Summary of major experimental covid-19 vaccines, as of August 2020

 Vaccines must undergo a series of tests in order to establish that they are safe and effective before they are available to the public.  In the US, the FDA must grant approval for a drug or vaccine to be sold. A company outside of the US can apply for FDA approval, but of course they still must meet the FDA standards. Other countries have their own regulatory systems for approval. 

The FDA requires three phases, although two phases are often combined. In order to even start phase 1, though, a vaccine will first be tested in animals.  Animal trials test for safety, and in the case of a vaccine, it's much easier to test for efficacy, because you can expose the vaccinated animal to the pathogen to see directly if the immune system fights off the pathogen. It is possible for a vaccine to produce a good immune response, but once the pathogen is introduced the immune response from the vaccine ends up being harmful.  There was some real worry that this would be the case for SARS CoV-2, as some animal trials with a different coronavirus found that the vaccine actually made the pathogen worse.  But happily, none of the animal trials for SARS2 vaccines have found any hint of that sort of outcome. 

Normally this sort of direct challenge trial with a potentially fatal pathogen would not be done in humans.  But in this case, the AstraZeneca team has said that they intend to do human challenge trials by the end of the year, in parallel with regular phase 3 trials.

Phase 1 is technically just to test for safety, although if you're going to give an experimental vaccine to some people, you might as well do the tests to see if it is likely to be effective, in which case it becomes a combined phase 1/2 trial. Phase 2, if you are doing it separately, tests for likely efficacy.  Both phase 1 and 2 are small studies, with dozens to maybe a few hundred volunteers, who must be young and healthy. 

Phase 3 is similar to phase 2, but with more people (thousands) and a wider range of people in terms of age and health status.  We know that in general, older people have weaker immune systems, and tend to have weaker responses to vaccines. At this point, only Pfizer has published data on older people, but all of the large phase 3 studies ongoing now are testing older people.  Unfortunately, the only country that is testing in children is China.  So this is going to leave parents in other countries with the decision of whether or not to give their kids a vaccine that has not been tested in kids. 

At this time, two vaccines have been approved for conditional use, although neither has been approved for use in the US or EU. One is the CanSino Biologics vaccine approved for limited use by the Chinese military. It has finished phase 2 testing, but not phase 3. The other is the vaccine developed by the Gamaleya Research Institute in Russia.  It has finished phase 1 testing.  

Eight vaccines are currently in phase 3 trials.  These are the ones that most of the world is waiting for. The three that are most relevant to the western world are Moderna's mRNA-1273, the Pfizer / BioNTech collaboration's BNT162b2, and the U. of Oxford / AstraZeneca collaboration's ChAdOx1 nCoV-19. I'm going to call these by the names of the largest company involved:  Moderna, Pfizer, and AstraZeneca. I will outline what we know about these three below.

The other five include four developed in China: CanSinoBio (the one approved for military use in China), Wuhan Institute of Biological Products, Beijing Institute of Biological Products, and Sinovac each developed a vaccine based on inactivated virus.  The last one is an Australian trial of the BCG vaccine, normally used to prevent TB, but in this case it's being tested against covid-19.

AstraZeneca / Oxford -- ChAdOx1 nCoV-19

This one was initially the front-runner in the competition to be the first through the approval process, but Moderna and Pfizer are catching up.  Although a common concern is that these vaccines are being developed too quickly, the people at Oxford have been working on the technology for this vaccine for a very long time, which gave them a big head start. They were trying to make a MERS vaccine, and so had inserted the MERS spike protein gene into their fancy vector, ChAdOx1.  This is a chimp adenovirus that is missing a gene needed to replicate.  In order to grow it for the vaccine, they inserted that one missing gene into a cell line, HEK293, which is used to grow the viruses.  These adenoviruses containing the gene for the MERS spike protein are injected as a vaccine.  Although they can't replicate to make new viruses, they can enter cells and do what viruses do -- hijack the cell's protein-making machinery to read the code of the foreign genes that it has brought into the cell.  So the cell makes the MERS spike protein, which the immune system recognizes as foreign, which triggers the development of immunological memory. The reason that they are using a chimp adenovirus is that many humans already have immunity against human adenoviruses.  They screened many different adenoviruses to find one that would infect human cells and not be attacked by the immune system before it can deliver its payload. If you search Google Scholar for ChAdOx1, and restrict the date to 2019 or earlier, there are 303 academic papers available. So the vector is not new.  And importantly, the vector has been tested in older people, who had about the same immune response as younger people.  When covid-19 happened, the researchers could quickly put the gene for the SARS2 spike protein into the vector and start animal trials immediately. 

