Adaptive Immune Responses after Natural Infection and Vaccination

TRANSCRIPT:

Alessia Ortega
All right and let’s get started. Hello and welcome everyone, and thank you for joining us for our S3 webinar, Adaptive Immune Responses After Natural Infection and Vaccination. Our speaker for today’s presentation is Dr. Daniela Weiskopf, a research assistant professor at La Jolla Institute for Immunology. We’re going to be taking questions later on in the webinar, so please submit any questions that you have using the Q&A button at the bottom of your screen. And now it is my great pleasure to introduce Dr. Daniela Weiskopf.

Dr. Daniela Weiskopf:
Thank you so much. Yes, thank you everybody for tuning in. It’s my pleasure today to present our work from the recent last 18 months, where we are interested in studying the adaptive immune responses to SARS CoV-2 after natural infection and also in the last year after vaccination.

Dr. Daniela Weiskopf:
So there is a lot of questions that are related to adaptive immunity. The first one, of course, was like, well, is there even an immune response induced after infection with SARS CoV-2? What are the targets of SARS CoV-2 adaptive immunity? What is the duration of immunity induced by natural infection? Is there a heterologous or homologous response? Meaning like everybody responds the same, or there is broad a difference. Are there correlates of protection? What is the duration of immunity induced by vaccination? And what is the issue of pre-existing immunity and development of a pan corona vaccine? I will touch based on some of these points today, and I’m happy to answer any questions after the presentation, as [Alessia 00:01:47] was finding out.

Dr. Daniela Weiskopf:
So when I talk about adaptive immune response, what specifically do I talk about? And this is basically the three arms of adaptive immunity. We are looking at antibodies, CD4 T cells and CD8 T cells. And all of these have individual functions in the immune system. So it’s important to study all of these individually. And also it’s important to study these all simultaneously in the same donors so that you can actually identify if any of these are correlated. Like for example, like high antibodies mean high CD4 T cells, or the other way around. And also it’s important to look at all of these different adaptive immune system parts to see what is important against infection against COVID-19.

Dr. Daniela Weiskopf:
So antibodies are what’s typically measured against infectious disease, are important in almost all currently licensed human vaccines. So it’s only natural that we have also been looking at this. It’s also something that is fairly easy to study because you just need plasma or serum samples from donors that have been infected or vaccinated. Then we also always look at the cellular immune system, which is CD4 T helper cells and CD8 killer cells. We know CD4 T cells are critical for antibody responses. TFH cells of CD4, T follicular helper cells are what helps B cells actually produce highly functional antibodies. And we know CD4 T cells alone have been shown to be protective independent of antibodies in SARS mouse model.

Dr. Daniela Weiskopf:
CD8 T cells are important in many viral infections. So we have seen that, in example, for a lot of different viral infections where CD8 T cells are necessary to clear the virus. Because one thing I like remind people, so antibodies can help prevent infection, but once the virus is in the cell, it’s invisible to antibodies. So that’s when you need cell immunity that can actually then clear the virus. And that’s mostly done by CD8 T cell killer cells, which recognize virus infected cells, and then can clear these infected cells.

Dr. Daniela Weiskopf:
So very early on, we were interested in like, what are the targets of T cell responses? So we measured all the different proteins, 26 proteins of the source coronavirus. And we were identifying which ones are actually highly recognized. And early on, we found out that the spike is a strongly recognized CD4 T cell and also CD8 T cell target, which is something that was very good news back then, because vaccines containing this spike protein were already developed in a lot of different places by a lot of different vaccine manufacturers.

Dr. Daniela Weiskopf:
But what we also identified was that there’s other proteins that are recognized after SARS CoV-2 infection by the T cell responses, and that I think becomes important when you see that there might be vaccines developed or second generation vaccines with additional targets. So not only containing the spike, but also other ones, you have definitely have added T cell targets in the case of other non-spike proteins.

