Coronavirus news & views

BioX Wins The Nobel!

“If you start to take Vienna, take Vienna”— Napoleon (reportedly)

What’s the fuss? BioX won the Nobel Prize….er rather it was the mRNA vaccine that won. Correction—it was the scientists, Katalin Karikó and Drew Weissman of the University of Pennsylvania, who developed the RNA technology that went into the novel vaccine who won the prize. But their work directly led to the vaccine, a first fruit of BioX.

Readers of these blog pages might remember that about this time in 2020, that year’s Nobel award for Medicine or Physiology went to three scientists for their decades-long search to discover what caused hepatitis type non-A, non-B. It turned out to be a whole new virus, the hepatitis C virus (or HCV) that took four decades to identify. Even though it still remains a huge health problem, there still is no vaccine for it. I compared that four decade slog just to find the pathogen to how fast the novel viral cause of COVID-19 was found and a vaccine developed—all done in less than a year! I anointed the new biology that did that amazing feat, ‘BioX.’ That was rather prescient of me, since three years later, the co-founders of the COVID vaccine using BioX too were awarded the Nobel Prize.

I dubbed the new amazing post-molecular biology science that enabled such a quick identification of the novel coronavirus and development of a vaccine against it, ‘BioX’ after SpaceX. SpaceX, of course, is the name for the new way space travel is now being done. Shortly before the Nobel award for the discovery of HCV, Elon Musk’s SpaceX took astronauts in an unpiloted vehicle to the International Space Station. Then the launch vehicle, rather than being discarded as usual, was landed, upright, in the center of a bullseye on a barge off the coast of Ireland, to be reused on a future space flight--maybe to Mars? The whole thing was developed in a fraction of the time at a fraction of the cost of what NASA had historically been doing. NASA’s technology was rendered archaic by SpaceX, which introduced us to a new era of space travel.

The breathtaking speed with which a new biology discovered the SARS-CoV-2 virus and then developed a safe and effective vaccine against it ushered in a new post-molecular biology world I dubbed ‘BioX’.

Now the details. But as breathtaking as SpaceX is, it was not developed overnight in a vacuum. It arose on the back of decades of NASA engineering R&D, which included some spectacular failures and even a few tragic deaths. Similarly, as breathtaking as BioX was with the rapid identification of a novel virus and development of the new mRNA vaccines to a wholly new disease, that technology too was built on the back of decades of hard work, punctuated with many failures, but also flavored with impressive perseverance on the part of a few individuals.

There are two major components to the novel COVID vaccines—the mRNA which generates the viral protein to which the immune response is made, and the lipid nanoparticles that encapsulate and protects the fragile mRNA from a world that is hostile to mRNA. Both components took very separate, decades long, twisting, uphill roads to develop. Both nearly met with failure. And both came together with spectacular success. BioX!

• The mRNA. Weissman, and especially Karikó, languished for years on the fringes of science with a, then, very weird idea of using mRNA to produce drugs or vaccines. Their collaboration began with a chance encounter at a UPenn copy machine in the 90s and went downhill from there as recently told in the Wall Street Jounal. Funding for their work was hard to come by. Karikó was banished to an office on the outskirts of the campus and languished in a non-faculty position for years. At one point, she had to take a demotion to simply keep a job at Penn.

They just could not get their idea to work. The mRNA was too fragile and too short-lived to work with and produce the desired proteins when they tried to express it in cells or animals. The fact is that there are ubiquitous enzymes all around us called RNases that have a ravenous appetite for mRNA. RNA molecules, especially mRNA disappear almost as fast as one can purify or make them, let alone then try to get them into cells in tissue culture or into bodies. On top of that, when naked mRNA is injected into a body, it elicits a powerful immune response that further quickly degrades it. Note that there are several different types of RNA, and mRNA is the most fragile and hardest to work with, but it is the type that provides the message that turns a genetic code into a protein molecule like a spike protein, which is why it is used in the vaccine.

The researchers had great difficulty getting grant funding for their research because no one believed it would go anywhere. When they could produce some data, they had a very hard time finding journals to publish it. No one was interested because no one believe that there was any utility in the whole premise of using mRNA as a therapeutic tool. In the publish-or-perish world of academia, such negative peer pressure usually is the kiss of death. They should have seen the writing on the wall and been teaching high school biology. But for some reason, Karikó continued to have faith in her idea even though no one else did. For some reason, she persevered.

