Undiagnosed Pneumonia...
I like to keep an eye on the ProMed mailing list. ProMed was one of the first news source to report on (what became) COVID-19 outside of China1.
The first cases of COVID-19 are suspected to have occurred in late November 2019… which is why I guess when ProMed started reporting “undiagnosed pneumonia” a few days ago everyone got a bit… excited:
A more recent comment on ProMed suggests reports are consistent with Mycoplasma, Why exactly we don’t know at this point if this is even a bacterial of viral infection in a mystery to me…
In any case “it’s probably going to be ok”… but it’s an interesting chance to review how we've progressed since 2019 in diagnostics and surveillance… what do we have that would help us through a new pandemic?
Honestly the answer is “pretty much nothing”. But let’s review!
At-Home Molecular Tests
These things are pretty cool. It’s like having a little qPCR machine that you can use once to see if you’re infected and throw away. The engineering and cost optimization that went into devices like the Lucira is impressive.
Unfortunately most of these seem to have been commercial failures and made a limited impact on the pandemic.
People are just unwilling to pay $50+ for a single use test, even if it is more accurate than lateral flow…
These products were already in development prior to COVID-19 but the pandemic likely helped push them to market.
Surveillance Infrastructure
We’ve build and expanded a bunch of (sometime questionable) infrastructure for COVID-19 variant tracking. There are also generally accepted methods and protocols for COVID-19 variant tracking. Getting this up and running and communicating the importance of variant tracking in a new pandemic would likely be far easier next time round.
While a lot of the labs doing variant tracking disappeared or refocused, I suspect we could spin them back up quickly.
Environmental Surveillance
We have things like the national wastewater surveillance system. And we’ve talked a lot about meta-genomic waste water surveillance. We’ve talked about it, and we’re moving towards it. And we think it could be a really good idea…
Companies also think you should spend money on it.
But I’m as yet unaware of anyone actually doing it in a coordinated way, with significant funding, on a global level.
But perhaps we could shift our COVID-19 wastewater monitor systems over to the next pandemic.
It’s Embarrassing And We Should Feel Embarrassed
To be frank, none of the above puts us significantly ahead of where we were in November 2019.
I suspect our oligo synthesis pipelines might have got a bit better, we can probably deploy qPCR kits a bit faster than the 4 months it took to ship 1M tests in the US for COVID-19.
There are have been no advances in sequencing from which a future pandemic would benefit. The NextSeq 2000 was probably the most cost effective instrument for variant tracking… it probably still is.
We have no new tools which will give us an early warning of an impending pandemic or potentially help us contain its spread.
It’s kind of embarrassing! And as someone who works in this area, I’m particularly embarrassed!
We could have cheap, effective tools for identifying new pathogens… helping bootstrap vaccine development and contain spread.
But somehow humanity has decided that it’d rather react to crises than create safeguards against them.