>”Despite the slightness of difference between the two coronaviruses, the antibody binds much less tightly to SARS-CoV-2 than it does to the SARS virus, and cannot neutralize SARS-CoV-2 in lab dish tests as it does SARS-CoV.”
There are different antibodies being tested though. So there's a good chance a properly working mAb (not inducing Antibody Dependent Enhancement) will happen.
One of the main reasons (most likely) is that these antibodies are already purified and in stock in the laboratories. So I'd be relatively easy to start researching the binding sites to SARS-COV-2. And since there is a relationship between the 2 viruses you can get useful information even if it's not perfect.
Labs definitely are. People are working on basically every avenue you can imagine - this is a true global emergency and it's been stunning to see how strong the response has been from the scientific sector. Just about everyone that provides my reagents are all on backorder, but they're still working to make things available for covid work / making it easier etc, even with the immense demand
>Labs at Scripps Research and throughout the world are currently seeking antibodies, via blood donations, from people who have recovered from COVID-19 for further studies along these lines.
Antibodies to this influenza HA trimeric interface epitope [that we studied before SARS-nCov-2 came along] do not exhibit in vitro neutralization activity but can confer in vivo protection. Similarly, antibodies to another conserved epitope that partially overlaps with the influenza HA trimeric interface also are non-neutralizing in vitro, but protective in vivo (26). Examples of antibodies that do not have in vitro neutralization activity but confer in vivo protection, have also been reported for influenza virus (27), herpesvirus (28), cytomegalovirus (29), alphavirus (30), and dengue virus (31). Therefore, although CR3022 does not neutralize SARS-CoV-2 in vitro, it is possible that this epitope can confer in vivo protection.
So the lack of in vitro neutralisation isn't a showstopper.
Still, that bit reads like reaching to me. We shouldn't expect this antibody to be that useful, although we can hope.
Moreover, i suspect we shouldn't think about manufactured antibodies as a treatment for COVID-19 at all, as i doubt we have the manufacturing capacity for biologicals to use them against a pandemic on this scale.
Rather, i think this points towards this part of the virus being a good target for vaccines. If you can make a nice little edited version of that epitope (the SARS-nCov-2 version), you might be able to use it to make a vaccine which raise neutralising antibodies.
Having an antibody bind the virus is good, but not enough. The antibody needs to end up activating the immune system. Sometimes antibodies binding to the virus can sometimes enhance the infection:
It's the light chain that binds, you can modify heavy chain to do what you need and said.
This is what's done when humanizing antibodies too.
The extra infection potential is when the virus or bacteria can survive or thrive inside macrophages or monocytes, which react to opsonized particles, such as with antibodies.
You can make IgA or IgM instead to prevent this mechanism. They work by polymerization to bind whatever they attach to. Former is typically not activating the rest of immune system, while IgM would activate everything strongly perhaps inducing your own production.
Monoclonal antibodies, or mAb are made usually by fusing a right B cell or splicing a gene sequence for the right light chains (V, D) into a leukemic cancer cell line producing a so called hybridoma. Those cells are damaged in such a way as to produce tons of antibodies and are immortal.
By using a different starter cell line you can get different antibody classes. Also by providing a different interleukin stimulus to the cells.
From my understanding when an antibody attaches to a virus it causes a signal for T-cells to eat the and destroy the virus. So the antibody would be effective in getting the body to destroy any virus found. However I don't think it would create any sort of immune memory which is what a vaccine or recovering from the illness by yourself would do.
That said it would be fantastic in that it could provide some immunity protection for a while why the antibodies are active in your body allowing health care workers to be safer. Might also be very helpful in creating firewalls in institutions like old folks homes or hospitals.
This is exactly the problem. It would only work in the short term - but would not provide any immunity. It might not even eliminate the virus - so once you stop the antibody treatment - the patient might relapse.
Still better than nothing and in extreme situations, it would give your body more time to produce an adaptive response.
Are there some examples of antibodies like this being employed successfully like that?
I find it fascinating how the body is able to adapt to new entrants and the immune system figures out how to uniquely bind to the virus - but seemingly based on the article only when it changes into an active infection mode and exposes a certain part. Potentially ignoring it unless it’s an active threat to the body.
It may simply be the normal predator-prey dynamic. Even if the predator is infinitely more powerful than the prey it's not in their interest to wipe the prey out. They want to leave enough prey for tomorrow. And if there are defector predators that try to gain an edge by eating more than is sustainable, other predators will try to stop them from doing so.