After dogged determination and ignoring all the naysayers, she eventually had a major breakthrough after a doing a simple experiment. They found a simple way to protect the mRNA from the immune response and published this in 2005. It opened the field and colleagues minds about using mRNA as a possible therapeutic tool. But there still was the problem that mRNA was exquisitely sensitive to RNase enzymes that were everywhere—on your fingers, in your breath and blood, even on sterilized surfaces—the enzymes are incredibly stable molecules and very hard to destroy. Life intended mRNA to be short lived molecules, not to be used in vaccines.

It wasn’t until folks paired the immune-stable mRNA of Karikó and Weissman with a way to protect the molecules from RNase enzymes that mRNA vaccines became possible so they could win the Nobel Prize. Lipid nanoparticles did the trick.

• The lipid nanoparticles. The story behind the development of the lipid nanoparticles used to deliver the CoV-2 viral spike mRNA sequence to cells so they could use their normal gene expression machinery to put the spike protein on their surface and generate an immune response is a long one. In that regard it is quite similar to the long, arduous story behind the development of the therapeutic mRNA. Early on, neither technology was believed possible or useful by the scientists’ peers. Both groups had very hard times getting their scientific feet on the ground. Both nearly failed. I described Karikó’s struggle above and in March 2021 I wrote in these pages about the professional plight of Bob Langer who, in the 70s, had a vision for using liposomes (short for lipid nanoparticles) for delivering fragile bio-molecules and drugs to cells (you can read that post here). Briefly, his idea was to create mini-cells in which to package and protect fragile therapeutic molecules and then deliver them to cells and tissues in the body. The liposomes containing the fragile therapeutic molecules would fuse with the lipid membranes of cells and disgorge their contents into the cells. Many people told him it was not possible and he had his first nine grant applications rejected—and this was a time when medical science research grants were easy to get (when I was in graduate school in the early 80s, NIH grant applications had a 50% success rate. By the time I became a faculty member in the late 80s that dropped to 10%). Langer, like Karikó, also could not get a faculty position because people did not believe in his research. Also like Karikó, for some reason Langer persevered.

Also like Karikó, Langer too succeeded—eventually. It took a long time. The technology he successfully developed was first used to package a drug used to treat a rare genetic disease that causes nerve and heart damage. It also was used to package mRNA for an Ebola vaccine. From an ignominious beginning, Bob Langer became a professor at MIT where there now is a bioengineering lab named after him. That is not quite as nice as winning a Nobel prize, but high recognition still.

Along the way, he also co-founded a small biotech company named Moderna that was focused on developing mRNA vaccines for infectious diseases, cancer and other diseases. Then COVID came calling and Moderna immediately pivoted, and along with BioNTech, NIH, and Pfizer, quickly gave us mRNA vaccines delivered in liposomes that saved millions of lives from COVID.

That is how BioX technology led to the Nobel prize this year.

The bottom line. BioX, like SpaceX, was built on decades of hard research that was punctuated by painful failures, but highlighted by dogged determination. Both technologies, BioX and SpaceX, are here to stay at least until the next amazing thing replaces them. You can bet that that next amazing thing will have been developed on the back of determined researchers who very possibly will be working at the fringe of their professions and may flirt with professional failure early on. You can also bet that the next amazing things will be built on the backbone of SpaceX and BioX. That is how science and engineering painfully progresses.

So, when you hear someone say that the mRNA vaccines are experimental like I very often do, tell them the truth. They were built on decades of hard research going back to the 70s.

Stay tuned for a coming post on the future of BioX, which is here to stay for a while. New mRNA vaccines are being developed for previously vaccine-impossible diseases including HIV, cancer, and various animal diseases. Work also is underway for a universal flu vaccine.

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The Differences Between The Moderna And Pfizer mRNA Vaccines

Since the vaccines rolled out, people, including me, have talked about the Pfizer and Moderna vaccines as simply being interchangeable versions of mRNA vaccine technology platforms. They both use part of the CoV-2 viral mRNA sequence to temporarily express parts of the viral spike protein on muscle cells in order to stimulate a protective immune response against the live virus. Since mRNA is very unstable and would quickly degrade if it were injected by itself, both vaccines encapsulate it in lipid nanoparticles, or liposomes, which both protects the mRNA and helps it fuse to cell membranes and insert the genetic material into the cells where it is translated into the protein. So, the Pfizer and Moderna technologies are very similar.  But they are not identical. At first blush, the differences appear subtle, but we are learning that they seem to manifest themselves in different, not-so-subtle biological ways. Let’s take a look at the how the vaccines differ.

