Covid-19 Tests?

Discussion in 'Biology & Genetics' started by KUMAR5, Jan 6, 2022.

  1. KUMAR5 Valued Senior Member

    Messages:
    1,221
    If all anticipated Omicron patients are or could not be specifically tested fir Omicron, how can anticipated hospitilízation and desths due to it, can belong tó this infection? Probably those are being overestimated in anticipation that Omicron pademic is dominating currently. When all these 3 are existing at a time now, if anyone claim serrious outcomes are due to previous varisnts, how can he can be oroved wrong for sure? Here official oublished data of Omicron infected is hardly about 2000 out of about 200000 total covid infected per day. But still 80 to 90% estimated as Omicron infected. Seriius outcome and deaths are just about .5% abd .2%. Then how can it is said fir sure which variant has caused what?
     
  2. Google AdSense Guest Advertisement



    to hide all adverts.
  3. billvon Valued Senior Member

    Messages:
    20,575
    Via statistical analysis.

    Insurance companies do it. Public health organizations do it. Aircraft pilots and route planners do it. Schools do it. Phone system designers do it. IC designers do it.

    It's pretty useful; might be worth learning about it.
     
    exchemist likes this.
  4. Google AdSense Guest Advertisement



    to hide all adverts.
  5. KUMAR5 Valued Senior Member

    Messages:
    1,221
    Yes it should probably if all such patients are specifically tested for Omicron and décidion is taken on the basis of such test results not on predicted value. I think all statics suggest sny recent outcome from z zcovud in gernal not from Omicron specific?, However due to dominance of pademic of any varisnt it is taken as granted that it should be of that variant infection. Moreover since many or early symptoms of all variants match to each other confusion or mistake in understanding should be possible. So unless statics of all Omicron infected is supported by soecific test reports, confusion is always possible.
    Do you find statics of say eg if 5 lacs Omicron infected, all these are soecifically tested for zOmicron for genome screening?, Here it is not pravctical.
     
  6. Google AdSense Guest Advertisement



    to hide all adverts.
  7. billvon Valued Senior Member

    Messages:
    20,575
    Nope.

    It's going to be effectively impossible to explain this to you if you don't understand statistics. I'll try below to simplify, and use large words to try to indicate its importance:

    YOU DO NOT NEED TO TEST EVERYONE TO KNOW WITH GREAT CERTAINTY WHAT IS HAPPENING.

    That's the bottom line, and that's why not everyone gets a differential test.
    Yes. In this case, you are confused.
    If you have 10,000 people with one of four unknown infections, and you test 500 randomly chosen people, you will know with a very high level of certainty what the level of infection of each pathogen is.
     
  8. KUMAR5 Valued Senior Member

    Messages:
    1,221
    Do officisls or competent authorities publish data under these heads specifically i.e. ' infected by Omicron, Hospitalisation due to Omicron infection and death s due to zomicron infection,? I want to see any such published data.
     
  9. Hercules Rockefeller Beatings will continue until morale improves. Moderator

    Messages:
    2,815
    This is a complex question. There are many qRT-PCR kits designed for clinical detection of SARS-CoV-2 produced by many different manufacturers. Different pathology companies and hospital pathology labs will use different kits that are capable of different things.

    Important to note is that no single RT-PCR test can detect all variants. In fact, many cannot distinguish between any variants. Here in Melbourne, Australia, my good friend works at a major pathology company that performs many thousands of SARS-CoV-2 clinical tests per day. He told me that they use a kit that amplifies the “stalk” region of the S protein. The stalk region is needed for viral attachment and, thus, is functionally constrained and is not subject to mutation.

    So, in this instance, this test cannot distinguish between any SARS-CoV-2 variants; it only produces a positive or negative for SARS-CoV-2 in general. The Department of Health determines the prevalence of specific strains by genomic sequencing, not RT-PCR. A subset of clinical specimens from hospital patients and a subset of tests from mass testing centres are chosen for genomic analysis (ie. sequencing of most, or all, of the viral genome as opposed to amplification of selected regions) in order to assess what strains are circulating in the community, and to match specific strains with specific symptoms in hospitalized patients. Community-wide prevalence of strains is extrapolated from the targeted genomic tests.

