4 ms·

I’m an epi professor and longtime HN lurker. I wrote a short essay yesterday about how to think about these mysterious outbreaks [1]. Briefly, the most common o

I’m an epi professor and longtime HN lurker. I wrote a short essay yesterday about how to think about these mysterious outbreaks [1]. Briefly, the most common outcome is they are determined to be an endemic disease. Less likely is an emerging infectious disease. The most concerning possibility is something novel or highly unexpected. [1] https://caitlinrivers.substack.com/p/understanding-mysterious-outbreaks https://caitlinrivers.substack.com/p/understanding-mysteriou...

etiam 2y ago
Are you willing to hazard a guess how long it will take to get material analyzed to determine which of your categories this is in?
- cmriversepi 2y ago
  The first round of test results should come in Friday or this weekend. The longer it goes undiagnosed, the more we tip into categories 2 and 3.
  - etiam 2y ago
    Thanks. So basically, if it's any of numerous reasonably well-known but very local diseases a fluid's probably going to go colored in some field test kit and say which one, else it could be something known (and often of known substantial concern for large-scale contagion) but too rare or understudied to have cheap robust quick tests yet so that has to be shipped to a real lab (probably with very high biosecurity rating), and if the lab doesn't recognize what they're seeing in their electron microscope and has to do fundamental research first to get a good biochemical profiling it's something truly expanding the boundaries of known infectious pathology? Something like that?
jonny_eh 2y ago
> Less likely is an emerging infectious disease. The most concerning possibility is something novel or highly unexpected. What's the difference between an emerging and novel disease?
- JumpCrisscross 2y ago
  > What's the difference between an emerging and novel disease? Novel is new. Never before seen. SARS-Cov-2 was a novel virus. Emerging means identified but changing [1]. The Covid variants were EIDs. So are antibiotic-resistant strains. [1] https://en.wikipedia.org/wiki/Emerging_infectious_disease#Classification https://en.wikipedia.org/wiki/Emerging_infectious_disease#Cl...
  - etiam 2y ago
    I don't exactly want to dispute that, but I would like to remark it's not entirely clear-cut. SARS-CoV-2 response could be as rapid as it was in no small part because two decades of research on SARS-CoV more or less was applicable, and looking at genetic similarity alone contemporary variants of SARS-CoV-2 are now more different from the original strain isolated in Wuhan than that strain is different from SARS-CoV. So was the threat from pathogenic Coronaviruses really novel? To a degree, and depending on what aspects one chooses to emphasize maybe. Also, I'd say the pathogen itself doesn't necessarily need to do the changing in the context of emerging diseases. I'd take it to mean they have potential to become more prevalent or have a more significant impact, but that could easily also be due to changes in conditions, including human behavior.
    - JumpCrisscross 2y ago
      > I would like to remark it's not entirely clear-cut Are you saying this as an epidimeologist? (I'm not an epidimeologist. I've only studied the math.) > looking at genetic similarity alone Epidimeology is the study of disease in a population. You can't look at the virus alone. The dividing line between emerging and novel is brighter than between emerging and existing. It has to do with whether the population has pre-existing immunity. SARS-CoV infection conferred no immunity to SARS-CoV-2. Getting infected with the Alpha variant, on the other hand, conferred immunity to Omega. > I'd say the pathogen itself doesn't necessarily need to do the changing in the context of emerging diseases. I'd take it to mean they have potential to become more prevalent or have a more significant impact, but that could easily also be due to changes in conditions, including human behavior Literally in the Wikipedia. "EIDs may also result from spread of an existing disease to a new population in a different geographic region, as occurs with West Nile fever outbreaks."
tptacek 2y ago
This is a great article, and for anyone that wants a cheat sheet for the thread (and to double check my read): * The "endemic disease" bucket describes things like cholera and known influenza strains, and what we're seeing is hazy reporting of flare-ups that happen in low-resource areas around the world on the regular. * The "emerging infectious disease" bucket describes stuff like Ebola, which is scary but we've got something like a reasonable history of responding and containing to it, if we take it seriously. * "Novel" is C19, or the first outbreaks of Ebola at the time, the point presumably at which we'd start thinking about novel precautionary measures applied preemptively.
itsaride 2y ago
The article says it's an area where malnutrition is endemic, couldn't it just be a flu variant that's killing already vulnerable people?
- gosub100 2y ago
  Starving people are more likely to eat bush meat, which is one way viruses can jump from one host species to another.