The formulation: The lipid nanoparticles that carry the mRNA are a bit different between the Pfizer and Moderna vaccine platforms. While the exact formulations are proprietary intellectual property owned by each company, we do have a little bit of information about how they are similar and how they differ. Both platforms are concoctions of several different lipids designed to spontaneously assemble in aqueous solutions into small, “artificial cells” that encapsulate the mRNA payload. The lipids in both vaccines include polyethylene glycol (PEG), which can have multiple effects on the properties of lipid nanoparticles; they can affect particle size and particle stability. Certain PEG modifications can also prolong the blood circulation time of nanoparticles by reducing clearance of the liposomes by the kidneys and by scavenger immune cells called phagocytes.

The Pfizer vaccine also contains two proprietary lipids known as ALC-0315, and ALC-0159 as well as cholesterol, all in a very precise ratio. The Moderna vaccine platform consists of lipids that are not as well-known publically because the company is in litigation over the intellectual property with Arbutus, which developed the lipids that were licensed by Moderna.

Basically, viruses are naturally occurring liposomes encapsulating genetic material. The nanotechnology community has long been trying to create “artificial” virus-like nanoparticles that do not replicate or spread like a live virus in order to deliver fragile molecules, like mRNA, to cells for therapeutic reasons. Therefore, the goal of therapeutic liposomes is to create a virus-like lipid bilayer membrane (see figure) in order to deliver a drug or vaccine payload to cells. Mixing amphiphilic fatty acids, which are lipids where one end is water soluble (hydrophilic), while the other end is not (hydrophobic), in an aqueous solution allows them to spontaneously assemble into virus-like nanoparticles, or mini-cells. A water soluble payload (mRNA in this case) is captured in the central blue area and is protected by the outer lipid membrane. When these artificial cells bump into a live cell, the lipids on the two membranes fuse dumping the therapeutic payload into the cell’s cytoplasm.

There are endless combinations of amphiphilic lipids which can form such pseudo-cells, the properties of which can be modified depending on which lipids are used. For example, the selection of lipids used in both vaccines give the surface of the liposomes a mild positive charge, which facilitates their ability to stick to the negatively charged membranes of live cells.

What all this means is that the specific lipid formulation used in the Pfizer and Moderna vaccines affects the delivery of mRNA to cells, but we do not have enough detail to be able to suss the effects of the different liposome compositions on the efficacy of the vaccine. Those details mostly remain trade secrets.

lipid nanoparticle mimics a cell bilayer membrane

mRNA sequence. Both the Moderna and Pfizer vaccines use mRNA that encodes part of the spike protein of SARS-CoV-2, which sits on the surface of the virus and binds with the ACE2 receptor on the cell surfaces of many tissues. mRNA molecules are chains of four nucleosides arranged in a gene-specific sequence code that cells then translate into a specific protein. However, when a foreign mRNA is injected into a body, the mRNA itself can be recognized by the immune system and neutralized before it can enter a cell and express its cognate protein. For this reason, both the Pfizer and Moderna mRNA vaccines have been modified to incorporate a synthetic non-natural nucleoside, 1-methylpseudouridine, which reduces the ability of the immune system to recognize the foreign mRNA and improves its stability and expression of its protein.

The spike molecule consists of two protein subunits, the first of which is responsible for the initial binding with ACE2, while the second promotes the fusion between the virus and the cell membranes. The mRNA sequence incorporated into the Moderna vaccine, mRNA-1273, specifically encodes the pre-fusion form of the second spike protein subunit that is found on the surface of the virus before it binds to the ACE2 cell receptor. The mRNA sequence is modified to produce a spike protein with two amino-acid substitutions at positions 986 and 987 on the protein that help to keep it in the pre-fusion state. In contrast, the mRNA utilized by the Pfizer-BioNTech vaccine (BNT162) only encodes part of the spike protein on the first subunit that specifically binds to the ACE2 receptor. Thus, the two vaccines drive immunity to different parts of the spike protein molecule.

