[HN Gopher] Derek Lowe: Omicron Update (Dec 17)
___________________________________________________________________
Derek Lowe: Omicron Update (Dec 17)
Author : herodotus
Score : 71 points
Date : 2021-12-19 17:56 UTC (5 hours ago)
(HTM) web link (www.science.org)
(TXT) w3m dump (www.science.org)
| kevinmchugh wrote:
| A minor point in here corrected a misconception I didn't realize
| I held:
|
| > T-cell mechanisms are also crucial, and T-cell data are much
| harder to come by. Since you don't see the number of papers in
| that area as you do for antibody profiling, it easy to think that
| they don't matter as much, but that's not true.
| ethbr0 wrote:
| I'd be really interested to hear someone in microbiology opine
| on the difficulties in measuring T-cell and other non-antibody
| data? What makes it so much harder?
| VeninVidiaVicii wrote:
| You're probably looking for an immunologist.
| rossdavidh wrote:
| Not the expert you're looking for, but I recall a past Derek
| Lowe article mentioned in passing that it was much more
| labor-intensive (presumably by a trained lab tech) to get
| T-cell data. Again, this is just my memory of a past Derek
| Lowe article, which I might be misremembering.
| KaiserPro wrote:
| There are mechanisms for t-cell testing in reasonably wide
| use now. from what I understand its not done that much
| comparatively is because its bloody expensive.
|
| I think one of the mechanisms is here: https://en.wikipedia.o
| rg/wiki/ELISpothttps://en.wikipedia.or...
|
| However I would take all of this with a pinch of salt. I
| asked my doctor friend about it, they said "We use t-cell
| tests for a bunch of things, but its really expensive. I
| can't remember what thing we were looking for, probably TB,
| everyone had TB in that ward, so it might be that."
| thatsamonad wrote:
| One thing I'm curious about and on which I haven't been able to
| find any good data/information is whether the drop in vaccine
| efficacy is a function of time since last dose (i.e. due to
| waning over time) or whether the third dose drives up total
| antibody or T-cell activity and/or broadens the immune response
| which leads to it being more effective against Omicron.
|
| My spouse and I have both had boosters but my child has only had
| two doses because they only recently authorized use for children
| ages 5-11. I think my spouse and I are fairly well protected but
| it's uncertain if my child is well protected or not given the
| timing of everything.
| jlokier wrote:
| No scientific data unfortunately, but this BBC article explains
| that even though it's the same substance each time, the effect
| develops further over multiple doses, and goes on to describe
| what that means using metaphors.
|
| BBC News - Omicron: Why do boosters work if two doses struggle?
| https://www.bbc.co.uk/news/health-59639973
|
| Excerpt:
|
| "Fortunately for us - while the contents of the syringe may be
| identical, a booster is not just more of the same for the
| immune system.
|
| The protection you're left with after the third dose is bigger,
| broader and more memorable than you had before."
| SkyPuncher wrote:
| We have a 1 year old. We try to avoid intentional exposure, but
| the knowledge I have indicates COVID is no more of a threat for
| children than many other viruses. Flu, RSV, etc all have
| similar risk profiles in young kids. As such, we approach COVID
| the same way we approach many other things.
|
| Wash hands, avoid known sick people, monitor conditions, avoid
| known bad situations.
|
| We are avoid daycare facilities for now since that would
| introduce a many-to-many situation where an outbreak is
| inevitable.
| johnisgood wrote:
| I am not updated on this, but is COVID-19 much of a concern
| when it comes to your child, especially after having received
| two vaccines already?
| Loic wrote:
| 3 boys at home, all with a COVID-19 infection last December.
| The one already after the puberty got long COVID, the one "in
| the start of puberty" had only mild long COVID and the
| youngest one (7) was asymptomatic.
|
| Some friends noticed also this puberty "cut". But
| statistically, I cannot tell if this is significant or not,
| because you never have the information "12 good in puberty"
| or "11 no signs of puberty yet".
| thatsamonad wrote:
| Fair question. My general understanding is that the risk is
| very low for children, especially when it comes to severe
| disease and/or death (though there are still some questions
| about long-term effects), and even more so now that they have
| been fully vaccinated with two doses.
|
| I'm mostly just curious if we'll see booster recommendations
| for children as we have for adults and if the efficacy impact
| of Omicron is due to time or something inherent to the two-
| dose vs three-dose mechanisms at play.
|
| And generally as a parent I'd prefer to see my child not get
| sick at all, though I know that's basically unavoidable. That
| being said, I like to understand what the risks involved are
| if possible.
