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30th November 2021, 03:44 PM | #481 |
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The whole problem with the world is that fools and fanatics are always so certain of themselves, and wiser people so full of doubts.Bertrand Russell Zooterkin is correct Darat Nerd! Hokulele Join the JREF Folders ! Team 13232 Ezekiel 23:20 |
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30th November 2021, 04:04 PM | #482 |
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I think you might be overstating things. First of all, we should probably wait and see, but even if the vaccines are less effective against the new variant it doesn’t mean that they will do nothing.
It seems to me the problem has been not getting them around the world. If you don’t do that, THEN you have more chance of the virus mutating to escape the virus. Surely the smartest thing to do is to keep vaccinating until we know more and not rely on treating the illness or using even less well-attested medication. |
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30th November 2021, 04:24 PM | #483 |
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Our Scottish outbreak of omicron seems associated with a party (with no identifiable African link). So certainly highly transmissible, and in country transmission occurring in Scotland. Most of the infected were young and double vaccinated, including one person who was both double vaccinated and had been recently (> 30 days before) infected with delta. So it seems to be transmissible despite vaccination and prior infection with delta. All our outbreak were young so low risk for serious disease anyway, but no cases of serious illness. This does not mean in an unvaccinated person it is less virulent than delta or alpha, it just means if you are young (<40yr) and doubly vaccinated your risk of serious illness with omicron is not high.
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30th November 2021, 04:27 PM | #484 |
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30th November 2021, 04:50 PM | #485 |
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Gee, it's almost like I didn't just post the link to BioNTech saying just that their vaccine is very likely to continue to protect against severe disease.
And if you read my post carefully, you'll see it starts with an "if". That should signify that I'm discussing what happens if that comes to pass. I'm beginning to see this "vaccinate everyone, everywhere" as pure red herring. We aren't vaccinating under 5s, so there's 10% of the population for starters. Add to that the 10% absolute refuseniks, and then you have the issue of vaccinating people in Afghanistan, Syria, Yemen, Libya, North Korea and Turkmenstan, and that's before you tell me how you're going to deliver vaccines to the >90% of Africans who haven't been vaccinated. We need to face up to the fact that vaccination isn't actually an endgame. They're great at stopping deaths, but they're not the nail in Covid's coffin. Obviously, in places where vaccines are available. Sure - I'm not a doctor or scientist and I'll take your two opinions as much better informed than me! |
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30th November 2021, 05:22 PM | #486 |
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proofreading function of nsp14
ExoN (nsp14) has the function of checking for mistakes as RNA is being polymerized. Suppose that the polymerase makes a mistake and puts an A (adenosine) where (by the Watson-Crick rules) it is supposed to put a G. The function of the exonuclease is to remove the A by hydrolysis, then step aside and let the polymerase put a G in and then keep adding more nucleotides. The polymerase is the writer of the growing strand, and the exonuclease (ExoN; nsp14) is the proofreader.
An exonuclease act at one end of a nucleic acid, using water to break (hydrolyze) a bond. Most RNA viruses do not have this enzyme, but coronaviruses do. A number of antiviral compounds are analogs of nucleosides, and they work in slightly different ways stop RNA polymerization or to make it error-prone. Some are ineffective against coronaviruses. At least one analog (Ribavirin) is chopped back off by nsp14. One way that a nucleoside analog might evade being removed by nsp14 is if the polymerase adds another base first, thus shielding the analog from nsp14. As long as the now internalized analog can still disrupt RNA replication in some way, it will be successful. I had hoped that Remdesivir might do so. See this link. Unfortunately, molnupiravir's ability to fight this disease is not looking as good, as a previous comment of mine indicated. That is why I was thinking about how one might inhibit this exonuclease and combine it with a nucleoside analog. To the best of my knowledge, there is no human counterpart to nsp14 most RNA polymerases do not proofread, unlike DNA polymerases. "The exoribonuclease function of ExoN 3ʹ–5ʹ is a central player in a variety of essential life‐cycle processes for coronaviruses and has made many previously active antiviral compounds ineffective against CoVs. ExoN is a logical therapeutic target for new technologies in genomics." link |
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30th November 2021, 09:11 PM | #487 |
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Doc in Israel becomes their third case of omicron and transmitted it to another to make the fourth case.
