How to get URL link on X (Twitter) App
https://twitter.com/siamosolocani/status/1813483639306346530Most spike mutations affect ACE2 binding similarly in BA.2, XBB.1.5, & JN.1—e.g., Y453F confers a large incr in ACE2 affinity in all—so the XBB.1.5 deep mutational scanning info from @bdadonaite & @jbloom_lab is still invaluable. But Q493E is different. 2/
https://x.com/jbloom_lab/status/1791652758141141238
https://twitter.com/LongDesertTrain/status/1808468615991091601When I Googled that name, a clear AI hallucination dutifully copied & pasted by "journalists," I accidentally stumbled on another.
https://x.com/LongDesertTrain/status/1781121832155824138@suprion_verlag @dfocosi @yunlong_cao @RajlabN @BenjMurrell @SystemsVirology @SimonLoriereLab @EricTopol @TRyanGregory @tylernstarr @JPWeiland @siamosolocani @CorneliusRoemer Then, after such a variant begins circulating, it begins to pick up mutations, primarily in the spike protein, which evade antibodies that are widespread in the population. The specific mutations vary somewhat with each new variant, but there's a lot of common ground as well...
https://twitter.com/siamosolocani/status/1802658772025766376It can be a difficult to decipher the meaning of these graphs if you don't have an encyclopedic knowledge of the latest variants—which I think only @siamosolocani possesses—so I tried to add some context to Ben's graph, which I'll explain below. 2/15
https://twitter.com/JosetteSchoenma/status/1785353182144610773Q493E involves the rarest of all nucleotide mutations, C->G, and occurs at a key residue that we've seen very little action from of late. 493 mutations, however, are common in the Cryptics, usually Q493K I believe. (@SolidEvidence can correct me if I'm wrong on that). 2/8
https://twitter.com/LongDesertTrain/status/1727852946291892367
https://twitter.com/TheMenacheryLab/status/1770959155093705059They proved that the N:1-25 region, esp. the ITFG AA motif from N:15-18, is the essential element in N's ability to suppress the formation of stress granules (SGs) in cells, which capture & disable long viral RNAs & help organizing innate antiviral immune responses. 2/6
https://twitter.com/LongDesertTrain/status/1775807031649198306BN.1.3 is a BA.2.75 descendant that emerged in Aug 2022, but much older variants still exist.
https://twitter.com/LabWaggoner/status/1769809271615570283"High receptor-binding affinity virus particles exhibited increased resistance towards IFN-I-mediated inhibition of viral entry & replication... eventually leading to impaired T cell immunity and prolonged virus load."
https://twitter.com/dfocosi/status/1767841861425643957In some ways, BA.2.87.1 is reminiscent of BJ.1, an obscure BA.2 chronic-infection lineage that emerged in India but hardly grew at all. It vanished quickly, but >75% of its genome lived on in XBB (a BJ.1/BA.2.75 recombinant) & went on to dominate globally. 2/10 image: @PeacockFlu
https://twitter.com/MIID_alex/status/1763392811423141914In case you forget what BA.2.87.1 is, here's a previous thread on it. BA.2.87.1 has not spread at all since then, so it is not a major concern at the moment.
https://twitter.com/LongDesertTrain/status/1753195705638760582
https://twitter.com/SolidEvidence/status/1762255568117387576My extremely amateur attempt to align these Cryptics with some SARS-CoV-2-like Clade 1a sarbecoviruses and SARS-CoV-1-like Clade 1b sarbecos. 2/4
https://twitter.com/SolidEvidence/status/1756467929242022203I've analyzed 1000's of chronic-infection sequences, yet this Cryptic has 9 mutations I've never seen in any of those: G413R, T415E, Y421F, N440T, V445N, G446K, Y449T, K462Q, and G482T—*in the RBD alone.* Two others I've only seen once. 2/22
https://twitter.com/LongDesertTrain/status/1752320762537525489
https://twitter.com/Tuliodna/status/1752996491948327126Will this new BA.2 sputter and disappear without making much impact? We've seen many chronic-infection BA.2 saltation variants do exactly that: BA.2.83, DD.1, BP.1, BA.2.10.4, + multiple undesignated ones (exceptionally divergent BA.2s in Chile & Ukraine come to mind). 2/