Kiki’s Comments                                                                                                        June 2020

                        TWiV 620: Antibodies and T cells in COVID-19 Patients

            Key Points:

*Moderna is making an mRNA vaccine encoding S (spike) protein that will be injected intramuscularly

*T cells are important for B cell evolution

*test, trace, and isolate will be critical to a successful reopening—this will be particularly important once the number of cases are lower to prevent the next outbreak

*previous infection with a coronaviruses does not appear to have a clinical benefit for patients 

*stem antibodies may be an option for COVID-19 therapeutic

*the persistent presence of CoV-2 viral RNA in patients likely comes from a yet undiscovered locus of infection

*some people who have clinical COVID-19 do not appear to make neutralizing antibodies or specific antibodies in response to the infection; some people have an undetectable amount of antibody (10-20% tested in some COVID-positive populations, termed “undetectables”)

*vaccination could provide better immunity than natural infection due to B cell activation but limited neutralizing antibody production in some patients for COVID-19

*there is a recurring convergent evolution of neutralizing antibody sequence with very high affinity found in many patients

            Immunology & General Discussion:

*T cell epitope and vaccination: there are CD4 (helper) and CD8 (killer) T cells. CD4 recognize MHC-II and CD8 traditionally interact with MHC-I. For an antibody response to become an IgG response, it has to have T cells. A good IgG antibody response means that there was a good helper T cell response. After vaccination, we will have B cells that recognize surface proteins of the virion, typically the spike protein, and this will give the B cells a huge advantage in antigen presentation. This is because the B cell no longer requires a way to stick to the antigen to present it; instead, now with a high affinity receptor and super high avidity, the B cell will bring the antigen in and process it much more efficiently. This means that even naive individuals will have antigen presentation in the lymph nodes. This will foster competition that selects for B cells producing the most progenitors—a very niche micro-evolution that occurs during infection. This process is called affinity maturation within which antibody affinity sequences are changing all the time; T cells are driving B cell evolution. Helper peptides are the peptides that the T helper cells are going to recognize. 

*Moderna Vaccine—mRNA vaccine: this is an mRNA vaccine that encodes the S (spike) protein. It will be injected into the muscle. Even though the muscle cells can be transfected, the relevant cells for this vaccine and immune system response will likely be the dendritic cells (DCs). The DCs will be transduced and will start expressing the antigenic protein. B cells will then have direct presentation (where the B cells synthesize the protein) and cross presentation because DCs can acquire antigens from other cells.This will ideally prime the immune system to be able to identify and neutralize SARS-CoV-2 immediately upon entry.

*Cross dressing: when the professional antigen presenting cell (APC) picks up a pre-form complex from a cell that is transduced

n.b. class I system is geared to this rapid presentation system, which is very important for combatting viruses

n.b.ii. epitopes are randomly distributed among the proteome

*Clinical outcomes and T cell immunity: those with pre-existing T cell immunity from cross-reactivity may lead to better or to worse disease outcomes in patients—it is possible that outcome course is T cell driven. We will have to look at outcomes and vigor of the antibody response to determine the effect.

n.b. Cross reaction is almost entirely based on the homology of the peptides. Sequence changes have to be conservative (which is necessary to maintain function)

*No protective effect from previous coronavirus infection: previous infection with a coronaviruses does not appear to have a clinical benefit for patients 

*neutralizing monoclonal antibodies: this is not the only type of antibody that could work. The use of stem antibodies does not work in classical antibody tests—in humans they do not appear to be working in most cases for most viruses. On the other hand, the stem antibodies do appear to be working for this virus, so we will have to analyze this further.

*persistence of RNA without PCR: persistent RNA without constant production of RNA is very unusual. In patients where this appears to be happening, it is important to locate where these viruses are reproducing and possibly persisting. In other words, there is likely a source in the body where the virus is reproducing, and we will have to identify that as it is incredibly unlikely that the RNA is persisting for so long without such a replicative source.


*New York Paper: made a serological antibody ELISA assay and performed neutralizing tests. Found there are people who have clinical COVID-19 who do not appear to make neutralizing antibodies or specific antibodies in general.

*Cal Tech Paper

1. undetectables: many people make a pretty average antibody response in response to CoV-2, but there is a group of “undetectables” (10-20% of the tested population) that make an undetectable amount of anti-viral titres to CoV-2. Possibly could indicate an effect of the virus on B cells. Even though there are patients that don’t produce good neutralizing antibodies, B cells that make those neutralizing antibodies could be detected in patients; this means that it is possible that those B cells could be boosted upon reinfection. This could be the first example that vaccination would provide better immunity than natural infection. This would be the point of the respiratory syncytial virus (RSV) vaccine, which is particularly important if natural infection is not great. 

n.b. it is possible that people with these very low levels of circulating antibodies could have infections similar to that with other coronaviruses, i.e. that they could possibly be reinfected within a year—we do not know this yet though

2. Convergent antibody sequence: Another interesting feature of this paper is that they are finding the same antibody sequence in different patients. This means that there are probably not a lot of ways that antibodies can bind the virus, so the antibodies have to converge upon a common strategy. It also could that there is a selective advantage for this kind of mutation or sequence. To accomplish this finding they took B cells from some of these patients and cloned the IgG heavy and light chains in people with high and low B cell counts, although not from any individuals in the undetectable category. They found a large amount of highly potent neutralizing antibodies in these specific B cells. There was a very high affinity in the monoclonal antibodies found. 

n.b.ii. antibodies are created by mixing and matching domains that creates a very diverse repertoire that differs between individuals. Once B cells are activated there is usually more divergence because of B cell hypermutation. This paper found the same antibody sequence in different individuals, meaning they are both binding the same epitope of the spike protein. The similarity of finding between individuals indicates convergent evolution rather than chance, which is not typical. Identical variable regions of antibodies in different people is unexpected. 


*If and when people are reinfected with the coronavirus (CoV-2), will infection be worse or better? We don’t know, but if upon reinfection the disease course is worse, we will really be relying on antivirals. If the second infection is milder, then there are many possible reasons for this, such as resident memory cells making the infection more mild. Time will tell.

By Kiki Warren (