Some very good "let's-not-make-a-scariant" coverage from @NOLAnews..it was a pleasure to talk to @emily_woodruff_ about the B.1.630 variant.. Also.. it's important to note that I'm speaking of "Collection Dates" NOT "Submission Dates". Backstory 🧵:
Why was this news? Our team recently sequenced some Aug 2021 samples from the Baton Rouge clinic & found 2 that were B.1.630. B.1.630 is a noteworthy variant 👀 with a freaky number of convergent Spike mutations shared by "Variants of Concern".. BUT... outbreak.info/situation-repo…
Even tho B.1.630 shares L452R with Delta, D950N with both Mu & Delta..and its T478K is almost like Delta's T478R, and it has H655Y like Gamma, & its E484Q is analogous to E484K found in many VOC/VOI, .......B.1.630 just can't complete with Delta.
Case in point: B.1.630 has not been detected from samples from anywhere in the world collected more recently than very early September.. Most everything collected here and everywhere else is now Delta and her AY.x sublineages..
Even so, I'd stress that it is so so important to keep sequencing viruses to keep tabs on variants.. someday a new VOC or VOI will rise to knock out Delta & the sooner we detect it, the sooner we will be able to protect ourselves, --if necessary--by updating vaccines, et cetera.
Globally & nationally we are still far behind where we need to be to detect & sequence circulating viruses.. we desperately need a new system to reward people (e.g. free diagnosis & medical care) for sharing samples of their mild colds & other respiratory infections.
Sharing these viral genome data in real-time is hugely valuable (big economic benefits) & will prepare us to detect and stop the next 'would be' pandemic in its tracks.. the data are inexpensive to generate & also help protect us from currently known 'seasonal' viruses..
it strikes me as absolutely nuts that for over a decade we've had the technology to inexpensively sequence & track all kinds of virus activity in real-time.. but even 21 months into a pandemic there are almost zero serious discussions happening re: how to tackle this challenge!
It's not that hard but we need leadership, innovation, public engagement, trust, international collaboration, funding & of course, entrepreneurs. It's really important that we get patients' full consent & "buy-in" lest we end up in a HeLa Cell / Henrietta Lacks type situation...
Scientists & public health agencies must not be seen as exploiting for private gain viral genome sequence data taken from patient samples. (I cannot stress this enough).
If people are being paid to sequence virus genomes from patient swabs, then we ought to compensate the patients, too. If not with money find at least some way to make it worth their while and not feel used /exploited. Give the patient their data. Be equitable. Be transparent. 🙏

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More from @macroliter

2 Oct
Hey, y'all.. I deleted my earlier tweet relaying a concern that #Molupiravir might also mutagenize our own DNA. Why did I delete it? Because I was wrong. An expert who I absolutely trust DM'd me to say the following: 🧵 (TL;DR: my concern is unfounded)
"People don’t realize how much sequencing & safety studies have been done just to get to this point. And it is far far less mutagenic (if at all) than the deoxy nucleotide analogs that have been used long-term for HIV patients for decades!"
My colleague added: "Molnupiravir is only used temporarily and has a short window of therapeutic efficacy (as for any respiratory pathogen drug). This will be more life saving for flu treatment than oseltamivir when it gets finally approved for flu." #AntiviralsWork
Read 4 tweets
30 Sep
The only problem is there isn’t just one route to disease susceptibility. There are lots of things that matter besides your “general health” (1) dose of virus you’re exposed to (2) genotype .. eg can you express prenylated OAS1, (3) do you have interferon auto-antibodies? 🧵
And… Not all humans can express the membrane anchored version of the viral “sensor” OAS1
Read 4 tweets
30 Sep
One of my favorite —but sadly, quite common —misconceptions is that people who eat a healthy diet & exercise a lot are naturally resistant to influenza & coronaviruses…
NO YOUR VITAMIN D, CROSS FIT ROUTINE, & FRESH GOJI BERRY SMOOTHIES WON’T HELP YOU… the virus likes to replicate in well fed cells. 🦠 😋
Even though immune suppression, high blood pressure, and chronic disease in general does predispose to worse outcomes, a virulent virus by definition can make a healthy person sick or even kill them.
Read 7 tweets
29 Sep
Interesting B.1.1.1.0 sub-lineage, short PANGO name: "L.3" uploaded to @GISAID from Nigeria by @WHO pandemic hub leader, Dr. @Chikwe_I, & co-authors. It has Delta-convergent S mutations L452R & P681H.. plus S98F, and D614G, of course.. Accession: EPI_ISL_4578066
I've been keeping my eyes peeled for anything non-Delta that might begin to show up. . so far not much "new" out there.. we need more non-Delta subsampled / enriched trees!
If you search @GISAID for all complete/ high coverage SARS2 sequences collected globally since Sept 15, 2021, the only non-Delta lineages that show up are: B.1, B.1.1.519, B.1.1.7, B.1.361, B.1.429, B.1.526, B.1.621, B.1.637, L.3, P.1, P.1.11, P.1.2, P.1.4, P.1.7, & Q.3
Read 5 tweets
24 Sep
Clickbait Variant Porn: R.1 has not been detected in the USA since mid-July...Most recent collection date for any R.1 sample in USA was July 16, 2021 in Kentucky. EPI_ISL_4172126
Here's the receipts.. So what happened? On Sept 14th, someone finally got around to submitting a sequence from the July 16 sample.. Is the SF Chronicle hard up for Clorox ad dollars?
R.1 doesn't even have that many Spike mutations! Aside from good ol' D614G, it's just del H69-V70, I100K, F342L, T716I, K1181N. This is nothing like Delta. CHILL THE EFF OUT, @sfchronicle!
Read 4 tweets
23 Sep
The Wild West situation with how coronavirus (and other microbial pathogen) genome sequence data are acquired, shared and monetized is in desperate need of professional #bioethicists & open, transparent debate.
Currently patients are not told their tests are being flipped around and turned into viral sequence data. Though it makes sense in certain setting, I disagree with this approach in terms of its long term sustainability…
Microbial pathogen genome sequence data are inherently valuable when rapidly generated & shared after a sample is collected from a patient.
Read 5 tweets

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