
HIV overcomes CRISPR gene-editing attack - aroch
http://www.nature.com/news/hiv-overcomes-crispr-gene-editing-attack-1.19712
======
chris_va
With the caveat that I have only had this explained to me ...

The one location in the HIV genome that consistently doesn't mutate is the
hexamer boundary of the viral capsid. Seems like that would make a better
taerget sequence as a result.

Anyone here know why they chose the sequences that they did?

~~~
IndianAstronaut
Is that area accessible to the enzymes. Not all parts of the stand are equally
accessible.

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im3w1l
Let's very pessimistically say this attack killed 50% of viruses, and only
those lucky enough to have a mutation at the cleavage site managed to survive,
and then multiply after, making the virus immune to that specific cleavage.

Couldn't you then cleave at a few sites at once? With 64 different cleavage
sites, only 1/2^64 viruses will survive, meaning it's pretty much completely
certain you will kill every last virus.

This assumes none of viruses have some general anti-CRISPR defence, but I
think that should be a pretty good assumption.

~~~
johnm1019
From the article...

> Both he and Liang think that the problem can be surmounted, for instance by
> inactivating several essential HIV genes at once...

~~~
nonbel
They don't really offer any argument for this though. Apparently one infected
cell can infect 10k new cells after a day or two[1], the mutation rate is 4
per kbp per cell[2], and the HIV genome is 9 kbp long[3]. That would mean 36
new mutations for each newly infected cell.

I'm not positive this is right... but I would think a rough estimate on the
upper bound could be arrived at assuming each mutation is equally likely and
independent. Then the probability of a single mutation at any given site would
follow a Poisson distribution with k=1 and r=.004:

    
    
      r^k*exp(-r)/k! = r*exp(-r)= 0.00398
    

Then the probability of a mutation at n=2 sites in the same cell would be:

    
    
      (r*exp(-r))^n= 1.58 x 10^-5
    

If each infected cell infects N=10,000 new cells each generation g, after one
generation (g=1) the expected number of cells containing a set of two specific
mutations would be:

    
    
      N^g*(r*exp(-r))^n= 0.158
    

However after two generations there would be 10^8 infected cells and 1587
would be mutants at any two given sites. Then for any n=3 sites there would be
about 6 cells containing mutations at each.

As I said, that would definitely be an upper bound. Some sites will be less
likely to mutate than others, eventually you run out of new cells, etc.

Also, this ignores that cutting the DNA may be killing the cells.

    
    
      [1] http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000906
      [2] http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002251
      [3] http://www.ncbi.nlm.nih.gov/nuccore/AF033819

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nonbel
I am wondering how they know these mutations were not present to begin with.
Also, how many cells were there before the CRISPR treatment vs after? What was
the rate at which they divide under these conditions? Perhaps they just killed
off enough of the cells with the CRISPR/cas-9 treatment and it took a few days
for them to recover to the point of producing detectable CA-p24 (an indicator
of HIV) levels.

~~~
tosseraccount
Original paper is here :

[http://www.cell.com/cell-
reports/fulltext/S2211-1247%2816%29...](http://www.cell.com/cell-
reports/fulltext/S2211-1247%2816%2930298-4) _CRISPR /Cas9-Derived Mutations
Both Inhibit HIV-1 Replication and Accelerate Viral Escape_

Supplement here :
[http://www.cell.com/cms/attachment/2052606220/2059839343/mmc...](http://www.cell.com/cms/attachment/2052606220/2059839343/mmc1.pdf)

Known strain to start with. They claim "Both viral targets are very conserved
in HIV-1 sequences that are registered in the HIV database (Figure S1B)."

See explanation of figure S1 in supplement for more info.

~~~
nonbel
Ah, I was looking at the other paper so haven't inspected the one you linked
to. The two papers used the same method though:

"The HIV-1 LAI stock was produced by transfection of 293T cells with the pLAI
molecular clone."

"HIV-1 was first produced by transfecting HEK293T cells with HIV-1 DNA"

Sounds like they produced a bunch of virus in 293T cells, during which time it
could mutate.

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foota
Perhaps a stupid question, but the article says "HIV has already shown the
ability to evolve resistance to all manner of antiviral drugs (as well as the
human immune system). This happens because its genetic material is copied by
enzymes that are prone to error. Most mistakes stop the virus working, but
occasionally a mutation is beneficial for HIV, allowing it to evade attack."
is it possible to fix the gene copying mechanism in HIV and thereby eliminate
its ability to mutate so quickly?