Now, before you object: it's not always perfectly balanced like this. Sometimes the prey does go extinct.
> And if there are defector predators that try to gain an edge by eating more than is sustainable, other predators will try to stop them from doing so.
You're talking about a virus, you know... an inert molecule.
Ye but by the same token predators don't try to consciously manage the population numbers of their prey.. rather through evolution self replicating organisms either pick up traits that helps their replicated copies be around at time point x.. or they dont. And u don't see them at time point x.
An inert molecule that kills all its prey will not survive.
The natural selection will favor those molecules that are able to spread without extinguishing all their guests.
My background is nothing to do with biology, but it has struck me for years that natural selection is just a broad statement about probabilities that can be applied almost everywhere.
It is something like: if something has high odds to exist, given enough time to possibly exist, it will exist.
So an inert protein coming into existence? Sure. Better odds to be replicated? Then it'll happen. We ascribe agency or will to survive. Those probably help the odds in a lot of cases. But the concept is broader than that.
natural selection applies to any self-replicating things... viruses are considered non-living, but they are still self-replicating.
(technically, the self-replication need also admit mutations into the replication process for natural selection to apply. viruses do mutate so, they qualify)
Viruses evolve in a way that's very similar to living things (and some scientists consider them living, but that gets into philosophical definitions of life). They have genotypes that can mutate, and some of these mutations find ecological niches where they reproduce better than others, which leads to those genomes reproducing themselves more, i.e. evolution by natural selection. They're taxonomized similarly to living organisms as well, into phyla, orders, families, genera, species, etc.
Maybe they can't fight it off and die. OTOH, a spider can lay hundreds or even thousands of eggs, so it's enough if a tiny fraction will be able to reproduce.
We’ve had many viral outbreaks. SARS, MERS, Zika, Swine flu, HIV etc. some of them have been with us for decades. Why don’t we have vaccines for all of them yet?
Also how likely is that COVID-19 will mutate like influenza and become a seasonal deadly killer ?
How does one isolate a specific antibody from the blood? Presumably there are thousands (millions?) of different ones in there for all kinds of pathogens.
Typically, you first test the blood to see if there are any antibodies in that blood of interest. E.g., collect blood sample, harvest serum from blood by coagulation and centrifugation, apply serum to surface coated with COVID protein(s), wash away unbound material, detect whether antibodies to serum have bound to surface coated with COVID proteins. If yes, then this is a blood sample of interest. You could also test for neutralizing antibodies in parallel/before/after/instead in a viral replication assay. Once you have identified the blood as containing what you want, you then harvest more and collect mature B cells. Mature B cells each produce one antibody. You isolate the B cells by limiting dilution and/or immortalize them by fusion with a special type of cell to make a hybridoma to isolate clonal populations of single cells that are maintainable. Then you test each clonal population for whether it produces the antibody of interest, isolate the nucleic acid that encodes that antibody and put it into a cell type suitable for manufacturing. There are other ways to do it, but the above is fairly standard. It is laborious and easy to mess up and takes time (1 to 2 months) to do correctly. Any step can go wrong and require starting over.
> You isolate the B cells by limiting dilution and/or immortalize them by fusion with a special type of cell to make a hybridoma to isolate clonal populations of single cells that are maintainable. Then you test each clonal population for whether it produces the antibody of interest
Do people actually still do it this way? I would have thought that you would use more targeted approaches where you use an antigen to fish for cells of interest before culturing. There are a few such techniques described here:
Naively, i would have thought you could do something with affinity columns or magnetic beads, too - coat beads with antigen, then use those to extract B cells expressing a matching surface immunoglobulin.
Magnetic bead filteration is commonly used to filter immune cells, but they are expensive. I used to work for a lab that did this on a daily basis. Common problems with it were getting enough cells to run the assays, and the process of extraction is damaging to the cells. So you need a lot of starting material and then after that they don't stay alive for very long. You can treat and freeze after isolation but thawing only decreases the amount of healthy cells.
Here’s a noob question. The coronavirus is made out of a whole bunch of proteins. Have we fully mapped out all the protein structures and corresponding DNA code?
The antigen is also a protein, I assume the DNA sequence for it is well known. Right?
How far are we in terms of tech to print custom proteins from arbitrary DNA sequences?
Is understanding protein folding and protein to protein interaction the holy grail of making massive improvements in molecular biology? What are the big unsolved problems?
