Virology thread.

>>8170460
Alright, since OP didn't really put any possible topics up, I'll help.

Does anyone here care about retroviruses and their applications in genetic design?

when will Herpes be cured?

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>>8170473
Adding a new gene segment is probably safer with adeno-associated virus, which integrates with host DNA at a specific location in chromosome 19 nearly every infection.

Manipulating genes or needing to insert at a specific location with is harder with retroviruses because they integrate at random locations. Pretty sure they have ways around that at this point but I don't know how viable they are for humans

>>8170487
Herpes simplex is a pain because of the fact it can establish latent infections in immune privileged sites (nerve cells). Finding a way to remove the virus from nerve cells without causing collateral damage is hard. Basically you can reduce outbreak frequency and severity

>>8170473
>retroviruses and their applications in genetic design?

Pleb you come out of a coma or what. Retroviruses are so 2013, we got crisper cas9 now 9 million % better. It's so easy even high school kids can experiment with creating cat girls now.

anyone here actually in the field? how is it?

>>8170460
>double gloving it

Why hasn't someone come up with something better than this awkward as fuck solution?

>>8170509
Fuck. Retroviruses are the absolute assholes of biotic life.
Can't you use electroshock or something like that to fry them out ? Even if its not electroshock, there must be something that the nerves can endure and they can't.

>>8170487

Medfag here…

3/5 cases involve no symptomatic presentation.

1/5 cases involve symptoms so mild that they typically go unnoticed.

1/5 cases present with obvious symptoms.

Of that 1/5, the overwhelming majority of cases are limited to an initial breakout and then a much milder secondary outbreak, whereafter the virus remains dormant.

Some individuals experience recurrent outbreaks, typically those exposed to high levels or stress or those with some form of immune deficiency.

Most people have herpes simplex 1 (estimated at 80%) and a smaller amount have herpes simplex 2, however they experience no symptoms; the virus merely remains dormant.

>>8172498

viruses in general have no metabolism so they're more like rocks, except that they react biochemically to your body with more viruses.

Therefore... no, the only way to destroy them is to starve them out, deal with them like foreign objects or have your DNA prepared to recieve them.

>>8170473
literally why would anybody do this instead of crispr?
>>8170509
>integrate at random locations
OH BOI

poor, poor retrovirus labs.

>>8172550
Man I got herpes in my upper lip area and this is like the 4th outbreak I had over 2 years. When the outbreak starts it covers a huge area in a really short time. I'm still walking around with herpes medication and blister stopping cream in my pocket all the time.

Stress doesn't really trigger mine though, it almost seems to hit at random times. Although getting exposed to sunlight dries the skin and can kickstart it as well. I'm desperate for a permanent cure but all the doctors I met said that it's impossible for the reason some anon stated above. It nests in the nerve cells and stays dormant there until the next strike and its almost impossible to reach there and kill it.

>>8172555
How do you starve them out ? Don't they hijack your DNA and keep spreading all the time ?

>>8170460
>Virology thread.

>>8172565

if you consider that virus "eats" cells, you starve them out by blocking their entrance to cells.

There is at least 10% of the population inmune to VIH just because they have faulty receptor in white inmunitarian cells, so the virus can't infect the cell.

Bacterias have ways to take out DNA from bacteriophages.

And so on... the usual defense is pasive, although your body can attack invading viruses by using proteins that attach to them and make them heavier so they precipitate and become "deactivated"(just rally unable to infect anything but not dead)

>>8172561

Damn, I'm sorry to hear that man.

A small percentage of the 1/5 of cases, is still a lot of people to be fair.

Say it's 5%, that's still over 200,000 people a year in the US who have recurrent breakouts.

>>8172574
>>8172576
Excuse my lack of knowledge but if we know their structure isn't there any way to kill them or attack the components of them in anyway at all ? They're already progressing on vaccines for Zika, Herpes have been around forever and I'm just surprised that there isn't already a permanent solution for such a common disease that literally hijacks the thing that makes you what you are.

