Clues to Covid-19 coronavirus’s vulnerability emerge from antibody against SARS

Re:Clues to Covid-19 coronavirus’s vulnerability emerge from... by hcknwscommenter on Saturday April 04, 2020 @11:40AM (#22778872)

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.

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Re:Clues to Covid-19 coronavirus’s vulnerability emerge from... by twic on Saturday April 04, 2020 @02:51PM (#22780525)

> 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:

https://www.frontiersin.org/articles/10.3389/fimmu.2019.0169...

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.

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Re:Clues to Covid-19 coronavirus’s vulnerability emerge from... by biophetik on Saturday April 04, 2020 @05:14PM (#22781567)

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.

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Re:Clues to Covid-19 coronavirus’s vulnerability emerge from... by nojvek on Saturday April 04, 2020 @03:29PM (#22780789)

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?

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Re:Clues to Covid-19 coronavirus’s vulnerability emerge from... by biophetik on Saturday April 04, 2020 @05:23PM (#22781628)

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/

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Re:Clues to Covid-19 coronavirus’s vulnerability emerge from... by hcknwscommenter on Monday April 06, 2020 @03:07AM (#22791471)

"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.

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Re:Clues to Covid-19 coronavirus’s vulnerability emerge from... by martimarkov on Saturday April 04, 2020 @01:10PM (#22779639)

Honestly I think I learned more from this one comment that most of my biology classes. :D

Any materials you can recommend for complete novices in industrial biology processes?

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Re:Clues to Covid-19 coronavirus’s vulnerability emerge from... by dzhiurgis on Saturday April 04, 2020 @04:23PM (#22781198)

> 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?

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Re:Clues to Covid-19 coronavirus’s vulnerability emerge from... by hcknwscommenter on Monday April 06, 2020 @03:02AM (#22791453)

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.

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Re:Clues to Covid-19 coronavirus’s vulnerability emerge from... by hyperpallium on Saturday April 04, 2020 @02:36PM (#22780395)

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.

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Re:Clues to Covid-19 coronavirus’s vulnerability emerge from... by hcknwscommenter on Monday April 06, 2020 @02:58AM (#22791438)

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.

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