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COVID-19 technical discussion

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    #32
    lozenges
    Registered Users Posts: 290 ✭✭lozenges


    dermob wrote: »
    Out of my depth a bit here, but looking for answers:



    The current testing methods that we are using for this virus, can someone answer these questions in relation to it:

    What does the test specifically detect, as in does it detect prescence of coronavirus, Sars-Cov-2, or Covid 19

    There are several (?5) different strains of coronavirus, most of which cause common cold type symptoms. Covid 19 is one of these. Sars-CoV-2 is the scientific name for Covid-19 i.e. they are identical.

    The tests we are using check only for the presence of Covid-19 ie not for the other 'common cold' type coronavirus.


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    #33
    dermob
    Registered Users Posts: 110 ✭✭dermob


    from what i understand, Covid 19 is the disease that is borne from the virus Sars-cov-2.

    How is it determined that you have covid 19?


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    #34
    lozenges
    Registered Users Posts: 290 ✭✭lozenges


    dermob wrote: »
    from what i understand, Covid 19 is the disease that is borne from the virus Sars-cov-2.

    How is it determined that you have covid 19?

    The terms are interchangeable, Covid 19 refers to the virus and also the disease, Sars CoV2 is the scientific name for it.

    The RNA (virus genes) are isolated, converted to a different form and amplified so that they are detectable. RT-PCR is the name of the process (Scientists feel free to correct me if this is inaccurate, to my knowledge this is the test currently in use).


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    #35
    dermob
    Registered Users Posts: 110 ✭✭dermob


    lozenges wrote: »
    The terms are interchangeable, Covid 19 refers to the virus and also the disease, Sars CoV2 is the scientific name for it.




    The RNA (virus genes) are isolated, converted to a different form and amplified so that they are detectable. RT-PCR is the name of the process (Scientists feel free to correct me if this is inaccurate, to my knowledge this is the test currently in use).

    i disagree with the above based on this https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it

    i still dont know what the test actually test for?


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    #36
    lozenges
    Registered Users Posts: 290 ✭✭lozenges


    dermob wrote: »
    i disagree with the above based on this https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it

    i still dont know what the test actually test for?

    Fair enough. Certainly in clinical practice currently Covid 19 is being used to refer to the virus/disease interchangeably, nobody is referring to the virus as Sars-CoV-2 and the disease as Covid-19.

    Re what the test checks for, I've answered as best I can as to how the test works so I'm not quite sure exactly what you're asking.


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    #37
    dermob
    Registered Users Posts: 110 ✭✭dermob


    Re what the test checks for, I've answered as best I can as to how the test works so I'm not quite sure exactly what you're asking.[/QUOTE]


    No worries on the name.

    Im askiing if the test is a positive or negative to any of the following:
    1. coronavirus
    2. Sars - Cov-2
    3. Covid 19


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    #38
    lozenges
    Registered Users Posts: 290 ✭✭lozenges


    dermob wrote: »
    Re what the test checks for, I've answered as best I can as to how the test works so I'm not quite sure exactly what you're asking.


    No worries on the name.

    Im askiing if the test is a positive or negative to any of the following:
    1. coronavirus
    2. Sars - Cov-2
    3. Covid 19[/quote]

    It tests positive for bits of SARS -CoV-2 virus particles essentially. (SARS -CoV-2 is the same to me as Covid-19, but anyway)

    SARS -CoV-2 is one of a family of viruses called coronaviruses. The test only tests for that one kind of coronavirus, but not the other kinds in the family.

    Hope that makes sense


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    #39
    dermob
    Registered Users Posts: 110 ✭✭dermob


    It tests positive for bits of SARS -CoV-2 virus particles essentially. (SARS -CoV-2 is the same to me as Covid-19, but anyway)

    SARS -CoV-2 is one of a family of viruses called coronaviruses. The test only tests for that one kind of coronavirus, but not the other kinds in the family.

    Hope that makes sense[/QUOTE]




    Thanks, it doesnt really make sense.

    i know every country hase different testing methods and i cannot find any specific reference to what we are testing for in ireland.

    you state above that the test is specific to Sars - Cov -2, yet the FDA have published this https://www.fda.gov/media/136151/download, and extracted from this is the following, paragraph2, line 5 " Positive results do not rule out bacterial infection or co-infection with
    other viruses. The agent detected may not be the definite cause of disease"

    On this basis, as i understand it, your statement is incorrect.


