Scary virus outbreak in China

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  • Gardenstater
    Gardenstater Posts: 2,014
    edited March 2020
    No I don't think so. I think it's a mouth swab that is done, but then it requires a special instrument (Applied Biosystems 7500 Fast DX Real-Time PCR Instrument with SDS 1.4 software) to run the test. I should've said that they are working on a serology (blood) test but that will only show the antibodies, not the actual virus like a PCR test does.
    George / NJ

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  • Willow
    Willow Posts: 10,435
    BlueFox wrote: »
    In California NOBODY drinks water from the tap. Period.

    I do. All day, every day.

    and you are worried about this virus?
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  • tonyb
    tonyb Posts: 32,356
    I saw the pic of that test kit, what does it look like to you. To me, it looks like 3 well sealed vials to put specimens in. That's a kit ? The process to test happens in the lab, not in these vials.

    I do admit though, the CDC screwed up demanding their own test kit instead of accepting the WHO one. Which I don't get if they are just vials like it appears to be.
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  • treitz3
    treitz3 Posts: 14,664
    e21qbd35627q.png

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  • Gardenstater
    Gardenstater Posts: 2,014
    tonyb wrote: »
    I saw the pic of that test kit, what does it look like to you. To me, it looks like 3 well sealed vials to put specimens in. That's a kit ? The process to test happens in the lab, not in these vials.

    I do admit though, the CDC screwed up demanding their own test kit instead of accepting the WHO one. Which I don't get if they are just vials like it appears to be.

    Well are you knowledgeable about laboratory viral testing? Cause I sure as heck am not. What looks like an empty vial isn't necessarily empty, but I believe the 4 (not 3) vials are assay controls that contain certain reagents necessary to do the test in the way the CDC has approved. You also need the special equipment and software to do the test. Here's the instructions if you want to wade through it:

    https://www.fda.gov/media/134922/download
    George / NJ

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  • BlueFox
    BlueFox Posts: 14,783
    Thanks. Interesting document.

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  • motorhead43026
    motorhead43026 Posts: 3,817
    edited March 2020
    DOW made a comeback end of day, 600M shares traded with a lot of buying late in the session. I suppose we can count on an up day Monday. The entities that are holding over the weekend will want to be rewarded.

    Seems like manipulation that they don't even try to hide anymore.

    All JMHO.
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  • tonyb
    tonyb Posts: 32,356
    That's why I'm asking, I don't know and googling the test kits is vague.

    I'm going by the explanation of the process in the link I posted earlier. Call me crazy, but the way they explained it, you'd think every lab had those tools at hand already.

    .....and if they don't, we should be asking why not, and if the almost 9 billion we just gave them might cover some of that.
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  • Gardenstater
    Gardenstater Posts: 2,014
    edited March 2020
    tonyb wrote: »
    That's why I'm asking, I don't know and googling the test kits is vague.

    I'm going by the explanation of the process in the link I posted earlier. Call me crazy, but the way they explained it, you'd think every lab had those tools at hand already.

    .....and if they don't, we should be asking why not, and if the almost 9 billion we just gave them might cover some of that.

    Well ok. I did read the instructions and I think I understand more or less. There are actually 2 boxes in the kit. That box contains the "primer and probe" reagents, which are enough for 1000 test reactions. Don't ask me what that means. The 2nd box has 4 tubes with the Positive Control in them, which provides enough for 800 5uL test reactions. These pics may explain it enough, but clearly the contents of the vials are crucial for testing the patient sample AND verifying that the test equipment and procedures were done properly so that a fair amount of confidence can be had that the result is a valid one.
    The Negative (NTC) control and the Extraction (HSC) control are provided by the lab, not the CDC:

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    George / NJ

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  • Joey_V
    Joey_V Posts: 7,804
    Give me a few and I'll explain the tests in detail.
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  • Gardenstater
    Gardenstater Posts: 2,014
    edited March 2020
    I really think the media is fear mongering. Take a look at this data from link below and note how the deathrate for confirmed cases in people under 80 and people with no pre-existing conditions is 0%:

    https://www.worldometers.info/coronavirus/coronavirus-age-sex-demographics/

    s1pu895ppkbk.png

    pd1h9aqdlg69.png
    George / NJ

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  • treitz3
    treitz3 Posts: 14,664
    I sneezed today. Should I quarantine myself?