Like if we know the virus’s DNA and it’s 3D protein architecture, we can solve for antigen proteins in a computer that outputs possible DNA sequences and we can manufacture them the next day in a protein printer. How far away are we to that future?
Protein folding is part of it. The other is finding which parts are antigenic to the immune cells. Epitope mapping is a common method to screen small bits of the proteins to see if any are hits for immune cells to recognize and kill. There are algorithms that can take the RNA/DNA, predict proteins, and then guess a percentage of those that may be important. But you still need to synthesize those in mass quantities and start testing each. Once you have candidates you then test them in mouse models (typically) to see if they actually provide an immune response. If interested check out the iedb. https://www.iedb.org/
"Have we fully mapped out all the protein structures and corresponding DNA code [of the COVID-19 virus]?"
Yes
"The antigen is also a protein, I assume the DNA sequence for it is well known. Right?"
Yes
"How far are we in terms of tech to print custom proteins from arbitrary DNA sequences?"
Generally that is something a first year graduate student can accomplish.
"Is understanding protein folding and protein to protein interaction the holy grail of making massive improvements in molecular biology? What are the big unsolved problems?"
There are too many unsolved problems to count. There have been great advances lately in de novo prediction of protein folding and to a lesser extent protein:protein interactions. But even if you had perfect knowledge of all that, you still can't just like design the perfect vaccine.
"Like if we know the virus’s DNA and it’s 3D protein architecture, we can solve for antigen proteins in a computer that outputs possible DNA sequences and we can manufacture them the next day in a protein printer. How far away are we to that future?"
We (the world) accomplished that within a couple of weeks of identifying the COVID virus.
> It is laborious and easy to mess up and takes time (1 to 2 months) to do correctly.
Sounds like a manual software testing. What are the chances of automating entire process? Whenever I see bio/chemists working it seems very manual job. I assume someone already tried it, but perhaps only for specific area rather than making universal robot?
Complete automation would be tricky. We are dealing with a lot of starting and intermediate materials that need to be precisely incubated under demanding and entirely sterile conditions. You need incubations at liquid nitrogen temperatures (for storing cell lines), -80 C, -20 C, 4 C, room temp, 30 C, 37 C, 37 C 5% CO2, etc. THen you need a way to go to and from each of these environments and a way of sterilizing in between steps. I'm not saying it's impossible, but it seems difficult.
IIRC the virus was isolated last year, so wouldn't at least some antibodies have been identified by now? Or, it's just very common to have to start over?
Is it unusually difficult for this coronavirus? eg I've heard it's unusually large.
Antibodies have been identified by now. They are being tested as we speak. Coronavirus is not more difficult than any other target really. It just takes time.
They're far too large and complex to be synthesized from scratch, that is simply not possible.
They are produced in various biological systems, with nature doing the synthesis. As far as I understand you can scale that up reasonably well with some effort.
To add to this, you don't even need to know what the antibody looks like, or even if it exists. Very simplified example: It's possible to grow a dish of cancer cells (because they divide quickly and are immortal, e.g HeLa cells), "purify" away everything that isn't protein (cell lysis), then run the proteins through a gel that separates them by size (Western blot). Comparing these to a control will show you which proteins enabled survival, which gives you your candidates for sequencing and further tests.
However, right now we have humans synthesizing large amounts of antibodies that are proven to work (because the humans creating them survived and cleared the virus). It may ultimately be faster to isolate antibodies from the serum and engineer cell cultures (through adding DNA to them, "recombinant DNA") to create more of those antibodies, resulting in much stronger synthesis of a single antibody (so-called "monoclonal antibody drugs").
It's nearly certain that both of these are happening many times over around the world right now. All of the science here was already in lab use the first time I worked in a bio lab in 2003, and nowadays we have methods that didn't exist then (such as CRISPR for DNA manipulation and fast sequencing of both nucleic acids and proteins).
The reason it's not researched much is because giving someone an antibody will not confer immunity - it will only treat the immediate virus.
It has value, but there are usually better treatments available that more broadly fight a variety of viruses and don't need to be so specifically customized as an antibody.
I suppose testing would be easier for a cure (compared to a vaccine)? Given that only the "adapter" needs to be specialized, I was wondering why there don't seem to be any approaches based on antibody mass-production....
Apparently it's grown quite a bit since I've spoken to my friend. When we last checked in, it was a little startup. Now, it's a $2.4 billion dollar operation. I guess my friend is probably worth a few hundred million right now.
Oh.