Dr. Daniela Weiskopf:
Something that I will touch back later on in my presentation is something that we noticed also early on. We did see responses also in unexposed donors, meaning these are donors that have never seen this virus. And the reason we know that because we have banked their PMCs years before, 2015 to 2018, and we saw responses in these donors. And I will touch back in a couple of slides later in my presentation.

Dr. Daniela Weiskopf:
So that was something that was good news early on. So yes, the immune system can recognize SARS CoV-2 by CD4, CD8, and also antibody responses. And there’s also responses against the non-spike protein. What was not known back then, and what we did next was like, what are the exact epitopes that are identified? Because what we have done originally was just doing this on a protein level. This protein is recognized, this protein is recognized, this protein is recognized, but we did not know what is the individual sequence of the epitope that is recognized.

Dr. Daniela Weiskopf:
And why this is important is because that is, first of all, helping you understand the diversity, the heterogeneity in human populations, because based on the different HLA a donor expresses, and that is something that is unique to an individual. So everybody has a different one. You have a different one, I have a different one. So it’s important to understand what is the different in your response, CD4 and CD8 response based on HLA phenotype of a population.

Dr. Daniela Weiskopf:
Also what we wanted to make sure is that there is representatives of different disease severities and also ethnicities in our population. So originally when we started just testing the proteins, this was mostly done on a Southern California population. We recorded here in San Diego, but we wanted to … and mostly also donors that have recovered from mild infection because that is what we originally to get our hands on. But we wanted to make sure that what we see also represents people that had severe disease. And most importantly, as I just pointed out, the different HLA phenotypes. We also wanted to make sure it has all the different ethnicities in the local population represented. And that’s something, so you know this webinar is hosted by Sanguine, but that is also something that we used Sanguine’s help to fill in the holes of different disease severities and also different ethnicities to match our local population, to just provide a comprehensive picture of the T cell response.

Dr. Daniela Weiskopf:
We then developed a screening strategy based on the overlapping peptides spanning the entire proteome, and then deconvolute that and identify the actual epitopes. And so, as I pointed out, it’s important that the HLA expressed in our cohort are representative, not only of a Southern California San Diego population, but are representative of the worldwide population. So that’s why we made sure that we have all the different HLA phenotypes represented. We then screened overlapping 15-mers that allows the coverage of HLA class II responses irrespective of HLA. So that was something that we then put together to infer restrictions. So we knew that these donors have this kind of phenotype. And we know this is the actual sequence that is recognized. And for class I, we selected 28 different class alleles, which cover at least three out of the four A and B in 75% of the donors. So that’s important, as I said. We made sure that this is also representative of a worldwide population.

Dr. Daniela Weiskopf:
And this is in a snapshot of our results. So you can see here for CD4 T cell response is in blue and CD8 T cell response is in red. So we see all the different proteins, and the more it lights up, the more white it becomes, the more this protein has provided specific epitopes for the individual donors. And as I just pointed out before, we knew that the spike protein is highly recognized. We also saw the membrane at the nuclear capsid, and also Nsp3 for CD4 T cell responses. And similar for the CD8 responses, we saw the same proteins be very dominant, spike protein, membrane, nuclear capsid, and also the Nsp3. We also saw some Nsp12 for CD8 T cell responses.

Dr. Daniela Weiskopf:
So overall we identified 280 different CD4 restricted epitopes. We also noted that dominant epitopes are highly promiscuous, which means they are recognized by many different HLA phenotypes. So multiple different donors recognize the exact same epitope. We identified more than 500 different CD8 epitopes, and that’s also just reflective of the different … the breadth of the phenotypes that we have represented in our population.

Dr. Daniela Weiskopf:
One thing I want to point out your attention to is that, because we did this on an individual basis, and we did this for all these different HLA phenotypes, we could draw a map and we saw that each individual recognized multiple epitopes and antigens. So a conservative estimate is like every donor recognizes 15 to 20 epitopes. And this is important, because if you think now what we hear every day or every couple of months, we hear about a new variant. So you have to imagine that you have to have mutations in a lot of different positions to completely evade T cell responses, because it’s such a broad response, 15 to 20 epitopes on average.

