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rotting sea cow

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Posts posted by rotting sea cow

  1. 18 hours ago, Zorral said:

    "‘I have no intention of getting infected’: understanding Omicron’s severity

    Like for many there is a choice.

    I respect many of these scientists and experts, but they really need to get a dose of reality. They have been sitting their arses in their comfy home offices, shitting their pants while learning about the virus, pontificating about measures and restrictions while billions of workers had to go out to earn a living and make this dysfunctional society to function, somehow, without getting any recognition.

    They have been driving the trucks, collecting the garbage, delivering the mail and parcels, packaging and processing food, manning the supermarkets and other essential shops, etc, etc, etc. 

     

  2. Unfortunately I didn't have the time to follow some previous interesting discussions regarding the evolution of the virus (and thus of the pandemic). Dealing with a number of personal and work related issues... on top of rising numbers of infections all around.

    Two little tidbits.

    1. There is growing concern about BA.2 (also dubbed "stealth" Omicron) rising in prevalence in a number of countries (e.g. Denmark). Compared to vanilla Omicron (BA.1) is has enough different mutations to get a different greek letter. In fact, the differences between BA.1 and BA.2 is larger than among other variants of concerns. Little is known regarding immune escape (expect to be high), cross-immunity and disease severity. Something to watch.

    2. First results from Israel regarding a second booster (4th dose). It raises the antibodies but it's unclear yet if it does something else.

     

     

  3. 9 hours ago, LongRider said:

    Fascinating article about Covin being spread by aerosol airborne transmissions, and why it has taken so long to understand this.  

    Don't let me started with this. Probably the second greatest mistake during the pandemic. Many warned about this very early on and it was considered a scientific fact in mid 2020. Instead, we have been disinfecting every surface with dangerous chemicals and washing our hands into oblivion. Good quality masks and air filtration should have been a priority, at least in developed countries that can afford that.

     

  4. 11 hours ago, The Anti-Targ said:

    If Omicron becomes the ubiquitous strain globally one would expect the next strain to be a descendant of omicron, and so an omicron vaccine should be reasonably effective. Unless there is a variant brewing in another animal species that will jump back to humans and is as distinct from all existing strains as Omicron is from Delta.

     

    11 hours ago, Impmk2 said:

    I think the problem is probably overstated for covid: See this recent data on immunity to a common cold coronavirus (229E) over time

    https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009453

    Serum collected from people is always pretty good at neutralising the virus from around the years it was collected - as well as extremely good neutralisation of the virus they've encountered over their lifetimes - though dropping off pretty rapidly for future 229E. Ie they haven't had a problem 'updating' the new antibodies and they've been significantly backboosted for what they've already encountered, but the virus has continued to mutate to evade immunity.

    I've seen that. But what they describe is the effect of antigenic drift which is not what we are observing with SARS-CoV-2

    We all thought we would be battling Delta and its descendants forever. Instead we got Omicron which come from another direction, maybe even from a second spillover after reverse zoonosis (or from a second lab leak?). With SARS-CoV-2 being such a promiscuous virus, it is not warranted that next variants will come from Omicron. It can perfectly come from that deer variant. Now, Omicron definitively has such competitive advantage, that is really hard to imagine something that could replace it, so maybe?

    11 hours ago, Impmk2 said:

    However there are also ways around this if it turns out to be a big problem - you could (for example) conjugate the RBD and other epitopes to a different protein scaffold so this problem wouldn't occur.

     

    One of the BionTech candidates was around that idea and one of the Cuban vaccines has the RBD attached to the tetanus toxoid. Of course there are advantages and disadvantages. If the virus mutates too much, you have basically zero protection. I read somewhere that another possibility is make a vaccine of conserved regions of the spike, but I guess you don't get such potent neutralizing antibodies.

    Overall, I think that after 2020 groundbreaking development, there was little interest in looking for new ways to make vaccines, despite that the threat of variants started to become more obvious.

     

     

     

     

  5. 1 hour ago, Padraig said:

    Moderna is talking about Autumn/Fall for its Omicron booster.  I suppose its lucky it isn't talking about earlier boosters!

    I'm not that hopeful regarding variant specific boosters. Two potential problems

    1.- Serotype replacement is occurring faster than vaccine deployment. Vaccines were designed around the ancestral strain. Since then few variants have come and go. In the Europe/US Alpha, Delta and Omicron have driven waves of infections. In other places you had Beta, Gamma, Lambda, Mu and few others. Fortunately until Omicron, there was more immune erosion rather than immune escape. But you see the problem. If Omicron follows that pattern, around mid year there should be another variant popping up that it's not necessarily a descendant of Omicron.

