HKer. RNA Virologist working on nidovirus/immune system interactions. Insomniac. Life before death. Journey before destination. 一个健康的社會不該只有一種聲音. 解散警隊. ★ she/佢 ★
it's called a cutoff, you colonial dipshit. every cycle you double your primer-matching DNA. if after fourty repeats of this you have still not detected viral DNA (here reverse-transcribed from RNA first), it's generally agreed upon your viral loads see too low to be infectious.
none of this is fucking true, this is a bog-standard BA.2 Omicron lineage (multiple sequences up on GISAID). as has been noted to death by many people incl. myself, this death rate is 100% a factor of a dismal elderly vax rate (<40% in 80+, <15% in RCHEs).
The entire planet needs to be paying attention to Hong Kong. Catastrophic loss of life is underway, with an unknown BA 2 variant emerging out of here. 🚨🚨🚨🚨🚨
too many people on here have either forgotten what a
#COVID19
ward looked like in 2020 or just flat-out never seen one & good lord does it *EVER* show.
once again. if i have *any* choice in the matter i want my primary immunity to be via vaccination. every time. no matter the virus, age, complication rate from the virus at that age.
if there's a vaccine for it i'm taking it.
as a virologist, if i have the choice of getting immunity from a virus via infection, or vaccination that is available to me, i'm picking vaccination. every time. no matter what the virus.
to the various people who took one look at that one particular paper & somehow came to the conclusion that Omicron doesn't induce immunity against itsself, what do you think caused the BA1/BA2 waves to stop growing, magic elves?
extremely mild take: cervical cancer is, almost entirely, now a vaccine-preventable disease. if you are arguing against HPV vaccination, you are quite plainly arguing for more cancer.
with all due respect this is simply not even remotely true.
even if VE against symptoms is indeed reduced saying the vaccine is *useless* after 6-8 months is just factually incorrect.
"huh, i wonder what could explain East Asia's success w/keeping COVID19 contained? could it be robust, well-funded public health systems, many which were recently battle-tested on SARS or MERS?
nah, it's got to be random mystery genetic factors! somehow!!!"
quick glance at B.1.640.2 before anyone asks me about it: it's basically B.1.1.7 w/a large Spike NTD deletion.
i see no reason to expect this to have a fitness advantage over Delta *or* Omicron. meh.
again, 1-2 week incubation period & it takes generally another 1-2 weeks for you to hit ICU, so the deaths we are seeing now are from cases around the New Year, which would've been pre-vaccination.
i feel like this point is being massively understated inexplicably.
this is some of the worst messaging i have *EVER* seen in my life. the tweet literally contradicts itsself; how is a non-specialist supposed to make *ANY* sense of shit like this?!?
Right now, there’s not enough data to support getting an mRNA
#COVID19
vaccine (COMIRNATY/Pfizer-BioNTech or Moderna) booster after getting Johnson & Johnson’s (J&J) vaccine.
However, people who received J&J will probably need a booster dose.
More: .
i really do not understand the sheer amount of surprise from so many that widespread reinfections are possible every year or so. like, the other 4 HCoVs do so via antigenic drift periodically so why would *this* HCoV be any different?
the extent to which people seem to have just fucking *completely* memory-holed the horrors of 2020 is genuinely mystifying. & horrifying in its own right.
i think a lot of people are misunderstanding the mechanism behind "shift to endemicity" in a CoV.
it's not at all due to the *virus*. yes, endemic HCoVs have certain mutations (such as a preference for closed RBDs on Spike where the CTD is the RBD) but those are from...
take it from someone living in a place that went from (relatively) free to police state in *three years*: this is how fast it happens.
fight. now. b/c they're not stopping otherwise, & they sure as hell aren't going to slow down on their own.
Roe V. Wade could represent a tidal shift in American society
This was so unthinkably impossible to happen that nothing should be dismissed or underestimated moving forward
The speed of the collapse is bewildering
@dieworkwear
scarf dude is just jealous he will never look this cool:
(seriously tho really curious on your thoughts on scarves; even as a woman i think that scarf style wouldn't be too different between genders or am i wrong?).
okay, here we go. so as i've said numerous times, DEFUSE could not have given us SARSCoV2 b/c:
1) there is no evidence that WIV had a viable progenitor sequence (something very clearly stated in the ODNI report)
2) it was not funded, i.e. the grant proposal went nowhere
i fucking swear, trying to set the record straight wrt the massive churn of terrible
#SARSCoV2
papers that now are increasingly hitting the terrible
#SARSCoV2
news cycle & inciting panic is increasingly feeling like trying to bail out an ocean liner w/a teaspoon.
so tired of seeing "we're back to March 2020" takes. not with this level of population immunity, fuck no.
like god fucking damnit you can be terrified while still having a grip on reality how is this so difficult.
hoo boy.
this is not a good paper at all. it pains greatly me to have to debunk claims made by a former colleague whom i respected a lot, but... yeah. here we go.
