Coronavirus news & views

New Coronavirus Mutation Enhances Spread

The Wall Street Journal reports that countries across Europe and beyond are banning travel from the UK in order to stem a more-infectious strain of Covid-19 that has been found in the London area. The new strain was first reported last Monday, and on Saturday, England announced that it is imposing fresh lockdowns in London and surrounding areas, which also include a ban on households mixing at Christmas. Similar restrictions have been taken across Europe with Italy announcing a complete lock down across the country. Germany and the Netherlands imposed lockdowns through Christmas, and Austria said Friday that nonessential businesses will be closed starting Dec. 26. However, it also appears that the new strain has popped up in Denmark and South Africa. Holland reported one case with the new virus variant.

Scientists believe the new strain of the coronavirus could be as much as 70% more transmissible than previous strains, but there is no evidence at this time that it is any more deadly or more resistant to the vaccines.

It seems that the virus mutated to change the spike protein on the surface of the virus, increasing the protein’s ability to cling to and chauffeur the virus into human cells. These changes allow the mutation, known as N501Y, to spread faster than other versions of the virus. Early analysis suggests the variant first occurred in September either in London—where it was identified on Sept. 21—or in the nearby county of Kent, where it was found on Sept. 20. That might explain why quarantine restrictions that have been effective elsewhere in England have not been effective in Kent. By mid-November, 28% of cases in London were attributable to the new variant. In the week starting Dec. 9, it was responsible for 62% of cases in the capital. In other words, this variant is winning the infection race against all other CoV-2 strains out there. As of December 19, there has been no evidence of the new strain in the US.

Viruses mutate all the time, but coronaviruses do so less than, say, the flu virus. Mutations happen when rare, random errors are made while cells copy millions of viral genomes. Most mutations are innocuous, but sometimes these accidental changes alter the behavior of the virus. Scientists have identified 23 genetic changes in the genome of the new variant, an unusually large number, some of which are associated with small changes in the proteins the virus makes, which, therefore, can change viral behavior. Those include changes in areas known to be associated with how the virus binds and enters cells, which probably explains why it spreads more quickly. While efforts, including quarantine measures and the new vaccines, are designed to drop the infection rate of the virus, or the R₀ number, these mutations threaten to work against those efforts and increase the virus R₀ value.

Two main questions are now being investigated: Is the new variant more likely to cause increased morbidity and/or mortality, and is it more likely to avoid the body’s immune responses, including those encouraged by vaccines? The provisional answers to those questions are no and no, but the research continues, so these conclusions are preliminary. We will see.

The new variant isn’t the first time a more-transmissible CoV-2 strain has emerged. As reported in these pages last summer, scientists in July described a viral variant that displaced an older strain of coronavirus to become the dominant strain in the global pandemic. Experiments showed that the variant replicated more quickly in tissue culture, but appeared to be just as susceptible to antibodies that targeted the earlier strain, and was not associated with more severe illness.

The bottom line is that as viruses replicate in cells, spread, and replicate some more, they acquire small mutations in their genome. It is like playing the lottery, an occasional mutation will be the “winner” and the ability to spread and even cause new diseases can arise. Like the lottery, the more you play the greater the chance of a winner. This is why calls for “natural herd immunity” by letting people get infected are really bad ideas--they are gambling that while spreading through a population, the virus does not become even more virulent. This also is why health professionals recommend quarantine measures to limit the reproduction-spread-more reproduction of the virus until we have vaccines that effectively block the reproduction and spread and mutation of the virus.

Otherwise, we are just playing the virus lottery.

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.

CoV-2 Virus Budding Fom Lung Cells

This is a colorized scanning electron microscope image of CoV-2-infected lung tissue that was recently published in the New England Journal of Medicine, by pediatric pulmonologist, Camille Ehre, at UNC-Chapel Hill. Human lung cells were cultured in a lab dish then infected with the virus. The image shows the great number of viral particles that can be released from infected cells in the respiratory tract. The dish contained about 1 million cells and Ehre noted that in just a couple of days, the virus produced by the cells exploded from about 1000 particles to 10 million.

