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Jeremy Kamil Profile picture
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Jan 27 • 5 tweets • 4 min read
SARSCoV2 trajectory toward #Omicron is AFAIK 1st 🥇 example of science watching trajectory of viral evolution to fulfill #CanyonHypothesis (more closed entry protein that hides receptor binding domain from antibodies). Beginning of pandemic was opposite: S became more “open” 👇👇
..cc: @EricTopol @carlzimmer h/t @GISAID community @Mizimmer90 @renegadenarwhal
The #CanyonHypothesis was first put forth by the late Michael G Rossmann, a prominent viral structural biologist who died in May 2019. Anyone interested in SARS-CoV-2 Spike evolution should read the paper. Nothing short of prophetic pubmed.ncbi.nlm.nih.gov/2670920/
Though Rossmann AFAIK didn’t theorize that a Spike could first move in *reverse* the trajectory of #CanyonHypothesis during early host adaptation during a pandemic, before heading back like a pendulum in that direction. 🔥
More here, Maxwell and coauthors also predicted (pre-Omicron) that SARS-CoV-2 would ultimately move in the direction of a more “closed RBD” Spike, based on their own independent computer modeling studies 👇👇

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More from @macroliter

Jeremy Kamil Profile picture
Jan 28
Yes.. BA.2 is increasing in USA.. but total is still only 180 entries in GISAID from all of USA, while BA.1 is at 132,497..
If we filter to only samples collected since Jan 10, it's: 127 BA.2 in USA versus 16,407 BA.1
If BA.2 takes over as % of new U.S. cases, as seems plausible, this will happen much more slowly than Omicron displacing Delta... Not maybe as slow as AY4.2 (LOL!) but I'd guess it'll take at least another month.. & will coincide w/ overall waning of the Omicron (BA.1+BA.2) wave
Keep in mind that although BA.1 and BA.2 might compete with each other, BA.2 didn’t evolve / emerge to escape anti-BA.1 antibodies..
Read 11 tweets
Jeremy Kamil Profile picture
Jan 28
Sad to learn that Dr. Mia Brytting has died. She contributed hugely to surveillance of RNA viruses: IAV, RSV, echovirus, norovirus, SARSCoV2, etc, studying their epidemiology & evolution & evaluating real-world vaccine efficacy. An incalculable loss! 😢scholar.google.com/scholar?hl=en&… Image
So much important work ... eurosurveillance.org/content/10.280…
pubmed.ncbi.nlm.nih.gov/29704733/
Read 4 tweets
Jeremy Kamil Profile picture
Jan 27
"Learning immunology without the pathogen is like watching a football match without seeing the ball-- you're just seeing players run around and have no idea what's going on.. you'd probably think they are just going mad.." - @askia_tm... 1/5 🧵
.. @askia_tm is a phenomenally intelligent young viral immunologist from Liberia.. He's now studying virology in West Java, Indonesia. The guy is not only smart at science, but is also a blossoming advocate for global public health & for decentralizing competence.. 2/5
He worked with the "Ebola awareness team" during the response to 2014-15 outbreak in Liberia. He understands the importance being able to reach communities in their own language, and was surprised how few Liberian scientists were publishing on Ebola from that outbreak and.. 3/5
Read 5 tweets
Jeremy Kamil Profile picture
Jan 22
“Mr. Moreau caught the coronavirus during its second wave in 2020 & suffered a stroke while working at his desk. A friend of his died just last weekend. But vaccination has plateaued at 39%, ~24 percentage points lower than the U.S. over all” #VaccinesWork theglobeandmail.com/world/us-polit…
“It is places such as East Feliciana that are increasingly suffering the consequences. The parish has seen 154 deaths in a population of 19,500, a per-capita rate more than double those of Los Angeles & Chicago, and triple that of New Orleans.”
“Out of the 100 U.S. counties with the highest death rates, 95 have populations of fewer than 100,000 people. None contain major cities.”
Read 4 tweets
Jeremy Kamil Profile picture
Jan 21
When it comes to #wastewater (ww) detection, all COVID-19 variants — and more broadly, all respiratory viruses, are not created equal. 🧵
Going forward, we need combined approaches to track all sorts of viruses & microbes that threaten our health & our economies: air samplers, ww, and yes: direct samples from people, too (saliva, nasal swabs) & even animals #OneHealth. 2/
Importantly, however, I cannot stress enough the need to look beyond the pure technology driven solutions. It’s not just genome sequencing machines, library prep, read QC, 🧬 consensus assembly & phylogenetics. Community engagement & “buy-in” from general public is PIVOTAL. 3/
Read 5 tweets
Jeremy Kamil Profile picture
Jan 16
Excellent work, as always, from @VirusesImmunity lab. Particular kudos to first author @michelle_monje 👏. 🧵
Sadly— as highly important as such work is, I’m concerned about the inevitable sound bytes & memetic take away tweets & headlines about how “mild COVID will give you brain damage”... /2
..& on the other side, COVID-contrarians will point to these apocalyptic takes & say: “My kid recovered from COVID 4 months ago and his latest report card is straight A’s. We need to quit it with vaccines & masking” /3
Read 10 tweets

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