percentage as the only relevant statistic to consider is falderal. For example, the Spanish flu also killed “only” 2% of those infected, but in just 24 weeks, that virus killed more people around the world than were killed in WWI AND WWII together! The percent figure is meaningless without considering the percent of what. Why do they continue to ignore the devisor and, hence, the total number of deaths?

A small percentage of a very large number is, in fact, another large number.

Those who wish to downplay the significance of the pandemic only focus on this mortality percent, but mortality is NEVER the whole story for any pandemic. A serious person will also consider the morbidity caused by the disease. In fact, the major CDC publication on health in the US is called the Morbidity and Mortality Weekly Report. Notice that it considers both morbidity and mortality, and further notice that morbidity is listed first in the title. I have made three prior posts in this series on Long COVID, about the significant lasting morbidity of COVID-19. You can see these posts here, here, and here. In those posts, I shared data showing that some ~10-30% of COVID survivors suffer serious health problems that last months.

In those posts, I mentioned the cases of a young, healthy MD, and of a young, healthy journalist, both of whom struggled with long COVID, and how it affected their careers and cost them thousands of dollars in out-of-pocket expenses for the dozens of tests and doctors they needed. In an article in Maclean’s magazine, a reporter interviewed many Canadian long COVID patients and heard how their lives have been turned upside down. They reported that they are unable to live like they used to and care for their families, do anything mildly strenuous, or even cook their meals. They spend long stretches of time in bed. Many of those interviewed had not returned to work several weeks after recovering from the acute disease.

Anecdotes like these have been repeated millions of times around a world that, according to the Johns Hopkins University COVID tracker, has seen more than 330 million cases of COVID (and this is a significant undercount since many countries do not record these data well). Research has corroborated these anecdotes.

+++

Common long-term symptoms include debilitating fatigue; respiratory problems; and “brain fog.”  Other common symptoms include compromised function of the heart, and kidneys, which sometimes require transplantation. Wide-spread clotting problems can cause significant illness and even limb amputation. There also are frequent neurological and neuropsychiatric symptoms as highlighted in Part 3 of this series. Surprising manifestations continue to emerge, such as new-onset diabetes.

Lung scarring often occurs in patients who experienced COVID-caused acute respiratory distress syndrome (ARDS), a common problem seen in acute COVID patients who required ICU care. ARDS is a serious respiratory problem that can be caused by different respiratory viruses and other things. About a third of patients with ARDS arising from any cause were unemployed 5-years later because of their lung damage. It is fully expected that patients with COVID-related ARDS will be found to fare similarly.

There also is the dysfunctional immune response common in many moderate to severe COVID cases that can cause long-term multi-organ damage, particularly in the liver and kidneys. It can also disrupt coagulation control of the blood, sometimes leading to amputations, mostly in patients in their 30s and 40s. It was reported that amputations due to vascular problems have doubled since the CoV-2 virus arrived. Compromised coagulation control in COVID patients can also precipitate adverse cardiovascular events such as heart failure, or hemiplegia due to strokes. Data from the COVID Infection Survey on long-COVID suggest that the risk of major adverse cardiovascular events and long-term illness is about ten times higher in COVID patients (even after mild COVID) compared to non-COVID matched controls. A Dutch study found that 31% of COVID ICU patients suffered thrombotic complications. These problems can unexpectedly pop up in people who had completely recovered from COVID.

A global survey tallied 205 different symptoms across 10 different organ systems that can persist after COVID infection has cleared. Typically, these manifold long COVID symptoms do not appear in isolation, but in multi-symptom clusters. A long hauler typically has several of these problems at a time.

While it is estimated that overall, 10-30% of COVID patients become long haulers, reports on the number of people suffering long COVID vary widely. Depending on the report, anywhere from 30-90% of COVID survivors suffer long term health problems. And even at the lower end of that range, 30% of over 330 million people world-wide who have been infected is a very large number. It represents an enormous personal toll in terms of lost health and diminished quality of life. Some of these reports are summarized below.