• Lung cells are purple.
• They are covered in hair-like cilia (blue) that clear mucus (yellow-green, of course) from the lungs.
• Red particles are budding CoV-2 particles.

CoV-2 In Animals

Coronaviruses are promiscuous critters. We know that the several coronaviruses that cause significant human disease passed from bats to other species and then to people. The virus that caused SARS came from a bat that infected a civet that then infected a human who passed it on to other people. MERS was similar—a bat virus infected a camel that spread it to people. There is good evidence that the SARS-CoV2 virus also came from a bat to infect humans, but we are not sure what animal was the intermediate vector.

Usually there is a biological barrier that limits virus spread between species. When viruses do jump between species, it usually is a result of chance mutation that makes a different non-host species a more hospitable home. That doesn’t seem to be the case with many coronaviruses, which seem to jump between species without markedly changing their genome. Notably, early in this pandemic, we realized that humans were spreading the virus to lions and tigers in the Bronx zoo. Since then, there have been increasing reports of pet cats and dogs catching the virus from their owners and even spreading it to other animals. Also there are reports that monkeys, ferrets and hamsters have caught the virus.

Human to animal spread is not confined to zoo and pet mammals. It has devastated mink farming activities around the world as well. Denmark recently announced plans to cull one million mink after finding extensive spread of the virus in several mink farms. Last May, Spain ordered the culling of 93,000 mink at one farm. The Netherlands also undertook a large cull after two, maybe four people, were reported to have caught the virus from infected mink. Several cats that roamed the affected mink farms were also infected, meaning that the virus was spreading between three different species. And on October 9, it was reported that 10,000 mink died at fur farms in Utah and Wisconsin following COVID-19 outbreaks. It was noted that the virus progressed quickly in mink, with most infected animals dying in one day.

It is unclear why mink seem more susceptible to the virus than other animals, but it is concerning. Similarly, we also do not fully understand why some people, but not other others are highly susceptible to the disease. What would it take for the virus to change and become even more deadly to more humans like it is in mink?

All this suggests that animals that are in very close contact with humans might become a growing reservoir for the virus. So, when a vaccine for humans is available, should we also vaccinate our pets to also give them herd immunity, which would protect them and us? That probably would be easier than trying to make your cat wear a face mask! Experts also are advising people to keep their pets safe by avoiding contact with other people and animals. They even advise to isolate pets from household members who catch the virus.

Another concern is that as viruses pass between animal species, they often acquire new behaviors via genetic drift and rearrangement between different viral genomes. It is believed that a simple mutation increased the ability of CoV-2 to infect human cells. We have found about 500 different coronaviruses in bats alone, while other animals often carry coronaviruses typical to their species. There might be thousands of different coronaviruses out there. When a coronavirus from one species enters a cell from another species that has its own endogenous coronavirus, the viruses can shuffle their genes creating new strains with new capabilities. And when we are talking about viruses infecting an animal, we are talking about billions of virions being produced that are capable of shuffling genomes with endogenous viruses. All it takes is one particularly nasty and overly competitive virion to emerge and find a new host that has not seen it before.

It is relevant here that a new coronavirus that causes gastrointestinal distress in pigs has emerged in China. It is especially lethal to baby pigs, killing 90% of them. It is called swine acute diarrhea syndrome virus, or SADS-CoV and is 98.48% genetically identical to a virus collected from horseshoe bats in China. Research recently published in the Proceedings of the National Academy of Science (PNAS) show that the virus can also infect human cells, but, so far as your humble blogger knows, no human disease has been associated with SADS-CoV. Yet.

Seeing as how coronaviruses readily transmit between different species, I predict that we can expect more novel human coronavirus disease in the future. Hopefully, things we continue to learn about the current CoV-2 virus and COVID-19 disease will translate to more rapid and effective responses to new coronavirus pathogens that are likely to pop up in pigs, people and pets.

We will see.

