SARS cov2 and Covid 19


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  • #61688
    Clark

      I think it’s extremely unlikely there will be any “forcible mass vaccination”. It isn’t even yet known whether any vaccine can impart a worthwhile period of immunity, nor indeed whether the risk of Antibody Dependent Enhancement rules out effective vaccines altogether.

      The Mail story is just the usual anti-restrictions propaganda from the Right; they attack anything that impedes flow of profit to the richest. What were the health authorities meant to do? The government left the borders open too late and applied restrictions too late. In March, the health authorities were facing an impending tsunami of covid, staff shortages from both infection and increased demand, and hospitals likely to become infection hot-spots – remember that as late as mid-March, the government “plan” was to do nothing and let it rip through the population. Cancer sufferers, and chemo patients in particular, are vulnerable to infection; keep’em coming into hospital for treatment, when staff are the most likely infection vector?

      Still, when the fatalities are mostly old people it has been popular to just write them off, “they’d have died soon anyway”, but apparently different logic applies to cancer treatment – when it suits the Right-wing media.

      #61717
      Clark

        SA, October 18, 10:51, #61615:

        “the CFR is lower this time round. […] patients admitted to ITU now have, I think, 80% chance of surviving, compared to figures nearer to 50% in April-May.”

        This is good news, but it makes it even more important not to overwhelm the hospitals. In April/May, the death rate would have doubled had the hospitals been overrun (100% / 50%), but now the death rate would increase by a factor of five (100% / 20%).

        It has been fashionable in the anti-restriction propaganda to cite an IFR Infection Fatality Rate of around “just” 1% (“99% survive”), but this is the IFR with treatment. The “raw” IFR was – and will remain – nearer 2.8%, over 1.8 million people in the UK.

        In our favour, the rate of spread has been much lower so far during this increase, making it easier not to overrun the hospitals.

        #61751
        SA

          Clark
          You spoke too soon! Our host has now published on the main thread as you know, and the conspiracy theorists are flooding in.

          #61846
          Dredd

            Yes the conspiracy theorists are flooding in, and they’re presenting dubious testimony from alleged experts proclaiming that there’s no virus, or if there is a virus it’s harmless, and the tests for it are made up anyway, etc. Of course these commenters know diddly-squat about what they’re commenting on and haven’t checked whether their extraordinary revelations withstand any critical scrutiny: they’re just copying stuff posted on other covid-conspiracy websites – and trying to drag Mr Murray’s blog down to the same level in the process.

            #61809
            SA

              In the discussion in the main webpage on Covid-19 and fearmongering, there was a discussion started by someone calling him (her) self John Piliger about an interview with Mike Yeadon. This prompted a discussion and I responded in that thread but would like to elaborate a bit more here.

              Mike Yeadon’s basic hypothesis is that SAGE got it all wrong, because there is an absence of immunologists and virologists and a preponderance of mathematical modelers and herd psychologists (sorry my term) in SAGE. This has led to a rather skewed discussion and recommendations. I basically agree with this, having discussed the folly of relying on mathematical modelling as a main tool to combat a new pandemic, rather than on reflex applying traditionally tried and tested, pre-prepared plans for dealing with the pandemic. The aim would have been to reduce transmission to near zero, something achieved by China, New Zealand and Australia and others. This would have been a single bite at the cherry as wider transmission make any measures more difficult to implement. Just to recap: an early use of PPI amongst frontline workers, widespread testing and tracking followed by effective supervised isolation was what was needed. The first lockdown was merely effective at ‘flattening the curve’ to buy time, but no more than that, and the time bought has been squandered; not entirely, because the NHS has become more stream lined to deal with cases and some treatments and better management is leading to improved survival. I maintain that it is now too late to apply lockdown, unless it is really draconian, which would be unacceptable- so it is too late to apply another lockdown. Other measures need to be taken. And this highlights the on the hoof nature of the decision making in this pandemic, that our government and its advisers have taken. A detailed long term plan with targets and regular reviews was needed, and strong involvement by all parties and local councils and public health. Instead there was a centralised, inefficient and privatised response.

              To return to Mike Yeadon. Of course he has a point but there are also some problems with what he says. He says that SAGE made two errors.

              • Error 1: Assuming that 100% of the population was susceptible to the virus and that no pre-existing immunity existed.
              • Error 2: The belief that the percentage of the population that has been infected can be determined by surveying what fraction of the population has antibodies.

              He then analyses these. He states that the first error assumes that because this is a new virus

              It’s ridiculous because while SARS-CoV-2 is indeed novel, coronaviruses are not. There’s no such thing as an ‘ancestor-less virus’. You will recall at least two, then-novel coronaviruses in the recent past: SARS in 2003 and MERS in 2012 (Zhu et al, 2020). While they didn’t spread worldwide, they are very similar, both at a sequence level and at a structural level, to SARS-CoV-2.
              But there’s much more than these infamous coronaviruses. For reasons I don’t understand, given the significance of what I’m about to tell you, none of the so-called medical correspondents and science journalists on radio and TV have ever (as far as I know) spoken of the four, endemic, common-cold inducing coronaviruses. It’s well understood by clinicians and scientists who’ve spent any time reading the scientific literature that at least four coronaviruses circulate freely in UK and elsewhere where they’ve been studied. They have names: OC43, HKU1, 229E and NL63 (Zhu et al, 2020). .

              There is the assumption therefore that there is some background immunity to SARS Cov2 because of some similarities to other coronaviruses. And even if this cannot be shown by cross reacting antibodies, Yeadon states that this may be due to innate immunity and cross reacting memory T cells and that this has been shown for other viruses. In the case of corona viruses, this cross reactivity may be due to the similarities in the spike protein between the different viruses.