  • Half of 70,000 hospitalized UK COVID-19 patients experienced long-term complications, according to a study published in July. Complications occurred regardless of age group: For instance, 25% of adults aged 19-29 developed complications, as did 33% of those aged 30-39. Complications affecting the kidneys and respiratory system, liver injury, anemia, and arrhythmia were the most common.
  • Many COVID-19 survivors require extensive and prolonged rehabilitation. An European study found about one-third of 1,837 non-hospitalized COVID patients (i.e., those with mild disease) needed a caregiver three months after their symptoms started.
  • In April the CDC reported in its Morbidity and Mortality Weekly Report that 69 percent of nonhospitalized adult COVID patients in Georgia required
  • one or more outpatient visits 28 to 180 days after their diagnosis.
  • A study published last February in the Journal of the American Medical Association found that roughly one-third of 177 people who had mild COVID disease not requiring hospitalization reported persistent symptoms and a decline in quality of life up to nine months after illness.
  • 70% of people hospitalized for COVID-19 in the UK had not fully recovered five months after hospital discharge. They averaged nine long COVID symptoms requiring continued medical care.
  • A study in South Korea found that 90% of patients who recovered from acute COVID experienced long-term side effects.
  • According to a report in the journal, Lancet, 75% of people hospitalized with COVID-19 in Wuhan early in the pandemic, reported continued problems with fatigue, weakness, sleep problems, anxiety and depression six months after being diagnosed with the disease. More than half also had persistent lung abnormalities.

Data like these have been commonly reported around the world, pointing to a more chronic and expensive health problem than seen with the flu or common cold, which often is caused by different coronaviruses. A July 2021 article in Scientific American talked about how all of this indicates that long COVID will cause a “tsunami of disability” that will affect individual lives as well as create enormous strain on the health system. Consider the numbers: More than 60 million Americans (this is an underestimate since many COVID cases are not reported) have been infected with the CoV-2 virus. Therefore, if only 30% of these suffer long COVID, we are talking about 20 million long haulers and counting.

The related health care and disability costs of all of this are also still being calculated. How many “long haulers” will not be able to return to work for months, or at all? How many will need short-term disability payments, and how many will become permanently dependent on disability programs? As increasing numbers of younger people become infected, will we see a generation of chronically ill? This then moves us to consider the economic and financial cost of long COVID, which will be the topic of the next installation in this series.

Stay tuned.

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Gain-Of-Function Viral Research: What’s The Big Deal?

Senator Rand Paul and many others have raked Dr. Anthony Fauci, long-time director of the National Institute for Allergy and Infectious Diseases (NIAID), over the coals for supporting research at the Wuhan Institute of Virology, and especially for supporting “gain-of-function” (GoF) research at that facility.

This needs some ‘splaining.

First, Senator Paul and the anti-Fauci crowd need to give us their definition of GoF research and then explain why it is bad. If they mean research that gives viruses new capabilities, then most labs seeking to learn how a virus functions is guilty. For example, University of Wisconsin flu researcher, Yoshi Kawaoka, did research that exchanged genes from the 1918 H1N1 Spanish flu virus with less virulent H1N1 viruses in order to learn why the Spanish flu caused so much death back then. That is classical gain-of-function research and it was done under strict quarantine and safety conditions (disclaimer, your blogger was on the safety review committee that vetted and approved Kawaoka’s Spanish flu research). It is legitimate and important research.

The Wuhan Institute of Virology had a small bit of indirect funding from Fauci’s NIAID to support a genetic registry of coronavirus sequences that is freely available to all researchers around the world. As new coronaviruses were discovered and their genomes sequenced, the lab investigators cataloged them. They also inserted the new spike protein genetic sequences into incipient, harmless viruses to see how well the new spike proteins allowed a virus to infect mammalian cells in tissue culture. This was done to help assess how much of a risk a new coronavirus was for spreading among mammals. Strictly defined, this research gave the engineered test viruses new capabilities—they acquired new spike proteins and gained the new functions that came with that. This is legitimate research and not some nefarious plot to weaponize coronaviruses that Rand Paul, et al., dishonestly allude to in their allegations.