COVID-19 Immunity: Too Little Can Be As Bad As Too Much

Precis: When two brothers fell critically ill with COVID-19 around the same time in March, their doctors were baffled. Both had been young and healthy, but within days they were unable to breathe on their own and one of them died. It suggested a genetic risk factor for severe COVID-19 disease. Two weeks later, a second pair of stricken brothers appeared in the Netherlands, and geneticists were called to investigate. They found a flaw in the brothers’ DNA that affected their resistance to the virus.

From the beginning of the COVID-19 pandemic, medical scientists have been baffled by the ferocity of the disease in some patients but not others. Especially baffling is the severity of the disease that sometimes even appears in healthy young people who have no preexisting high risk conditions. As we gain experience with this new pathogen and its disease, we are learning that there are several distinct factors related to viral pathology as well as to how the host responds to infection that lead to the disparate responses to CoV-2 infection.

Story: A pair of studies by the international COVID Human Genetic Effort research team that was recently published in the journal Science reveals novel aspects about what causes severe COVID-19 disease in certain patients. The studies report that about 15% of severe COVID-19 patients are deficient in a single cytokine called interferon. In other words, their severe disease is linked to an insufficient early immune response, which is the opposite of the over-reactive immune response called a “cytokine storm” that has been linked to severe disease in other patients.

“Cytokines” is the collective term for  a wide range of small proteins secreted by a wide variety of immune cells, and even by non-immune body cells in response to infections. They play many roles in modulating the immune response, resisting infection, promoting inflammation, regulating temperature, blood pressure, and more. Some cytokines are important for mediating the earliest immune response we make to an infection, which is called “innate immunity.” This early response provides the first line of defense against a pathogen while a second, slower-developing response, or “adaptive immunity,” gears up to provide a more pathogen-specific, robust, and long-lasting protection.

Interferon (IFN) is one of the many cytokines that mediate the early innate immune response. There are several types of interferons that can interfere with viral replication, hence their name and role in innate immunity to viral infection.

In the first paper, investigators sequenced DNA from several genes known to affect early IFN responses. Genes from 659 critically ill patients who did not show signs of a cytokine storm, and from 534 patients with mild disease were compared. About 3.5% of the critically ill patients carried mutations in IFN regulatory genes and had almost undetectable IFN function. None of the control group showed any mutation in these genes or reduction in IFN levels or function. Notably, some of the IFN genetic defects also have been linked to life-threatening influenza pneumonia.

In the second study, scientists examined blood samples from 987 gravely ill patients and found that >10% of them had anti-IFN antibodies that neutralized their IFN activity leaving their cells unprotected against the early stages of CoV-2 infection and spread. None of the 663 patients with mild COVID-19 had the anti-interferon antibodies.

Intriguingly, 94% of the very ill patients with anti-interferon antibodies were men, which might partly explain why men are more susceptible to serious COVID-19 disease. However, this preponderance of male patients was surprising since women generally have a higher incidence of autoimmune disease. This observation suggests that there is an unknown X chromosome-linked recessive trait that influences the production of anti-IFN antibodies. Since women have two X chromosomes, both of them would have to carry the recessive gene in order to develop the antibodies while men, who only have one X chromosome, would only need the recessive gene on their lone X chromosome, giving them a greater probability of producing the anti-IFN antibodies.

Bottom line: It seems significant that none of these patients with deficient IFN responses had a history of other severe viral illnesses requiring hospitalization. This suggests that we are more reliant on this IFN response to protect ourselves against CoV-2 versus other viral infections.

Also, these studies have practical implications for treating COVID-19 patients. Recombinant interferon made in the laboratory has long been used to treat other viral diseases and could be part of an important therapeutic toolbox to treat COVID-19 patients who fail to produce sufficient IFN response to infection. Of course, this will not work in patients who have anti-IFN auto-antibodies that neutralize the activity of any IFN. But from years of experience dealing with auto-immune diseases, we do have an arsenal of other therapies that can mitigate these damaging auto-antibodies. Finally, recognition of these new high-risk subtypes, which can be identified via genetic and immunological screening, can identify individuals who should take extra precautions to avoid exposure to the virus, and those who should be at the head of the list to receive a vaccine when they are available.