>>8172583
Latent viruses like herpes remain in your cells and as a result, it's hard to get a vaccine to work. There has been cure research in the past which haven't been unsuccessful, but they are unreliable and do not work the same, if at all, on each patient.

But about why they haven't hurried the research, one question:

Is herpes fatal?

Not to mention there's already cures in the flaviviridae family (think yellow fever), making the vaccine research faster, unlike with herpes.

>>8170603
the only thing blocking proactive genetic research from continuing are the moral issues. playing god gets us everywhere, but we have to get there first.

>>8172550
>Medfag here
do you like starting your posts like that?

>>8172754
>Is herpes fatal?
No. Unless you are seriously immunodepressed, then it can attack eyes and/or the brain (HSV-1).
HSV-2 don't do anything.

>>8173423
I think any diseases is fatal if your immune system is crippled.

>>8173426
Depends how exactly, HIV is the best known example but also the worst case possible because you say bye to the CD4+ T cells, meaning no one is here to coordinate immune response : everything can destroy you.
There are other kinds of immunodepression.

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Bacteriophages exist to kill bacteria.

Why aren't there Viriophages?

>>8173452
you cannot kill that which is not alive

>>8173674
but I can destroy your car so that it doesn't work anymore.
So the question would be how to disrupt virus functionality

>>8170460
>yep it's a virus

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>>8173452
>>8173684
There is some mechanisms in bacterias (hey CRISPR/Cas9, bacteria immunity) and eukaryota (RISC complex, pic related) that can detected and disable virions.
For disabling viruses, we have the immune system : Antibodies for free capsides and killers (NK and effector CD8+) for infected cells.

>>8170460
>Virology
You guys are so stupid sometimes.

>>8173674
define life

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>>8173684
Increase the free energy of the surrounding state to decouple the molecular bonding that the virus structure has. Thus neutralizing the virus.

>>8172498
>Can't you use electroshock or something like that to fry them out
lol
>>8172555
>or have your DNA prepared to recieve them.
What?
>>8172583
>or attack the components of them in anyway at all
Yes there is! Go look up HIV protease inhibitors for example.
Eliminating them is another thing, but imagine if you had some kind of technology that could efficiently and precisely cut in a specific DNA sequence, oh wait, we already do. It's called CRISPR-Cas.
Weaponizing it for actual therapy is probably hard as balls though.

>>8173819
so fuck up the viruses along with your nerves ?

any recommended textbooks for virology or pathology?

>>8174067
There already has been multiple attempts at targeting lysogenic viruses with CRISPR to finally remove it from the body, particularly HIV. In a surprise twice it did not work. CRISPR does not simply remove a gene usually what happens is that a CRISPR causes a double stranded break at the target gene which is repaired by nonhomologous end joining commonly resulting in indel mutations that can essentially knock out the gene. However every so often there is an indel mutation caused by the CRISPR that does not hurt the viruses ability to reproduce but makes the gene no longer recognizable by the CRISPR cas9 system.

Tldr: CRISPR makes mutations in the virus which makes the virus immune from CRISPR.

I know this because this was one of my intended research projects :,( in the future I might pursue it again assuming that we increase the efficiency of CRISPR cas9 induced homology directed repair

>>8170603
nigga how we gon deliver dem cas9 shits into hard-to-transfect/transduce cells hmm??

>>8175441
Can't you engineer a virus to attack HIV or herpes virus ?

has there ever been an attempt at cultivating mycoviruses to treat drywall mold? like how they treat chestnut trees infected with chestnut blight.

>>8175903
Spray and pray. You might laugh but we are doing just that with homologous recombination.
>>8175905
You can't have a virus infect a virus but you have something called satellite viruses, like hepatitis D, that follow another virus around and use it's replication cycle. We can imaigne a satellite virus that hijack the replication cycle of HIV or herpes.
Problem : It's a lot complex and hazardous for nothing.