| [deleted]
| pygy_ wrote:
| I'm in a similar position: I've had three mRNA doses,
| vaccines here may start to be available to my children next
| week
|
| I wouldn't want them to be the weak link, but having them
| partially immunized during a delta/omicron peak may be sub-
| optimal...
|
| Any data/analysis on the subject would be welcome
| johnisgood wrote:
| > South Africa is the furthest along in the Omicron world, from
| what we can see, and although their cases have rocketed up, their
| rates for hospitalization and death have only been a fraction of
| what was seen in the earlier waves.
|
| That is pretty good though, all things considered. Spreads fast,
| but is mild enough. If the next variant is going to be even
| better in this regard, we should be happy. It may, given enough
| people catch this variant with mild symptoms and develop
| immunity. Maybe we should re-think the strategies involving
| restrictions and vaccination.
| [deleted]
| mdp2021 wrote:
| > _given enough people catch this variant_
|
| Please see the point Derek Lowe makes in the first article, of
| Dec 2 (point which I have abridged in this page): cases of mild
| immune response which let the virus dwell for a long time in
| the organism can be the proper places for a virus to develop
| mutations.
|
| Also, the paragraph closing this article of Dec 17: that the
| main future mutations will be of high contagiousness and low
| impact is a non granted possibility.
| johnisgood wrote:
| Yeah, fair enough. I mean, after all, mutations are random,
| it can get worse.
| 2-718-281-828 wrote:
| > cases of mild immune response which let the virus dwell for
| a long time in the organism can be the proper places for a
| virus to develop mutations.
|
| that's practically irrelevant or you'd have to demand
| lockdowns for any virus and its uncle because they all mutate
| all the time. is that what you want?
| Zababa wrote:
| I'd really like to see an analysis comparing covid to the flu.
| There's the vaccine and omicron making it less deadly than
| before, but I have no idea by how much.
| TheSocialAndrew wrote:
| If the mutations continue, at some point the mortality rate
| will likely meet the mortality rate of the seasonal flu.
| Hopefully we can then compare COVID to the season flu on any
| large media outlet / platform without being canceled, so that
| we can accept it as such and not rework our lives a dozen times
| a year around restrictions.
| GDC7 wrote:
| > Hopefully we can then compare COVID to the season flu on
| any large media outlet
|
| It will never happen, humans take more and more to recover
| from traumatic events and people who claim that it's time to
| put the traumatic event behind our back and go on with our
| lives are singled out as irresponsible .
|
| See the 2008 financial crisis, we are still doing QE, Fed
| balance sheet would never go back to normal , we have scam
| companies worth hundreds of billions and perhaps the most
| scammy one just went above a trillion in financial value with
| no real tangible product presence in a market in which
| commands a 1% presence.
| saila wrote:
| I guess it depends on the person, but this doesn't square
| with what I see, and I live in what's considered a very
| liberal area with relatively strict mandates. People are
| going to bars & clubs, eating out, holiday shopping, etc.
| Even people who are being more cautious right now are
| itching to get out and do stuff. I think we'll recover just
| fine.
| dnautics wrote:
| > likely meet the mortality rate of the seasonal flu
|
| We should consider the possiblity that _we are already there_
| with omicron.
| 1shooner wrote:
| I thought the pushback on the comparison to flu was the
| conclusion that's intended to draw. The 2018 flu outbreak
| hospitalized approximately 710,000 Americans[0]. Public
| health professionals generally thing flu should have more
| public attention, so saying we should be unconcerned because
| now we have another disease as impactful as flu, I can see
| them objecting.
|
| 0. https://www.cdc.gov/flu/about/burden/index.html
| gentleman11 wrote:
| There is no guarantee of that at all. Many diseases get worse
| over time
|
| https://www.politifact.com/factchecks/2021/dec/08/facebook-p.
| ..
| mkolodny wrote:
| According to the CDC, the flu caused 12,000-52,000 deaths a
| year in the US between 2010-2020 [0]. While covid caused more
| than 800,000 deaths in the US over the past two years, and
| more than 36,000 US deaths over the past month alone [1]. At
| this point, covid is still orders of magnitude deadlier than
| the flu.
|
| [0] https://www.cdc.gov/flu/about/burden/index.html [1]
| https://covid.cdc.gov/covid-data-tracker/#trends_totaldeaths
| wk_end wrote:
| ...it's 12k-50k _per year_. So just ("just") one order of
| magnitude or so.
| ipspam wrote:
| Can't compare apples and oranges. For flu seasons, regular
| classification applies. For pandemics, all persons that die
| with Covid are Covid deaths.
