Tag Archives: vaccine

How The Pandemic Ends

The gold standard, the ones to beat, the top dog, brain trust magnate, 800 pound gorilla, paragon, cream of the crop, and the one head and shoulders above all others, in the matter of a Covid-19 vaccine, is Oxford.

The group at Oxford already made a Coronavirus vaccine, for MERS, but it never underwent final testing and deployment. Not enough people were getting sick from MERS, and it was under control.

This group is optimistic about having a vaccine in September of this year. Give them a month leeway, a few months for emergency intensified field testing, and some extra time to ramp up production and negotiate liability issues, and we could have a world wide vaccination program well under way by the end of January.

Between now and, say, August 15th, the medicos will have developed and deployed a half dozen nursing, ER, and IC procedures that drop the death rate of the most severely ill well below its near 90% level, to maybe half, and various treatments, therapies, and all will drop the number who go from diagnosed to severe down by a double digit percent.

Although natural herd immunity would take multiple waves and years, a certain reduction of infection rate happens at any percentage. New normal practices will have adapted to slow the disease. By mid September there will be parts of the US, and various smaller sized countries, where COVID-19 will become rare or nearly non existent, even as new hotspots emerge. But even those hotspots will be dealt with better than the US addressed this disaster in the early week.

But the flareups will be severe, and in most cases, caused by politically driven Republican strategies cheered on by Trump and sullenly overseen by Pence. The carnage will continue to be so bad, and the response to it by Trump and his gang of Republicans so inept and inextricably linked to nefarious side bets and deals, that there is a non-zero chance his administration will not still be in place on election day, November 3rd. Either way, Trump will be voted out of office on November 3rd, and probably dragged from the White House and impaled with a broom stick well before inauguration day by angry tourists and DC residents after he attempts to annul the election results. There is a non-zero chance that the 46th President of the United States will be Speaker Pelozi, for the several days between Trump and Pence’s awkward and painful departure (captured on hundreds of cell phones) and the inauguration of President Joe Biden.

There will be no Biden Inaugural Ball and his Inauguration speech will be on Zoom, But his first act will be to sign the 2021 Rapid Immunization Order, speeding up the delivery of the vaccine already developed by Oxford and manufactured everywhere but the United States even as Jared Kushner tries to get his vaccine (which is fatal to 1 in 200 who are injected with it, and does not actually protect against COVID-19) to be the legally required stick.

But I digress.

Schools will not reopen in the Fall, but by Spring it will be possible to have limited activities, as vaccination spreads faster than COVID-19 itself ever did. Kids who come from anti-Vax families will be shunned, and hate their parents forever, because they won’t be allowed to go to the 2021 proms and graduation ceremonies, which will be endlessly televised and smeared across social media until we are giddily sick of them.

By the end of 2021, the virus will be history (except in the Congo, where all diseases go to retire securely), social distancing will be a fond memory (for everyone with sensory processing disorder), and our new society, led by science and reason, will begin the process of building windmills instead of tilting at them.

Problems conceptualizing Covid

The Covid-19 pandemic is serious, scary, real, and kills. And there is a fair amount we don’t know about it.

There I said it. You don’t have to worry about me thinking Covid-19 isn’t serious. That happens to me a lot. Someone says “OMG, the COVID-19 is just like a grizzly bear eating your face off!” and I point out that a virus and a face-eating grizzly bear present distinctly different problems. Then the person gets all pissy and mad because I did not share their specific horror. Generally, I prefer it if people do not shove their fears in my face at the expense of reason. We have real fears, we don’t need to add on the ones that are bogus, unsupported, panicked, or untethered from reality.

You might say, jeezh, Greg, what harm does it do if people don’t understand every little thing about COVID-19 and, in their conceptualizing this disease, stray away from actual science and reality and stuff? Most of the time it probably does’t matter. But people make decisions on the basis of what they think they know. If you think the SARS-CoV2 virus doesn’t really live on surfaces, you won’t be careful about door knobs and push plates in heavily used public places, and you may thus contribute to the spread of this disease. If you think COVID-19 can be spread by eating food from a can, you might waste your energy, my energy, everybody’s energy, by campaigning against canned food. And so on.

So what kinds of things are people getting wrong? Here’s a sampling.