    2. Immune imprinting (related to the Original Antigenic Sin). A variant specific vaccine would boost the immunity against conserved regions of the antigen instead of the mutated parts. As those parts in Omicron are also the most antigenic regions (like the RBD), the booster would not do necessarily better in comparison to what we have.  I believe that Moderna already ran into this problem with its Beta specific booster that didn't perform better than the original recipe. Of course, with Omicron being heavily mutated, it's possible that the immune system will able to "see" those mutated regions. I suppose that clinical studies will be out soon and tell us whether this is a real problem or not.

     

  6. 1 hour ago, Padraig said:

    I thought Denmark had the highest level of boosters in Europe?  

    I misremembered this plot. It's UK that has a similar booster rate, not US. In fact, the US has a very low rate compared to other countries

     

     

    1 hour ago, Padraig said:

    I'm actually a little less positive.  Europe hasn't been overrun (yet) but most metrics are negative at the moment (with a few weird exceptions).  Rising hospitalisations.  Rising fatalities.  Terrible case numbers.  Hospitalisations may not be as bad as last winter (although Canada/US are) but they are still going in the wrong direction.

    I'm not optimistic at all, but neither too pessimistic.  I think that there is too much recklessness in the face of an unknown and while Omicron dominates the numbers, many countries had significant Delta waves with the respective backlog of hospitalizations.

     

  7. I've never liked to comment on other countries internal issues but I was reading about the shitshow about a famous tennis player and this comment taken from the BBC cracked me up.
     

    Quote

     

    Abul Rizvi, a former official in Australia’s Department of Immigration, told the BBC that even if Djokovic is allowed to play, "the Australian public will be angry at what’s happened here", and angry that the star "did not get himself vaccinated".

    “Assuming that the Australian government doesn’t try to cancel his visa again and he is actually allowed to play at the Australian Open, I think there will be a lot of difficulties for Djokovic from the Australian crowds," he said.

    “I think if Tennis Australia and Mr Djokovic were to think this through, they would announce some very significant health measures to ensure that there is no risk to public health from the tennis tournament more generally and from Mr Djokovic in particular."

     

    What level of mental contortionism is required to state something like that?

    Australia is currently having an uncontrolled Omicron outbreak and as far as I can tell, they aren't doing anything in particular to try to control it. Stating that a single unvaccinated represent a "threat to public health" in that context is laughable and reflects a high level of mental dissonance.

     

  8. Olympic games aren't fun to watch anymore since the Cold War ended. Since then, all mystic has been lost. It's all about the money.

    Anyway, what you describe with international sports can be seen all across the board, maybe they are more exposed and they are more obvious.

    I've met enough scientists to know that most of the "big names" are a bunch of egocentric and abusive pricks and better to not speak about the sycophants that are abundant in politics and business right now.

    We are immersed in an economic and social system that positively selects people with the worst personal traits for the top positions. Sure, in times of yore wasn't better (probably) but I don't think the problem is restricted to sports.

     

  9. 11 hours ago, Impmk2 said:

    I think the big issue for both Aus and NZ is that because the outbreaks in both countries have been so (comparitively) small the unvaccinated populations in both are basically entirely naive. So a good 10% of adults - hundreds of thousands of people in NZ, and millions in Aus are completely unprotected. Those people alone is enough to completely overwhelm the healthcare system, let alone the breakthrough infections. Most overseas countries dealing with large outbreaks would have had the virus rip through those populations already.

    Thing is, outbreaks are looking completely different across countries. UK's outbreak is worse than S. Africa's and US outbreak definitively worse than UK's. Why the difference?

    At the same time, Denmark outbreak is as old as UK's and they aren't seen any strain and they did have low levels of infections and the fraction of boosted population is not much higher than US.  I was reading some days ago they had around 50 persons in ICU with Delta and 5 with Omicron (they know) and epidemiologists do not consider Omicron worse than the flu but they are reluctant to easy the comparatively light restrictions. So uh?

    39 minutes ago, DireWolfSpirit said:

    I glimpsed a headline about Omnicom and Delta combining for the new mutant virus Delticom or some such near future threat lurking.

    Lab error most likely from what I read in twitter.