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    #40
    TheChizler
    Registered Users Posts: 9,400 ✭✭✭TheChizler


    dermob wrote: »
    Thanks, it doesnt really make sense.

    i know every country hase different testing methods and i cannot find any specific reference to what we are testing for in ireland.

    you state above that the test is specific to Sars - Cov -2, yet the FDA have published this https://www.fda.gov/media/136151/download, and extracted from this is the following, paragraph2, line 5 " Positive results do not rule out bacterial infection or co-infection with
    other viruses. The agent detected may not be the definite cause of disease"

    On this basis, as i understand it, your statement is incorrect.

    They're saying you can also be infected other things at the same time, which the test doesn't test for. The symptoms might be caused by something else, even though they are likely positive for COVID-19.


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    #41
    dermob
    Registered Users Posts: 110 ✭✭dermob


    Thanks Chizler, it states "The agent detected may not be the definite cause of disease"

    So by my reading the test indicates the prescence of Sors-Cov-2, but it could also indicate the prescence other virus.

    is this an incorrect asumption?


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    #42
    Breezer
    Registered Users Posts: 3,228 ✭✭✭Breezer


    dermob wrote: »
    Thanks Chizler, it states "The agent detected may not be the definite cause of disease"

    So by my reading the test indicates the prescence of Sors-Cov-2, but it could also indicate the prescence other virus.

    is this an incorrect asumption?
    It doesn’t say anything at all about the presence of other viruses. It says whether RNA fragments (bits of genes) from the Sars-CoV-2 virus are detected on the swab that was taken.

    It can’t say that you definitely don’t have SARS-CoV-2 in your system, just whether or not it was detected on the swab.

    It can’t say whether or not you have other viruses or bacteria in your system, or whether the disease you have is being caused by these organisms or by Sars-CoV-2.

    This is standard reporting jargon for any type of microbiological test. In reality, PCR is an extremely sensitive test method, and will only miss Sars-CoV 2 if the swab wasn’t taken properly. And in reality, if you are presenting with the symptoms Sars-CoV-2 is known to cause, and only those symptoms, and you have a positive test, then your symptoms are due to that.

    All medical tests need to be interpreted in the context of the patient’s clinical presentation. It’s why a doctor will ask you questions and then examine you before ordering a test.


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    #43
    dermob
    Registered Users Posts: 110 ✭✭dermob


    Breezer wrote: »
    It doesn’t say anything at all about the presence of other viruses. It says whether RNA fragments (bits of genes) from the Sars-CoV-2 virus are detected on the swab that was taken.

    As far as i am aware i cannot find a test that that detects Sars-Cov-2 specifically, can you link information to this?


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    #44
    lozenges
    Registered Users Posts: 290 ✭✭lozenges


    dermob wrote: »
    Breezer wrote: »
    It doesn’t say anything at all about the presence of other viruses. It says whether RNA fragments (bits of genes) from the Sars-CoV-2 virus are detected on the swab that was taken.

    As far as i am aware i cannot find a test that that detects Sars-Cov-2 specifically, can you link information to this?

    Not sure how much use it will be to you, but this is a link for the RT-PCR kit in use in France. I don't know which kits are in use in Ireland but they are all the same just by different manufacturers.

    https://www.generon.ie/read/newsletter-26/ce-ivd-qpcr-covid-19-test-in-2-2261.html


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    #45
    Breezer
    Registered Users Posts: 3,228 ✭✭✭Breezer


    dermob wrote: »
    As far as i am aware i cannot find a test that that detects Sars-Cov-2 specifically, can you link information to this?

    I can’t I’m afraid, I’m a clinician, not a lab scientist, and would have no idea where to find the specific information you’re looking for. My answer was based on my understanding of the principles of PCR, which is a highly sensitive and specific test based on knowledge of a microorganism’s unique genetic sequence.

    I hope you don’t mind me saying, but you seem highly suspicious of this test. Do you mind if I ask why?