Furthermore, there are the thousands of other labs around the world, including mine at UCLA and the University of Wisconsin that use viruses as tools for gene transfer in order to study the activity of newly discovered genes. For example, my lab discovered an aberrant gene that was associated with a particular human leukemia that used to be untreatable. We wanted to learn how the abnormal gene affected blood cells, so we cloned it and inserted it into a virus that could infect mouse cells. We then gave mice leukemia by infecting them with a virus that expressed a human cancer gene. That recombinant virus gained the function of the human cancer gene. Rand Paul, et al., would call that sinister gain-of-function virus research. However, from that and other research, that incurable leukemia now is 95% curable. Sinister?

Sure, using modern molecular technology, a minacious actor could help a pathogen gain super-lethal function and develop a super-pathogen, or a weaponized bug, like antibiotic resistant anthrax or super-spreading Ebola virus. It would be pretty easy to do. But, by far, the GoF research routinely done in labs around the world is done for learning not for killing.

When Paul accuses Fauci of supporting GoF research, that accusation is attached, without evidence, to an implicit accusation that the Wuhan labs are creating more virulent pathogens for nefarious reasons. So, why does Paul not go after Kawaoka or me for using NIH money to create viruses that might be able to kill people (Kawaoka’s flu construct) or that could cause cancer (my virus expressing a human cancer gene)?  

Could it be for political reasons?


Has Omicron Rendered Vaccines Ineffective?

Early in the pandemic, when we realized that the CoV-2 virus was quickly producing mutated progeny, some of which were becoming more deadly and transmissible, some (including your humble blogger) warned that viral mutation could feasibly give rise to a variant that ignored immunity to previous iterations of the germ—in other words able to ignore the current vaccines. We have arrived—almost.

The so-called omicron variant partly avoids immunity conferred by the current vaccines (and by prior infection), meaning that we are seeing “break-through” infections in fully and partially  immune people. Popular news sources are running headlines declaring that vaccinated patients with COVID are filling hospital beds, leading many to leap to the conclusion that the vaccines have failed.

But, that is not fully accurate. Many vaccinated people are indeed getting infected with omicron, yet the vaccines are still quite effective, and much better than no vaccine. Let me explain.

First, about two-thirds of Americans are vaccinated—a definite majority of the population. This means that for a hypothetical virus that can fully evade immunity, there are more vaccinated than unvaxed viral “targets” available; meaning more vaccinated than unvaccinated people will be infected. The reality, however, is that the vaccines are still partly protective so that many vaccinated people still catch omicron COVID. Yet, compared to vaxed people, unvaccinated people remain at significantly greater risk of infection, hospitalization, and death. Numbers in my State of Wisconsin, bear this out.

Currently, 69% of the State adult population is vaccinated. According to the latest data* (as of January 15, 2022), out of 100,000 vaccinated people, 1573 caught COVID, 18.5 were hospitalized, and just under 4 died. In contrast, out of 100,000 unvaccinated people, 4,746 got infected, 176 were hospitalized, and 51 died. In other words, many more unvaccinated adults are feeling the effects of COVID, despite representing only 30% of the State population. Clearly, there were breakthrough infections in vaccinated people, but just as clearly, unvaccinated people fared way worse than they would have if they had the shot.

Yet, the headlines persist, proclaiming things like, “Similar numbers of vaccinated and vaccinated people hospitalized for COVID.”   Does this not show that the vaccines are no longer effective? Not at all. Because many more people are vaccinated and partly susceptible to the virus, more and more vaccinated people are showing up with infection, but at a much lower rate than unvaccinated people do. The graphic below illustrates how this works.

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The benefits of the vaccines also are reflected in national and world-wide numbers. The US has one of the lowest vaccination rates among developed countries such as the UK, Canada, Norway, Denmark, etc. And despite omicron’s “milder” nature, which means it kills fewer people but still kills, the COVID death rate in the less vaccinated US is greater than seen in more vaccinated countries, attesting to the efficacy of the shots. Also, new hospital admissions in the US have now reached an all-time high and far exceeding hospitalization rates in better vaccinated countries. Current data from New York State shows that hospitalization among the unvaccinated is 14x higher than among fully vaccinated people.

