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Epistemic Status: intended to answer this question, other considerations came up.  Figured I should ask the forum rather than throw the question away, as it seems like it could be important to think about. <3h research done on even framing this question well, not claiming at all to have an answer.

The main reason not to be worried about existential risk from naturally-occurring pandemics is 'it hasn't happened yet'; humans have been around for a long time, and even ignoring anthropic problems, there don't seem to have been many near-miss events.

One reason this argument might not hold is based on three claims:

  1. Most pandemics are zoonotic, particularly emerging pandemics
  2. Humans interact with animals more than ever before (currently ~7x as many animals are slaughtered daily as in 1960)
  3. Humans interact with animals in very different ways than ever before (factory farming involves close animal-animal contact and human-animal contact)

If the rate of zoonotic 'near-miss' events is increasing, we may be undervaluing interventions specific to natural pandemics or interventions which would apply to any pandemic (relative to how we value interventions specific to man-made pandemics).

Some sub-questions I think might be useful, if research exists to answer them:

  • Is the rate of zoonotic pandemics going up?
  • What proportion of pandemics are zoonotic?
  • How common are zoonoses in farmed animals?
  • Are farmed animals more/less susceptible to disease than wild animals?
  • Are there examples of near-miss/'important' pandemics originating in farmed animals?

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I think it's good to have in clear mind if we mean x-risk pandemic vs bad pandemic. Factory farming already has done many bad pandemics, but as you seem to note the majority of EV from pandemics comes from x-risk cases

The best solutions to pandemics are ones that can tackle all vectors of deadly pandemics(natural & man made)

Hear this idea podcast has a great recent episode on this topic

This is a good point, and I think most EV in general is in X-risk. I'd include COVID-level or HIV-level emerging pandemics as being worth thinking about even if they don't represent X-risk, though. 
It's not obvious to me that generalised solutions (for both natural & man-made andemics) are the most efficient answer. For instance as a random and un-researched example, it could be really cheap to encourage farmers to wear gloves or surgical masks when handling certain animals (or in certain regions), but this is only worth doing if we're worried about farm animal pandemics. 

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