In summary, both an over-exuberant immune response in the form of a cytokine storm, as well as an unenthusiastic immune response in the form of IFN deficiency can lead to severe COVID-19 disease. The optimal middling response is true for much of bioscience. You do not want to have a too high or too low blood pressure; ditto for body temperature; ditto for respiratory rate, blood pH, blood sugar, cholesterol, and so on.

Gotta love that happy middle.

COVID Kids

Recently, as school districts, teachers, parents, pundits and politicos across the country have debated about re-opening schools for in-person instruction vs going to virtual classrooms, many people, including Dr. Scott Atlas, a new Whitehouse medical advisor and coronavirus contrarian,  have claimed that school kids don’t often catch COVID-19, and when they do, rarely die from it, and they don’t spread it to other kids or adults in their families. Therefore, they argue for fully opening the schools where kids do not need face masks, or to worry about personal distancing measures.

There are, of course, other issues in this debate, such teacher safety, and how keeping kids at home would hinder the ability of parents to go to work, etc. I don’t intend to lobby here for restarting schools or not. The only issues I will address are whether kids can get COVID-19, be significantly affected by the disease, and spread it to others. In brief, the science informing these three issues says “yes, yes, and yes.”

Kids do catch and spread COVID-19. The science showing that children can readily be infected by CoV-2 is unequivocal. Nevertheless, some people point to other observational data showing that kids do not often get infected and, from that, conclude that children somehow are resistant to the virus. However, these people fail to consider other reasons why children are infected at a low rate. The answer, as I discuss in more detail below, is not due to some intrinsic biological factor that better protects kids than adults from the virus. Rather, the lower rate of infection in kids is due to the early school, playground, and activity closures that have limited their exposure to the CoV-2 virus. In other words, mitigation efforts were effective in preventing virus spread among school kids. And as these social restrictions gradually have been lifted, CoV-2 infections and hospitalizations have increased in children.

According to the latest data from the Centers for Disease Control and Prevention COVID-19 data tracker, about 245,000 US youth from birth to 17 years old have tested positive for the virus. Pediatric cases of COVID-19 increased by 21% in the two weeks between August 6 and August 20 (>70,000 new cases of the disease). Between July 9 and Aug 9, the number of pediatric COVID-19 cases in Florida jumped 137%, while hospitalizations increased 105%. This upward trend in infections and hospitalizations is seen across the US as recently reported by the CDC. One reason for rising infection rates in kids is increased testing, but increased testing does not account for increased COVID-19 diagnoses or hospitalizations. An increase in infection and disease is expected as children are also increasingly being less isolated than they were when schools first closed and playgrounds locked. Relaxation of quarantine measures, along with the persistent and rising CoV-2 infection rate in the US, means that it is expected that more children are being exposed to the virus and coming down with COVID-19.

In March, childhood COVID-19 cases were just 2% of the total, now they are 9% according to a recent weekly report from the Children’s Hospital Association and the American Academy of Pediatrics. Pediatric COVID-19 cases in the US rose 90% between mid-July to mid-August. Also, examples of superspreader events among children are becoming more common around the world (these events are the major drivers of viral spread). There are several reports of such outbreaks among children at foreign schools. A superspreader event also was recently reported at a summer camp in Georgia where one young staffer initiated the spread of the virus to 76% of campers. A total of 260 kids (median age 12), and staffers (median age 17) were infected in just a couple of days—clearly kids can catch and spread the virus. This confirms results reported earlier by the Korea Centers for Disease Control and Prevention, which  examined >59,000 contacts from ~6000 pediatric COVID-19 patients and found that infected children between ages 10-19 spread the virus as readily as adults do. Yet another study published in late July in JAMA Pediatrics, reported that kids in this age range carried similar upper respiratory viral levels as adults. Surprisingly, kids five and younger carried 10-100 times the viral genetic material as adults and older kids. The reason for this unexpectedly high viral load in very young children is not clear, but it could be due to the immature immune system children have in their early years that might be less effective in controlling the virus. This finding raises concern that very young infected children could be highly efficient vectors for viral spread, which would fit the pattern seen with other respiratory viruses.