What a mess! Came back from a conference in London. With a mask and 3 #Pfizer vaccines I managed to get #Omicron (case #3 in Israel). https://twitter.com/maor_elad/status...00588314791947 Neg PCR test before leaving and upon return to Israel. Went to work and infected another doc. They are both doing well so far. -CNN story. |
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30th November 2021, 09:41 PM | #488 |
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Antimicrobial Drugs Advisory Committee Meeting Briefing Document
Molnupiravir https://www.fda.gov/media/154421/download Efficacy against hospitalization 30%, down from earlier 50% estimate. However, only 1 death v 9 in the placebo grp. https://www.statnews.com/2021/11/26/...ks-covid-pill/ |
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1st December 2021, 12:58 AM | #489 |
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1st December 2021, 01:35 AM | #490 |
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Interesting thread here on Omicron from Kristian Andersen who has returned to Twitter after being hounded off it by the lab leak fanatics.
https://twitter.com/k_g_andersen/sta...629821442?s=21 |
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1st December 2021, 03:13 AM | #491 |
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The whole problem with the world is that fools and fanatics are always so certain of themselves, and wiser people so full of doubts.Bertrand Russell Zooterkin is correct Darat Nerd! Hokulele Join the JREF Folders ! Team 13232 Ezekiel 23:20 |
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1st December 2021, 09:58 AM | #492 |
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May as well have: https://www.ft.com/content/27def1b9-...6-72e432e0838f
Quote:
The only they could possibly have data from is RSA, and given the close relationship of the two countries, I'd say it's possible they have an early look, but I'd think it's very soon to know the levels of protection they're claiming. Still, encouraging. Those T cells look to be the key. |
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1st December 2021, 02:36 PM | #493 |
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1st December 2021, 04:39 PM | #494 |
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I'm not sanguine about Omicron. The damned thing continues to grow like Kudzu with an exponential 4x/week if not higher in SA. Further the fraction of tests coming back positive is now over 16% more than doubling in a week. This indicates the actual Covid-19 incidence is growing even faster than the cases indicate. It also means they aren't just expanding testing in search of Omicron. The growth rate is clearly higher than any previous wave there including when Delta hit. And this is with a majority of the population previously infected and a quarter vaccinated.
As for virulence, jury's still out. Hospitalizations are up but the case ramp is so fast it's hard to model. Generally, about 5% of cases in most of the West are hospitalized. However, the age distribution in SA skews much younger so I would expect maybe around 3%. What I don't have is a distribution of time of first symptoms/positive test to hospitalization. I believe the median is a bit over 1 week. But I need a distribution day by day to model it. Could be anywhere from milder to just as bad as Delta. |
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1st December 2021, 05:16 PM | #495 |
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Yep. We just don’t know. I thought one of the interesting theories that was raised by Andersen in that thread is that it is possibly caused by spillback (or reverse zoonosis from humans to animals) then a subsequent spilllover again. This kind of dynamic would be really worrying as it would suggest a lot of possibility for subsequent spillovers that are far removed from what our vaccines and other meds can handle. Too soon to tell but that would be perhaps the worst case scenario.
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1st December 2021, 05:17 PM | #496 |
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Pre-omicron, but numbers from Singapore show quite starkly that one you get above 90% vaccination, you can return to normal.
As long as omicron doesn't bust the vaccines, things are looking up! https://www.stuff.co.nz/world/asia/3...gy-is-on-track |
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1st December 2021, 05:30 PM | #497 |
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1st December 2021, 09:28 PM | #498 |
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Effectiveness and durability of protection against future SARS-CoV-2 infection conferred by COVID-19 vaccination and previous infection; findings from the UK SIREN prospective cohort study of healthcare workers March 2020 to September 2021
Preprint: https://www.medrxiv.org/content/10.1....29.21267006v1
Quote:
The surprise in this study is that prior infection confers greater immunity than either 1 or 2 dose vaccination. Note that boosters have not been measured. Table 2. Prior infection plus either one or two vaccine doses provided the best protection. Table 3. |
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2nd December 2021, 12:20 AM | #499 |
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FTFY A similar development can be seen in Cuba where everybody is also still masking up - and children are getting vaccinated, three jabs for everybody, and and vaccines against Omicron are being developed. Daily new confirmed COVID-19 cases per million people: Cuba, Singapore Daily new confirmed COVID-19 deaths per million people: Cuba, Singapore Share of people vaccinated against COVID-19: Cuba, Singapore Population density per km2 should be taken into consideration: Singapore 8,358, Cuba 106. |
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/dann "Stupidity renders itself invisible by assuming very large proportions. Completely unreasonable claims are irrefutable. Ni-en-leh pointed out that a philosopher might get into trouble by claiming that two times two makes five, but he does not risk much by claiming that two times two makes shoe polish." B. Brecht "The abolition of religion as the illusory happiness of the people is required for their real happiness. The demand to give up the illusion about its condition is the demand to give up a condition which needs illusions." K. Marx |
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2nd December 2021, 03:56 AM | #500 |
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SARS-CoV-2 sequences by variant, Nov 29, 2021 (Our World in Data)
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/dann "Stupidity renders itself invisible by assuming very large proportions. Completely unreasonable claims are irrefutable. Ni-en-leh pointed out that a philosopher might get into trouble by claiming that two times two makes five, but he does not risk much by claiming that two times two makes shoe polish." B. Brecht "The abolition of religion as the illusory happiness of the people is required for their real happiness. The demand to give up the illusion about its condition is the demand to give up a condition which needs illusions." K. Marx |
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2nd December 2021, 06:08 AM | #501 | |||
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Nice TWiV episode.
