“Detecting Genetically Engineered Viruses With Metagenomic Sequencing” by Jeff Kaufman

This is a link post.

This represents work from several people at the NAO. Thanks especially to Dan Rice for implementing the duplicate junction detection, and to @Will Bradshaw and @mike_mclaren for editorial feedback.

Summary

If someone were to intentionally cause a stealth pandemic today, one of the ways they might do it is by modifying an existing virus. Over the past few months we’ve been working on building a computational pipeline that could flag evidence of this kind of genetic engineering, and we now have an initial pipeline working end to end. When given 35B read pairs of wastewater sequencing data it raises 14 alerts for manual review, 13 of which are quickly dismissible false positives and one is a known genetically engineered sequence derived from HIV. While it's hard to get a good estimate before actually going and doing it, our best guess is that if this system [...]

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Outline:

(00:22) Summary

(01:15) System Design

(02:36) Evaluation

(02:50) Simulation

(05:28) Real World Evaluation

(08:29) System Sensitivity

(11:34) Future Work

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First published:
June 27th, 2024

Source:
https://forum.effectivealtruism.org/posts/da6iKGxco8hjwH4nv/detecting-genetically-engineered-viruses-with-metagenomic

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Narrated by TYPE III AUDIO.

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