etiam 2y ago

Are you willing to hazard a guess how long it will take to get material analyzed to determine which of your categories this is in?

cmriversepi 2y ago
The first round of test results should come in Friday or this weekend. The longer it goes undiagnosed, the more we tip into categories 2 and 3.
- etiam 2y ago
  Thanks. So basically, if it's any of numerous reasonably well-known but very local diseases a fluid's probably going to go colored in some field test kit and say which one, else it could be something known (and often of known substantial concern for large-scale contagion) but too rare or understudied to have cheap robust quick tests yet so that has to be shipped to a real lab (probably with very high biosecurity rating), and if the lab doesn't recognize what they're seeing in their electron microscope and has to do fundamental research first to get a good biochemical profiling it's something truly expanding the boundaries of known infectious pathology? Something like that?

jonny_eh 2y ago

> Less likely is an emerging infectious disease. The most concerning possibility is something novel or highly unexpected. What's the difference between an emerging and novel disease?

JumpCrisscross 2y ago
> What's the difference between an emerging and novel disease? Novel is new. Never before seen. SARS-Cov-2 was a novel virus. Emerging means identified but changing [1]. The Covid variants were EIDs. So are antibiotic-resistant strains. [1] https://en.wikipedia.org/wiki/Emerging_infectious_disease#Classification https://en.wikipedia.org/wiki/Emerging_infectious_disease#Cl...
- etiam 2y ago
  I don't exactly want to dispute that, but I would like to remark it's not entirely clear-cut. SARS-CoV-2 response could be as rapid as it was in no small part because two decades of research on SARS-CoV more or less was applicable, and looking at genetic similarity alone contemporary variants of SARS-CoV-2 are now more different from the original strain isolated in Wuhan than that strain is different from SARS-CoV. So was the threat from pathogenic Coronaviruses really novel? To a degree, and depending on what aspects one chooses to emphasize maybe. Also, I'd say the pathogen itself doesn't necessarily need to do the changing in the context of emerging diseases. I'd take it to mean they have potential to become more prevalent or have a more significant impact, but that could easily also be due to changes in conditions, including human behavior.
  - JumpCrisscross 2y ago
    > I would like to remark it's not entirely clear-cut Are you saying this as an epidimeologist? (I'm not an epidimeologist. I've only studied the math.) > looking at genetic similarity alone Epidimeology is the study of disease in a population. You can't look at the virus alone. The dividing line between emerging and novel is brighter than between emerging and existing. It has to do with whether the population has pre-existing immunity. SARS-CoV infection conferred no immunity to SARS-CoV-2. Getting infected with the Alpha variant, on the other hand, conferred immunity to Omega. > I'd say the pathogen itself doesn't necessarily need to do the changing in the context of emerging diseases. I'd take it to mean they have potential to become more prevalent or have a more significant impact, but that could easily also be due to changes in conditions, including human behavior Literally in the Wikipedia. "EIDs may also result from spread of an existing disease to a new population in a different geographic region, as occurs with West Nile fever outbreaks."

tptacek 2y ago

This is a great article, and for anyone that wants a cheat sheet for the thread (and to double check my read): * The "endemic disease" bucket describes things like cholera and known influenza strains, and what we're seeing is hazy reporting of flare-ups that happen in low-resource areas around the world on the regular. * The "emerging infectious disease" bucket describes stuff like Ebola, which is scary but we've got something like a reasonable history of responding and containing to it, if we take it seriously. * "Novel" is C19, or the first outbreaks of Ebola at the time, the point presumably at which we'd start thinking about novel precautionary measures applied preemptively.

itsaride 2y ago

The article says it's an area where malnutrition is endemic, couldn't it just be a flu variant that's killing already vulnerable people?

gosub100 2y ago
Starving people are more likely to eat bush meat, which is one way viruses can jump from one host species to another.