They criticize the punishing of South Africa for doing good work in sequencing the variant. They tend towards the idea that we should just not freak out, and just get vaccinated.
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2nd December 2021, 01:13 PM | #502 |
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SA case rates continue to roughly double every 3 days (over 4x growth per week). Same with positivity rate which is up to 22% today compared with 16% yesterday which means actual infections are growing even faster.
https://www.nicd.ac.za/latest-confir...december-2021/ Unbelievable. Also: https://twitter.com/jburnmurdoch/sta...80113487392769 NEW: today’s update from Gauteng, now on a log scale to better show current trajectories. Steepness of lines shows how much faster the growth in cases and positivity is now vs past waves, and hospital admissions are now steepening too as the acceleration in cases feeds through. And this indicating Omicron has 3 fold lower protection from prior infection: https://twitter.com/miamalan/status/1466460836143239179 |
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2nd December 2021, 03:03 PM | #503 |
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One bit of bright news - another treatment has been added to the armoury: https://www.aljazeera.com/news/2021/...gainst-omicron
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2nd December 2021, 03:27 PM | #504 |
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Yep. At the rate this bugger is growing there really isn't much time for the Vax makers to tune and make available targetted vaxxes.
So we can hope the current vaxxes have some efficacy. At least against hospitalization and death. I've found zero info on vax efficacy so far but if probably provides some benefit. In any case I'm ordering some N95s. I've been using kf94's so far but time to upgrade before the rush. Lots of treatment possibilities near and they may be the big thing if vaxxes turn out to be marginal. Merck, Pfizer, fluvoxamine, etc. may have their big day. Is sotrovimab an IV drug. Supposidly monoclonals may be effective against Omicron too. |
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2nd December 2021, 03:38 PM | #505 |
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I saw a comment by some scientist the other day that made a lot of sense.
The premise was that new vaccines will target the new spike strongly. If it mutates again, it might miss entirely, while vaccines that target the whole thing have a better chance all round. Still too early to know, and while opinion is divided, I see lots of scientists saying they should. We're just starting to take them off here. Sotrovimab is IV for 30 minutes, so they'll obviously choose who gets it. Pfizer's take-at-home pill sounds a better option right now. |
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2nd December 2021, 04:55 PM | #506 |
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More from South Africa - it looks like omicron is doing what P1 did to Manaus in Brazil: infecting everyone who'd already had Covid.
Early indications are: Previous infection offers minimal protection May be less severe High probability vaccines are working Spreads much faster https://www.theguardian.com/global-d...frican-experts |
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2nd December 2021, 06:20 PM | #507 |
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Guardian story is a bit out of date. 16% positivity rating was yesterday (Dec. 1) . Today it's 22%. Monday a week ago it was 1% per the article.
While there is published evidence prior infection is 3x less protective against Omicron, it's still around 60%. There is actually prepint data on this. Since most of Omicron's mutations are in the spike, I would expect vaccine immunity to be slightly harder hit than prior infection immunity. All depends on how lucky we are. Only data so far is against prior infection. I'm suspicious that the frequent statement "the vaccines are expected to provide protection against serious disease" is more just public messaging because Delta is the current killer and it might get some people to get themselves vaccinated. My guess is that vaxcines will provide some covid-19 immunity but somewhat lower than that of recovered cases because the vaccines are also targetting just the spike and that's the most mutated. Prior infection will likely target a broader range. Financial Times has a piece on it too. https://www.ft.com/content/df3738ab-...d-aa7eb75451a2 |
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2nd December 2021, 10:24 PM | #508 |
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Omicron is going to be a huge problem for China.