    I know there are some RT-PCR kits that might distinguishing between a few strains. However, I am not sure whether they are approved for clinical diagnosis, as opposed to non-human laboratory R&D. I suspect there is at least one that is used clinically because the so-called “S gene dropout” is a result that indicates the omicron variant as opposed to other variants.
     
  10. billvon Valued Senior Member

    Messages:
    20,575
    Yep. Most PCR tests test just for the existence of SARS-CoV-2, not any particular strain.

    Some PCR tests using specific antisense preparations can tell strains apart. However, they have to be designed for that strain; they can't detect new (i..e unknown) strains. A fraction of the total PCR tests are run through these tests as well. That's how we get relative ratios of (say) omicron to delta.

    And very few are sequenced 100%. This gives the entire genome of the virus, and can be used to detect new strains as well as existing strains. (That's how we discovered omicron was a new strain, for example.)
     
  11. Hercules Rockefeller Beatings will continue until morale improves. Moderator

    Messages:
    2,815
    They are, all of them. The full genome is acquired for genomic surveillance. The SARS-CoV-2 genome is only ~30kb. I don’t know what platform relevant authorities around the world usually use for their genomic surveillance, but I’d bet many use an Illumina platform. I have some familiarity with Illumina NGS platforms. Depending on the precise system, the number of amplicons and the desired coverage, I expect that an NGS approach could fully sequence at least a thousand genomes (samples) in a single flow cell (run), maybe two or three thousand. The sample prep (using automated microfluidics and robotics) and flow cell run would take ~24 hours. Of course, an institute charged with SARS-CoV-2 surveillance would be running many machines in parallel.
     
  12. billvon Valued Senior Member

    Messages:
    20,575
    That would be great - but they are not.

    We are getting better, though. A year ago we were sequencing about .5%* of all COVID cases, which was about .5-1% of all positive PCR tests (since more than half of the COVID cases back then wound up getting a PCR test.) That's the stat I remembered when I described it as "very few" above.

    After your comment I checked - and we are now we are sequencing about 14%** of all positive PCR tests. Which is good; that will give us better surveillance of variants, and will detect new variants (like the BA.2 subvariant) sooner.

    *Dr. Ingrid Katz, director of the Harvard Global Health Institute, Nov 2021: "Back in January, the numbers were quite low. It was really I think under half a percent in terms of the Covid infections that were prevalent were getting sequenced."

    **CDC Director Dr Rochelle Walensky, Jan 24 2022: "We are now sequencing approximately 80,000 samples per week -- about one in every seven PCR positive cases."
     
  13. KUMAR5 Valued Senior Member

    Messages:
    1,221
    Thanks a lot for explaining it for me in detsil. In nutshell, i feel specific geme rests for different variants for all infected people are not practiced. So my question is that when all variants of same virus exist in community at a given time with slight variation in symotoms, how serious outsome and deaths van be attributed to any one varian esp if nature of that variant is thought to be or observed as less severe than other preceding variants? Suppose if I claim most of recent hospitalization and deaths actually belong to Covid 19 or Delta not to Omicron, how I can be proven wrong esp if genome test is not done for them?
     
  14. KUMAR5 Valued Senior Member

    Messages:
    1,221
    Btw, when RT PCR test of all infected people is positive and gemome test for specific variant is done only in certain percentage and when all three variants exist at a given time, what can resist infected people to get infection from two or three variants at a time? Inharent nature differenciste in aggressiveness abd severity between these variants so is the observed symoptoms and outcomes. Do these varisnts have some kind of compromise that if one is infected from one other will not come into picture?

    Yes if there would had been different viruses altogether in existsnce at a time with no matching symptoms, they could had been differencisted altogether but here we are considering varisnts with some matching Symptoms. So probably in serious cases they might be infected be multiple varisnts so the apoarent outcome.
     