Dr. Daniela Weiskopf:
And the same is true for the proteins. If you just look at the number of proteins that are recognized by CD4 and by CD8 T cells, on average, it’s three to four proteins for CD4 T cells, and two to three proteins recognized by CD8 T cells. So this is just to illustrate why it’s important to know the exact targets, because look, first of all, we can now know immediately when there is a variant that has mutations in one of the different epitopes, if that’s in a T-cell epitope-rich region or not. And also, if you have like 20 epitopes recognized in the donor, and there is mutations in two, maybe the other 18 cover enough for that. So that’s why this is important. I wanted to point out that the T cell response is very broad.

Dr. Daniela Weiskopf:
So what this also allowed us to actually design optimal pools to study natural infection, what I’ve shown here of the natural infection, but also vaccination. So you can see here, these are the pools that we have newly identified, and they all, for CD4 and for CD8, have a higher specificity and a higher significance based on the pools we have previously utilized, which were done on predictions.

Dr. Daniela Weiskopf:
So the other thing I want to point out is we have been developing two different assays to study T cell responses. And it’s important to look at two different of these assay because they give you very different information. So one assay we have been highly utilizing was the AIM assay, which is shown here. AIM stands for activation-induced markers. That means any T cell that is activated by a peptide upregulates these markers. In contrast to cells that, for example here, when we do interferon gamma fluoroscopy, you are relying on the cytokine that is produced based on antigen-specific stimulation.

Dr. Daniela Weiskopf:
We do know that there are certain subsets of T cells, for example, T follicular helper cells that do not produce readily like cytokines based on activation. So it’s important to have an agnostic assay, which is the AIM, to actually allow you to identify all of these different antigen-specific cells. So we have been openly sharing these mega pools with a bunch of labs around the world. So more than 160 different laboratories have received our pools, we have already result that this has already resulted in more than 25 different collaborative of studies. And this is counting we’re still on the situation where we’re still working with people and also sharing other pools.

Dr. Daniela Weiskopf:
This was overall the good news, that we have a broad immune response, and this is irrespective of the HLA phenotype and irrespective of disease severity. The next question we had is like, well, how long does this immunological memory to SARS CoV-2 last? So are we after three months, everything is waned and we cannot detect any memory responses, or do we induce stable memory? That was the next question that we were asking. So this is just an overview of the cohort. So we made sure that we have from young to old human subjects are represented in our population, because we did not want to just make statements just in the young population or just in the old population.

Dr. Daniela Weiskopf:
We also made sure that gender is almost equally distributed. So we had 43% male, a little bit more than half females. And then you can see here, I don’t know why this is always changing. And you can see here that we had PCR positive confirmed cases, but also cases that were not confirmed by PCR, but they were collected for the [inaudible 00:14:12] infection so that they were confirmed by other antibody tests. And also we made sure that we have a representation of peak disease severity. So you see that we have heavily represented mild infections. That’s also what is reflective of what’s actually happening in a population. So majority of people does have mild infection, but we also have asymptomatic moderate and severe cases in there.

Dr. Daniela Weiskopf:
And in terms of the day, for symptom onset, we collect everything from six to 240 days. So this is up to eight months. And that’s important because we wanted to see when the immune response drops off and when can we see a waning of the antibody and/or the T cell response.

Dr. Daniela Weiskopf:
This is the overview of all these different parameters that I’ve just been mentioning to you. So overall we studied almost 200 subjects. 41 subject of these were all the way out to six to eight months post-infection. That doesn’t sounds very long as of right now, because we are so much further in the pandemic. But back then, this was exactly how long we could study, six to eight months was exactly the cutoff of people that we could study back then. And you can see that all these different immune parameters have very different memory kinetics. So one is slowly declining. CD4 and CD8 T cell responses, as seen here, have half-life calculated, as you can see here, of 125 days for CD8, 94 days for CD4 T cells.