|
| Apples and oranges.
| 2-718-281-828 wrote:
| is this also a thing in the states? in germany even
| people who died from accidents but have tested positive
| for covid (either pre or post mortem) are counted as died
| from corona - not kidding.
|
| - https://www.zdf.de/nachrichten/panorama/corona-tote-
| rki-stat...
|
| - https://www.heise.de/tp/features/Wer-zaehlt-als-Corona-
| Toter...
| ugjka wrote:
| If only we had endless medical capacity for those who will not
| have it "mild"
| johnisgood wrote:
| Well, it is better than the mild ones not having it mild
| either, but worse.
| matthewmacleod wrote:
| I think it's _really_ important to stress that while it is
| obviously great to see fewer people in hospital, that alone
| doesn 't tell us very much about the severity of the variant,
| or the expected outcome in other countries.
|
| We would already expect the number of hospitalisations second
| wave to be way lower, because of the effect of higher levels of
| immunity through vaccines and previous infection versus the
| first wave. The Discovery Health research from South Africa [1]
| suggests that Omicron might result in about 30% fewer
| hospitalisations versus an equivalent Delta infection, but it's
| still early days and it's hard to get clear data given the
| number of confounding factors. The early research from Imperial
| in the UK [2] says:
|
| "The study finds no evidence of Omicron having lower severity
| than Delta, judged by either the proportion of people testing
| positive who report symptoms, or by the proportion of cases
| seeking hospital care after infection." with the notable
| qualification that "hospitalisation data remains very limited
| at this time."
|
| Even if it's substantially less severe, it does seem certain
| from the way it's ripping through the UK at the moment that it
| spreads extremely quickly - and even with a lower chance of
| hospitalisation, we could quickly see a very large spike in the
| number of people requiring care, with the corresponding stress
| on already overstretched healthcare.
|
| I'm definitely a bit concerned about the amount of "it's
| basically just a cold now!" chat we've been seeing - something
| we'd all like to be the case because pandemics are shite. But
| anecdotally I have witnessed first-hand quite a few people I
| know here in the UK being pretty blase in the run up to
| Christmas and getting quite sick as a result.
|
| [1] https://www.discovery.co.za/corporate/news-
| room#/pressreleas...
|
| [2] https://www.imperial.ac.uk/news/232698/modelling-suggests-
| ra...
| gentleman11 wrote:
| > And notably, the virus that causes COVID-19 is most
| transmissible before symptoms set in, so its harmfulness to its
| host may not be as strong an influence on how it evolves as the
| trade-off model suggests.
|
| > "The virus, speaking anthropomorphically, just wants to
| spread and have its genes replicated," said Dr. Amesh Adalja,
| an infectious disease specialist at Johns Hopkins University,
| in an interview. "If the best way for it is to spread by
| causing severe symptoms, it will continue to do that."
|
| https://www.politifact.com/factchecks/2021/dec/08/facebook-p...
| Barrin92 wrote:
| not sure I understand the reasoning here because the
| behavioral response to covid at a collective level will
| always depend on the harmfulness of the disease regardless of
| when symptoms set in.
|
| We are going to take stronger measures against harmful
| diseases, and that reduces their fitness inevitably. The
| claim that a disease _always_ evolves towards being more
| harmless is obviously not true due to mere chance, but in the
| long run there is a clear advantage to it. Rather than
| cherry-picking examples to prove the point I think it 's more
| accurate to say the article cherry-picks counterexamples like
| multiple Malaria strands competing against each other in the
| same host or a rabbit disease that became more deadly to
| overcome an immune response. None of which is long-term
| adaptive.
| k__ wrote:
| As far as I know, mild cases are only confirmed for vaxxed
| people.
| juanani wrote:
| Interesting, you must not know far.
| gentleman11 wrote:
| Did you find any statistics saying that?
| wk_end wrote:
| SA was only around 20% vaxxed when the omicron wave started
| and everyone with boots on the ground there seems to be
| saying it's milder.
| k__ wrote:
| Could be.
|
| I also heard SA has a much younger population than most
| western countries, so "mild" should be used with caution.
| johnisgood wrote:
| I wonder about, say, how non-vaccinated 16-25 years old
| people are affected by Omicron vs. Delta.
| soperj wrote:
| Where were all the people saying "I told you so" about viruses
| getting milder over time when Delta came around?
