Scary virus outbreak in China

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  • Joey_V
    Joey_V Posts: 8,600
    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: 4,742
    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: 712
    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.
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  • Gardenstater
    Gardenstater Posts: 4,742
    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: 712
    Gardenstater 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?
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  • halen
    halen Posts: 712
    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.
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  • Gardenstater
    Gardenstater Posts: 4,742
    edited March 2020
    halen wrote: »
    Gardenstater 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: 712
    And yes. Quest is not the only lab. LabCorp went live with it as well.
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  • BlueFox
    BlueFox Posts: 15,251
    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: 4,742
    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: 712
    Gardenstater wrote: »
    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.
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  • halen
    halen Posts: 712
    edited March 2020
    ...
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  • Gardenstater
    Gardenstater Posts: 4,742
    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: 3,353
    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.
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  • daddyjt
    daddyjt Posts: 3,031
    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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  • F1nut
    F1nut Posts: 51,680
    She's an idiot for waiting 12 days to get medical attention.
    Political Correctness'.........defined

    "A doctrine fostered by a delusional, illogical minority and rabidly promoted by an unscrupulous mainstream media, which holds forth the proposition that it is entirely possible to pick up a t-u-r-d by the clean end."

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  • BlueFox
    BlueFox Posts: 15,251
    daddyjt wrote: »
    I’m telling you, this virus is going to run it’s course - it’s got too much of a head start.

    That is the current issue. Nobody knows how long it will continue. Will it subside with warm weather? Will it mutate into a more fatal virus? Nobody knows.
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  • Gardenstater
    Gardenstater Posts: 4,742
    edited March 2020
    daddyjt wrote: »
    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.

    According to the CDC website, healthcare providers are supposed to report PUI (Persons Under Investigation) to their local and State Health Departments, so I guess the question is what are they doing and are they understaffed/overwhelmed?

    https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-criteria.html

    https://www.cste.org/page/EpiOnCall

    Here's an article about how it was handled back in late Jan in WA:

    https://www.wsna.org/news/2020/update-on-statewide-response-to-2019-novel-coronavirus-contact-investigation-continues

    NJ Dept. of Health link for healthcare professionals (my state):

    https://www.nj.gov/health/cd/topics/covid2019_professionals.shtml
    https://www.nj.gov/health/cd/reporting/
    Post edited by Gardenstater on
    George / NJ

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  • kevhed72
    kevhed72 Posts: 5,126
    Kex wrote: »
    It’s possible that she has no healthcare coverage, or coverage with a high co-pay, possibly a plan with 100% copay until a minimum out-of-pocket has been met.
    I know from first hand experience many people with serious healthcare issues avoid the doctor or ER because of the high costs involved, but thats a whole other issue nobody is willing to tackle....except maybe for Amazon? Weird world we live in....

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  • tonyb
    tonyb Posts: 33,065
    Thanks Garden and Halen for posting more details on the kits. Still, one would think that the same process used in a lab for detecting the coronavirus, is also used to confirm other contagious viruses.

    and if so, wouldn't these kits be more universal in their application across the board ? If so....one has to ask, why the heck we don't have a stockpile of them unless they can't be stored for periods of time. This isn't going to be the last virus to come around, I think we all know that.

    My brother has a trip to Sicily in May, has to re-think that. If any of you are planning a trip, airlines are discounting flights big time. Not you old folks, you stay home under the covers with a flashlight. :)
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  • Gardenstater
    Gardenstater Posts: 4,742
    According to the CDC website, healthcare providers are supposed to report PUI (Persons Under Investigation) to their local and State Health Departments, so I guess the question is what are they doing and are they understaffed/overwhelmed?

    https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-criteria.html

    https://www.cste.org/page/EpiOnCall

    Here's an article about how it was handled back in late Jan in WA:

    https://www.wsna.org/news/2020/update-on-statewide-response-to-2019-novel-coronavirus-contact-investigation-continues

    NJ Dept. of Health link for healthcare professionals (my state):

    https://www.nj.gov/health/cd/topics/covid2019_professionals.shtml
    George / NJ

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  • Gardenstater
    Gardenstater Posts: 4,742
    Be careful with editing your posts. It seems like there is a risk that Vanilla will make your whole post go POOF ! Just happened to me again.
    George / NJ

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  • tonyb
    tonyb Posts: 33,065
    It's an impossible task, for a country our size and the travel in and out that happens daily, to completely protect everyone against infectious diseases/viruses. It's also impossible to test everyone, especially since this type of virus can test negative one day, and the same person can have it again after being declared cured.

    We going to shut tight the borders, nobody in or out, no trade of goods. Cancel all overseas flights, all shipping goods at ports, use of paper money and coins. You'll never stop the spread, but you can slow it down. Pretty much what everyone is doing right now.