COVID-19 is caused by a virus. Most life lessons about pathogens are not transferable across types of pathogens. A coronavirus can’t be compared usefully to malaria or sleeping sickness because those are single celled eukaryotes. COVID-19 can’t be compared to bacterial infections. All these different kinds of pathogens have different effects, do different things, act in different ways, and need to be dealt with using specific actions (or avoiding specific actions).

COVID-19 is caused by a particular type of virus. There are many kinds of viruses, and the different kinds have distinctly different biologies. Comparing the behavior of SARS-CoV2, the virus that causes COVID-19, to the influenza virus, is like comparing the behavior of eels to eagles. How they reproduce inside a cell, how they avoid a body’s immune response, how much they mutate, and how a vaccine might work for each type of virus, are really very different, in fact, astonishingly different. Comparisons are not helpful at all.

Immunity is a tricky concept to understand. I wrote about it here. I think immunity (to a pathogen) is often viewed as an absolute, and as a somewhat magical thing. If I’m immune to a particular pathogen, that pathogen can not infect me, right? If I’m walking down the street, and a pathogen is coming the other way and I’m immune to it, it crosses the street to not get anywhere near me, right?

No. If I’m what we call “immune” to a pathogen, that means that the pathogen still goes inside me. It starts to do whatever that pathogen normally does in a human body. It is, in fact, infecting me. Then, because I’m “immune” a particular part of my immune system quickly responds to that pathogen’s presence, because I’ve acquired an immunity to it either by prior infection or by vaccination. Other parts of my immune system also work against a pathogen whether I was previously vaccinated or exposed or not.

The acquired immunity that comes with vaccination or prior exposure causes my body to respond more quickly. The best kind of immunity is where my body responds well within the time period where the pathogen hasn’t made me sick yet, attacks the pathogen, and kicks the crap out of it before it can do anything. I don’t get “sick” from the pathogen not because it did not infect me — it did infect me — but because the illness that pathogen typically causes never got of the ground. The natural biological course of the pathogen did not advance sufficiently to either make me feel bad or to be passed on to another person. Or, in a less ideal immunity, common with many pathogens, I do actually get somewhat sick, and maybe I can even pass the disease on, but acquired immunity makes me much less sick and much less contagious.

And as noted, a person who is “not immune” is typically a little immune anyway. That is because the immune system has several parts that try to stop a pathogen, and because the above mentioned acquired immunity is still an immunity before it is trained up in your body. It just takes longer.

The difference between a typical “non-immune” person and a typical “immune” person, as the term is usually applied, is this and only this: For the immune person, the adaptive immune system (only one part of the immune system) acts faster because it is trained by prior infection or a vaccine (which simulates a prior infection) so the body is prepared.

Indeed, a normal immune response to a pathogen is often to get sick and seem not very immune at all. Little kids get colds all the time, and they can last a long time. It seems like from a certain young age until a few years later, still at a young age, a kid is sick all the time. Adults go around bragging about how they haven’t lost a day of work in 20 years. (Not all adults, but some.) This is largely because kids don’t have a very strong immunity to the handful of different viruses that give us regular colds. But over time, a human will typically develop a stronger and stronger immunity. All these humans are immune to those viruses to some degree, just not perfectly and totally immune.

With COVID-19, we hear stories of “reinfection” and this has led many people to believe that humans do not develop an immunity. The numbers of possible re-infections is very very small compared to the number of people infected, and it is highly likely that those instances are bad reports, or individuals who never really got rid of the disease to begin with. Of the remaining, much smaller number of individuals, re-infections may have happened because that person’s immune system just didn’t produce a strong immunity in that person. A very small number of possible re-infections is expected for any disease and isn’t alarming.

Usually, an exposure to a pathogen that we can develop an immunity to results in an immunity that lasts for a while. Usually, years.Sometimes enough years that it seems like a life long immunity, or close to it. In other cases, you get a modest immunity that gets better with more exposure. Remember, SARS-CoV2 is a particular virus, and should not be compared willy nilly to other viruses. HIV gets around the human immune system, but it is a very different virus. Not a valid comparison at all.

Sometimes our immunity does not help us much with a later infection, or so it seems. You get a Yellow Fever shot and later they tell you you need another one. Or, the flu shot from last year isn’t helpful this year. This might be a linguistic matter. We call the pathogen by a certain name, but underlying that name is a wide range of different species or strains of that pathogen. We use the word “flu” for “influenza” but there are many different major types of influenza. If influenza was a “canid” then there would be foxes, wolves, coyotes, and domestic dogs. All in the same family but not really the same.