Dr. Daniela Weiskopf:
Interestingly, we notice that memory B cells are actually increasing over time, as you can see here. And then we could calculate also on the left side, antibody parameters. And overall, we noticed a couple of different things. First of all, all of these different parameters, CD4, CD8, and antibodies have very different kinetics. And the other thing that you can realize, appreciate is there is a broad heterogeneity. So some donors basically have a hundred fold range of responses six to eight months out. So there’s a broad heterogeneity in responses. And there’s also results in wide half-life confidence intervals because of this heterogeneity.

Dr. Daniela Weiskopf:
And we have tried to probe it, like, what is the reason? We looked if the different clinical severity may be responsible for that. No, it didn’t trend with anything. A little bit with sex or gender. So we haven’t found a smoking gun, so to say. We are still looking into this, but again, that’s also a reason why it’s so important you have a broad heterogeneity in your population.

Dr. Daniela Weiskopf:
And one thing we all also don’t know yet, we noticed that in about 10% of individuals, they have very low levels of immune memory at eight months. And we don’t know what’s different in these 10% and how you would recognize them early on after infection. So there’s still a lot of questions to answer, but the important question that we back then could show was like, yes, we do see a good response six months after infection. So the majority of donors had three out of the five immune parameters still present. So 90% of the donors had a good response and it did not look like it’s going to fall off the cliff anytime soon. So it looks like you have a somewhat stable immune memory for three out of the five different parameters.

Dr. Daniela Weiskopf:
This was all now about natural infection after SARS CoV-2 infection, but what about vaccines? This was obviously the next question that came up with the release of vaccines earlier this year. So we studied that and we had access to a very early phase two clinical cohort, which was the Moderna mRNA-1273 vaccine cohort. And importantly to point out that this was the quarter dose of what the vaccine that’s given right now, because the vaccine that’s utilized right now is a 100 microgram dose of the exact same vaccine. But this was the cohort we had access to. And this was also where we had access to up to seven months after first immunization. So that was the cohort that we had basically samples from first, in fact, first immunization, second immunization, and then all the way up to six months after second immunization or seven months after first immunization.

Dr. Daniela Weiskopf:
Again, what was important in this cohort is that we made sure that we have different groups represented. So in our cohort, we had 15 subjects 18 to 55, 10 subjects 56 to 70, and then also 10 subjects older than 70 years. Again, just to have a representative presentation. So the first question was like, okay, we now, again, look at the different parameters that I’ve been just illustrating to you. Antibodies, CD4, CD8 T cells. How does this look like after vaccination? And we could see that there are significant responses compared to day one at all three time points after vaccination. The peak of the response for antibodies was at day 43 compared to day 15. And this was also maintained all the way up to seven months after vaccination.

Dr. Daniela Weiskopf:
So these responses were maintained. And as you can see for both RBD and spike, as you see, antibodies in 100% of the donors seven months out of the vaccination. So that was good news because that’s what we’ve seen in natural infection where we saw seven to eight months induction of new memory, at least seven to eight months. We also saw after vaccination, and remind you this was a low dose, all of the donors recognized antibody responses, and I’m going to touch base on the CD4 and CD8 T cell responses now.

Dr. Daniela Weiskopf:
So when you ask the same question, how long does CD4 T cell memory is induced after vaccination with the low dose of the Moderna vaccine? We can see that it induces durable immune responses. So 97% of the donors had a response induced after the second shot. So that’s just to get to show you that about half of the people had responses after the first shot, which was almost elevated to 100%, just illustrating the importance of getting the two shots instead of just one.

Dr. Daniela Weiskopf:
And this response then was maintained in 100% of the donors after day 43, and then again in 97%. So almost everybody still had detectable CD4 T cell memory after seven months after the second shot. And importantly, I’ve told you that CD4 TFH T cells are necessary to induce highly functional antibody responses. And we could see that this vaccine also induced TFH T cell responses as we have defined by these marker here. And again, first vaccination, second vaccination, and then all the way out seven months after the first dose.