Perhaps more importantly, the dose of mRNA in the two vaccines differs. The Moderna vax delivers a 3-fold higher dose (100 mcg) of mRNA compared to the Pfizer vaccine (30 mcg). This  means that more spike protein antigen to stimulate an immune response is expressed from the Moderna shot.

What does it all mean? Initially, these differences in lipid composition, mRNA sequence, and mRNA dose do not seem to affect vaccine effectiveness. Both are extremely effective at protecting against COVID-19 within a few months after the second shot. But, over time, differences in the effectiveness of the vaccines are showing up.

Last month, the Mayo Clinic released a preprint of a large study of 645,109 patients after vaccination. This assessed the level of protection from infection in people vaccinated with the Moderna or Pfizer vaccines, or who were unvaccinated between January–July, 2021. Both vaccines continued to be very effective at preventing hospitalization, ICU admission, and death relative to unvaccinated people over the period of the study. However, prevention against mild to moderate COVID-19 was somewhat lower for both vaccines in July compared to January. Vaccine immunity faded a bit over that time. Importantly, the efficacy of the Pfizer vaccine faded faster over this time compared to the Moderna vaccine. A more recent CDC analysis of COVID-19 emergency room or urgent care visits for ~33,000 people between June-August 2021, when the Delta variant was predominant in the US, showed that overall the vaccines were 86% effective at protecting against serious COVID-19. But, vaccine efficacy for those who received the Moderna vaccine was 92%, while those receiving the Pfizer vax showed 77% protection.

Similar results were found in another study of 196 vaccinated elder nursing home residents in Canada. Compared to those who received the Moderna vaccine, residents who received the Pfizer shot mounted a 3.89-fold lower antibody response. A Belgium study published August 30, also found that the Moderna vaccine stimulated ~3 times the antibody response as the Pfizer vax. This study looked at 1,647 vaccinated workers at a Belgium hospital. Finally, a Qatar study largely found the same thing; that the Moderna vaccine stimulated a more robust antibody response.

What accounts for the different responses to the different vaccines over time? That is impossible to pinpoint at this time. It could be due to the higher dose of mRNA in the Moderna vaccine. The difference in response over time could also be due to the different mRNA sequences the vaccines contain, or due to the slight differences in the chemical composition of the lipid nanoparticles. Or, any combination of the above could drive quantitatively different immune responses.

Most importantly, though, both vaccines continue to work amazingly well against serious COVID disease, hospitalizations and death. Even while the more infectious Delta variant rages around the world in the face of slowly fading vaccine efficacy, about 95% of COVID-19 hospitalizations and deaths today are in unvaccinated people.

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Vying With Viral Variants

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The back story: There are four known CoV-2 variants in the US that are more transmissible than the parent strain. They are the UK variant, which is 70% more infectious and 60% more deadly than the original strain. There also are Californian and Brazilian variants that are more transmissible, but it is not yet known if they are more deadly. However, in Brazil, their variant is associated with a significant increase in infections and ICU stays for young, healthy, unvaccinated people. Fortunately, the current vaccines seem to be effective at preventing infection with these strains.

More worrisome is the South African variant that is 50% more transmissible. It is worrisome because the AstraZeneca vaccine is not very effective against this variant, and a very recent, but a small study out of Israel suggests that the Pfizer vax might have reduced efficacy against the S. African variant. It is not yet known if this strain causes more serious disease. These findings provide evidence that mutation can produce new viral strains that can evade the immune response to the viral spike protein.

Two other variants, the so-called New York variant, and a second Brazilian variant have early signs of being more infectious or even being able to reinfect people who previously had COVID-19. Data are still being collected in order to better understand the risk that these variants pose. Stay tuned.

You can follow the variants in the US here.

The bottom line is that the world is in a race to roll out vaccines faster than troubling virus variants can arise. The UK is expected to reach herd immunity​ early next week. Infections there dropped by 60% during March, with deaths dropping more rapidly, indicating that the vaccines are helping prevent severe illness and viral spread. Meanwhile, the US leads the world in total vaccines administered (175 million), with 43% of the adult population having received at least one shot. More than 700 million doses have been administered world-wide.

