A few points about the H5N1 outbreak that I'd like to share.
1. If we had a pan-influenza wastewater screen in place nationally that differentiates the influenza sources by sequencing (which isn't that hard to do), we probably would have detected this outbreak months ago.
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BTW, we submitted a CDC proposal earlier this year to do exactly this, but the topic was pulled from the BAA so the proposal wasn't even reviewed.
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2. We should not panic about the current outbreak in cattle. You aren't going to get influenza from pasteurized milk, and this virus isn't ready for human-to-human spread (yet).
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3. What we should be concerned about is that fact that the viruses is getting way too many chances. It keeps expanding its tropism. The more animals it replicates in, the more chances it gets to sample new configurations.
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4. When the virus makes it way it to pigs, that is when we need to start getting really nervous. Pigs are a mixing vessel where flu is more likely to adapt to respiratory spread in humans.
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5. In my opinion we should be focusing our attention on wastewater testing downstream of meat processing plants (for all types of animals). It wouldn't matter what tissue the virus is in, it would end up in the water and give us an early warning.
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We've detected and sequenced pig influenza from such sewersheds before (not H5N1), so I know it can work.
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6. Most important, we shouldn't shy away from surveillance because we want to avoid a panic. There is still time to stay ahead of this, but if we aren't careful I think it's just a matter of time before H5N1 makes it to humans.
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This is cool. I was poking around at the Rhinovirus (common cold) data and realized that my perception about these viruses was completely wrong. 1/
Rhinoviruses (Rhino is Greek for nose) are picornaviruses in the enterovirus genus (same as polio). Enteros can be GI or respiratory (or both), but Rhinos are usually respiratory, and are the main cause of the common cold.
The first big improvement is that the output is more precise, and interactive. For each data point we tell you the date, the reads mapped, the total reads in each sample, and the reads/billion for each pathogen.
The heat map color is dictated by reads/billion.
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As before, we have a dropdown menu (now divided into categories) where you can do a city-to-city comparison of the different pathogens.
There haven’t been a ton of changes to the manuscript since I wrote a post on the preprint, so I’ll make this summary brief and focus on the things that changed. 2/
Cryptic lineages are anachronistic, evolutionarily advanced SARS-CoV-2 lineages detected from wastewater. We are pretty certain they are all from persistent infections.
We developed techniques for finding these lineages and partially reconstruction their genomes. 3/
For the last 18 months we have been getting weekly composite wastewater samples, isolating the viral fractions (the virome) and randomly sequencing everything.
The project started with Columbia, MO in late 2023, but we’ve expanded to include Chicago, Boston, Boise, and Riverside. We are doing other sites too (and expanding), but these are the first we are reporting. 3/
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.
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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.