Dr. Daniela Weiskopf:
And you can see here that we do see a very heterologous response. So we see in some donors having a strong induction of TFH cells after the first dose, some after the second dose, and we still see in about two sorts, we still have detectable T follicular helper cell responses after that second dose of vaccination.

Dr. Daniela Weiskopf:
So overall, we were then interested in the CD8 T cell responses and also what is shown here on the right side, in the functionality of these cells. I told you originally that CD8 T cell responses are important to clear infected cells. And we see the majority of T cells, so 70% of the donors had induction of strong CD8 T cell responses, about half of them had still detectable CD8 T cell responses seven months after the first shot. And importantly, because we wanted to not only see the activation induced response but also the cytokine response, we measured the different cytokines and the different number of functions these CD8 T cells can produce. And you can see here that after the first dose, second dose, and all the way out to memory phase, the number of functions, meaning the number of different cytokines these people can … these CD8 T cells can induce is basically expanding.

Dr. Daniela Weiskopf:
And as a control, we measure the exact same response for CMV in the exact same donors, which you see here were not affected by the vaccine-induced responses. So overall, we did see a strong induction of memory responses after first, second, and all the way out to memory responses for antibodies where 100% of the donors were induced, had either ELISA or neutralization titers. We saw that the majority of donors still had detectable CD4 T cell responses and a good number, up to 88% after the second dose, 60 some percent after the … in seven months after infection still had detectable CD8 T cell responses measured by either AIM or by cytokine responses. So this was good news, because also for the low dose of vaccination, we saw a strong induction of immune memory. And we saw a strong detectable immune response in the majority of donors seven months out after vaccination.

Dr. Daniela Weiskopf:
I have not shown you this here in the slides, but we also compared that to the 100 microgram dose. And of course, because you have higher antigen profile, it’s stronger than what I’ve been showing you. So, but like I point out, even the low dose has responses detectable all the way out to seven months.

Dr. Daniela Weiskopf:
At the beginning of the presentation I showed you that we have also detected responses in unexposed donors. And in more detail, 50% of the donors had CD4 T cell responses detectable against spike, also non-spike proteins. 20% for CD8 T cell responses. So this phenomenon seemed to be much more pronounced with CD4 T cell responses. As I pointed out, we knew these donors have not seen this virus because they were [inaudible 00:24:38] way before the pandemic started. And this is a also phenomenon that was not only this discovered by us here in Southern California, but by the time we seen that in groups around the world and populations around the world. So this was discovered by us, by a group in Singapore, by a group in Germany, by a group in the Netherlands, by a group in the United Kingdom. So a phenomenon that was not, was basically seen in multiple different populations around the world.

Dr. Daniela Weiskopf:
What was not known, where this pre-existing T cell memory derived from, and we have shown in one of our earliest studies that we could map the majority of these responses to the exposure to common cold. So you might have heard that SARS CoV-2 is part of the coronavirus family. That also is the same family that is containing viruses that we refer to as common cold coronaviruses, such as listed here, 229E, HKU1E, NL63, OC43. So all of these four common cold coronaviruses are circulating in the worldwide population on a basically rotating level.

Dr. Daniela Weiskopf:
So that also makes sense why not only us, but also groups around the world have discovered this phenomenon. So we could actually map some of these epitopes to cross-reactivity with common cold exposure. So we could identify where this pre-existing T cell memory is derived from. What we did not know, does it make a difference if you have this pre-existing immune memory, or does it maybe even hurt you? Or maybe it doesn’t matter at all?

Dr. Daniela Weiskopf:
So the vaccine cohort that I have been just showing you actually provided the perfect opportunity to ask this exact question. Because we could measure responses before they have received the vaccine, and we could see which ones do have this pre-existing immune memory and which ones do not. And this is basically exactly what we have been doing. So if you look here in the blue bars, these are all the donors that do have pre-existing CD4 T cell memory on day one, which is before these people even received the vaccine. In contrast to the white bars here, where none of these donors have been demonstrating pre-existing CD4 T cell memory.