Animal trials

The results of the animal (mice and monkeys) trials are published here.  I'm looking primarily at the monkey data, since they are more similar to humans than are mice. They used three groups of six rhesus macques -- one got a single shot of the vaccine, one two shots 28 days apart, and one got a placebo vaccine of the vector containing the gene for GFP.  

All of the monkeys that got the real vaccine had an immune response.  In the graph below, red symbols are the moneys with the single shot, blue are those with the shot plus booster, and green are the controls.  The left graph shows antibodies, the middle neutralizing antibodies (which can block the virus from infecting cells) and the right graph shows T-cell responses.  Both antibody and T-cell responses are better for the monkeys with two shots rather than just one, which is not surprising.  The booster shot is designed to mimic a natural infection, where the immune system sees foreign material for an extended time, rather than just once. All of the monkeys that got the vaccine had an antibody response.  Unfortunately, the T-cell response was above baseline for only 4 of the 6 monkeys.  

 

The monkeys were then given a high dose of virus in both the upper and lower respiratory tract.  The result was good but not as good as we'd like.  The best result is shown in the graph below.  The green symbols show the control monkeys are testing positive for virus growing in fluid from their lungs, whereas the immunized monkeys have at most a low level of virus that goes away quickly. This is why the title of the paper is "ChAdOx1 nCoV-19 vaccine prevents SARS-CoV-2 pneumonia in rhesus macaques."  The best news is that the vaccine protects the monkeys lungs. 

The less-good news is that the nose swabs are showing virus growing in the upper respiratory tract.  This is virus detected by PCR, so not the same as infectious virus. They did test for infectious virus as well. That data in "extended data table 1" below shows that the monkeys with two shots (prime-boost) had less infectious virus for a shorter period of time. The monkeys with one shot (prime) were about the same as the controls with respect to live virus in their nasal swabs. Less infectious is good, but we'd rather see not infectious at all.

Something I missed the first time I read this paper in preprint form is that the vaccinated monkeys were not free of symptoms when they were exposed to the virus. This data is presented differently in the preprint than in the final paper that is now available. Below, the left graph is from the preprint, and the right one from the final paper. The left graph looks like the vaccine led to milder symptoms for a shorter period of time, although the error bars are larger than I'd like to see.  The right graph, which separates out the monkeys that got one shot vs two, looks like a rather messy result, with the two-shot monkeys actually doing worse than the one-shot monkeys at later time points.  If you lump all the vaccinated monkeys together, the difference is statistically significant, but still, this is a bit concerning.

They then killed the monkeys (sorry animal lovers!) and looked at their lung tissue. The left image is from a one-shot monkey, the middle a two-shot monkey, and the right a control monkey.  The left and middle look totally normal.  The right looks like a really nasty case of pneumonia. This is good news, and consistent with the finding of low or no virus in the vaccinated monkeys' lungs

They also looked at cytokine levels for the monkeys. The little paired asterisks show statistically significant differences. Interferon gamma, is higher for the vaccinated monkeys, probably due to T-cells formed during exposure to the vaccine. IL-10 and IL-13 are both lower for vaccinated monkeys. These are both cytokines associated with a Th2 response, which makes sense.  Fighting a virus requires a Th1 response, so the exposure to the viral vaccine pushed the immune system toward Th1 and away from Th1.  The bad thing here is that there isn't a reduction in IL-6 with the vaccine.  This is an inflammatory cytokine that is highly elevated in people who have the most severe cases of covid-19. On the other hand, none of the control monkeys are showing the crazy high IL-6 levels that are happening in some humans, so maybe monkeys are not a great model for that particular part of covid-19.

Human trials 

The combined phase 1 and 2 results for testing this vaccine in humans are available here.

1077 healthy people aged 18-55 were randomized to receive the ChAdOx1 vaccine or a different vaccine as a control.  The nice thing about using a different vaccine is that subjects don't know if their side effects are due to the experimental vaccine or the control vaccine, so they can't guess which group they are in.  This is a fairly large group for phase 2, so we have the potential to get more data about rare side effects.  The dose was twice that given to the monkeys, which makes sense given that humans are larger than the monkeys.  Ten people who received the ChAdOx1 vaccine were given a second shot as a booster.  Those ten people were told that they were getting the real shot and not the control.

The side effects from the real vaccine were clearly worse than for the control (meningitis) vaccine. The symptoms experienced were the sort of thing you'd expect from activation of the immune system -- fatigue, chills, headache.  Think flu-like symptoms.  A few people described these as severe in the days following the injection, but none had severe or even moderate symptoms a week out from the injection. I suspect that those individuals are the ones who would have been more likely to have a nasty reaction to the real virus.  Remember, severe covid is severe at least partly because of immune system overreaction. 