Police in Central China's Wuhan arrested 8 people spreading rumors about local outbreak of unidentifiable
#pneumonia
. Previous online posts said it was SARS.
folks there is too little hospitalization data for Omicron, let alone data that has vaccination status, that it is literally impossible to empirically compute a VE against hospitalization for it at this moment in time.
can y'all please fucking stop until we have that data???
anyone trying to throw the words "vaccine escape" around has to explain to me how a non-integrating virus incapable of nuclear latency is supposed to escape a polyclonal *ADAPTIVE* immune response or shut the fuck up.
it's fucking lineage C.37, so L452Q & F490S on a D614G Spike (plus usual NTD & nsp3/4/6 crap).
i know NYpost is total garbage but this is journalistic malpractise of the highest grade.
(also nothing at P681 or even anywhere near FCS for that matter so i'm not even blinking).
it is 2021, 2 years into this pandemic, we've known about HCoVs since 1965 OH & WE HAVE YEARLY FLU SEASONS.
HOW HAS *ANTIGENIC DRIFT* BECOME THE LATEST CONCEPT IN IMMUNOLOGY THAT WE ALL COLLECTIVELY FORGET ANOUT THEN PANIC ABOUT AS WE REDISCOVER IT?!?!?!?!?!?!?!?!?!?!?!?!?!?!?
"Herd immunity may not even be possible to reach with this virus".
'By the time you get enough people vaccinated, you get a new variant that arises that escapes previous immunity', says clinical epidemiologist Dr Deepti Gurdasani.
#COVID19
:
i know i'm a bit late to the party, but to anyone who thinks
#SARSCoV2
FCS is engineered, if you were actually engineering in an FCS:
1) you'd use something you've seen before, say RRSRR in HKU1. turns out this particular one *does* show up in some strains of FIPV but it's rare.
so uhh... genetic info has been released on the Oct. 2022 H5N1 outbreak in farmed mink & it's uhh... let's just say nature is trying a little too hard to replicate Fouchier's H5N1 study:
like, we need to have vaccines for this thing at the ready.
*puts on hard hat, respirator, asbestos gloves* (hey i haven't used these in awhile!)
okay. i'm seeing the same claims on my TL over & over that quite frankly, make no sense. & now they're starting to broken-telephone into each other so:
my thoughts on vaccine schedule.
the speed & extent of this pivot is just insane. from massively overstating the dangers of this to most (as long as they are vaccinated) to almost going full GBD in literally weeks.
almost as if much of this never was about public health to start.
#Omicron
is not scary, and about 99% of those infected with Omicron can fully recover within 7-10 days, China's top respiratory disease expert Zhong Nanshan said at a national academic video conference of respiratory diseases on Friday.
at this point there's a consistent clear picture that Omicron has massively decreased fusogenicity when taking the TMPRSS2-dependent path & also that infectivity via that route is correlated w/LRT pathogenicity.
In sharp contrast, Omicron is less fusogenic (left panel) and its spike is faintly cleaved (right panel). Our data suggest that the efficacy of spike protein cleavage, fusogenicity and pathogenicity are well correlated each other. 3/5
*really* wish people would categorize any potential intrinsic severity reductions in Omicron against D614G Wuhan-Hu-1 & not Delta.
like yeah, it's likely *somewhat* less severe than Delta. that's not a high bar, Delta is *horrifying*.
so a bunch of people have asked me about my thoughts on AY.4.2, so here we go.
it's Delta plus a mutation in the second NTD loop.
anyhow, let's go thru the usual...