Dr. Daniela Weiskopf:
So if you now ask the question, if you separate these two groups into either people that have or do not have pre-existing immunity, and is there any difference? We could see that for almost all parameters we measured, so this is shown for CD4 T cells. They have a stronger and faster induction of CD4 antigen-specific T cells compared to the group that did not have pre-existing immunity. And that was true also for TFH T cells. That was true for antibodies. You had a stronger and higher antibody response induction, and also a faster multifunctional in response as shown here by the pie charts.

Dr. Daniela Weiskopf:
So this was the first time that we could actually demonstrate that, yes, it actually has a benefit if you have this pre-existing immunity, because you can induce faster and early multifunctional T cell responses.

Dr. Daniela Weiskopf:
This is basically the overview I wanted to give you today. And we’ll close with my final slide here. So this has not only been done by my laboratory, but also I’ve been working closely with Alex Sette’s lab and Shane Crotty’s lab here at the La Jolla Institute that have been basically, all been a part of the coronavirus team here at the La Jolla Institute and all of these people that have been involved in this. And I’m thanking you for your attention, and I’m happy to take any questions.

Alessia Ortega:
All right. Thank you so much, Daniela, for that amazing presentation. And now it is time to get into our questions. So let’s begin with our first question for you, which is, could mRNA vaccines be generated for congenital forms of cancer?

Dr. Daniela Weiskopf:
Yeah, so I think this platform has a lot of different applications, and I’m not involved in that, but I know that there’s people that are trying to develop mRNA vaccines against different cancer platforms, autoimmune platforms. So of course also other infectious diseases. So yeah.

Dr. Daniela Weiskopf:
It remains to be seen. Yeah.

Alessia Ortega:
Yeah. All right. Thank you. Our next question is, could you explain how the immunity system is being impacted by such emotions like stress or sadness or happiness?

Dr. Daniela Weiskopf:
Yeah, certainly. That is something that has not been studied in my lab, but there’s certainly parameters that are connected with suppression of the immune system. So that is something that is outside of the focus of my work, but yes. So I have not looked into this in detail, but there’s certainly groups that look into this. If people are stressed, the immune system goes down, but yes, not part of my research.

Alessia Ortega:
Okay. All right. Thank you. Next question is, what are the differences between human and veterinary immune responses?

Dr. Daniela Weiskopf:
Yeah, so that basically looks into what kind of animal science you’re looking into it. There’s certainly a lot of different groups that look into veterinary science, mostly for other vaccines, because SARS CoV-2 is maybe not so directly influencing the livestock, for example. But there’s certainly animals like cats and dogs have CD8 and CD4 T cells and antibodies. So there’s certainly parallels.

Alessia Ortega:
All right. Thank you. Next question is, how can we deliver this level of science to non-HCP people?

Dr. Daniela Weiskopf:
Yeah. So that is something that is very near and dear to the mind of the La Jolla Institute. We regularly host, we call it Live from the Lab webinars where we are trying to communicate stuff that happens in this institute, to a non-HCP population. So in order to also help spread what we find out here to the general population and help to improve understanding of science for the general population. Yeah. And I know that we are not the only ones that have programs like this. So that’s certainly something that we noticed within this pandemic that is more and more important that we learn how to communicate, not only with scientists or healthcare workers, but also the general population.

Alessia Ortega:
All right. Got it. Thank you. Our next question is, can you describe the differences between natural versus vaccine-induced immunity?

Dr. Daniela Weiskopf:
Yeah, so the immunity is the same. It’s just a matter of like, how does the immune system see the virus? But the CD4 T cells induced by the natural infection with the virus and the vaccination with any of the vaccine constructs, the result is the same. It’s just a matter of like, what’s the difference in the scene? So if the question is, is there a difference in the immunity? No, there isn’t.

Alessia Ortega:
Okay, thank you. What is the key difference in the response to infection versus vaccination?