Alternatively, later infection could be the result of a particular strain mutating enough to side step our immunity, somewhat. Or, it could be that our immunity wore off.

A common misconception about mutations is that they make a pathogen worse. Well, they can, but they usually don’t. We hear “COVID has had 29 mutations! Aieeeee!!!” I assure you that SARS-CoV2 has had many many more mutations than that. If you get COVID-19, the SARS-CoV2 inside you probably mutates hundreds or thousands of times as it replicates using your cellular machinery, as viruses do. But, the vast majority of mutations cause a viral strain to become broken, or to not change at all. A small number may make the virus a little better at what it does, or a little less good at what it does. From our point of view as the host of the virus, a small number of mutations might make it harder to pass it on, or easier to pass it on, or liable to make a person a little more sick or a little less sick. That any one of these mutations occurs in your body does not mean that that mutation will now be part of the general population of SARS-CoV2 viruses. The vast majority of mutations that both happen in an infected individual and that do not produce a dead-end variant will not be passed on to the next person. You will just sneeze them out and they will be killed by ultraviolet light, hand sanitizer, or the main thing that kills most individual virus particles: Time.

We hear a lot now about rare and scary things. Twenty-three year olds dropping dead of a stroke, or other odd blood clotting things, and so on. Those may be real or they may not be real. If tens of millions of people get a disease, there will be situations where a cluster of individuals were going to also have some other thing happen to them medically, and they happen to have this thing occur while they have COVID-19. Coincidence. Or, a disease like this might really have some other effect that is very rare, but that thing is, well, very rare. After the discovery of some possible odd effects on blood clotting, people started to say things like “it kills young people in this strange way and we didn’t know it until now! Aieeeee!!!!” but at the same time, the death-over-age statistics did not change. We did not find 300,000 dead 23 year olds. The strange new thing remained rare, and enigmatic. Important, interesting, something we must find out about. But still very rare.

I’ll end here with a dirty little secret of the immune system: Of all the different biological systems that make up the typical animal (including humans) it is with the immune system that the gap between all that can be known and what we confidently know is largest and deepest. We know a lot, but we also don’t know a lot. And, it is so damn complicated that it is impossible to expect the average non-expert to not make the sorts of mistakes mentioned above. I can add this: I’m heavily revising what I cover in my course on the immune system, to help future generations of pandemic victims have an easier time parsing what is happening around them. Assuming I can get back into a classroom with them!

A Coronavirus (Covid-19) Vaccine

There are no current vaccines for any coronavirus. I’m not comfortable explaining why that is the case, but I’m usually told that the actual killer coronaviruses (there are not many, most viruses of this kind are not big problems for humans) came and went too fast to “need” a vaccine.

This is not really true, since at least one such virus is endemic to a region, a continuous threat, but found mostly in domestic camels. There was a vaccine developed to address that virus, but testing was never completed, and deployment never happened, so we don’t know if it was really effective.

The question of “can there be a vaccine” and “do we develop an immunity to this virus” are related, and we still see the occasional panicked revelation that maybe humans don’t actually develop an immunity to this virus. Don’t worry, we do. If we didn’t the situation would look very different than it does now.

However, we don’t know everything we need to know about that immunity. We know that for this kind of virus, it is possible that a partial immunity develops in most but not all people, and that some people have a much stronger immune response than others. It is quite possible that we develop an immunity that lasts only a few years (for most people), and it is also possible that repeated exposures and/or vaccinations will build up a longer term immunity. These are all important questions, but they do not raise the possibility that we can’t be or won’t be immune to SARS-CoV-2 (the virus that causes Covid-19). Rather, they frame the issue of how a vaccine is actually deployed. We may see a world, in two years from now, where a Covid-stick is an annual event, but one that people take more seriously than they currently take the annual flu shot, and quite possibly, one that works better (SARS-CoV-2 and influenza are very different things).

There are several vaccines in development. In my experience tracking disease and epidemiology (I’m an immunologists or an epidemiologists, but both my wife and I play these roles in the classroom and she is actually a fellow in an immunology program for teachers), the assertion that “we’re close to a vaccine” is one of the Great Lies, which are “the check is in the mail” and two other ones.