    Edit: I found details of one test being used in Washington: [url] https://testguide.labmed.uw.edu/public/view/NCVQLT?tabs=no[/url]

    From the linked FAQ:
    How specific is the COVID RT-PCR test? Does it cross-react with the “coronavirus” test on an extended respiratory panel?

    All of the offered assays are highly specific for the SARS-CoV-2 virus, with no known cross-reactivity to either other human coronaviruses or to other human respiratory pathogens.

    I can’t find the details of the test the NVRL are using here in Ireland, but it would be based on similar principles.

    Still genuinely curious as to why you seem so sceptical (nothing wrong with that of course).

    Edit 2: So yeah, essentially what lozenges already said. Sorry, I’m tired.


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    #46
    TheChizler
    Registered Users Posts: 9,400 ✭✭✭TheChizler


    dermob wrote: »
    Thanks Chizler, it states "The agent detected may not be the definite cause of disease"

    So by my reading the test indicates the prescence of Sors-Cov-2, but it could also indicate the prescence other virus.

    is this an incorrect asumption?

    No is says nothing about a different virus. Just that SarsCov2 was detected.

    Imagine someone has allergies that can result in flu-like symptoms, and at the same time gets infected by the SarsCov2 virus. If they end up with breathing difficulties it's possible that they're caused by the virus, the allergies, or something else entirely. The test shows they have the virus, but doesn't tell you what's causing symptoms. Doctors would have to use their judgement in that unlikely situation.

    Caveat, I'm not a health professional, just very familiar with technical documentation like that paper.


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    #47
    Miike
    Registered Users Posts: 2,021 ✭✭✭Miike


    dermob wrote: »
    As far as i am aware i cannot find a test that that detects Sars-Cov-2 specifically, can you link information to this?

    The specific test you're looking for is Real-time Reverse Transcription Polymerase Chain Reaction or "rRT-PCR". Which in very simple terms is a test which is used to detect a very specific part the genetic material of a pathogen, and in this case it's part of the genetic material (RNA) unique to SARS-CoV-2 (the virus responsible for COVID19). The current problem cited in the literature with this test is the sensitivity and specificity of current testing methods (which has gotten better as the disease timeline moves on).

    For clarity:
    COVID19 = Coronavirus Disease 2019 (The ILLNESS)
    SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2 (the virus responsible for the illness)


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    #48
    dermob
    Registered Users Posts: 110 ✭✭dermob


    My concerns/sceptisim are borne,initially over my parents being older and falling into the over 70 category and member of my family being immuno compromised. Some of them are quite scared and I was seeking to get my head around this situation in an attempt to offer some levels of comfort.

    also the fact that there are a lot of names on this thing and all are being talked about in mainstream media (coronavirus, Ncov, Sars-cov-2, Covid 19 etc). And i feel that its confusing to older people, including my parents.

    Some of the media i have seen are as follows, im not going to link as i dont want to add to confusion etc but namely:

    - the downgrading of Covid 19 by the uk goverment that its no longer classified as a HCID.
    - Italys publications on 99% of cases having previous conditions
    - Number of professiors comming out and questioning this pandemic.
    (Stanford’s John P.A. Ioannidis, Dr Sucharit Bhakdi)
    - the different approaches some countries are taking (sweden)

    The queries on testing are based on the fact that every country is using differnt methods (of the same test) to find the virus and im wondering is there any discrepencies in how they are reported or classified, and also the different view on mortality rates.

    I do think we are in a terrible situation, but there is a huge amount of contradicting information around about it, and just trying to make some sort of sense of it all.


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    #49
    lozenges
    Registered Users Posts: 290 ✭✭lozenges


    dermob wrote: »
    My concerns/sceptisim are borne,initially over my parents being older and falling into the over 70 category and member of my family being immuno compromised. Some of them are quite scared and I was seeking to get my head around this situation in an attempt to offer some levels of comfort.

    also the fact that there are a lot of names on this thing and all are being talked about in mainstream media (coronavirus, Ncov, Sars-cov-2, Covid 19 etc). And i feel that its confusing to older people, including my parents.

