A comprehensive analysis and resource to use CRISPR-Cas13 for broad-spectrum targeting of RNA viruses, 2025, Lin et al

Paddler · May 17, 2025 at 2:07 AM

Abstract
A comprehensive analysis and resource to use CRISPR-Cas13 for broad-spectrum targeting of RNA viruses
Xueqiu Lin 1,6, Yanxia Liu 1,6,7, Augustine Chemparathy 1,2,6, Tara Pande 3, Marie La Russa 1,7, Lei S Qi 1,4,5,7,8,∗

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and variants has led to significant mortality. We recently reported that an RNA-targeting CRISPR-Cas13 system, called prophylactic antiviral CRISPR in human cells (PAC-MAN), offered an antiviral strategy against SARS-CoV-2 and influenza A virus.

Here, we expand in silico analysis to use PAC-MAN to target a broad spectrum of human- or livestock-infectious RNA viruses with high specificity, coverage, and predicted efficiency. Our analysis reveals that a minimal set of 14 CRISPR RNAs (crRNAs) is able to target >90% of human-infectious viruses across 10 RNA virus families. We predict that a set of 5 experimentally validated crRNAs can target new SARS-CoV-2 variant sequences with zero mismatches.

We also build an online resource (crispr-pacman.stanford.edu) to support community use of CRISPR-Cas13 for broad-spectrum RNA virus targeting. Our work provides a new bioinformatic resource for using CRISPR-Cas13 to target diverse RNA viruses to facilitate the development of CRISPR-based antivirals.

CRISPR/Cas13 could be used as broad anti viral for RNA viruses:

https://pmc.ncbi.nlm.nih.gov/articles/PMC7985958/

https://www.genengnews.com/gen-edge...iosciences-uses-crispr-to-target-rna-viruses/

Dr Hanson and Dr Chia support the theory of chronic enterovirus non cytolytic infection as the driving mechanism in MECFS. This potential treatment would be worthy of consideration/investment.

Kitty · May 15, 2025 at 9:17 PM

Paddler said: ↑

do enteroviruses incorporate themselves into host genome
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Pretty sure that's only retroviruses.

Paddler said: ↑

Dr Hanson and Dr Chia support the theory of chronic enterovirus non cytolytic infection as the driving mechanism in MECFS.
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This kind of idea's been around for a long time, but no one's produced any evidence for it.

Paddler · May 16, 2025 at 12:59 AM

Kitty said: ↑

Pretty sure that's only retroviruses.

This kind of idea's been around for a long time, but no one's produced any evidence for it.
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Fortunately, CRISPR/Cas13 could serve as diagnostic tool as well.

Hutan · May 17, 2025 at 2:23 AM

Interesting to read the article. Excerpts:

Stealth startup Carver Biosciences has turned a different CRISPR RNA-cutting nuclease enzyme—Cas13—into an antiviral that can be programmed to detect and destroy RNA-based viruses in human cells.
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During his postdoc with Pardis Sabeti at the Broad Institute, Myhrvold helped to harness Cas13’s programmable RNA-targeting activity to develop an end-to-end technology platform called Cas13-assisted restriction of viral expression and readout (CARVER). Myhrvold has since teamed up with CEO and Carver Bioscience co-founder Walter Strapps, PhD, who has worked at Merck, Intellia Therapeutics, and Gemini Therapeutics.
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Myhrvold: One of the things that got me excited about Cas13 when I started my post-doc was this notion that we now have a CRISPR protein that can be targeted to RNA. In particular, RNA viruses cause so many of the infections that make us sick. About two-thirds of the viruses that infect humans are RNA viruses—there are hundreds of them— and almost all have no good treatment options or vaccines. We’ve made some progress in that regard, but only a few dozen have suitable treatments. I got excited by the notion that maybe we could use Cas13 to target then destroy the RNA of these viruses as they are replicating, which would represent a fundamentally new way of dealing with antiviral infection.
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In many ways, we’re taking these CRISPR systems back to their roots. They evolved initially to go against RNA bacteriophages. That’s why I like the idea of repurposing them for viruses that can affect people. And we were successful, demonstrating in cell culture experiments several beneficial properties like efficacy and multiplexing capabilities, which is nice because we’re so concerned about the evolution of resistance. That’s not something we worry about here because we can simply re-target the CRISPR easily to go after different sequences.
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Finally, we did some preliminary work looking for off-target effects because that’s something that everyone is concerned about in the CRISPR field. While we didn’t see evidence for a ton of that, we will continue evaluating that going forward. Fortunately, in this scenario, those would be effects just on the transcriptome and nothing permanent. Even if there was some modulation of gene expression, hopefully that would not be too harmful.
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RNA viruses are an excellent place for us to go while allowing us to demonstrate the platform’s utility against anything that uses RNA to replicate itself. You could envision going from viruses to somatic disease, directly targeting the RNA. But before you can dream that big, it’s important to demonstrate that you can do what you think you can do with the technology. That’s the advantage of going after viruses is for us. We can target those directly, and they’re transient.
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