All of this demonstrates how effective the vaccines remain at preventing infection, hospitalization, and death from omicron-driven COVID. Places with higher vaccination rates, such as the UK and Canada, are not experiencing an increase in base case rates of patients admitted to the ICU or deaths, even with omicron cases skyrocketing. The US is.

Get your Fauci boo boo.

*Note on Wisconsin State data sources: State data mentioned here are from the Wisconsin Department of Health Services, Public Health Madison and Dane County, and the Wisconsin Hospital Association as reported Jan 15, 2022 in the Wisconsin State Journal.


Lions And Tigers And…Deer? Oh My!

First it was bats and humans, then domestic cats and dogs, farmed mink, and big zoo cats; now gorillas, hippos, and wild deer that have been infected by the SARS-CoV-2 (CoV-2 for short) virus. Many of these animals have become ill and several have died of COVID-19, most recently three snow leopards in South Dakota and Nebraska zoos. This is quite a wanton virus.

Of course, before CoV-2 and COVID-19 were known to the world, we knew that bats, humans and a few other animals, notably civets and even camels, were ready hosts of several different strains of “‘rona” viruses. We also knew that domesticated animals are also susceptible to their own coronavirus diseases—in fact veterinary coronavirus vaccines have been in use for years. Humans are known hosts for several coronaviruses, including those that cause the common cold, as well as the viruses that cause SARS, MERS, and now COVID-19. And we know that humans often catch these germs from bats and other intermediate hosts as diverse as civets and camels. After we genetically identified CoV-2 and were able to follow its spread, we quickly noticed that domestic pets also could be infected. This was closely followed with news that seven big cats at the Bronx zoo had become infected, and that mink farms across Europe were hotbeds for CoV-2 spread between humans and the animals and back. In fact, mink farms became such a hotbed of CoV-2 zoonotic spread that a couple of European countries completely shut down mink farming and culled all their animals. Several US states have also sharply curtailed mink farming. PETA probably applauds.

More recently two snow leopards at the Lincoln, NE children’s zoo and one in a zoo in South Dakota died from COVID. The Lincoln zoo also had two infected Sumatran tigers who recovered after being treated with steroids and antibiotics to prevent secondary infections and pneumonia. How the animals were infected is uncertain, but the most likely scenario is that they caught the virus from a caretaker. The problem is, none of the caretakers tested positive for the virus. Bats? Something else?

Since April 2020, when a tiger tested positive at the Bronx Zoo, dozens of other animals in zoos around the world have caught COVID. This month, the Denver Zoo reported the first coronavirus cases in hyenas, and the St. Louis Zoo found eight positive cases among its big cats, including two snow leopards. Abroad, the virus has killed a lion in India and two tiger cubs in Pakistan. Big cats seem especially susceptible since three other snow leopards at the Louisville Zoo were infected last December, and another snow leopard tested positive at the San Diego Zoo in July. The virus doesn’t just infect our fuzzy friends either; two hippos, named Imani and Hermien, at a zoo in Antwerp recently tested positive for COVID-19. Zoo keepers were first alerted to a potential problem when they noticed that the colossi had “runny noses.”  One reckons that a runny nose for a hippo is a big deal. One also wonders who gets to dab that nasal maw in order to test for the virus.

In fact, zoo and domestic animal infections have become so prevalent that an animal COVID vaccine developed by Zoetis, a NJ-based veterinary pharma company and former Pfizer subsidiary, has been authorized by the USDA for experimental use. The Cincinnati Zoo, for one, has vaccinated  80 animals, from giraffes to apes, against COVID.

Deer too. Oh my! It is one thing for zoo animals to acquire COVID—their captivity makes it easy to limit their interaction with other animals and humans to prevent spread of contagions, and they seldom complain that their rights are being infringed when they are quarantined. However, COVID in wild animals is a different story, as we have seen with bats and how easily they transmit the virus to humans. Scientists now have evidence that CoV-2 also readily propagates in white-tailed deer. In fact, the virus is already widespread in cervids across the US, which likely has significant implications for the long-term course of this pandemic.

