1/10 This shouldn't even be a debate. Who could argue against this? Knowledge is the ultimate public good, & to restrict access to scientific papers to those at academic institutions w/subscriptions to journals is a crime.
2/10 Out-of-control, continually strengthening copyright & patent laws are an economic weapon wielded by the rich against the poor and by enormous, monopolistic firms against small firms. This is a major driver of inequality that receives scant attention. cepr.net/technology-pat…
3/10 The alleged justification for strong IP laws is that they incentivize & facilitate innovation. But as @DeanBaker13 points out in his indispensable (& free) book Rigged, in their current form, IP protections greatly impede innovation. See Ch. 5 deanbaker.net/books/rigged.h…
4/10 How much has medical progress been stifled by the patent-driven secrecy under which private research is cloaked? And by the gross distortions that drive companies to pursue expensive, patentable treatments & ignore cheap, often greatly superior treatments? (Rigged, Ch. 5)
5/10 Apart from the baleful economic & scientific effects of our IP laws, it's worth considering some more indirect effects these laws have on public health. Patent monopolies unquestionable cause corruption in the pharmaceutical industry. @DeanBaker13 on the opioid crisis:
6/10 Understandably, the rampant corruptions & recurrent scandals in the pharma industry have led to public distrust. Skepticism about Big Pharma claims is of course justified, but it has led some to reject anything connected to pharma, including vaccines. statnews.com/2019/02/26/ant…
7/10 The anti-vaccine movement's claims are of course absurd & tremendously harmful to public health, but their outright rejection of all scientific evidence largely stems from the never-ending flow of pharma-industry scandals, which are a predictable result of patent monopolies.
8/10 There's been much discussion of how to combat misinformation during the pandemic, but little talk of one of the root causes: patent-monopolies. Public financing of drug research could eliminate patent monopolies & allow drugs to be sold at generic, free-market prices.
9/10 Until we reform our rotten, corrupt, patent-monopoly-driven pharma industry, public skepticism of even impeccable medical research will remain, and such distrust will continue to be exploited by charlatans & mountebanks peddling noxious nonsense, w/grave public consequences.
10/10 Chart in tweet #8 is from chapter 5 of @DeanBaker13's book 'Rigged.' The book is freely available in digital form, & an awesome intro into some of the most pressing economic issues of our time. Definitely give Ch. 5 a read if nothing else. deanbaker.net/books/rigged.h…
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Incredible how quickly @yunlong_cao & co provide us w/info on the latest emerging SARS-CoV-2 variants.
Already, we have great data on BA.3.2 (the divergent saltation lineage detected in South Africa & the Netherlands & NB.1.8.1, an emerging contender for global dominance. 1/9
BA.3.2 is a clear outlier on the antigenic cartography map—as expected given the enormous differences between its spike protein & every other circulating variant. 2/9
It's unsurprising, therefore, that BA.3.2 evades antibodies from human sera more effectively than any other variant, though the degree of its superiority is striking. 3/9 biorxiv.org/content/10.110…
About 1 month after this monster BQ.1.1 appeared, an even more extreme sequence has shown up in Alberta. Like the BQ, it has 50 private spike mutations, but it also has >40 AA mutations elsewhere in the genome. 1/6
They include the full panoply of NSP3, NSP12, & N muts I've written about previously. ORF1a:S4398L is the most common mutation in the 4395-4398 region, this has ∆S4398, a rarity also seen in a few other extremely divergent seqs w/this constellation. 2/6
In a theme that's become familiar, it's added two spike NTD glycans, N30 (via F32S) and N155 (via S155N+F157S).
Another chronic-infection leitmotif (first noted by @SolidEvidence): reversions to common or consensus residues in related Bat-CoVs, including SARS-1. 3/6
A fascinating SARS-CoV-2 sequence was recently uploaded—collected from a dog in Kazakhstan in July 2022.
Usher places the seq 1 nuc mut from the Wuhan ref seq—C21846T/S:T95I—i.e. pre-D614G. Could this seq somehow have a close connection to the first days of the pandemic?
1/19
Of the sequences near this one on the tree, all are low-quality & clearly bad BA.1 or Delta sequences. The only genuine one is from the UK, collected April 2020. So it's likely even S:T95I was not inherited.
This sequence has several fascinating aspects. 2/
(This all assumes the sequence is accurate and that C241T & C14408T (ORF1b:P314L) are genuinely absent. Its mutational characteristics make me certain this is a good sequence, though it's not impossible there's dropout not indicated hiding C241T and/or C14408T.) 3/
Do you remember BA.3—the weakling cousin of BA.1 & BA.2 that seemed to take the worst from each & had weaker ACE2 binding than even the ancestral Wuhan Virus?
After 3 years, BA.3 is back.
And it is transmitting.
Who saw this coming?
1/13
While the full extent of the new BA.3’s spread is not known, it’s been detected in 2 different South African regions through regular (not targeted) surveillance by @Dikeled61970012, @Tuliodna, & the invaluable South African virology community.
2/13 github.com/cov-lineages/p…
After nearly 3 years of intrahost evolution in a chronically infected person, the new BA.3 is almost unrecognizable. It has ~41 spike AA substitutions (4 of which are 2-nuc muts) to go with 14 AA deletions (∆136-147+∆243-244). We’ve seen nothing like this since 2023.
3/13
Fantastic review on chronic SARS-CoV-2 infections by virological superstars Richard Neher & Alex Sigal in Nature Microbiology. I’ll do a short overview, outline a couple minor quibbles, & defend the honor of ORF9b w/some stats & 3 striking sequences from the past week.
1/64
First, let me say that this is well-written, extremely readable, and accessible to non-experts, so you should go read the full paper yourself, if you can find a way to access it. (Just realized it’s paywalled, ugh.) 2/64nature.com/articles/s4157…
Neher & Sigal focus on the 2 most important aspects of SARS-CoV-2 persistence: its relationship to Long Covid (including increased risk of adverse health events) & its vital importance to the evolution of SARS-CoV-2 variants. I’ll focus on the evolutionary aspects.
3/64