Not looking good for the hope that delta + S:Y145H is just a founder effect or fluctuation, its prevalence continues to increase in the UK, now up to ~8%. Only a matter of time before this hits the US and rest of the globe
scalding take: highly vaccinated countries are currently in the process of undergoing a transition to endemicity, perhaps in some like the UK a bit more rapidly than i think they should, but in the end people *will* need to update their mental model of a
#SARSCoV2
infection.
where the hell did public health messaging go so wrong that it seems a nontrivial amount of the public believes that "vaccine-resistant" viruses are a thing you *can* have happen??? (it's not. at all).
when people tell me that
#SARSCoV2
is unlike other HCoVs "since there's no indication that it will stop evolving & changing in fitness"... what the bloody hell do you think the other 4 HCoVs in circulation do?!? just exist in perfectly preserved evolutionary stasis for centuries?
literally *all* of these viruses w/the exception of HCV become permanently *LATENT* in cells & actively mess w/both anti-apoptopic factors & the cell cycle in order to maintain persistence. this can go awry in the predictable manner.
#SARSCoV2
does not establish latency.
Some viruses are cancer-causing ("oncogenic"). HPV and anogenital and head and neck cancers, Hepatitis B and C viruses and liver cancer; Epstein Barr virus and lymphomas etc…
I'd be surprised if SARS-CoV-2 doesn't join the list.
good lord, the comments to this are... christ.
anyway: yes, for healthy young *vaccinated* adults, reinfections from antigenically-drifted variants will, on average, be less severe. we've already gone from "the entire hospital is a
#COVID19
ward" to flu-level morbidity ffs.
Scientists say that for most healthy adults, COVID-19 reinfections should get easier to deal with as the immune system gains repeat training on how to handle the pathogen.
astounding. certainly would explain everything but now makes me wonder how this couldn't've been caught *before* the multitude of breathless, panicked press releases about "waning immunity" & whatnot.
You’ve probably seen reports from Israel on low vaccine effectiveness in this wave. Is it because of Delta? Waning immunity? We think the reason is mostly that we got the denominator wrong.
my suspicion: most of this is CureVac using uridine instead of m1Ψ in the mRNA itsself... you're likely to accidentally hit RIG-I/MDA5 before the ribosome that way & wind up w/translational shutdown via phosphorylation of eIF2α after induction of ISGs...
If anybody is interested in learning more about the reverse transcription of HIV this video explains it: Covid has also been found to reverse transcribe into genes: what it means is Covid should be considered a retrovirus:
the sheer number of people desperate for BA.2 Omicron, or BA.2 Omicron+whatever to be the Andromeda Strain instead of just the boring, obvious answer of VACCINATION IS GODDAMN KEY is absolutely *infuriating*.
Tom. please explain to me, mechanistically, how this is supposed to happen even in theory or stop bloody saying it.
"vaccine escape" is not a bloody thing.
1) The emergence of future variants that can escape vaccine-induced immunity. Delta may not be the worst variant the virus deals us. Continued uncontrolled spread around the world makes this scenario more likely.
Updated data: The COVID death rate among unvaccinated people is 25-times higher than among vaccinated people who received a booster.
This is the latest age-standardized data from Chile.
[From this post with
@redouad
: ]
Quite interesting. Figure 6D 👀
Omicron appears to have switched cell entry preference to endosomal fusion (rather than ACE2+TMPRSS2 mediated cell surface fusion like previous variants, incl. the well adapted Delta).
Pre-print from Glasgow Uni:
hot take: we should be teaching people research skills & critical thinking skills so they *can* do their own research w/o easily falling prey to misinformation/disinformation vendors.
dear clowns in my menchies demanding that we specifically, somehow, eliminate this virus, while it's still in pandemic phase, try & recall that we have a sterilizing vaccine for polio, have been running an elimination campaign for decades, it's not airborne & we're *almost* done.
...selection pressure *once in the endemic state*.
what causes the shift is the virus going from antigenically novel to us having prior immunity.
@dylanhmorris
wrote a great article on this that is *highly* worth a read:
just saw some in vitro Omicron cell entry data & like.
it's like looking down a microscope at a cell culture & seeing a thousand dancing hamsters.
fairly convinced we've reached the stage of pandemic where this virus is just openly trolling us.
it is deeply morbidly hilarious to me that there are a zillion "look the novel β-CoV emerged in same city as a big CoV lab" takes & yet nobody points out the novel β-CoV emerged in the city where the "banned" wildlife trade was quietly allowed, then turned into a hub for it.