The major concern is that a too-slow vaccine distribution, such as what has happened in Brazil, will encourage more virulent variants to arise. If we don’t quickly achieve herd immunity across the world, it probably will just be a matter of time before a variant arose that renders the current vaccines useless, and we would have to start over.

What is a world to do? Besides increasing surveillance of viral variants, a couple more prevention initiatives are in the works. One is economic and the other scientific.

Economics of viral mitigation: The economic approach is detailed in an article by the Associated Press Economics Writer, Martin Crutsinger. Basically, the International Monetary Fund (IMF) proposes giving $650 million to support vulnerable countries struggling to deal with a global pandemic. Along with that, the Group of 20 major industrial countries issued a joint statement that announced a six-month moratorium on debt payments by 73 of the world’s poorest countries.

The rationale behind these actions is to ensure that poor countries, where vaccinations are lagging due to lack of resources and infrastructure, can pick up the pace of vaccination. Their lag in rolling out shots is a threat to the whole world, even while wealthy countries are approaching herd immunity. In order to beat the variants, vaccines are needed to quickly create herd immunity and stop viral spread before a variant that can avoid vaccine immunity appears. When countries lag in vaccinations, the virus continues to spread increasing the chance for an immune-avoiding variant to pop up. Such a variant can then spread to countries that are highly vaccinated, starting the pandemic over again because the current vaccines would be ineffective. We would be back at square one.

Science to the rescue: So far, all the vaccines, except one from China, which uses the whole virus, direct the immune response to the viral spike protein that is used to attach to receptors on the surface of cells in your body. The viral variants we are concerned about show mutations in the spike protein that allow them to become more infectious, and in one case, to be less affected by some of the vaccines. In addition to trying to  nip the virus in the bud by quickly building world-wide herd immunity, new vaccine strategies are being developed to quickly respond to newly arising CoV-2 variants, and even to respond to entirely new strains of viruses that will arise in the future.

• One way to do this is to begin developing booster shots as soon as a coronavirus variant becomes a significant concern. With the new mRNA, and adenovirus vaccine delivery technology, this is eminently possible. It just requires scientists around the world being vigilant for new variants. Pfizer, Moderna, AstraZeneca, and Johnson & Johnson have all said they’re starting work on developing booster shots to the known variants.

• Last week, the US government announced a pact with CureVac to tackle variants, pairing artificial intelligence to predict future mutations that can be quickly addressed with modern vaccine technology. London-based GlaxoSmithKline is also working with CureVac on mutant-quelling vaccines.

• Another strategy is to identify viral molecules other than the spike protein that the immune system can recognize. Efforts are underway to test the immunogenicity of what is called the CoV-2 nucleocapsid, or N protein, which wraps itself around the viral RNA. If successful, future vaccines could incorporate both the N and S (or spike) proteins, which would require the virus to mutate both of those genes in order to avoid vaccine-induced immunity, a greatly tougher task for the virus.

• Researchers at Moderna, Novavax, and the University of Oxford are designing multivalent vaccine strategies to protect against multiple CoV-2 variants with a single shot, and even against new viruses that might emerge in the future. A similar strategy is used with the annual flu vaccine, which usually incorporates four different influenza strains in one shot. It is also used with measles, mumps, and rubella vaccines. Some vaccines against pneumonia target as many as 23 variants of that pathogen.

• Finally, a wholly new vaccine technology has shown recent success in animal studies. It works by chemically attaching many short viral protein sequences from different CoV-2 variants, and even from completely different coronaviruses, to engineered nanoparticles that are then injected. In mice, this single vaccine induced an antibody response capable of neutralizing many different coronavirus strains. If successful, this could represent a universal vaccine capable of neutralizing CoV-2 and its variants, as well as other coronaviruses such as SARS and MERS with a single vaccine. And it can be easily modified to quickly respond to future viral epidemics caused by novel coronaviruses or other viruses that will certainly arise. The technology is being developed at Cal Tech using technology developed by collaborators at Oxford University. The nanoparticle platform is a “cage” made from 60 identical proteins. Each of those proteins has a small protein tag that functions like a piece of Velcro to which the viral protein sequences stick resulting in a vaccine nanoparticle with short protein sequences from four to eight distinct coronavirus strains on its surface. If successful, this could prevent infection and disease for several different viruses with a single shot.
  

 We are in a revolutionary era of vaccinology. BioX marches on.