    Tom
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  • Gardenstater
    Gardenstater Posts: 2,014
    edited March 2020
    Another thing. In mainland China you have 54,158 people recovered of the 80,573 cases up to this point. Since this is the origination point it is the best data (assuming it is accurate) to assess the recovery rate and mortality as this progresses.
    Post edited by Gardenstater on
    George / NJ

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  • Gardenstater
    Gardenstater Posts: 2,014
    Deathrate is probably MUCH less than the 2.3% (or whatever) that was initially reported:

    Why the Death Rate From Coronavirus is Plunging in China:

    https://www.npr.org/sections/goatsandsoda/2020/03/03/809904660/why-the-death-rate-from-coronavirus-is-plunging-in-china
    George / NJ

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  • Joey_V
    Joey_V Posts: 7,804
    edited March 2020
    @tonyb

    The tests are nasal swab, nasopharyngeal swab, and expectorated sputum samples.
    PCR takes a few days to return.
    However, certain cities like Dallas will have labs that will have a less than 1 day turn around.

    I used to do PCR when I was in college for research.

    Basically the sample is collected with a swab, the swab is then placed in a reagent.
    The vial is brought to a lab.
    The lab then breaks down the dna (zipper down), down the middle, cleaving it to a single strand rather than a double helix. Usually at >90C heat.
    A Dna polymerase enzyme is then added, Taq or whatever, which allows for the primer to bond prior to the anneal (zipper up) process, IIRC. At a lower temp, I recall 50C.
    Then the peptides in the solution bond like a zipper, I believe around 70C.

    Then the process is repeated for 40 cycles or so, creating billions of DNA units.

    Then the solution can be measured.

    That's why it takes a while.
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  • Gardenstater
    Gardenstater Posts: 2,014
    edited March 2020
    Joey_V wrote: »
    @tonyb

    The tests are nasal swab, nasopharyngeal swab, and expectorated sputum samples.
    PCR takes a few days to return.
    However, certain cities like Dallas will have labs that will have a less than 1 day turn around.

    I used to do PCR when I was in college for research.

    Basically the sample is collected with a swab, the swab is then placed in a reagent.
    The vial is brought to a lab.
    The lab then breaks down the dna (zipper down), down the middle, cleaving it to a single strand rather than a double helix. Usually at >90C heat.
    A Dna polymerase enzyme is then added, Taq or whatever, which allows for the primer to bond prior to the anneal (zipper up) process, IIRC. At a lower temp, I recall 50C.
    Then the peptides in the solution bond like a zipper, I believe around 70C.

    Then the process is repeated for 40 cycles or so, creating billions of DNA units.

    Then the solution can be measured.

    That's why it takes a while.

    So again, it is clear that those 4 vials are not simply empty vials as tonyb suspected, but they are the Primer Reagents that the lab needs to complete the process you describe, but according to the CDC's complicated and probably more accurate process (4 different reagents) than the rest of the world (but was it worth the delays?). They have enough in them for something like 1000 patients to be tested.

    Now the CDC and the FDA are allowing labs like Qwest Diagnostics and Labcorp, etc.. to develop their own "test kits" or Primer Reagents I guess, with samples of the virus that they have obtained from the CDC, cutting through all the red tape that would normally exist for FDA approval. We should see the testing numbers skyrocket in the coming days.

    George / NJ

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  • halen
    halen Posts: 639
    tonyb wrote: »
    I saw the pic of that test kit, what does it look like to you. To me, it looks like 3 well sealed vials to put specimens in. That's a kit ? The process to test happens in the lab, not in these vials.

    I do admit though, the CDC screwed up demanding their own test kit instead of accepting the WHO one. Which I don't get if they are just vials like it appears to be.

    That is correct. It still needs to be sent to a lab for tests. It is not like a fish tank PH strip that you dip in and have instant results. Also kind of like the at home HIV or ancestry test kits.

    I just happen to be one of the guys that wrote the code to communicate with the lab instruments. ASTM comm over both TCP/IP or Serial using MD5 hash checksum standards.

    With that said. I have boarded up all windows, added a 5th dead bolt door lock, took home three bears to guard the front, and back doors. Honey Badger in back yard. No snakes. I just don’t do effin snakes. Garlic for vampires and pics of Rosie O Donnel for democr... ahem zombies. Lol.
  • Gardenstater
    Gardenstater Posts: 2,014
    No it isn't correct. The vials are in the posession of the labs that have the qualifications and equipment to do the tests and they have enough reagent to do tests on something like 1000 patients. The doctors offices that take the swab samples have to follow a certain procedure as far as what sort of preservative tube they put it in but that is standard procedures, and then they ship it off to the lab or have it get picked up.
    George / NJ

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  • halen
    halen Posts: 639
    No it isn't correct. The vials are in the posession of the labs that have the qualifications and equipment to do the tests and they have enough reagent to do tests on something like 1000 patients. The doctors offices that take the swab samples have to follow a certain procedure as far as what sort of preservative tube they put it in but that is standard procedures, and then they ship it off to the lab or have it get picked up.