COVID-19 morbidity in children: As I wrote this blog post, a radio talking head in the background announced that since the CDC reports that kids seldom die from COVID-19, there is no reason to keep schools from opening. However, the pundit, like so many others, only considered COVID-19 risk in terms of mortality and failed to take into account the significant morbidity of the disease. While it is true that, compared to adults, fewer kids die or get seriously ill with COVID-19, many children, even those with mild or asymptomatic forms of the disease, develop a post-infection condition called multisystem inflammatory syndrome in children (MIS-C) that can lead to organ failure and possibly long-term health problems. This is a condition reminiscent of toxic shock syndrome where different organs including the heart, brain, lungs, kidneys, skin, eyes and GI system become inflamed. As early as last May, the CDC issued a health advisory to pediatric doctors alerting them to this new complication of COVID-19, which was first reported in April by doctors in the UK. More than half the MIS-C cases are under nine years old with the median age being eight. As of August 20, A CDC tracker reports that the US has seen almost 700 serious cases of MIS-C, and about 5000 children were reported with a less severe form of MIS-C. Because the disease is so new, the long term consequences of this systemic inflammatory response is not known. For that reason alone, caution is warranted as we try to get a handle on this novel complication and understand  its long-term consequences.

Most children with MIS-C require ICU hospitalization and can experience symptoms that last for weeks. It is often accompanied by subtle changes in myocardial function where the heart’s left ventricle, or main pumping chamber, is impaired. This is the chamber that pumps oxygenated blood arriving from the from the lungs to the rest of the body. At the Children’s Hospital of Philadelphia, 17 of 28 MIS-C patients showed this myocardial injury as reported in the Journal of the American College of Cardiology. Over a brief followup period, affected patients tended to recover systolic (pumping) function, but diastolic (resting) dysfunction persisted.

A recent report in Nature Medicine, indicates that MIS-C isn’t a direct result of the virus, but is likely due to an intense autoimmune response, akin to a cytokine storm, to the infection. This very unexpected consequence of the disease represents one of the several novel aspects of COVID-19 that we have had to very quickly recognize and just as quickly learn how to deal with. The good news is that we are steadily learning more about the disease and making headway in knowing how to treat it. The bad news is that it will be years before we can fully understand what all this means for the long-term health of these pediatric patients.

Biomedicine is wonderfully interesting for those who have patience.

Bottom line: As of July 24, the CDC recommended that K-12 schools reopen this year. On the other hand, a study published last month in The Journal of the American Medical Association estimated that by closing schools in March, we  reduced the rate of new COVID-19 cases by 66%. If the JAMA report is accurate, it means that about 1.4 million fewer people became ill and about 40,600 fewer people died, which argues against re-opening schools for in-person instruction.

What would you do?

Good Progress On The Vaccine Front

At last tally 197 vaccine candidates against the CoV-2 virus are being developed around the world. On May 12, that number was 125. It seems that vaccine candidates are spreading as fast as the virus. According to the World Health Organization, 23 of these experimental vaccines already are in human trials. As reported two months ago in these pages, the vaccine that seems to have the early lead is being developed at England’s Oxford University in partnership with the pharma company AstraZeneca. On Monday, they reported encouraging results from their combination phase 1/2 study in the journal The Lancet.

The Jenner Institute, Oxford University

It also seems that two other vax candidates have caught up to the Oxford efforts and also have reported encouraging results in early combination phase 1/2 or phase 2 studies. One of the vaccines is being developed by the Chinese company CanSino Biologics, which also published its results from early phase 2 trials on 500 subjects in the same issue of The Lancet. Both the Oxford and Chinese labs are developing a recombinant vaccine in which the genetic sequence for the CoV-2 spike protein is engineered to be expressed as part of a crippled adenovirus genome. The adenovirus will infect human cells, but not replicate or cause disease. 