With all due respect, please don't do this. It's incredibly confusing public messaging when people see different estimates of efficacy each week from data that we just can't infer these from. PHE will analyse the full data & produce robust estimates. We need to be sure about this
brief break from China protests to highlight: if you asked me what scares me the most right now virologically, it's H5N1. no contest.
people need to follow UK's lead & have vaccines for it on the ready. they *WILL* be necessary, & far sooner than some people realize.
genuine question, but is there really any motivation for US virologists to, like, give a fuck at this point? your warnings get ignored, repeatedly, & then when the scenario forecasted happens, the most mendacious midwits blame you for *causing* it.
it's just that b/c none of them are novel at an age where they are *likely* to cause disease do we consider them mostly harmless.
*this* is the projected final state of
#SARSCoV2
.
importantly, it'll only happen once we *all* (12+, at least) have immune memory to it. not sooner.
like maybe, JUST MAYBE, we could agree to practise due diligence BEFORE giving papers airtime? especially when this can influence vaccine allocation for the world?!?
AT LEAST READ THE FUCKING THINGS & THINK ABOUT THEM BEFORE GIVING THEM AIRTIME. IS THAT *REALLY* TOO MUCH TO ASK?
It's not like Harlan Crow is some apolitical pal of Thomas.
He CONSTANTLY has cases before the court. He funds groups that argue for outcomes that benefit him.
One group, CCI, filed 8 briefs before the Court. Thomas sided with Crow in all 8 cases.
also you are confusing primer sets (N1, targeting a sequence in
#SARSCoV2
nucleocapsid & N3, targeting a part of the coronavirus replicase that is conserved between all β-CoVs that we have sequences for) w/the genes they target.
well *this* is a deeply irresponsible shit paper.
shows escape from NTD nAbs which also put RBDs in the "up" position which might improve infectivity. somehow goes on to claim that loss of serum neutralization is the same as vaccine resistance (it's not).
in short, crap.
y'know, it's honestly pretty hilarious having a bunch of iSage-adjacent folks up in my menchies calling me a
#COVID19
"minimizer", like, uh, have y'all actually read like any of my tweets? like at all???
i am once again watching Western countries snatching defeat from the jaws of victory moments away from the finish line, a point which they are immensely privileged to be at, while in large parts of the world deaths from
#COVID19
are at record highs & honestly i feel so defeated.
just saw the most astoundingly hilarious take: "Jesus wasn't vaccinated!" & it's like.
look Jerry unlike Jesus i can't be resurrected 3 days after i die in the ICU from respiratory failure so i fail to see the relevance here.
look if you're going to tweet alarmist word salad, could you at least be consistent within tweets? (H78Y is in orf3a, *not* S). anyway i checked out the paper cited, it's small magnitude of effects in VeroE6 cells for various orf3a mutations, ***NONE OF WHICH ARE H78Y***.
According to this study, ORF3A protein is associated with COVID-19s immune evasive capacities, given that this H78Y mutation is on this spike protein, we must monitor closely the impact to vaccines and prior BA 1 infection.
to anyone that wonders why i'm falling apart lately: how do you not when your home is literally becoming unrecognizable before your very eyes, you can't do anything about it w/o risking jail & the people responsible actively want to rewrite our history on top of that?
seeing a lot of comments to the effect of "well EFD didn't *exactly* say
#COVID19
is airborne HIV..." (he just QTed someone saying that, heavily implied it & linked to no studies) & like.
look, i generally steelman people's arguments on principle but this isn't a debate.
if this were true (it's not), then why does "boostering every year endlessly for flu" not "deplete our pool of naive T cells"?
come on people, think more.
fuck's sake, i'm absolutely incensed w/the Israeli MoH now. like, they're claiming results that have powerful implications on how a lot of countries might decide vaccine distribution, are known to use dodgy-as-fuck methods & so *need* to release literally all the data they have.
i'm at such a loss for words i can't even think of which swearwords to use. one in THREE people??? AIDS?!? do you have *ANY* idea how abjectly horrifying that would look like in society if that were even *REMOTELY* true?
this is absolutely insulting to so many people.
the one thing about this that baffles me a bit is the lower lung TCID50s for *Delta*, which is known to cause *greater* lung pathology in the unvaccinated in vivo.
Omicron replicates much better than Delta in bronchus, but not in lung, explaning why Omicron is so transmissible. Excellent ex vivo studies from Michael Chan
@HKU_SPH
and John Nicholls in Department of Pathology
@hkumed