Looking at antibody responses, those that got the real ChAdOx1 vaccine had a good response.  There does not appear to be an advantage here for the booster shot. Compared to people who actually got covid, they had roughly the same level of antibody response. 

A subset of people were tested for neutralizing antibodies.  These antibodies block the virus from entering cells. Here there is a clear advantage to the booster shot. Some people had a weak neutralizing antibody response with one shot, but everyone who got he second shot had a solid response.

A subset were also tested for T-cell responses.  Happily, the humans had *much* better T-cell responses to this vaccine than did the monkeys. This suggests that humans will have better immunity when faced with wild virus than did the monkeys. The best monkey had about 175 activated T-cells per million, and the average human is peaking around 800. There are a few humans in the one-shot group that didn't have a T-cell response. But the worst-responding humans in the two-shot group are roughly the same as the best-responding monkey.  

The official phase 3 description is here. They've changed the name of the vaccine to AZD1222. They are in the process of enrolling up to 30,000 participants. This time it is double-blind (the phase 1/2 was single-blind), and uses a saline placebo instead of a control vaccine. Instead of splitting people 50-50, the experimental group is twice the size of the placebo group. The dose is the same as the phase 1/2 trial, but this time everyone is getting two shots, four weeks apart. They are not accepting kids, but there is no upper limit for old people. They are not testing immunodeficient or seriously ill people.  

They started injecting people in late July, and claim on the official forms that they expect to have their primary results by 12/2/2020. I think it's possible that they might have results sooner, since immunity is pretty clearly kicking in within a month. To see if the immunity is actually protecting people, we need to see if the placebo group is getting sick and the vaccine group isn't.  Right now about 0.7 per thousand Americans is officially testing positive every day. If you have a placebo group of 10,000, that's 7 people per day on average. That's going to add up fast.

They are also planning on doing human challenge experiments, which are much faster, as the subjects will be exposed to live virus as soon as they have had time to develop immunity. They haven't given a hard date on that, although the general "by the end of the year" may mean that they are holding the option as a last resort if they don't get enough data from people catching the virus in the wild.

In April, they said that they would release results in June, and they didn't. In May, they said that they would be approved by September, and that seems like a long shot now. They have also said that they expect the vaccine to last a year, although without giving any hint of why they think that. 

Moderna -- mRNA-1273 

Because Moderna is a company rather than a university, we have less background on the past development of this one. The technology is RNA, a type of genetic code.  RNA is notorious for degrading in the environment, but for the vaccine, it is wrapped in a protective lipid nanoparticle. Moderna had also been working on a MERS vaccine when SARS2 hit, although they were not quite as far along as the Oxford group was on theirs.  The gene being used here is the spike protein, with a slight modification to stabilize the protein.

Animal trials

Like the Oxford group, Moderna tested their vaccine first on mice, then on monkeys.

The most notable thing about their mice study is that even though the mRNA-containing lipid vesicles were injected into a muscle, most of the expression of a reporter gene showed up in the liver. Upon reflection, this makes sense. One of the functions of the liver is to scavenge lipids, and so it's probably taking up the lipid vesicles. There are lots of immune cells in the liver, so this might actually help the vaccine provoke a strong immune response. 

The monkey study is here. They used three groups of eight monkeys each. One group got a saline control, one got 10 ug of the vaccine, and one got 100 ug. All monkeys were given a second shot a month later of the same thing they got the first time. The units here are micrograms, commonly written as ug to avoid having to look up the keyboard code for the greek letter mu. To give you an idea of how much this is, find a ruler with millimeters. A cubic millimeter of water weighs one milligram.  The larger 100 ug dose is 0.1 milligrams, so a tenth of the weight of that cubic millimeter of water.  The vaccine is made synthetically, not grown in cells like the AstraZeneca vaccine.  Because RNA is unstable and won't just go into cells by itself, it is encapsulated in tiny lipid vesicles.  Unfortunately the papers describing these lipid vesicles in detail are behind paywalls.  

The monkeys all developed general antibodies.  All but one (in the lower dose group) had neutralizing antibodies.  The purple dots show same test run on humans who have had covid.  So far so good, especially with the higher dose.

They also looked at T-cell responses. Unfortunately, they are not doing exactly the same test as was done with the AstraZeneca vaccine, so we can't do a direct comparison between the two.  But we can say that with the lower dose, four of the eight monkeys had T-cell activation, and with the higher dose, all eight did. The responses were all Th1 rather than Th2, which is what you want to fight a virus. 