The third vaccine is being developed by the pharma giant Pfizer and the German biotech company, BioNTech. This is a highly novel RNA vaccine where just a simple genetic sequence from the CoV-2 virus is used to immunize patients. No virus is used at all, just some of the virus genetic material. They recently reported in a pre-print paper that has not yet been peer-reviewed, similarly encouraging results from a combination phase 1/2 trial on 60 subjects.

The results of the three studies were very similar. The vaccines were all safe and there were no serious side effects. The only problems were an occasional temporary fatigue, sore arm or headache, which were treated with Tylenol. These effects are much more pleasant than coming down with COVID-19.

Importantly, all three vaccines were shown to stimulate both arms of the adaptive immune response, which is a crucial factor for a successful vaccine. The first arm is the B cell, or bone marrow-derived lymphocyte response. B cells produce antibodies that neutralize the virus, but they fade away after the infection is cleared, not providing long term immunity. The second arm is the thymus-derived lymphocyte, or T cell, response. Activating a T cell response is particularly important for a successful vaccine because it is what oversees the whole immune response to a pathogen and, more importantly, produces long lived memory T cells that impart a long term sentry function to the pathogen, which is what “immunity” is. Memory cells are the basis for long-lived vaccine protection. A successful vaccination will produce memory cells that will sound an alarm if you are later exposed to the pathogen. This alarm rapidly mobilizes your immune system to make a very robust defense that prevents the infection from developing. Therefore, it is very encouraging that the experimental vaccines activated T cell responses.

The Oxford vaccine stimulated T cell immune responses within 14 days and antibody responses in 28 days. Both responses were also stimulated within 28 days in the Chinese study. The Oxford and Chinese studies showed that 85-90% of vaccinated subjects developed antibodies that neutralized the virus and that response was sustained up to 56 days, which is how long the longest study followed the recipients. T cell responses were also seen in 90-100% of the vaccine recipients. The Chinese study further reported that people over 55 developed weaker responses than younger subjects, which was expected. The Oxford study only enrolled volunteers under 55 years. While employing a much smaller sample size, the German study had results similar to the Oxford and Chinese studies.

It must be cautioned that these very encouraging phase 1 and 2 studies did not test whether the immune response could actually protect people from the virus. In other words, they did not test whether the vaccines produced memory cells that could confer long-term immunity. This will be tested in the large phase 3 trials that will begin as early as the end of July. These will be massive studies involving tens-of-thousands volunteers. Phase 3 studies also will take longer since they require the subjects to be naturally exposed to the virus and develop COVID-19. After a period of time, the number of unvaccinated control subjects who develop the disease will be compared to the COVID-19 incidence in vaccinated subjects in order to learn if, and to what extent, the vaccine can protect against the virus. These results should be forthcoming in a few months. Phase 3 trials also will pay attention to vaccine safety in a much larger cohort of subjects than tested in the earlier trials.

If the phase 3 studies show that the vaccines can protect people against future infection with the virus and are safe, then they will be approved. In anticipation of this, some large pharma companies, such as AstraZeneca and Pfizer are already producing the, still experimental, vaccines. This means that if they prove effective, there will be a stockpile of vaccine that can be immediately dispensed around the world. The companies also have pledged to provide the vaccines at cost.

Just a few weeks ago, worry was that the virus seemed to be petering out and that it would be hard to find sufficient numbers of volunteers to undertake large phase 3 studies. However, as the virus is rebounding in most US States and is gathering steam elsewhere in the world, that does not seem to be a problem anymore. Just one week after the National Institutes of Health launched a clinical trial network for vaccines and other prevention tools to fight the pandemic, they announced that 107,000 Americans have already volunteered for vax studies. It is estimated that 120,000 volunteers are needed to adequately test the four lead vaccine candidates under development in the US (assuming 30,000 subjects are needed to test each vaccine). So the high enrollment is a good sign that the vax studies will not be hampered by low enrollment.

