We are recruiting sewersheds for an expanding project. Basically, we want to learn everything that can be learned from wastewater.
Read on if you are interested. 1/
This is a collaboration with SecureBio that started about 18 months.
Basically, we isolate the viral fraction from wastewater and sequence the crap out of it (~1 billion reads/sample). This is unbiased sequencing; we don’t want to miss anything. 2/ securebio.org
There are three main levels to the analysis of the wastewater virome.
The first is SecureBio’s main focus, which is novel pathogen detection with a particular focus on engineered pathogens. 3/ naobservatory.org/blog/detecting…
This battle between Harvard and the administration is so befuddling. The latest plot twist makes less sense than the last season of Lost.
Let me give a very quick summary for those not following along.
1/11
The last few weeks Harvard had been talking with the administration about concerns over antisemitism on campuses, but the talks lacked details, and Harvard was told that they would get a letter last Friday with more specifics.
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Then last Friday Harvard got an email from the acting general counsel of HHS with a scorched earth list of demands that would have effectively ended Harvard’s autonomy in hiring, admissions and curriculum.
Last month there was an announcement that I thought was a major advancement in world health, but it got little attention.
I thought I would tell you all a little bit about it and why it is so important.
1/25
This breakthrough has to do with HIV, which was a zoonotic pathogen. The progenitor of HIV infects chimpanzees in Cameroon.
No one knows exactly when or how HIV crossed into humans, but the first undisputed HIV patient sample (discovered retrospectively) was from 1959 in what is now the Democratic Republic of Congo.
HIV smoldered for decades before becoming widespread in the early 80s.
At the time, being diagnosed with an HIV infection was a death sentence.
There was no real cure (still isn’t) and no treatment. By any measure, HIV was one of the worst diseases of the last century. 3/ nature.com/articles/d4158…
I briefly thought the SA BA.3.2 was in the US, but it turns out the virus was just messing with me again.
This was kind of interesting though.
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We've been screening all of the new wastewater data a few times a week for signs of BA.3.2.
One of the many screens we have is looking for reads that have C21846T+T21864C together, which are in BA.3.2 but no current lineages (it works better to look for pairs of changes).
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This week we had a hit. This was the genotype of the read:
Here’s the problem we hope this dashboard will help solve. SARS-CoV-2 remains very prevalent in the US.
However, sequence surveillance from patients has plummeted. In addition to fewer samples, the average sequence takes >3 weeks to be reported (and it’s getting slower).
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Fortunately, we have wastewater surveillance (primarily through CDC NWSS), which covers a large chunk of the population and has a fairly fast turnaround (<2 weeks).