    Anyway. It's something to keep a watch. I said earlier that Omicron is likely unstoppable but it doesn't mean we shouldn't do anything. Doing something even light things might help to decrease the genetic diversity of SARS-CoV-2 and reduce the risk of recombinants, pushing other nasty variants in the path of extinctions.

    Probably you have seen that Marseille's variant with lots of mutations too, which popped up in Canada too. Yes, it's not of concern right now, but letting things like that to spread is an unnecessary risk.

     

     

  10. 1 hour ago, DireWolfSpirit said:

    What I've been wondering, but haven't asked anyone yet, do they tell you whether it was omicron or delta?

    Is the strain specificity in your positive/negative test? How does one know which has afflicted them?

    Ideally, you will need sequencing, which is slow and expensive and cannot be done at that massive scale.

    But there is a trick. In some PCR tests, Omicron (and also Alpha) triggers a signal known as S-gene target failure, which can be used as proxy. Usually PCR tests look for particular pieces of genes and compare to a template. Due to mutations in the spike, that comparison fails. It doesn't happen with all variants, it does with Omicron, fortunately as that was the signal that triggered the alarm from S. African labs.

    BTW. There is sub variant of Omicron dubbed the "stealth' because it doesn't trigger that signal. It seems that it less abundant, but it's actually different enough to be considered a different variant.

    .

  11. I keep worrying regarding the hospitalization rate. Despite this excellent thread posted earlier.

    This is the situation in US with a somewhat deeper analysis here. Focused on the NYS situation that provides better data. Some info on the age specifics showing that hospitalization are unfortunately rising sharply in the elderly.

    and again, the situation seems to be markedly different to the UK.

    https://www.bbc.com/news/health-59862568

    A possible explanation is that some parts on the US had rising Delta waves before Omicron hit. Also the focus on Omicron "mildness" might have made the people to take unnecessary risks.

    Overall, I think governments (and people) are acting recklessly in the face of unknowns. Scientific results are being consistent regarding that Omicron will cause milder disease, but we are not facing Omicron in the vacuum. Also, that Omicron is possibly unstoppable is not an excuse to do nothing and try to spread the infections as wide as feasible. 

    This is another trend in governments policies regarding the pandemic. They react when the crisis hit instead of trying to prevent them and we pay the costs. 

     

     

     

  12. 6 hours ago, Lermo T.I. Krrrammpus said:

    It'll be interesting to see if any of the anti-vax / vax hesitant crowd will be more willing to get something like Corbevax if it starts getting approval.

    Hope this ends up being safe and effective as it's cheap and doesn't require new tech to produce. 

    Wow. That's great! I don't think it would move the ideological antivaccine, but I do think it might convince a number of vaccine hesitant and also provide options people who haven't tolerated well mRNA/Vector vaccines. Specially, if governments once for all, start changing the discourse regarding vaccine and measures, but my hopes of that are very low. Most of the people I know who haven't getting the vaccine are more in the contrarian "don't tell what to do" side.

  13. 5 hours ago, RhaenysBee said:

    I want to believe you, I just wish I didn’t read 30 headlines arguing to the contrary every single day. At some point it gets really difficult to believe that the world is getting better when everything and everyone are breaking their backs to convince you otherwise. 

    I think it's mostly they want to scare people into compliance. I don't think it's a good tactic. Honesty has been in short supply during the pandemic and has only created further skepticism.

     

    4 hours ago, Knight Of Winter said:

    Without trying to sound like a confrontational asshole, I think this is way overly simplistic view of the infection process. If if were "entirely down" to luck, then there would be no regularities whatsoever in cross section of the infected population. Thanks to overwhelming number of studies done, we know that this is not so. For example:

    I think she meant that despite the known risks there are always that odd case of a young health adult being badly hit by the disease despite all precautions. Or those elderly who have at the most blinked to the virus.

     

  14. 15 hours ago, williamjm said:

    I was reading this thread earlier which answers many of those questions from a UK perspective. I think it's fair to say there are a lot of moving parts when trying to understand the big picture at the moment.

    Thanks a lot for that twitter thread. It really clarifies things. Well, I'm fine if it's still from the UK's perspective. Turns out that UK has excellent data collection systems, which allow that kind of analysis. Data from US is on the other hand underwhelming.

    The increase of the cases in older adults is certainly concerning.