Dr. Daniela Weiskopf:
Yeah, that basically follows up to the question that I have just been mentioning. We have been looking into this, and that’s why it’s also so important that we always study natural infections. So people that have not … Because that will kind of help to benchmark. So in our case, we actually have seen a response after vaccination being just as good or better than induced by natural infection. And what I’ve not pointed out too, it looks that people that have seen both the virus and the vaccine actually have the most superior immunity, which is something that we call hybrid immunity. So it’s definitely important to study both so that you can actually see the difference and have a benchmark to if the vaccine is as good or better. In this case, we saw better induced responses.

Alessia Ortega:
Thank you. Our next question is a bit of follow up to that one as well. Which is, do you feel immunity from natural infection may prevent infection by new variants better than vaccines do due to the breadth of responses?

Dr. Daniela Weiskopf:
Yes. That’s a good question. And it’s certainly something that we’re constantly looking up. In general, if you think about it, this is basically how many times you have seen. The immune system is kind of like an exposure history. So if you have been infected and then vaccinated, you’ve seen the immune system, there’s the same pathogen twice. So you have stronger CD4, stronger CD8, and stronger antibody responses. We know that continuous exposure is also helping to make better antibodies, more diverse antibodies. So that’s why right now it makes a lot of sense that people are encouraged to get booster shots, because that means they have seen the same thing three times. So overall, I think there is … Now I forgot the beginning of the question. But overall, I think it’s important that it really is not so much, like if you get natural infection or vaccination, it’s more like also how many times you have seen a pathogen.

Alessia Ortega:
Thank you so much. Our next question has to do with T cell responses. The question is, do you think T cell responses will be much better when you prime with the mRNA vaccine and then boost it?

Dr. Daniela Weiskopf:
So it basically has been looked into the other way around. Because there’s a lot of people that have received AstraZeneca or the Johnson, which are adenovirus vector vaccines, and then have received the boosters. And they have seen actually strong induction of immune responses if they have been doing this way around. I’m not aware of any studies that have looked at the mRNA first and then adenovirus, which was this question I believe. So I don’t know if it’s the same or not, but it certainly has been shown for other vaccinations that if you first give heterologous, we call it a heterologous prime booster regime. So you first get a vector and then a protein or mRNA vaccine, that it induced stronger immune responses.

Alessia Ortega:
All right. Thank you so much, Daniela. Our next question is, what is the mechanistic basis for different immune responses to infection and vaccines?

Dr. Daniela Weiskopf:
Yeah, as I said, so the end result of a CD4 T cell induced by the virus or by the vaccine is the same T cell that’s induced. There is not a mechanistic difference. One difference that I’ve been pointing out is, of course when you’re naturally infected you have different proteins that are induced at CD4 or CD8, mostly CD4 T cell responses. However, for antibody responses, like spike is a dominant target for T cells. Spike is a dominant target. And that’s what’s contained in all of the vaccines.

Alessia Ortega:
All right. Thank you. Our next question is, what are the facts regarding the escape of humoral immunity by the currently predominant variants?

Dr. Daniela Weiskopf:
So the currently dominant variant before this weekend?

Alessia Ortega
Yeah.

Dr. Daniela Weiskopf:
Of course is Delta.

Alessia Ortega:
Dominant variant. Yes.

Dr. Daniela Weiskopf:
Yeah. So we have actually been showing in our cohorts and also other cohorts around the world, if you look at the T cells, there’s not much difference. So there is even no difference in the immune response compared to the ancestral [inaudible 00:36:45] spike response. And that very well is related to what I’ve been showing in the beginning, that you just have this broad, broad response of like 15 to 20 epitopes. So even if there’s mutations in some of them, certainly not on a population level, because everybody has such a different response. And also on an individual level, you would need to have mutations in like 15 different epitopes to actually have an escape mutation. And also for Delta, I believe antibody response was maybe a little bit lower in some of the cohorts, but certainly never like I’ve seen it being wiped out.