But, there is hope, and it might be real hope, that there will be a vaccine, and there is even the possibility that it will take less time than the several years. It may even take less than the oft-cited but pretty much made up “18 month” time span.

A few takes current, add to comments your newer information if you have some:

April 14: Microneedle coronavirus vaccine triggers immune response in mice

Researchers led by Drs. Louis Falo, Jr. and Andrea Gambotto from the University of Pittsburgh have been working to develop vaccines for other coronaviruses… They adapted the system they had been developing to produce a candidate MERS vaccine to rapidly produce an experimental vaccine using the SARS-CoV-2 spike protein.

…a method for delivering their MERS vaccine into mice using a microneedle patch. Such patches resemble a piece of Velcro, with hundreds of tiny microneedles made of sugar. The needles prick just into the skin and quickly dissolve, releasing the vaccine. Since the immune system is highly active in the skin, delivering vaccines this way may produce a more rapid and robust immune response than standard injections under the skin.

When delivered by microneedle patch to mice, three different experimental MERS vaccines induced the production of antibodies against the virus. These responses were stronger than the responses generated by regular injection of one of the vaccines along with a powerful immune stimulant (an adjuvant). Antibody levels continued to increase over time in mice vaccinated by microneedle patch—up to 55 weeks, when the experiments ended….

April 14th: Johnson and Johnson claim a vaccine is imminent

Johnson & Johnson (JNJ) said on Tuesday it plans to begin imminent production of its trial COVID-19 vaccine on an “at risk” basis, as the coronavirus pandemic infects nearly 2 million people around the world.

Manufacturing “at risk” allows the world’s third largest pharmaceutical company to produce a product before its ultimate design is finalized and released to the public. The company plans to produce its COVID-19 vaccine in the Netherlands, and a facility it is updating in the United States.

“We’re manufacturing at risk to ensure that should the clinical development and the trials be successful, we are in a position to kind of flip the switch and ready to go, to create great access across the globe,” J&J CFO Joe Wolk told Yahoo Finance in an interview.

J&J began developing its vaccine for COVID-19 in early January with its European subsidiary Janssen Vaccines & Prevention B.V. It’s using the same biological platform Janssen uses in developmental vaccines for Ebola, Zika and Influenza.

During J&J’s first quarter earnings call, Chief Scientific Officer Paul Stoffels said the company is also negotiating with partners in Europe and Asia to produce the vaccine, and partnerships will be announced in the coming weeks.

“Our goal is to enable the supply of more than 1 billion doses of the vaccine globally,” Stoffels said.

April 14th: Two Pharmaceutical Giants Collaborating To Develop One. GlaxoSmithKline and Sanofi are joining up …

” in an unprecedented collaboration. It brings together two of the world’s biggest vaccine companies with proven pandemic technologies and significant scale, all with the aim of developing an adjuvanted COVID-19 vaccine.”

An adjuvanted vaccine is one that includes a compound known as an adjuvant that enhances someone’s immune response to a vaccine. In the partnership, GSK will be providing the adjuvant and Sanofi will provide the specific protein component of the coronavirus that will generate the appropriate antibody response.

“… we’re planning to start trials in the next few months,” Walmsley said. “And if we’re successful, subject to regulatory considerations, we aim to complete the development required to make the vaccine available in the second half of 2021.”

There is an earlier reported vaccine in development at Johns Hopkins.

Science Gone Awry, Science Haters Mailing Mailers

I’m currently reading Paul Offit’s Pandora’s Lab: Seven Stories of Science Gone Wrong, in preparation for an interview with him that I’ll be recording later this week. I’ll let you know about the interview, but at this time I can say that I’m very much enjoying the book. The publisher’s description:

What happens when ideas presented as science lead us in the wrong direction?

History is filled with brilliant ideas that gave rise to disaster, and this book explores the most fascinating—and significant—missteps: from opium’s heyday as the pain reliever of choice to recognition of opioids as a major cause of death in the U.S.; from the rise of trans fats as the golden ingredient for tastier, cheaper food to the heart disease epidemic that followed; and from the cries to ban DDT for the sake of the environment to an epidemic-level rise in world malaria.

