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Discussion thread VI - COVID-19 (new coronavirus)

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  • JJackson
    commented on 's reply
    gs re #506.4 The virus will not make 'the big jump' seen in Omicron normally in humans as one or more of the intermediate steps will get weeded out by the immune system, however in severely immunocompromised hosts it may survive and get additional changes. If one of these multi-mutation variants happens to be fit it may survive and spread from any host that is subsequently infected by the immunocompromised host. The same could also happen in a non-human host with a very different immune profile however in either case I would expect the new hosts to rapidly apply immune pressure causing considerable genetic change to the epitopes they interact with. It will be interesting to see where these changes are applied. A very similar set of mutations were observed in an in vitro epithelial mono-layer, where there is intra-cellular immunity but no adaptive immunity, but they could not compete against wild type in an in-vivo model.

  • Emily
    commented on 's reply

  • Emily

    Robert W Malone, MD @RWMaloneMD

    This guy pulls his punches and will not speak the obvious truth. The selective pressure is the vaccines. Note where his funding comes from. Another intimidated, spineless academic.
    Will omicron – the new coronavirus variant of concern – be more contagious than delta? A virus...
    It’s too early to say whether the newly identified omicron variant is going to overtake delta. But particular mutations in the new strain have researchers deeply concerned.

    8:00 PM · Nov 30, 2021·Twitter Web App

    Leave a comment:

  • gsgs
    commented on 's reply
    it could have accumulated the mutations over time by selection due to respiratory spread,
    not just growth inside the body.
    in animals ?

    or maybe in some remote isolated community

  • gsgs
    what was that organisation, created last year, dedicated to find and stop new outbreaks like omicron ?
    Head was Ian Lipkin, I remember how I applauded at twitter. But now I can't find it.
    Only nichtssagende stetments by Lipkin now, no reference to that task.

    We were asking for it here since 2006's H5N1

    China stopped Wuhan-Hu-1 in Feb.2020
    But they let it escape to other countries
    and most of the rest of the world didn't stop it

    Alpha, Delta were detected too late.

    Omicron was detected early but spreads better and faster, but i think we should try to stop it to contain it now.,
    support ZA's measures financially. Although it's probably invain and too late.


    The key to global public health is global cooperation, transparency and investment."
    the lack of international, inter-institutional and interpersonal trust, respect and collaboration,
    [not the project that I had in mind. It was rather about early stopping emerging pandemics]
    pandemic prevention institute , Rockefeller Foundation

    from what I read so far I'm disappointed by their tweets

    Last edited by gsgs; December 2, 2021, 11:40 PM.

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  • gsgs
    commented on 's reply
    you mean, it was not created by finetuning ? Big achievement to create such a successful
    strain without some continuous adaption and selection (=finetuning)

  • sharon sanders
    commented on 's reply
    Masks are only part of disease avoidance practice. They help, but like vaccines, they are not guaranteed. As I have said many times, I am living a COVID life style. I do not eat inside any restaurants. I do not attend big events. I keep a distance from others - even outside. I carry an N95 mask, and I am fully vaccinated. Even these actions do not guarantee anything. It just gives me a chance. I am really enjoying my adult children and other relationships. I want more time and I am willing to make changes to my life style to get it.

  • JJackson
    commented on 's reply
    gs I do not think masks will stop any strain I think they will reduce the total amount of virus being transmitted from host to host making it easier for the immune system to get on top of any infection earlier hence reducing symptom severity. I do not think this will vary by variant.

    I forgot to include this in my earlier comment but I also expect this variant to undergo significant further mutation in the short term. With so many changes all at once I expect a fair amount of fine tuning will be needed as some of the changes are found not to be optimal in this new configuration and will need to be adjusted and some existing unchanged AAs need adapting to the new protein configuration.

  • gsgs
    commented on 's reply
    I don't think distancing, masks can stop it. This is like panflu. Even China, Israel will get it
    this winter (IMO).
    these mysterious multi-mutation strains will probably appear again.
    One per year ?! Makes it unpredictable like flu.

  • gsgs
    commented on 's reply
    yes, but once it gets into the community it spread very quickly and should be detected soon.
    Maybe this is only since one last decisive mutation, though, and it may have spread
    without that mutation earlier with lower speed.