Alessia Ortega:
Okay. Thank you. Next question is, how often does an immune response to natural and/or vaccines result in a serious autoimmune adverse effect?

Dr. Daniela Weiskopf:
Well, so that is something that is definitely looked into it in terms of collecting all of the side effects after vaccination, natural infection. There is cases, but it’s in the minority of cases that they have … and that happens after natural infection and vaccination that there can be side effects. But what we have learned so far from this virus and these vaccines, it’s very, very, very low. But that’s definitely a question maybe more for an epidemiologist, that they can actually track carefully these side effects.

Alessia Ortega:
All right. Thank you. Our next question is, can you share more on current efforts to develop a pan coronavirus vaccine?

Dr. Daniela Weiskopf:
Yeah, that’s certainly on everybody’s mind, and that’s something also the La Jolla Institute is very interested in. So what, not my group, but Alex Sette’s group is interested in is the T cell epitopes they have identified, are they present only in SARS CoV-2 or also in other coronaviruses? With the background and the thinking that, might this actually help to induce a pan coronavirus vaccine? So with one shot you would be able to protect yourself from SARS CoV-2, but also from the common cold, which I’m sure all parents of small kids are very much aware of, and also maybe also future upcoming viruses. So that’s certainly something that is in a lot of people’s mind and certainly also here at the La Jolla Institute. But I think it’s in the beginning stage of investigation.

Alessia Ortega:
Yeah, of course. Thank you. Our next question is, what are your thoughts on original antigenic sin, also known as immune imprinting, influencing immunity with boosters updated with new sequences?

Dr. Daniela Weiskopf:
Yeah, so original antigenic sin is certainly known from the field of dengue virus, for example, where there’s a lot of different sequences of this virus circulating. We have, in the case of dengue, it has not been shown to be related to anything that T cells are doing. And also if you look at the data that [inaudible 00:39:51] showing you right now, where you basically have imprint of the CD4 T cell response by exposure to similar sequences, which is basically exactly like what you’ve been just asking by the coronaviruses, and then you get the sequence of the SARS CoV-2, it actually has a beneficial effect. Because we’ve seen that there’s stronger and faster and more multifunctional responses induced.

Alessia Ortega:
All right. Thank you. Our next question is, is this method applicable to all infections?

Dr. Daniela Weiskopf:
If you are referring to the AIM assay, yes. That is applicable to all infections. We have used that successfully for also other viral infections. You can utilize that. Sometimes there’s a bunch of different activation markers. Sometimes one combination will work better for one infection versus the other, but the general concept of this method that you basically capture activated the T cells, regardless of the cytokines they produce, that is working in a lot of different contexts.

Alessia Ortega:
All right. Thank you so much, Daniela. We are now at our last question. This is our final question. Have you linked target specificities of serums with IgH CDR3 region AA sequences?

Dr. Daniela Weiskopf:
Can you repeat? Have you …

Alessia Ortega:
Yeah. Have you linked target specificities of serums with IgH CDR3 region AA sequences?

Dr. Daniela Weiskopf:
Yes. No, we have not looked into this. So we have mapped, as I showed you, the T cell responses. I have not looked at the individual sequences of like, which is … This question I think is related to antigen responses.

Alessia Ortega:
Okay. All right. Thank you so much, Daniela. Do you have any closing remarks that you would like to make before we close out our webinar today?

Dr. Daniela Weiskopf:
I’d like to thank everybody for the interest. And I’d really like to thank everybody that put out the questions that just shows that there’s a lot of questions that we still have. So maybe we will be back for another webinar where we can answer more of the questions that have been asked today. And I thank everybody for the attention and I thank you for inviting me and hosting this webinar.

Alessia Ortega:
Of course. Thank you so much, Daniela. And thank you everyone else for joining us in today’s webinar. For our upcoming webinars and to request samples, you can visit sanguinebio.com, that’s sanguinebio.com. Everyone, enjoy the rest of your day. Thank you so much.