    You taking to me?
  • halen
    halen Posts: 639
    edited March 2020
    If you want to talk about lab instruments. Either you have true first hand knowledge or you don’t. Don’t try to wiki it and spread it like facts.

    Couple questions. What is the turn around time for that instrument and it’s capacity? Does it do water cup? Wet run? Dry run? QC? And at what rate of QC and threshold?

    For those that don’t know QC, it is placed in with the patient samples at predetermined areas. And contains the known virus. If the instrument does not come back with results that it is a virus at those predetermined locations, the test could be compromised.
  • Gardenstater
    Gardenstater Posts: 2,014
    edited March 2020
    halen wrote: »
    No it isn't correct. The vials are in the posession of the labs that have the qualifications and equipment to do the tests and they have enough reagent to do tests on something like 1000 patients. The doctors offices that take the swab samples have to follow a certain procedure as far as what sort of preservative tube they put it in but that is standard procedures, and then they ship it off to the lab or have it get picked up.

    You taking to me?

    Yeah. You don't put the specimen in any of those 4 reagent vials in the CDC test kit. Those vials have enough reagent for testing 1000 patients, so the sample from any one patient is not put into one of those vials and it is only used by the labs during the PCR testing process.

    This whole thing started because tonyb had the suspicion that the vials were just empty sample collection vials, so I did the research into what they actually were. Nobody said anything about the test equipment, except what it was called and that the lab had to have it to do the PCR testing, so might as well cool your guns lol.
    George / NJ

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  • halen
    halen Posts: 639
    And yes. Quest is not the only lab. LabCorp went live with it as well.
  • BlueFox
    BlueFox Posts: 14,783
    Currently twenty states have the virus. I wonder if the additional testing will bring it up to fifty states.
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  • Gardenstater
    Gardenstater Posts: 2,014
    halen wrote: »
    And yes. Quest is not the only lab. LabCorp went live with it as well.

    Yeah I actually mentioned both of those. OPKO Health Inc. and Co-Diagnostics also have them ready and can be ordered pending review by the FDA under emergency-use authorization.
    George / NJ

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  • halen
    halen Posts: 639
    halen wrote: »
    And yes. Quest is not the only lab. LabCorp went live with it as well.

    Yeah I actually mentioned both of those. OPKO Health Inc. and Co-Diagnostics also have them ready and can be ordered pending review by the FDA under emergency-use authorization.

    You sound like someone within healthcare industry. State your name and alliance soldier. Haha.
  • halen
    halen Posts: 639
    edited March 2020
  • Gardenstater
    Gardenstater Posts: 2,014
    edited March 2020
    No just someone whose portfolio is getting hammered and trying to do research, and to also find out what's what with a media industry that can't really be trusted imho.
    George / NJ

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  • aprazer402
    aprazer402 Posts: 2,426
    edited March 2020
    First confirmed Covid-19 case in Omaha announced this afternoon. A 36 year old woman that had been in the UK recently. Claims to have had all the symptoms for the past 12 days. So it got so bad she drove to a west Omaha hospital Wednesday and walked in. She should have stayed home and called her doctor. So they had to transport her from the hospital she walked into, to UNMC where she is in their isolation section in serious condition. Very little word from UNMC about the 13 or so they've been treating from the first cruise ship.

    There was a discussion on local radio this afternoon, people calling in and venting asking for the woman's name or at least her place of employment to be released. I know
    HIPPA laws. But to protect the community, who investigates these infected persons contacts for the past two weeks? The medical professionals shouldn't have to, they have patients to treat.
  • daddyjt
    daddyjt Posts: 1,468
    aprazer402 wrote: »
    ...But to protect the community, who investigates these infected persons contacts for the past two weeks? The medical professionals shouldn't have to, they have patients to treat.

    There simply isn’t the depth within the system to investigate even this one case. Think about it - she’s been sick for twelve (12) days. Within that 12 days, let’s say she’s had contact with 60 people (5 per day, x 12 days). That’s probably WAY low, but just for example, the 5 she contacted on her first day each contact 5 (25) others, then those 25 each contact 5 (125), and so on... and that’s just from her day one. You’re talking thousands of people, and that’s just from HER.

    I’m telling you, this virus is going to run it’s course - it’s got too much of a head start.
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