Expect more, not less supply chain issues. |
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3rd December 2021, 12:57 AM | #509 |
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Well... to poke at this just because I stumbled across a link to it, here's a link for some Minnesota numbers.
COVID-19 Vaccine Breakthrough Weekly Update It's some data, at least. Predictably, unvaccinated numbers are wildly higher across the board. Elsewhere, it seems that a Missouri DOH study requested by the Governor found that mask mandates were highly effective at reducing cases and even more effective at reducing deaths. So, what did the Republican Governor of Missouri do? Buried it, apparently. I'd comment more there, but those comments would likely be more suited to the US politics thread. |
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3rd December 2021, 02:09 AM | #510 |
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3rd December 2021, 04:56 AM | #511 |
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Don't think for one moment that "natural immunity" survives encounter with omicron. Natural immunity is very weak if it exists at all and at fraction of induced immunity. And any antibody that is targeted on non-spike proteins is wasted one, because it will not prevent cell infection at all. (At best it is race between infection and destruction of virus particle)
Reminder: That's why vaccines target dominantly spike protein. it has very small mutation space before it no longer can bind to human ADE2. Anyway, here's Derek Lowe's rundown on Omicron: Omicron Time ETA:
Quote:
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3rd December 2021, 10:27 AM | #512 |
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mask information from the Show Me State
"State health department data alone can’t explain the effectiveness, or lack thereof, of mask mandates, without a fuller analysis of vaccination rates, behavior and time. But the data does show that in three of the four jurisdictions – Kansas City, St. Louis and St. Louis County – per capita case rates for the pandemic are in the bottom quarter of 118 local health jurisdictions, and per capita deaths are in the bottom third." Missouri Independent.
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3rd December 2021, 10:53 AM | #513 |
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3rd December 2021, 06:32 PM | #514 |
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And people who are vaccinated. This story from Norway is mind boggling. OTOH, it's not inconsistent with the unbelievable case ramp in South Africa.
Party where everyone was vaccinated: Norway is seeing the world’s first omicron superspreader event after a party downtown Oslo last Friday. Of 120 healthy non-symptomatic fully vaccinated individuals with a negative test, two had recently returned from South Africa and turned out to be positive, omicron. https://twitter.com/GANyborg/status/1466875096212119556 Understatement of the day: Now some 80-90 of the 120 are PCR pos, 13 of these confirmed omicron, the rest waiting for sequencing results. Some of those infected w omicron were not at the party but present at the same restaurant that evening. Not looking good re transmissibility. Omicron is a slam dunk. Delta doesn't come close to doing this. Now's the time to hope that Omicron's virulence is very low and that vaccines provide some protection against severe disease. Because it's coming for everyone. Soon. Of course hope isn't a plan. Love this comment: "I really hate this graph!" https://twitter.com/rid1tweets/statu...28284445040645 |
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3rd December 2021, 06:59 PM | #515 |
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That's unreal. On those numbers, it must be close to the most-infectious virus ever known. As you say, world spread is a done deal.
I see the same thread contains this disturbing piece:
Quote:
While it's horror news for kids, it may gel with the "more infectious, less dangerous" theory, because it conforms to things like RSV. Interesting times... |
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3rd December 2021, 07:24 PM | #516 |
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3rd December 2021, 07:53 PM | #517 |
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Airborne. Big time. Two quarantined in rooms across the hall from each other with strong evidence of aerosol spread.
https://wwwnc.cdc.gov/eid/article/28/2/21-2422_article
Quote:
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3rd December 2021, 08:07 PM | #518 |
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I'll just re-post what I said four days ago:
We still have no data on whether the vaccine is offering protection against severe Covid, which I expect it to. Meanwhile, let's get those drugs into doctors' surgeries and pharmacies as a matter of huge urgency. Paxlovid is a simple oral medicine that can be taken at home. I'm going to source some through the internet as soon as they get on the market - it's going to take months for our clowns to catch up. Pretty sure the drug dogs won't be trained to smell that out. Hell yes. Astonishing how things change. And people reckon a week is a long time in politics! |
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3rd December 2021, 08:10 PM | #519 |
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Sorry, I meant to address that the other day.
Their plan of staying Covid-free just got blown out of the water, alright. No way is anyone stopping this sucker. It appears to have reached measles level of infectiousness, which is the only other disease with that kind of action I can think of. We can only hope the harm angle doesn't turn out to be "too bright, too early". |
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3rd December 2021, 08:25 PM | #520 |
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