In September of last year, genetic analysis of the gene that encodes the ACE2 protein (i.e., the viral receptors expressed on many cells in the body) in many different animal species suggested that CoV-2 could easily infect deer (and several other animals too). A survey of white-tailed deer in the Northeast and Midwest found that 40% had antibodies against the CoV-2 virus, indicating prior exposure. Between April and December 2020, veterinarians at Penn State found active CoV-2 infections in ~30% of deer tested across Iowa. Then during the winter COVID surge in humans from Nov. 23, 2020, to Jan. 10 of this year, ~80% of the tested deer were infected. The prevalence of the virus in deer was 50 to 100 times greater than in Iowa residents at the time (and the deer reportedly did not wear face masks). The study, published about two months ago, indicates that white-tailed deer have become a permanent reservoir for CoV-2. While it is not fully understood how the virus entered the deer population, genetic sequence analysis of nearly 100 viral samples found that the variants circulating in deer matched the variants circulating in people. This suggests that deer caught the virus from people multiple times in Iowa alone. How that happens is not known since people usually do not have close contact with live deer. More concerning is whether viral variants arising in deer readily pass back to people.

Bottom line. Clearly, a lot of different animal species can catch Cov-2 and spread it. It is clear that people can spread coronaviruses to pets and other animals, but the FDA says that the reverse, animal-to-human virus transmission, is not common. But, it clearly happens as we have seen with this pandemic, and with many other viruses that cause SARS, MERS, AIDS, Ebola, flu, etc., that spread from animals to humans. The prevalence of CoV-2 infection in so many species of mammals, especially in animals that have close contact with humans, suggests that several animal species, not just bats, can serve as permanent reservoirs for the virus and the jump to humans is something that can happen over and over. This is not unprecedented. It is what we see with influenza, which is carried back and forth between the Northern and Southern hemispheres with migratory birds, in which different flu viruses shuffle their genomes to create the new strains of flu for which we have to vaccinate against each year. This animal reservoir for flu makes it next to impossible to eliminate influenza, and similar animal hosts for CoV-2 likely would make it nigh impossible to eliminate COVID too. I raised this specter some months ago in these pages when reporting that pet dogs and cats can carry the virus. Our furry friends represent a viral reservoir that is in even closer contact with people than bats, deer, and fortunately, hippos and leopards.

We also have to be worried about the CoV-2 virus mutating in the different animal species that harbor and spread it. We know that happens in bats, which makes it almost certain that new strains of the virus will arise in deer and dogs too. We have already seen this on mink farms in the Netherlands and Poland. Farmworkers passed the virus to captive animals where it spread, mutated, and then spilled back into humans. In fact, zoonotic transmission from animals to humans probably happens thousands of times a year. Researchers from the EcoHealth Alliance and from Duke-NUS Medical School in Singapore, estimate that each year many people are newly infected with SARS-related coronaviruses. Many may get sick, but there are many reasons why most of these infections never grow into noticeable outbreaks (for example see my earlier blog post about unusual respiratory infection clusters in China and Los Angeles just before COVID). The researchers also created a detailed map of Asian habitats of 23 bat species known to harbor SARS-related coronaviruses then overlaid it with data on where humans live to create a map of potential infection hot spots. They found that close to 500 million people live in areas where bat-to-human transfer is likely, and this risk is highest in southern China, Vietnam, Cambodia, and Indonesia. Other surveys done before COVID-19 showed that many people in Southeast Asia harbor antibodies against other SARS-related coronaviruses. Blending these data with data on how often people encounter bats and how long antibodies remain in the blood, the researchers calculated that ~400,000 undetected human infections with these viruses occur each year across the region.

That is just for bat-to-human transfer in Southern Asia. It now looks like we will have to also concern ourselves with zoonotic coronavirus transfer from Buddy and Bambi too.

For this reason, researchers are working to develop a universal coronavirus vaccine that will be effective against most viral strains and variants. I will write about this soon. Stay tuned.

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