     

  15. Two things are worrying me right now.

    1) As you may know, hospitalizations are rising steeply in many countries (including pediatric). Unfortunately there is little clarity regarding the exact situation. One news outlet is straight out calling you to panic, the next one is saying that there is no reason for that because decoupling and mild.

    It is very hard to get a clear assessment of the situation. At least from the distance. How many of these hospitalizations are incidental? How many are in-hospital infections? Age stratification? Vaccination status? Etc.

    That after almost two year into the pandemic it gets that hard to get an assessment of situation is disappointing. I really hope that policymakers have better overview of the data, however it seems that news outlets are just trying to gaslight people towards particular behaviors, which is of course bad. People need reliable information to take their decisions, thinking that you can manipulate into compliance is not only morally wrong, but it will backfire in the end, as it had during the pandemic.

    2) This one is more hypothetical. A new study on Omicron cell's entry and replication as well as immune evasion, in line with previous studies. However...

    Quote

    The SARS-CoV-2 variant, Omicron, shows rapid replication in human primary nasal epithelial cultures and efficiently uses the endosomal route of entry.

    At the end of 2021 a new SARS-CoV-2 variant, Omicron, emerged and quickly spread across the world. It has been demonstrated that Omicrons high number of Spike mutations lead to partial immune evasion from even polyclonal antibody responses, allowing frequent re-infection and vaccine breakthroughs. However, it seems unlikely these antigenic differences alone explain its rapid growth; here we show Omicron replicates rapidly in human primary airway cultures, more so even than the previously dominant variant of concern, Delta. Omicron Spike continues to use human ACE2 as its primary receptor, to which it binds more strongly than other variants. Omicron Spike mediates enhanced entry into cells expressing several different animal ACE2s, including various domestic avian species, horseshoe bats and mice suggesting it has an increased propensity for reverse zoonosis and is more likely than previous variants to establish an animal reservoir of SARS-CoV-2. Unlike other SARS-CoV-2 variants, however, Omicron Spike has a diminished ability to induce syncytia formation. Furthermore, Omicron is capable of efficiently entering cells in a TMPRSS2-independent manner, via the endosomal route. We posit this enables Omicron to infect a greater number of cells in the respiratory epithelium, allowing it to be more infectious at lower exposure doses, and resulting in enhanced intrinsic transmissibility.

    https://www.biorxiv.org/content/10.1101/2021.12.31.474653v1

    So, Omicron is not only bypassing immunity and becoming the fastest spreading pathogen known to humanity, but also shows enhanced potential to infect other animals, including domestic avian species. Given the rapid spread of Omicron and difficulty to contain it,  these reversed zoonosis events might be happening right now in multiple chicken farms all around the world. Then what?

     

     

     

  16. 8 hours ago, Impmk2 said:

    Omicron has completely swapped cellular entry mechanism(!), now entering via endosomal fusion - generally associated with lower inflammatory response, less cell to cell transmission and biases towards different tissues. It's a pretty huge shift. This is now one of a string of studies showing replication in different tissues and a decrease in surface fusion, but has some pretty great controls in there to really dissect the detail.

    I think I saw something similar. It might be the same study? Reportedly, Omicron also has reduced ACE2+TMPRSS2 cell entry and enhanced pure ACE2 attachment.

    We maybe should start calling Omicron the first true different strain of SAR-COV-2. It's anyway crazy that comparatively few aminoacids mutations can lead to such a change in viral behavior and pathogenesis.

    I agree that it's not a common cold yet, even if some people feel it like that. I still wonder what will happen when the vulnerable population starts to be hit by the massive waves.

    This is the study

     

     

     

  17. 48 minutes ago, Tywin et al. said:

    It's natural for those who've done everything right to feel increasingly resentful towards those who are unvaccinated by choice and are flouting the safety protocols. 

    I think some people have too "high expectations" regarding the outcome of doing "everything right" and what could have meant regarding the trajectory of the pandemic.

    As @Mlle. Zabzie succinctly put it some pages back. We were told that few weeks of lockdown will done the job. It didn't. That masking may be even enough to contain the virus (I even saw some analysis). It didn't. Test and trace, masking and some light restriction will avoid the next lockdown. It didn't. But vaccines were coming and a lot of discussions ensued how many people we needed to vaccinate to reach some magic "herd immunity" number. Well, that percentage has been going up and up and infections are soaring despite the "best vaccines to be had".

    The message was always insinuating that if everybody did "everything right" we could eliminate the virus of our lives. Nobody told us the truth back in March 2020 that the virus, bar all countries simultaneously agreeing going full China, was going to inevitably become endemic.