Stay tuned. We will see.

Misleading Media Reports That CoV-2 Immunity Quickly Disappears

The media is reporting that immunity to CoV-2 disappears in a few months. This is based on a pre-publication report from researchers at King’s College in London that shows that of >90 infected patients, only 17% maintained significant levels of anti-CoV-2 antibodies after three months. The antibody response to the virus decays pretty quickly after the virus is cleared from an infected person’s body. The implication is that we quickly lose immunity to the virus.

However, this is a good example of how poorly the media sometimes reports on medical science matters.

In every infection that generates antibodies, the antibody level always decays pretty quickly after the infection runs its course. And thank goodness for that because your blood serum could be overloaded with protein if you kept pumping out antibodies to everything you were ever exposed to. Most readers of this blog have had numerous vaccinations in their youth and remain immune to most of the pathogens they were vaccinated against or exposed to. You don’t keep producing antibodies to all those pathogens throughout your life, but you still remain immune to those pathogens. How does that happen?

Antibodies are just one arm of your immune response to an infection. Antibodies are produced by blood cells called lymphocytes, specifically bone marrow derived lymphocytes, or B cells. When you are first infected with a pathogen, it takes some time for the B cells to be informed that there is an invader, but they gradually begin producing antibodies to that bug. Once the bug is eliminated, the B cells cool off and go into a dormant mode.

There also is another type of lymphocyte called T cells because they originate in the thymus, a gland in your neck. They come in different forms. There are cytotoxic T cells which recognize virally infected cells and kill them. There also are T cells, called helper cells, that encourage B cells and cytotoxic T cells to attack the invader. All of these go dormant after the infection is over. However, a type of T cell, called a memory cell, arises during the infection and floats in your blood as a sentinel guarding, often for many years, against future infection.

Memory cells, not antibodies are the basis of vaccination and immunity. If you are subsequently exposed to the same pathogen, memory cells sound an alarm that immediately mobilizes your dormant B cells and cytotoxic T cells to provide a quick response to an infection with a previously experienced pathogen.

 So, the media articles implying that immunity to CoV-2 is short lived because the antibody response decays after three months are misleading. The fact of antibody decay does not mean that you are losing immunity. You are also developing memory cells while the B cells that produce antibodies are going into sleep mode.

A Simple Mutation Might Have Accelerated The Infection

70% of the sequences of ~50,000 CoV-2 genomes isolated from infected people around the world carry a simple mutation that might impart an increased ability of the virus to infect human cells. The mutation, first noticed by a researcher at Northwestern University Feinberg School of Medicine, designated D614G or "G" for short, has been found to affect the virus spike protein, which is the surface protein that gives the virus its distinctive “corona” and that binds to ACE-2 molecules on human cells in the lungs, GI tract and vascular endothelium. Lab studies suggest that the mutation in the spike protein enhances its binding to the ACE-2 receptor, thereby enhancing the virus infectability.

The mutation only changes one of about 1300 amino acid building blocks that make up the spike protein. It changes the spike protein amino acid #614 from “D” (aspartic acid) to “G” (glycine). The fact that 70% of viral isolates carry the mutation indicates that the mutation gives the virus variant an infectious advantage that has allowed it to dominate the original virus first identified in China.

The outer parts of the mutated viral spike protein are less likely to break off, which was a weakness of the original CoV-2 virus that originated in China. This weakness made the original virus harder to invade human cells. The “G” mutation makes the virus 10 times more infectious in lab experiments done at the Scripps Institute. Other researchers at the New York Genome Center and New York University, who were studying how the virus binds to and enters cells, but using the original strain isolated in January in China, had a very hard time getting the virus to infect human cells in tissue culture. When they switched to the “G” variant, they found a huge increase in infection, which agreed with what researchers at Scripps found. In human studies done at the Los Alamos National Laboratory, patients with the “G” virus variant typically carried a higher viral load, consistent with the greater infectious nature of the virus. A higher viral load would then make them more likely to spread the virus. In sum, a greater infectious ability and higher viral load, would likely accelerate the spread of the virus.