~~~
pdkl95
The problem is reverse transcriptase[1] (the enzyme that causes the copy
errors) is a key part of how HIV infects the cell[2]. If we could fix that, we
could simply block it from working at all, stopping the virus's ability to
copy itself into the cell's chromosome. This is actually how a lot of the HIV
drugs work (reverse transcriptase inhibitors[3]).

[1]
[https://en.wikipedia.org/wiki/Reverse_transcriptase](https://en.wikipedia.org/wiki/Reverse_transcriptase)

[2]
[https://www.youtube.com/watch?v=eS1GODinO8w#t=100](https://www.youtube.com/watch?v=eS1GODinO8w#t=100)

[3] [https://en.wikipedia.org/wiki/Reverse-
transcriptase_inhibito...](https://en.wikipedia.org/wiki/Reverse-
transcriptase_inhibitor)

~~~
marshray
So then why are retroviruses so relatively rare? Why aren't they the dominant
type of virus?

~~~
gozur88
_Are_ retroviruses rare? From what I can tell we don't know much about viruses
that don't clearly cause disease.

~~~
cowsandmilk
Wikipedia claims "Over 8% of the human genome is made up of (mostly decayed)
endogenous retrovirus sequences"[1]. So, it appears they are at least common
enough that we're all passing along endogenous viral elements[2] to our
children (and we got them from our parents).

[1]
[https://en.wikipedia.org/wiki/Noncoding_DNA#Repeat_sequences...](https://en.wikipedia.org/wiki/Noncoding_DNA#Repeat_sequences.2C_transposons_and_viral_elements)

[2]
[https://en.wikipedia.org/wiki/Endogenous_viral_element](https://en.wikipedia.org/wiki/Endogenous_viral_element)

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s_q_b
The biggest problem with HIV is that when you're dealing with one person with
"HIV" you're actually fighting dozens of different adaptations of the virus,
much like how cancer tumors differentiate into dozens of cell types.

My approach would be to compare and contrast SIV and HIV defense strategies in
humans and chimps. How does the TRIM5-alpha in chimps manage to fight off HIV,
and how does human TRIM5-alpha fight off SIV?

~~~
rpgmaker
What makes you think that they aren't doing that already? That seems like the
first thing anyone would think of doing.

~~~
s_q_b
Well, I keep up on my journal reading, and my sister's a medical doctor from
Penn. The first serious _proposal_ for preliminary trim5-alpha based gene
therapy was released in 2015, without much reaction.

Some previous work has been done. Modified human T-cells with a copy of new
world monkey trim5-alpha. The result was successful in vitro. I believe that
was 2008.

My point was really, "Why doesn't this rather straightforward mechanism
receive more time and research?"

*Disclaimer: I have worked in bioinformatics.

~~~
rpgmaker
Thank you. If that is indeed the case then I'm left asking the same question.

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awakeasleep
I wonder if it'd be possible to alter HIV into something benign instead of
killing it. If done properly, that'd eliminate the virus's drive to out-evolve
our treatment.

~~~
XorNot
HIV is relatively benign. People love for years without showing symptoms,
hence its success.

To beat that we'd have to find something which could deny it resources without
killing the host (us). But that's pretty much just 'a cure'

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known
Reminds me
[https://en.wikipedia.org/wiki/Jurassic_Park_%28film%29](https://en.wikipedia.org/wiki/Jurassic_Park_%28film%29)

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mentos
If every computer scientist studied medicine for the next 8 years I wonder how
much that would increase the likelihood of finding an HIV cure?

~~~
hatsunearu
What's with the attitude of "computer scientists can solve anything if they
displace the original researchers who are incompetent"?