    I understand that people are exhausted and looking for some scapegoat of the situation. The reality is that none of the policies implemented even taking together would have been enough.

    Now, we have a highly infectious and highly immune evading variant sweeping across the world that nobody could credibly claim that those "flouting safety protocols" are responsible for. It might well be that it's coming even from some animal.

    The pandemic has seen colliding the limits of scientific knowledge and technology against the complexity of natural phenomena. The problems of our economy and politic systems against the the complex nature of societies. And of late I'm increasingly seeing a conflict between our humanity and our exhaustion.

  18. 6 minutes ago, Lermo T.I. Krrrammpus said:

    Absolutely hilarious in a "people are going to keep dying" kind of way that Biden is pretty much just Trump when it comes to covid response.  

    Don't you have elections next year? Then, Biden definitively want this to be over by Easter, like a miracle. Doing something, anything will only prolong the pandemic. Maybe doing nothing will do the job?

     

  19. 2 hours ago, Zorral said:

    NYC Pediatric hospital admissions for covid continue to spike.

    They might be incidental cases according to some article. That is children being at the hospital for other reasons and then test positive. Still is something to keep an eye on. Hopefully, clear stats come soon.

    Meanwhile, several European countries are hitting new records regarding infections, 180k in France, 215k in Spain, 115k in UK, etc. Reportedly, testing capability is hitting its limits with Ireland reporting an insanely 50% positivity rate

    https://www.bbc.com/news/world-europe-59806119

    I'm having the strong feeling that by the end of February we will largely done with this shit, but first we need to endure some few hard weeks/months and the circus that the response has become.

    There is a storm raging in twitter because the new CDC guidelines, with few European countries considering to implement something similar.

     

     

  20. 1 hour ago, Clueless Northman said:

    It really depends. Key question is if Omicron can be actually genuinely bad for people with previous immunity (say at least 2 doses or infections). If for them it basically can't get worse than a mild flu, it makes no sense to keep such strict restrictions on the vaccinated ones - you're not legally obliged to quarantine for X days if you have the flu, despite the yearly toll, you do it as a social duty, and also because you won't be able to go out for a few days, with a real flu. If at least 95% of vaccinated people who get Omicron are asymptomatic or have cold-like symptoms for a couple of days, than we're close to the point where them quarantining exists merely to protect unvaxxed ones - a position that cannot be defended anymore, since we've had vaccines for one full year. It's not just people who want to be slaves to the economy, it's people who've fucking had enough of having to restrict their lifes for 2 years, specially when restrictions these last 6 months were entirely due to the anti-social behaviour of assholes; if Omicron turns out to be truly milder, as hoped for, then keeping quarantines, isolations and the like is basically allowing anti-vaxx to take the bulk of society as hostage.

    The jury is still out there about how dangerous Omicron is for various groups, but that's a matter of weeks. If it turns out that S. African results were a fluke or an outlier, and it's overall as bas as any previous strain, then a significant level of restrictions will have to be kept.

    Look. I know you are trying to give health authorities the benefit of doubt regarding this guidance. It has been hard, even in Europe, to keep employers from requesting their infected workers to come to work, citing they aren't actually sick, which remains to be true for many infected.  I'd guess that it's even worse in US. With this guidance, you will have actual infected individuals at work places. 

    Yes, in one hand is a way towards normalcy. On another, its only purpose is to not do further damage to the economy, so countries will not enter in an unplanned "soft lockdown"

     

  21. 9 hours ago, Tywin et al. said:

    Didn't you get the memo? The billionaire class hasn't grown their wealth by enough during the pandemic. Where's your sense of civic duty? Get out there and spend, Spend, SPEND, health be damned! 

    go back to work, you peasants!

    It was always about it, wasn't it? Health was only important as long as it was disrupting our neo-feudal economic system.

    At least the masks are falling.

  22. 8 hours ago, Paxter said:

    I’d like to believe the above bolder remark. But SA has a very young population compared to Europe, so I’m not getting my hopes up.

    This is an important and often neglected aspect of disease. Young people get it mild, regardless of vaccination status. In fact most people get it mild. That's few days bedridden. The problem are old adults, the high rate of hospitalization in middle aged adults (but with good prospects of survival) and some tragic cases of younger people which are hard to explain. So, when we make statistics, these problems get smoothed out.

     

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