A month after the second shot, the monkeys were challenged with live virus. The dose here was lower than with the AstraZeneca vaccine.  It was about 760,000 viruses for the Moderna study and 1.3 million for the AstraZeneca study. So again you can't do a direct comparison. We can say that once again, the vaccine is better at preventing the virus from replicating in the lungs than in the upper respiratory tract. With the higher dose of the vaccine, there is not much replication in the nose, but that could be due to the lower challenge dose. This group did not test the nasal swabs for infectivity, unfortunately.

They also killed the monkeys and looked at their lungs.  The placebo monkeys (top) had clear pneumonia, whereas the vaccinated monkeys did not.

Human trials

Moderna has said that they've done phase 1 and 2 trails, but they have only published phase 1, here. There is a supplement with additional data here. Being a phase 1 trial, it is small, only 45 people. They were divided into three groups of 15 that received 25 ug, 50 ug, or 250 ug, then the same dose 28 days later.  There was no placebo group, since this is phase 1 only. 

Once again, we see flu-like symptoms as a side-effect, some described as severe. One person was withdrawn from the study after experiencing a mild allergic reaction (hives) to the first shot. Unlike the AstraZeneca paper, this study does not give data on how long the side effects lasted. 

Unfortunately, one person in the highest dose group had a fairly serious reaction after receiving the second shot. Here is the description from the paper: 

"A participant in the 250 mcg dose group had severe fever, onset the evening of the second vaccination, along with severe chills and mild fatigue, myalgia, and headache. In the early morning of the day after vaccination the participant developed recurrent severe fever, chills, fatigue, and headache, moderate myalgia and nausea, and mild arthralgia. The participant was evaluated in an urgent care center and received symptomatic treatment prior to discharge. A nasal swab specimen was negative for SARS-CoV-2 by polymerase chain reaction and positive for adenovirus by a fluorescent antibody assay. After sleeping for several hours at home, upon standing the participant was lightheaded and nauseous, vomited, and then fainted. Lightheadedness persisted for several hours. Other systemic symptoms improved over the course of the day. Mild headache was present the next day and mild fatigue was reported through post vaccination day 6."

Because this is the age of covid, this subject has been interviewed about his experience, so if you want to read a more personal account, that's here.  There were several other people, also in the 250 ug group, who had abnormal labs, probably related to liver inflammation. Spoiler alert: Moderna is not using the 250 ug dose in the phase 3 trials. 

All three dosages gave good general antibody responses. This is seen in the top two rows below. The neutralizing antibodies were a bit weaker with the 25 ug dose.  Also, some individuals are losing neutralizing antibodies pretty quickly, but this happens with natural exposure as well.  Of course, not all immunity is antibody-based, which leads us to T-cells.

Here are the T-cell results for those that got the 100 ug dose. Once again the humans are showing a stronger T-cell response than the monkeys, about double.  The difference is not as dramatic as with the AstraZeneca vaccine, but in that case, the humans were given twice the vaccine dose as the monkeys, and here the doses were the same. As expected, the response is mostly Th1, not Th2. 

The official page for the phase 3 clinical trial is here. 

They are testing the 100 ug dose vs saline as the placebo. This makes sense, given that 250 ug had a lot of side effects, and 25 ug had a weaker neutralizing antibody response.  I do think that if the vaccine is made available to children, they shouldn't get the full adult dose.  If 250 ug causes problems in adults, 100 ug might cause problems in a child that has half the body weight of an adult. As with the AstraZeneca trial, the Moderna trial is enrolling up to 30,000 people.  They are not accepting kids or pregnant women, but they are accepting old people and those who have pre-existing medical conditions.  

Moderna has said that they need 150 people to test positive for the virus, after enough time has passed for the vaccine to kick in.

Pfizer --  BNT162b2

American biotech giant Pfizer has been quietly collaborating with the German company BioNTech. As far as I can tell, they have not released data from animal studies, although presumably they would have had to show those results to the FDA in order to go forward with human trials.  Their technology is very similar to that of Moderna.  They are using mRNA code for the spike protein, with slight modifications to stabilize the protein. The mRNA is wrapped in a lipid vesicle.  Neither company is making the composition of the lipids easy to find, so I don’t know if they are the same lipids.  The Pfizer vaccine has an additional modification.  Specifically, for the science people out there, it has pseudouridine in place of uridine.  This reduces the immunogenicity of the mRNA itself. You don’t want the immune system attacking the mRNA before it can be decoded. Theoretically, this should reduce side effects, and also reduce the dosage, since more of what you inject will get past the immune system to make the SARS2 protein that you actually want the immune system to attack. 