>>8173452
Well, there are satellite viruses

>>8174609
Principles of Virology is a good one to start off, plus you can use this guy at Columbia's lectures to supplement https://www.youtube.com/playlist?list=PLGhmZX2NKiNlKLVfVwFz8UhS720xIe6v5

>>8175441
Do you think you could replicate function on different targeted sites by engineering a protein similar to CRISPR? I imagine there has to be a fair amount of sequence similarity among different viruses' replication sequences. If you can target the same RNA/DNA sequence with CRISPR, why not engineer another protein to attack a different sequence in multiple viruses?

>>8177453
>>8177453
Hi, I am >>8175441

You do not actually have to re-engineer a CRISPR/cas9 like system to target multiple sequences due to the nature of the CRISPR/cas9 system you can target multiple sites by using normal components.

As the name suggests the CRISPR/cas9 system has two components
- CRISPR is usually refers to a DNA sequence that can be used to make RNA antisense to the target sequence. In lab settings we simply make guide RNAs (gRNAs)
- cas9 is a endonuclease which causes double stranded breaks where the guide RNA finds homology.

By having more than one cas9 protein molecule in the system (which is normally the case) you open up the oppurtunity of occupying them with a variety of different guide RNAs that target different sites of the integrated viral genome.

This is obviously a great idea so the researchers I mentioned previously are planning to do this "Both he and Liang think that the problem can be surmounted, for instance by inactivating several essential HIV genes at once, or by using CRISPR in combination with HIV-attacking drugs."


This news article refers to the papers and is where I got the quote, if you are interested:
http://www.nature.com/news/hiv-overcomes-crispr-gene-editing-attack-1.19712

>>8177453
Simply from the groundbreaking research I see everyday. I am optimistic that HIV and most cancers will be cured within the next decade or so.

>>8177453
Oh! I forgot something.

Using multiple guide RNAs to target multiple sites have a trade off. The more sites that are targeted by CRISPR the more likely that there will be some sequence elsewhere in the human genome which is similar enough to the target that it will also get hit. Uncontrolled mutations in potentially important genes are, to say the least, not optimal. This should not discourage any efforts in this direction. Regardless of what you, this problem is inevitable because of genetic variation that already exists in the human gene pool (something somewhere is going to get hit). If therapies were perfect we would not have chemo and surgeries

>>8177692
>>8177673
>>8177680
Awesome, thanks for answering my question. I personally haven't touched much more than metadata on genomes since I learned basic genetics a few years ago, so it's kinda nice to learn some new stuff going on in biotech. CRISPR/cas9 is something I've only heard about since being here on /sci/.

One question I have is that if cas9 proteins tend to target RNA strands, then would engineering a mechanism for the cas9 system to break down after treatment) be a good way to prevent side effects (ribosome damage comes to mind)? Or would that just damage their ability to target viruses while solving a problem that isn't there?

>>8177929
>then would engineering a mechanism for the cas9 system to break down after treatment) be a good way to prevent side effects (ribosome damage comes to mind)?

What the fuck does this mean? Why the fuck would the ribosome be damaged by Cas9?

>>8177692
You mean there are essential genes in the human genome with great enough sequence similary to viral genes to be recognized by CRISPR Cas? I'm somehow not totally concinved.
>If therapies were perfect we would not have chemo and surgeries
Pretty sure the main problem with this kind of therapy is inefficient delivery and cost.

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>>8177972
Ribisome is made of RNA, rRNAs. Also the RNA inside are the one doing the job (catalytic RNA called ribozymes), the proteins are just structural. If you fuck up the rRNAs, you fuck up ribosomes.

But Cas9 do not target RNA strands as >>8177929 said : Cas9 uses gRNA to cut double stranded DNA and only DNA.

>>8177977
Many viral genes were at one point genes on some kind of organism. For example a lot of viral oncogenes are exactly this and so are many other genes that are used to manipulate the host cells machinery to their needs.

Even if the gene on the virus was not originally from the same organisms that is its current host, the conservation of important genes would allow for enough sequence similarity for CRISPR to be target genomic dna.