Feels very timely today to be on the way to the #Nobel Symposium in Stockholm: The First Great Pandemic of the 21st Century.
Though I do not believe the #monkeypox outbreak will be a pandemic, it's a reminder there are many pathogens that can rear their heads in different ways.
Though I do not believe the #monkeypox outbreak will be a pandemic, it's a reminder there are many pathogens that can rear their heads in different ways.
Tomorrow, I'll talk about how phylogenetics played a critical role in #COVID19 #SARSCoV2 - but also outline what challenges we face when we look to tomorrow's pandemics. In particular we have to ensure: sequencing, sharing, software & sufficient background.
A lot of pandemic preparedness focuses on detecting a new pathogen, or what to do once we know it's bad news. But a lot of the critical work is a little more boring: encouraging #openscience, ensuring credit, maintaining & advancing software & building up our virus knowledge.
Even as I wrote out the framework for the talk, I feel like #monkeypox is highlighting exactly why these things are so critical:
Through available sequencing tech in affected countries & truly open sharing, we've got the first genomes fast & a community pouring over them.
Through available sequencing tech in affected countries & truly open sharing, we've got the first genomes fast & a community pouring over them.
We have software that's ready to handle big genomes (#monkeypox is 200,000 bases compared to #SARSCoV2 30,000) & (mostly ready) to do tricky alignments for a DNA virus with lots of repeats. We have great viz for trees & geography ready to go.
Critically, with truly open genomes scientists are able to share alignments with each other (so everyone doesn't have to figure out how to do those tricky bits) & feed these genomes into high-powered platforms that will spit out incredible stats (more on this later!).
And finally, sequences from previous outbreaks are allowing us to gain critically important insight into how this #monkeypox outbreak relates to previous ones. Still, how much is unsampled that might be giving us more clues now? Background is important!
Chances are, we won't perfectly identify in advance the next pathogen we have to tackle. But if we ensure the community, technology, sequencing, personnel, & background is in place widely, we'll be better prepared to tackle _whatever_ the next pathogen is that causes us alarm.
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