    Some of the media i have seen are as follows, im not going to link as i dont want to add to confusion etc but namely:

    - the downgrading of Covid 19 by the uk goverment that its no longer classified as a HCID.
    - Italys publications on 99% of cases having previous conditions
    - Number of professiors comming out and questioning this pandemic.
    (Stanford’s John P.A. Ioannidis, Dr Sucharit Bhakdi)
    - the different approaches some countries are taking (sweden)

    The queries on testing are based on the fact that every country is using differnt methods (of the same test) to find the virus and im wondering is there any discrepencies in how they are reported or classified, and also the different view on mortality rates.

    I do think we are in a terrible situation, but there is a huge amount of contradicting information around about it, and just trying to make some sort of sense of it all.

    Sure.
    Regarding Italy - I doubt it's 99%, but they have the second oldest population in the world after Japan, so it makes sense that they would have very high mortality rates and that many of those affected would have pre-existing conditions.

    Re different approaches taken by different countries - this is not really based on the biology of the virus. As I see it, it's more a political decision taken by each country's governments as to the balance of harm caused by the virus (hospitalisations, mortalities) compared to the harm caused to the economy by restrictions/lockdowns (job losses, possible recession etc).

    It also depends partly on social factors - e.g. in Italy multiple family generations living in one household is common, whereas Sweden apparently has a high proportion of one person households. So rapid spread would be more likely in the former situation than the latter.


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    #50
    sudzs
    Registered Users Posts: 8,718 ✭✭✭sudzs


    Also out of my depth!

    There seems to be a lot of variability in the severity of this disease, from extremely severe and needing hospitalisation to extremely mild and having hardly any symptoms at all.

    I'm wondering what could be the contributing factors to this variety in the severity of the illness. Could it just be how much of the virus someone is exposed to? Is it differences in individuals immune systems? Or could it be that some people have some sort of 'semi-immunity' to it as a result of previous infections with another coronavirus, possibly one closely related to covid-19??


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    #51
    Breezer
    Registered Users Posts: 3,228 ✭✭✭Breezer


    dermob wrote: »
    My concerns/sceptisim are borne,initially over my parents being older and falling into the over 70 category and member of my family being immuno compromised. Some of them are quite scared and I was seeking to get my head around this situation in an attempt to offer some levels of comfort.

    also the fact that there are a lot of names on this thing and all are being talked about in mainstream media (coronavirus, Ncov, Sars-cov-2, Covid 19 etc). And i feel that its confusing to older people, including my parents.

    Some of the media i have seen are as follows, im not going to link as i dont want to add to confusion etc but namely:

    - the downgrading of Covid 19 by the uk goverment that its no longer classified as a HCID.
    - Italys publications on 99% of cases having previous conditions
    - Number of professiors comming out and questioning this pandemic.
    (Stanford’s John P.A. Ioannidis, Dr Sucharit Bhakdi)
    - the different approaches some countries are taking (sweden)

    The queries on testing are based on the fact that every country is using differnt methods (of the same test) to find the virus and im wondering is there any discrepencies in how they are reported or classified, and also the different view on mortality rates.

    I do think we are in a terrible situation, but there is a huge amount of contradicting information around about it, and just trying to make some sort of sense of it all.
    All very understandable and relatable reasons. I hope you got some answers :)


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    #52
    echo beach
    Registered Users Posts: 1,252 ✭✭✭echo beach


    sudzs wrote: »
    Also out of my depth!
    Everybody is out of their depth on this one!
    There seems to be a lot of variability in the severity of this disease, from extremely severe and needing hospitalisation to extremely mild and having hardly any symptoms at all.
    That is the case with many infectious diseases, e.g measles is usually mild but can have serious complications and even be fatal in some cases.
    I'm wondering what could be the contributing factors to this variety in the severity of the illness. Could it just be how much of the virus someone is exposed to? Is it differences in individuals immune systems? Or could it be that some people have some sort of 'semi-immunity' to it as a result of previous infections with another coronavirus, possibly one closely related to covid-19??
    Probably all of the above and many other factors we aren't aware of. Age and pre-existing conditions, especially hypertension and obesity, look at this very early stage to be important. There is also in most conditions a random element or what could be termed sheer bad luck.