The mutation does not seem to affect the virulence of the virus. But, all of this points out that as mutations accumulate while the virus spreads, changes in its behavior due to changes in its genome are quite possible.

This is all very preliminary and the research has not been officially published, but it was made available as “preprint” research. The data have been submitted for publication. More research is needed to confirm the observations.

We will see.

Some People Say That A COVID-19 Vaccine Will Never Happen

It is amazing how many new “expert” virologists, immunologists and vaccinologists have popped up since the COVID-19 pandemic began. Over the last few weeks I have repeatedly seen claims from such “experts” that since we don’t have a vaccine for the coronavirus that causes the common cold, we will never have one for the coronavirus that causes COVID-19. Therefore, they conclude that the current efforts and expense to make such a vaccine simply waste time and resources. That syllogism assumes that someone has tried and failed to make a vaccine to prevent the common cold.

These are the facts: Only ~30% of colds are caused by a coronavirus; rhinoviruses and adenoviruses also cause what we call a cold. Therefore, we would have to develop several vaccines against several different viruses in order to prevent colds. Since colds do not cause serious morbidity or mortality, there has been little interest in developing several different cold vaccines. Thus, the first point in the “expert” syllogism falls apart.

Second, coronavirus vaccines that effectively prevent certain diseases in animals do, in fact, exist. Therefore, it is quite possible to develop a vaccine to a novel coronavirus. This defeats the second point in the “expert” syllogism.

I am pretty certain that in a couple of years, there will be several successful CoV-2 vaccines. In fact, there is a very good chance that by the end of this year, we might very well have one or two effective vaccines. This humble blogger predicts that the biggest problem we face is not in developing an effective vaccine, but getting enough people quickly vaccinated.

On May 18, this blog reported that 133 vaccine candidates were under development around the world. Today, the Milken Institute reports that 172 vaccines are under development.

Where Did This Coronavirus Come From? An Update.

On 5/21 I posted a blog, “Where Did This Coronavirus Come From?” This post is to update some of that information. However, the conclusion remains the same, we do not know.

In very early January, Chinese authorities took hundreds of samples from animals and from the Wuhan market. As I reported, they found several samples of the virus in drains and sewers in and around the market, but they had inexplicably refused to release the results of animal testing. The Chinese authorities have now confirmed that no animal samples from the market were infected. This suggests that a single person brought a virus that was already adept at human transmission to the market and infected others. This just confirms what was already known; the virus passed through the market, but this says little about where it originated. It, however, does, increase the doubt that it came from an animal in the market.

Recent work published in March by Andrew Rambaut of Edinburgh University, analyzing viral genomic sequences, calculates that the most recent common ancestor of the virus infected someone in late November or early December, though that comes with a “confidence range” stretching back into October. So it presumably fine-tuned its ability to infect humans sometime before this and likely somewhere other than the market in Wuhan, since Wuhan is not a home for the bat species that carries the ancestor virus.

The closest animal version of the virus remains a bat sample collected by scientists in 2013 a thousand miles away in Yunnan. A new paper by two scientists from the Agharkar Research Institute in Pune, India, show that it is the same as a published sample that was collected from an abandoned mineshaft in southern Yunnan in 2013, following an outbreak of pneumonia-like illness that killed three miners there the year before.

So what did happen? At present, the evidence points tentatively to a chain of person-to-person infections occurring somewhere outside the city before somebody brought the virus to Wuhan, where the market acted as an amplifier. The first case could have been a rural farmer or possibly a bat researcher collecting samples for virologists. Or it is possible that another animal was involved in some way, with the virus bouncing between a farmer and his animals, or a wildlife smuggler and his poor prey.

As I concluded in my previous article, “It seems clear that the ancestral virus came from a bat, but there is little certainty about what happened after that. At this point, the only thing certain about the virus is its uncertainty.” Except, a bit more data seems to support the notion that the virus originated outside Wuhan. That is speculative at this point, but it seems more possible.