    Read a few stories about some who were suppose to self quarantine and instead went to parties. How irresponsible can you be. Makes ya want to punch these people....with a glove on of course.
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  • Gardenstater
    Gardenstater Posts: 4,742
    tonyb wrote: »
    Thanks Garden and Halen for posting more details on the kits. Still, one would think that the same process used in a lab for detecting the coronavirus, is also used to confirm other contagious viruses.

    and if so, wouldn't these kits be more universal in their application across the board ? If so....one has to ask, why the heck we don't have a stockpile of them unless they can't be stored for periods of time. This isn't going to be the last virus to come around, I think we all know that.

    My brother has a trip to Sicily in May, has to re-think that. If any of you are planning a trip, airlines are discounting flights big time. Not you old folks, you stay home under the covers with a flashlight. :)

    I'm pretty sure the nature of the PCR testing where you are identifying a particular DNA strand makes the test kits for a particular virus totally the opposite of universal. joeyv or others with more knowledge can correct me if I'm wrong but I think those Primer/Probe Reagents that are in Box#1 are developed using the particular virus to be detected and are specific to that virus.
    George / NJ

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  • tonyb
    tonyb Posts: 33,065
    Gardenstater wrote: »
    tonyb wrote: »
    Thanks Garden and Halen for posting more details on the kits. Still, one would think that the same process used in a lab for detecting the coronavirus, is also used to confirm other contagious viruses.

    and if so, wouldn't these kits be more universal in their application across the board ? If so....one has to ask, why the heck we don't have a stockpile of them unless they can't be stored for periods of time. This isn't going to be the last virus to come around, I think we all know that.

    My brother has a trip to Sicily in May, has to re-think that. If any of you are planning a trip, airlines are discounting flights big time. Not you old folks, you stay home under the covers with a flashlight. :)

    I'm pretty sure the nature of the PCR testing where you are identifying a particular DNA strand makes the test kits for a particular virus totally the opposite of universal. joeyv or others with more knowledge can correct me if I'm wrong but I think those Primer/Probe Reagents that are in Box#1 are developed using the particular virus to be detected and are specific to that virus.

    Could be, I dunno. If they are specific to a virus, then you can't really make a kit until a particular virus becomes a problem. Then it becomes a manufacturing issue and how quick you can churn them out, right ? Which might explain some lag in the availability of kits here, aside from the dumb decisions of the CDC to use their own.
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  • verb
    verb Posts: 10,176
    I went to our state's Heath & Human Services website for the first time, ever. Michigan is clear, so far:
    d72e44r11ifa.png

    To date, there are no confirmed COVID-19 cases in Michigan. As of March 4, eight people have been tested for COVOD-19 in the state; five by CDC and three by MDHHS.
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  • treitz3
    treitz3 Posts: 19,947
    Serious question here....how long does this virus live in air? Does anyone know or has it been reported yet?

    Tom
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  • mhardy6647
    mhardy6647 Posts: 34,918
    The way PCR (polymerase chain reaction) works is that each test is specific for a unique DNA (or, in the case of these viruses, DNA 'reverse transcribed' from RNA, RT-PCR) sequence for that pathogen. This requires two primers that are complementary to the DNA sequences that are used as the diagnostic for the pathogen being tested for. The size (length) and precise DNA sequence of the primers used and the conditions for denaturing and re-annealing the DNA strands for each organism or virus sequence to be tested for has to be carefully selected and tuned to minimize false negatives (which are 'worst case' for a diagnostic). A false positive is preferable to a false negative in diagnostic tests like this -- because a false positive can always be retested. A false negative walks out the door and infects his/her friends and acquaintances! :(

    What's cool about PCR is it uses the biochemical DNA replication machinery to amplify the signal, so the tests are almost unbelievably sensitive. They're also automated and reasonably fast and as precise as biology allows them to be. The test can also
    quantitative (qPCR). I'll spare y'all the details unless you really want to know.

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  • deronb1
    deronb1 Posts: 5,021
    Thanks Doc! Now my head hurts!
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  • Emlyn
    Emlyn Posts: 4,623
    treitz3 wrote: »
    Serious question here....how long does this virus live in air? Does anyone know or has it been reported yet?

    Tom

    It's not entirely clear yet because it is still being studied, but there have been studies of other coronaviruses that give clues. From what I have read from the CDC, the main transmission source is through airborne droplets between people in close contact. Like on cruise ships! Once no longer airborne in droplets, the virus can remain live on hard surfaces for minutes or days depending on the temperature and humidity environment. Sunlight kills it. If people wash their hands often and avoid touching their faces while out and about that surface to person transmission risk goes way way down. It also helps to avoid touching things with bare hands that many other people touch throughout the day such as door handles and elevator buttons. These rules go for anything though, not just a coronavirus.


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