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    #53
    Miike
    Registered Users Posts: 2,021 ✭✭✭Miike


    Interesting replication of the Chinese data from New York
    CN: https://www.medrxiv.org/content/10.1101/2020.03.11.20031096v2.full.pdf

    NY: https://www.medrxiv.org/content/10.1101/2020.04.08.20058073v1.full.pdf


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    #54
    fryup
    Registered Users Posts: 18,069 ✭✭✭✭fryup


    ^^^^^^^^^^^^

    what does it implicate? there's a link in blood type and severity of infection?


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    #55
    Miike
    Registered Users Posts: 2,021 ✭✭✭Miike


    fryup wrote: »
    ^^^^^^^^^^^^

    what does it implicate? there's a link in blood type and severity of infection?

    Basically ABO blood groups are showing different association for risk of COVID19: O is significantly lower than A, where A seems to be quite high risk. We do not know why but definitely warrants further investigation.


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    #56
    darjeeling
    Registered Users Posts: 962 ✭✭✭darjeeling


    A couple of good podcasts:

    This Week in Virology
    https://www.microbe.tv/twiv/
    This is a very long-running podcast that has turned itself over to COVID-19 recently, and does a couple of long episodes a week, with interviews with coronavirus experts, immunologists, physicians.

    A more recently-launched second podcast hosted by the same main presenter, this time focusing on immunology:
    https://www.microbe.tv/immune/
    The last two episodes have dealt with immunology of COVID-9

    They cover many different scientific aspects of the pandemic - virology, immune response to the virus, immune pathology seen in severe cases, PCR & serological testing, vaccines and more - and review the papers being rushed out during the pandemic, and the evolving clinical treatments.


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    #57
    amandstu
    Registered Users Posts: 3,370 ✭✭✭amandstu


    I heard that dementia seems to be one of the most important underlying conditions affecting mortality (or severiity of outcome).

    I wonder why that might be? Could it just be that symptoms are treated at a later stage since those patients would less likely to communicate their ongoing symptoms to their careers as promptly as would the general population?

    Or would dementia lead to a general lack of physical resilience that would weaken their defences?


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    #58
    Miike
    Registered Users Posts: 2,021 ✭✭✭Miike


    darjeeling wrote: »
    A couple of good podcasts:

    This Week in Virology
    https://www.microbe.tv/twiv/
    This is a very long-running podcast that has turned itself over to COVID-19 recently, and does a couple of long episodes a week, with interviews with coronavirus experts, immunologists, physicians.

    A more recently-launched second podcast hosted by the same main presenter, this time focusing on immunology:
    https://www.microbe.tv/immune/
    The last two episodes have dealt with immunology of COVID-9

    They cover many different scientific aspects of the pandemic - virology, immune response to the virus, immune pathology seen in severe cases, PCR & serological testing, vaccines and more - and review the papers being rushed out during the pandemic, and the evolving clinical treatments.

    Been listening to TWIV for sometime. Absolutely love it. Highly recommend episode 599 with that lady who worked on Ivermectin for Merck. Fantastic information from possibly one of the best placed sources on the subject matter.


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    #59
    Miike
    Registered Users Posts: 2,021 ✭✭✭Miike


    Follow up re ARBs ACEIs from previous comments:

    http://ahajournals.org/doi/pdf/10.1161/CIRCRESAHA.120.317134


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    #60
    echo beach
    Registered Users Posts: 1,252 ✭✭✭echo beach


    amandstu wrote: »
    I heard that dementia seems to be one of the most important underlying conditions affecting mortality (or severiity of outcome).

    I wonder why that might be? Could it just be that symptoms are treated at a later stage since those patients would less likely to communicate their ongoing symptoms to their careers as promptly as would the general population?

    Or would dementia lead to a general lack of physical resilience that would weaken their defences?

    Dementia patients are vulnerable and some of the most difficult to protect. They don’t understand the situation, the need for social distancing, the importance of washing your hands. They don’t know why everything is closed and their routine disrupted which in itself worsens their condition.

    Sending some into hospital when they can’t be accompanied by a family member or familiar carers would be a cruelty so difficult choices have to be made.


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    #61
    amandstu
    Registered Users Posts: 3,370 ✭✭✭amandstu


    I am wondering about blood plasma from recovered patients.

    I know this is in the early stages of verification as to the benefits but I have heard that 1 person's blood can in principle treat 4 ill patients.

    Why ,does it not seem possible to grow the antibodies from the serum?

    Are there any trials in this direction?


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