  • JJackson
    Re. Omicron
    There is not enough data to say anything very definitive about this variant yet - not that that will stop the media from writing exciting headlines and worst case scenarios.
    Speculation is all we have so lets look at what we know and what it is reasonable to infer.

    It was first found less than a month ago - Given that very few positive test are fully sequenced it is very likely to have been circulating below the radar for some time and is likely to have spread to several other areas/countries by now so travel restrictions will probably not delay international spread by much.

    It has a bucket load of AA changes many in the Spike - This is unusual, while the virus will be continuously making small changes in any infection most will be weeded out in that host with only one or two making it to the next host. Viruses with this many changes as a single jump are almost always dead ends except where the host is immunocompromised allowing 'damaged' viruses to keep on adding mutations until a new viable progeny is achieved. The high HIV prevalence is a suspect here but we will never be able to pinpoint the index case.
    These Spike changes are almost definitely going to reduce vaccine efficacy to some degree which will increase relative viral fitness in areas with high vaccine coverage. If the virus is relying on this to out perform the Delta variant it will spread well in high vaccine/prior infection areas but not in countries that are naive.
    As we have never seen all these changes in one variant before there is no way of guessing what impact they will have on transmission, virulence or other properties of the phenotype we are just going to have to wait and watch.
    As with the Alpha variant it is easier to pick up by rt PCR as the Spike probe (normally 1 of 3 probes) gives a reduced signal which in turn tends to lead to more full sequencing of that hosts viral genome which will skew the data compared to random sequencing so be wary of the relative numbers of sequences deposited at GISAID.

    As far as the impact on health services is concerned the key here is if, in people whose immune system is primed, there is adequate protection to limit the replication in the host sufficiently for somatic hyper-mutation to adjust the B cells' antibodies to the new virus (I wrote an explanation of B cell maturation here In countries with high vaccination/prior infection rates (like mine, the UK) people have dropped their guard and are tolerating very high infection rates as it is only producing low hospitalisations. If this strain has retained its virulence and drifted away from vaccine strains enough to allow significantly more hospitalisation and we do not change our behaviour, physical distancing and masking, then our health systems hospitals are going to get swamped and will cause more lockdowns.

    A first look personal opinion only based on very little information - caveat emptor.

    Leave a comment:

  • sharon sanders
    So - ****

    I am really over it!

    I had a great Thanksgiving - designed with COVID-19 in mind. We ate outside, at a distance, at separate small tables. We did not have a buffet. The hostess put a little of everything on everyone's plate and served them. It was so much fun that we have planned the same type of event for Christmas.

    Now we have this Omicron development. I am waiting to see what science tells us. Since I am high risk I live a COVID-19 oriented life style anyway.

    I am a big fan of N95 masks and I have repeated this over and over. I always carry one even though I am fully vaccinated + booster.

    I do not support mass lockdowns or vaccine mandates. Societies are at the breaking point.

    I do support protecting our vulnerable populations, like nursing homes, etc.

    Please read this site, check the international and national news - and your local news.

    Always use at least two sources for your information, and use your common sense.

    Only you can take care of you.

    Leave a comment:

  • sharon sanders
    commented on 's reply
    It is hard to know at this point how the growth is because the focus on this variant is new. It might have been circulating undetected for a while.

  • gsgs
    it redoubles in 3 days !
    It started 10 days ago in Gauteng province and in the last
    4 days there was an increase also in neighboring provinces.

    unless there was some -still unrecognised- superspreading
    this is almost like pandemic influenza.
    2009 H1N1 reached its peak in just 3 weeks from zero in NY

    expect a wave starting in Jan.
    in 2 weeks we'll know how much the vaccines may help and how virulent it is ...

    Leave a comment:

  • gsgs
    commented on 's reply
    Dr. Angelique Coetzee, chair of the South African Medical
    Association and a practising GP based in Pretoria, said it
    was "premature" to make predictions of a health crisis.
    "It's all speculation at this stage. It may be it's highly
    transmissable but so far the cases we are seeing are
    extremely mild," she said.
    "Maybe two weeks from now I will have a different opinion
    but this is what we are seeing. So are we seriously worried ?
    No. We are concerned and we watch what's happening.
    But for now we're saying "OK; there's a whole hype out there,
    [We're] not sure why."