  15. Hercules Rockefeller Beatings will continue until morale improves. Moderator

    Messages:
    2,815
    Oh, we’re talking about different things! Crossed wires.

    I thought you were saying that, when a positive sample is chosen for genomic testing, the whole SARS-CoV-2 genome isn’t sequenced. It is, and that’s what I was referring to. I wasn’t trying to say that ALL positive clinical test samples are sent for genomic testing. That is totally impossible to achieve.
     
  16. billvon Valued Senior Member

    Messages:
    20,575
    Ah, that makes more sense. Thanks.
     
  17. billvon Valued Senior Member

    Messages:
    20,575
    It's very unlikely but possible. If you get a similar inoculum of two variants at once, and they reproduce at about the same rate, then you'll see both genotypes when testing. I have never heard of that happening, though, since invariably the infections happen at different times and/or they grow at different rates. (And an immune reaction against one variant will generally go after the other variant as well.)
    When you generate an immune response to a vaccine, the response (i.e. the antibodies and the immunologic memory) will recognize the specific antigens that the vaccine produces. They are chosen to be relatively immutable i.e. it will be hard for the virus to "evolve them out." There are a handful of antigens that it generates, so you get antibodies to several known antigens.

    When you generate an immune response to an infection the immune response is a lot more random. It generates both antibodies and memory against viral antigens, but since there are so many (thousands) which antigens your body will respond to is less well known. Since there are more of them you MAY get more robust immunity. Since they are random you MAY get immunity to antigens that are easily mutated, and thus will not protect you well against another strain.

    In addition, antibodies fade with time, and how fast they fade depends on what antigens they are designed to recognize. Your immunologic memory is much more durable.

    All that means that "it depends." Some studies have shown that naive infection (i.e. infection before vaccination) produces more durable immunity. In all cases, more recent vaccination or booster improves immunity, even if you've had it before.
     
  18. KUMAR5 Valued Senior Member

    Messages:
    1,221
    Thanks for telling these details. However can there likeky be such possibilty of multiple infection at a time in vieemw of::.

    1. Gemome testing of all existing varisnts are not done at sane time.
    2 SITEs of infection are different..
    3. Immune response to three variants is different
    4. Severity of symptoms and serious outcomes are different
    5. Immene protection amto these 3 are different. I think we do not not know if omicron or vaccination oriented immune protection actually happen or not to reinfection of Omicron. Why? Does body not take it as a long term threat?
    6. Statical data may also indicate such possibility.

    Hence logicalky it is quite dynamic to understand it
     
  19. billvon Valued Senior Member

    Messages:
    20,575
    How could you EVER do testing of all variants at the same time? They don't all exist at the same time.
    Nope. All COVID infections are found in the same sorts of tissues - just in different amounts.
    Yes, and that's why you have immunologic memory that protects you even if the antibodies denature and break down over time.
    Now you are getting it!
    If you mean "immunology is hard to understand" I agree. I've had several courses in biology and genetics - AND I have a wife who's a doctor who I can go to with questions - and I only know a small fraction of how our immune system works. It's a huge topic.
     
  20. KUMAR5 Valued Senior Member

    Messages:
    1,221
    What can resist these variants to remain present in body at a time ? These are variants not dufferent pathogens. Moreover site if infection is also different.
    [ Quote] Nope. All COVID infections are found in the same sorts of tissues - just in different amounts. [/Quote]
    .Still omicron infect differently than its preceding varisnts esp in lower respiratory tract and in other deep parts of body

    I think it is not yet clear if long term antibodies IgG or immunilogical memory are developed on or after Omicron infection or not? If early reinfection is possible, it may suggest these are not developed.
     
  21. KUMAR5 Valued Senior Member

    Messages:
    1,221
    Just asking casually.

    What negative Rapid Antigen test and RT PCR test for Covid 19 suggest?
    If low(below sickness) or nil antigen level?
    If low(below sickness) or nil viral load level?
     

Share This Page