These are today’s sins of science—as deplorable as mistaken past ideas about advocating racial purity or using lobotomies as a cure for mental illness. These unwitting errors add up to seven lessons both cautionary and profound, narrated by renowned author and speaker Paul A. Offit. Offit uses these lessons to investigate how we can separate good science from bad, using some of today’s most controversial creations—e-cigarettes, GMOs, drug treatments for ADHD—as case studies. For every “Aha!” moment that should have been an “Oh no,” this book is an engrossing account of how science has been misused disastrously—and how we can learn to use its power for good.

The story of opium reminds me of that movie, Very Bad Things. Remember that?

Also, I did a podcast, the guest rather than the interviewer (I go both ways), on Geeks Without God, which will be up on the 16h, here. I think that if you are a subscriber you can get it early, like, now. The interview was about the Heartland Institute‘s recent recent mailing of anti-science materials related to climate change, sent out to a very large number of teachers.

NewLink Genetics, of Ames Iowa, Implicated in African Ebola Genocide?

According to those intimately involved in the response to the West African Ebola outbreak, NewLink Genetics owns the rights to a piece of the puzzle needed to quickly test and deploy one of two likely Ebola vaccines and they are holding up the entire process because they are not entirely sure they are going to get rich on it. Other suggest it is incompetence. NewLink seems to be claiming it is just a lot of paperwork. In the end, tough, none of these excuses is convincing. This is one of those cases that gives Big Pharm a bad reputation.

From as story in Science:

Stephan Becker is tired of waiting. The virologist at the University of Marburg in Germany is part of a consortium of scientists that is ready to do a safety trial of one of the candidate vaccines for Ebola. But the vaccine doses he’s supposed to test on 20 German volunteers are still in Canada. Negotiations with the U.S. company that holds the license for commercialization of the vaccine…have needlessly delayed the start of the trial… “It’s making me mad, that we are sitting here and could be doing something, but things are not moving forward,” Becker says.

… it’s inexplicable that one of the candidate vaccines, developed at the Public Health Agency of Canada (PHAC) in Winnipeg, has yet to go in the first volunteer’s arm, says virologist Heinz Feldmann, who helped develop the vaccine while at PHAC. “It’s a farce; these doses are lying around there while people are dying in Africa,” says Feldmann,…

At the center of the controversy is NewLink Genetics, a small company in Ames, Iowa, that bought a license to the vaccine’s commercialization from the Canadian government in 2010… Becker and others say the company has been dragging its feet the past 2 months because it is worried about losing control over the development of the vaccine. But Brian Wiley, vice president of business development at NewLink Genetics, says the company is doing all it can. “Our program has moved forward at an unprecedented pace,” he says. Even if it took another few months, “we would still be breaking a record in terms of getting this into patients.” Wiley says the holdup is “the administrative process”: agreeing on a protocol, getting collaborators to sign the right contracts, securing insurance in case something goes wrong.

Marie-Paule Kieny, a vaccine expert and WHO assistant director-general, disputes that NewLink is dragging its feet. “We have so far been able to resolve issues along the way, to get moving as fast as possible,” she says.

A stock of the Canadian-developed VSV vaccine is stored at PHAC in Winnipeg. The Canadian government owned 1500 doses, 800 to 1000 of which it has donated to WHO; the rest are owned by NewLink Genetics.

Scientists say WHO’s vials could have already been shipped to the research centers planning to do phase I trials. One such trial is scheduled at the Walter Reed Army Institute of Research in Silver Spring, Maryland; other studies, by a consortium that includes WHO and Becker, are on the drawing boards in Hamburg, Germany, in Geneva, and at sites in Kenya and Gabon. PHAC is ready to ship the doses “at a moment’s notice,” a representative says.

But for a clinical trial to start, regulators require information about how the vaccine was manufactured, and that resides with NewLink Genetics, which has been slow to release it, people familiar with the negotiations say. …

Part of the problem may be that NewLink is a small company, with about 100 employees, that has concentrated on immunotherapies to fight cancer in recent years. The Biomedical Advanced Research and Development Authority—a U.S. government agency tasked with speeding up the development of emergency drugs and vaccines—recently sent two staffers to Ames to help NewLink file documents needed by the U.S. Food and Drug Administration, a U.S. government representative says. “Our engagement of outside help has nothing to do with our competence, but with the urgency around this matter,” Wiley says.