| mdp2021 wrote:
| > _A team in Hong Kong has announced that in their cell assays
| the Omicron variant seems to reproduce up to 70 times faster in
| the upper respiratory tract, while at the same time being much
| slower to reproduce in lung tissue_
|
| > _What About Immune Evasion? How Much Protection Do Vaccines
| Provide? This part of the story isn 't completely worked out
| yet... Most of that [information] is antibody-based data, and ...
| while this is important, it is not the last word on real-world
| immune protection[: ]T-cell mechanisms are also crucial, and
| T-cell data are much harder to come by_
|
| > _the Pfizer protease inhibitor ... does appear to be just as
| effective against Omicron, but its supply will not be enough to
| make any real difference at all in the coming weeks_
|
| From the "introduction" of Dec 2:
|
| > _Where Did It Come From? Omicron ... is not a direct descendant
| of the Delta strains ... An immediate hypothesis was that Omicron
| may have developed in a single immunocompromised human patient
| over a period of weeks or months[: ... y]ou don 't just
| immediately kill everything off - you give the virus or bacterium
| a chance to overcome a lesser challenge before turning up the
| pressure a bit more, letting mutations accumulate and try their
| worth over and over as the challenge slowly increases. That's
| just what's going on inside a coronavirus patient if they can't
| mount a full immune response. The virus and the immune system
| engage in a prolonged battle where neither one can land a
| decisive blow, and things just keep on evolving. This is why they
| tell you to take your full course of antibiotics when you have a
| bacterial infection, and why effective vaccines actually suppress
| variant formation: if you kill off the pathogens as quickly as
| possible, they don't have time to explore their mutational
| landscape_
| loeg wrote:
| > the Pfizer protease inhibitor ... supply will not be enough
| to make any real difference at all in the coming weeks
|
| Tautalogically so in the US, anyway, where the FDA has
| inexplicably still has not approved (or emergency authorized)
| it for use.
| tempnow987 wrote:
| For those following - these treatments are 40 pill
| treatments. For the 50M odd cases we've had we'd need 40*50M
| pills (2 billion pills).
|
| Assume a daily global rate of around 600K cases per day we'd
| need 24M pills per day.
|
| USA alone is perhaps 100K cases, so 4M pills per day. Do they
| really have this volume ready to go?
|
| --
|
| I'm not aware of a single study showing that for vaccinated
| folks the pills do anything. Not saying they don't, but it
| would be helpful to have ONE study.
|
| --
|
| As to why the FDA has not approved, they are reasonably
| clear. One issue is that COVID, and particularly omicron
| variant which dominates, is just not that lethal.
|
| EDIT: This part is incorrect below
|
| These pills work in interesting ways, ie, generating MORE
| mutations.
|
| b-d-N4-hydroxycytidine Inhibits SARS-CoV-2 Through Lethal
| Mutagenesis But Is Also Mutagenic To Mammalian Cells
| https://pubmed.ncbi.nlm.nih.gov/33961695/
|
| So before you jam 2 billion doses into folks there is going
| to be a bit of an evaluation.
|
| If Omicron turns out to have high fatality rates then I
| suspect things like these therapies will be fast tracked a
| bit more.
| tguvot wrote:
| you describing here merck treatment, not pfizers
| loeg wrote:
| > For those following - these treatments are 40 pill
| treatments.
|
| > These pills work in interesting ways, ie, generating MORE
| mutations.
|
| > b-d-N4-hydroxycytidine Inhibits SARS-CoV-2 Through Lethal
| Mutagenesis But Is Also Mutagenic To Mammalian Cells
| https://pubmed.ncbi.nlm.nih.gov/33961695/
|
| You're way off-base. You're talking about Merck's
| Molnupiravir (Lagevrio), which is both _less effective_
| (~30% vs ~88%) and _already approved_.
|
| Pfizer's Paxlovid (Nirmatrelvir) is not mutagenic.
|
| It is a 15 pill course (5 days x 3 per day), not 40.
|
| Also, Pfizer thinks as of Nov 29 that they can make 80M
| _courses_ by EOY. The US has purchased at least 10M of
| them.
| rossdavidh wrote:
| On one level I agree, but realistically I think they may not
| feel much of a hurry to do so since there isn't a significant
| supply ready to distribute. My understanding is that they
| already have authorization to use whatever they have,
| essentially as additional testing.
| loeg wrote:
| As of Nov 29,
|
| > Pfizer now expects to make 80 million courses of COVID
| drug Paxlovid by the end of 2022
|
| That's a ton of supply!
| mcguire wrote:
| Has Pfizer submitted the clinical trial data to the FDA? The
| last I heard (a week ago?) was that they were going to do it
| "in a few days".
___________________________________________________________________
(page generated 2021-12-19 23:02 UTC)