Pfizer was initially working on a slightly different vaccine, BNT162b1, which was a secreted form of the spike, with an extra immunogenic domain tacked on.  If you want to read those studies, they are here and here. But they switched to one that has the full code with membrane anchor, due to finding fewer side effects.  Their phase 3 trials are therefore testing BNT162b2.

The phase 1 trial for BNT162b2 is here.  

Although Pfizer is doing a similar vaccine to Moderna, their early experiments included a cohort that Moderna’s did not: elderly people.  As with the other vaccines, side effects were basically flu-like symptoms, and were lower in the older group.  This makes sense, as older people have weaker immune responses in general.

General antibodies were lower in the older group, but still higher on average than people who have had covid (far right bar)

Same goes for neutralizing antibodies:

They haven’t published data for T-cell responses with BNT162b2, but for the b1 version, their responses were good.  

The official clinical trial webpage lists both the b1 and b2 versions, but various media reports claim that they are moving forward with the b2, 30 ug dose, two-shot version.

Back in July, Pfizer said that they were on track to have 100 million doses of the vaccine available by the end of the year, and 1.2 billion doses in 2021.

A brief word about the BCG vaccine

Early on, there were lots of studies that showed a correlation between use of the BCG vaccine and lower rates of covid-19.  Correlation is not causation, so clearly more research was needed.  The Murdoch Children’s Research Institute in Australia is conducting that research. They are currently doing a phase 3 trial in which healthcare workers are given either a placebo or the BCG vaccine.  They are recruiting up to 10k participants, and already are following 2800 people from the first phase of the study. The fact that they have moved to phase 3 suggests that they found something interesting in phase 1/2.  But they have published nothing at all to that effect.  It’s possible that they found a benefit early on and are trying to prevent a run on the vaccine.  Currently, the main use of BCG is to prevent TB in children in the developing world.  If the manufacturer of the vaccine is notified secretly, they can ramp up production while phase 3 trials are being completed.  That’s pure speculation on my part, so take it with a grain of salt. 

There has been one non-randomized study done in the UAE that found that people who took the BCG vaccine didn’t get covid, while 8.6% of their colleagues who declined it did.  Because this isn’t randomized, it may just be showing that people who are taking the virus more seriously are more likely to take the vaccine if offered, and also to wear masks, wash hands, etc.  So we still need to see the Australian study, which is randomized and placebo controlled, finds a benefit. 

Concluding remarks

All three of the major contenders have good enough preliminary data that the vaccines are likely to show enough benefit for approval.  All three are also likely to have side effects that are worse than vaccines you’ve had in the past.  Still, it’s far better to have flu-like symptoms for a few days than to get actual covid, and if you’re someone who is prone to strong immune reactions, you are also someone who is at high risk from covid, because much of the severity in severe cases is linked to immune over-reaction.  It looks like 10-20% of young adults who get the vaccine will be curled up in bed for a day or two with chills/fatigue/body aches.  Older people have weaker immune systems, and so have fewer side effects.  I think this means that we should be cautious about giving the vaccine to kids, because they are both physically smaller, meaning the dose per body weight is higher, and they are also prone to strong immune reactions, like suddenly spiking a high fever.   If a vaccine is offered for kids, it could probably be given at a lower dose, as side effects for all three are proportional to dose, and we are giving a high dose to adults in order to protect the elderly people who are at most risk from covid, but also have weaker immunity to the vaccine.

Although the vaccines are likely to be good enough, they might not protect completely.  That is, it will probably still be possible to get a positive covid test after getting the vaccine, but with milder symptoms than you would have had without the vaccine.  We don’t know yet whether or not a vaccinated person will be able to give the virus to someone else, but at the very least, they will probably be less contagious than they would have been without the vaccine.  

I suspect that many people will rush to get the vaccine as soon as it’s available, but that many others will worry about safety, or in the case of the AstraZeneca vaccine, have objections to the HEK 293 cells (human embryonic, derived from an abortion in the 1970’s) used to grow the vaccine. Because the virus does not spread as quickly as does some other pathogens, we don’t need a very high percentage of the population to get the vaccine in order for spread of the virus to decline.  The percentage needed depends on a lot of other factors, like what percentage of people are wearing masks, but a rough estimate is 60%. That doesn’t mean the virus would go away overnight if 60% of the population gets vaccinated.  It means new cases would stop growing.   I think that there are many people who will let others go first, and then join in when they see that their friends and family got the vaccine and were okay. The more uptake there is with the vaccine, the faster we can all get back to normal life.