Those who are taken ill and die of Ebola are the victims of a natural disaster, until paperwork, incompetence, greed, or some combination of those delays an international response by weeks time. After that, it is something else.

Science Denialism: Some resources

The term “War on Science” comes from multiple sources, one being Chris Mooney’s book “The Republican War on Science” (see below) and another, the made up “War on Christmas,” a term attributed to Bill O’Really. Throw in a little “Culture War” rhetoric and I think we have a good basis for the origin of the term. The term “War on X” has been in used for decades if not longer, when some large perhaps organized group of people or institutions takes up the task of shutting down some thing or another. It does not mean an actual war with generals and troops and bullets, but the metaphor “war” is still quite apt because there are generals and troops and bullets, just metaphorical ones.

Anyway, I thought it would be a good idea to provide a list of current or recent books and other resources pertaining to the war on science. Where I’ve reviewed a book here, I provide a link to that review. There are also some helpful web sites and podcasts listed below. The listing of resources is divided up by “front” or “battle ground” where appropriate, keeping with the “War on Science” metaphor.

The War on Science, General

Continue reading Science Denialism: Some resources

Why isn’t there a malaria vaccine, and could there be one soon?

There are several reasons why there is no vaccine for malaria, but the thing you might want to know is that malaria is not a virus, and it is not even a bacterium. It’s a protist. Generally speaking, there are not really vaccines for such organisms. One metastudy that looked specifically at Malaria had this to report:

Continue reading Why isn’t there a malaria vaccine, and could there be one soon?

A Universal, One-Shot Flu Vaccine?

ResearchBlogging.orgA Better Grip: T Cells Strengthen Our Hand against Influenza Clinical Infectious Diseases, 52 (1), 8-9 DOI: 10.1093/cid/ciq018Flu vaccines are important and useful, but also relatively ineffective compared to many other vaccines. Immunity is imperfect, there are many ‘strains’ of influenza in a given year only some of which are addressed by the available vaccine (though often the most common ones) and one year’s vaccine does not provide immunity to subsequent years’ influenza because the virus changes so much. Well, actually that’s not exactly true: The influenza virus has various different parts, and the parts that the traditional flu vaccine uses to induce an antigenic reaction in the potential hose is highly variable. Other parts of the flu virus are not as variable. If only a vaccine could be developed that uses the less variable part of the influenza virus, then perhaps it would be a universal, long-lasting vaccine that you take once, and become pretty much immune to all future influenza.
Continue reading A Universal, One-Shot Flu Vaccine?

Vaccination vs. Disease: Which is worse?

It is very reasonable for a parent to worry about vaccines. For one thing, most of them involve sticking the baby or child with a sharp object, thus making the little one cry, and it would be abnormal to not have an automatic reaction to that. For another thing, they are drugs, in a sense. When the little one is ill, and you call in to the health care facility in the hopes that there will be some useful advice, most of the time you hear “No, we no longer recommend giving [fill in the blank with a medicine you thought might work] to children under [one or two months older than your child]. But if [symptom] persists for more than [amount of time that is 12 hours longer than the symptoms ever persist], call back.”
Continue reading Vaccination vs. Disease: Which is worse?

Study Confirms Link Between Autism and Use of Cells From Abortions in Vaccines?

First, let’s get this straight. I’m all for anti-science anti-vaxer right wingers not being vaccinated, as long as a) we take their children away from them (and vaccinate the poor dears) and b) isolate the adult anti-vaxers from the rest of the species, perhaps in Texas. But in the meantime, let’s look at the latest bit of (mis)information from the utterly insane side of our society. If nothing else, this story may serve to remind us all what we are fighting about…. not the attitude of this or that skeptics, or which movements should or should not be engaged in chopping the pope down to size. This, folks, is the real deal:
Continue reading Study Confirms Link Between Autism and Use of Cells From Abortions in Vaccines?

How do we know how bad the Swine Flu is so far?

I spent about 45 minutes yesterday in the local HMO clinic. They had turned the main waiting room into a Pandemic Novel A/H1N1 Swine (nee Mexican) Influenza quarantine area, and I could feel the flu viruses poking at my skin looking for a way in the whole time I was there.

Continue reading How do we know how bad the Swine Flu is so far?