              There is some evidence for this cross reactivity in antibody testing as

              Sequence similarities of the common viral proteins between SARS-CoV-2 and SARS-CoV, MERS-CoV
              or LPH-CoV (229E, NL63, OC43 or HKU1). The polyprotein 1AB, and spike (S), membrane
              (M), envelop (E) and nucleocapsid (N) proteins

              But the problem arises with inconsistencies with therefore arguing about the rates of antibody positivity, reported by the NHS/Imperial College study of 7%, and that of Ioannides in Santa Barbara of more like 30%. If you argue that one is an underestimate and the other is an overestimate then you will need to explain why. Are there methodological errors? Was the Ioannides test less specific, the NHS less sensitive, or perhaps less cross reacting, or was it a genuine difference in population exposure? If the antibody test is unreliable, why do we believe one set of figures and not the other? Yeadon makes no such attempt at explaining, he merely states that he thinks the NHS figure is wrong. When two sets of studies give different results it is important to know why, rather than to assume that one is right and the other wrong as it suits you.

              To turn to the second supposed error by SAGE. Yeadon produces two charts: on the left is one reflecting what SAGE believes that 7% of population is infested and 93% susceptible. On the right is another chart with figures postulated by Mike Yeadon as follows:

              • 30 percent prior immunity (assumed)
              • As many as 32% infected (presumably from Dr. Ioannides’ figures)
              • Only 28% susceptible.

              From these figures Mike Yeadon states that he therefore thinks the pandemic is virtually over in the UK and is now just doing its rounds about the country, and there shall be no second wave.

              Some of this may be true but we would need more robust reasons to believe this, hard figures, especially about this 30% and 32%. We need to know if there are genuine geographic and ethnic and other genetic susceptibility and many other factors. Measurable antibody T cell and antibody responses may or may not be different or may or may not be protective.

              In fact there may be other observational data to suggest that there may be geographic and environmental and ethnic factors that may lead to variability. The pandemic seems to have hit hardest in Europe and North and South America, but much less so in Asia and perhaps also Africa, although the data there may be more difficult to get. Some countries have had very few cases and deaths, notable amongst them are Vietnam, Taiwan and Thailand. I do not have information as to whether these countries applied particularly stringent rules, I could be advised. On the other hand BAME communities seem to suffer more from the burden of the disease in the West, suggesting that the difference is not genetic and that other factors may come into play. Could it perhaps be that there is more prevalent cross immunity with other corona viruses in Asian countries but not in Asian communities in the West where exposure to some of these viruses is less common? I have no idea but this could be looked at.

              In conclusion, I agree that the constitution of SAGE should be looked at to be more inclusive, I also think that the public health aspects should be left to experts and not politicians, but I do not believe that this pandemic is over. Only time will tell.

              #61815
              Clark

                Mike Yeadon:

                “For reasons I don’t understand, given the significance of what I’m about to tell you, none of the so-called medical correspondents and science journalists on radio and TV have ever (as far as I know) spoken of the four, endemic, common-cold inducing coronaviruses.”

                See? Science is really a conspiracy. Which is exactly the perspective that James Delingpole has been pushing trying to wake us up about for decades regarding the icecaps melting away great Global Warming Swindle.

                #61818
                SA

                  Clark
                  I wrote the above with no knowledge of Delingpole. I am glad that at least I was not ‘biased’ when I wrote what I wrote.

                  #61845
                  Steph

                    SA – I am glad that you were not biased too! It is good to try and look at what people have to say objectively. Only in that way do we move forward. There is such a widespread tendancy to tenaciously hang on to one’s own viewpoint and simply discount any differing perspective by discrediting the proponent in some way. ‘Ah well, he’s spoken on RT’. ‘Yes, but he spoke in favour of the IRA’. ‘But his reasearch was funded by a tobacco corporation’ And on and on. No matter how tenous the link, these things seem to be quite sufficient reason to simply discount whatever is being said. I’ve seen it over and over again.
                    Thank you for your post re Mike Yeadon. As you say, quite a short time will tell I think.

                    #61854
                    Clark

                      It’s clearly Yeadon who’s biased, or he’d publish in the scientific literature as scientists should rather than hinting directly to the public that science is a conspiracy. Delingpole has for decades consistently denigrated climate science as a conspiracy, so it’s unsurprising that he offered Yeadon some publicity. They appear to be collaborating in prioritising profit above human and ecological welfare by promoting public distrust of science. Both have made a lot of money from the current commercial system.

                      Publishing in the scientific literature and forums exposes propositions to expert scrutiny. Publishing directly to the public influences public opinion and behaviour without expert scrutiny. As such, it is a form of propaganda. Hinting that science is a conspiracy is an effective cover story for not publishing in the scientific domain.

                      Is this what you’re advocating Steph? Do you wish the public to be influenced by certain highly specialised arguments, insulated from the appropriate context which would provide equally technical scrutiny? If so, why?

                      #61855
                      Clark

                        Did the government assemble the SAGE committee? I could be suspicious of government motives, in that mathematical modellers are far more easily dismissed and mathematical models far more vulnerable to denigration than a board of epidemiologists, virologists and immunologists would be.

                        #61856
                        Clark

                          Steph, my prediction is that you would simply ignore my question at 13:27 above if you could. However, I hope this prediction might change that.

                          #61857
                          SA

                            I understand both stances in a way. But the answer to Steph is that the forum chosen and the company kept are important when you look at the message, but I agree that to counteract these often propagandistic and self advancing individuals it is also important to refute their insidious methods. In fact your mention of RT has reminded me of why I now do not get as much news from there as I used to. RT is splendid in reporting from the point of view of Russia and in certain other political reporting. But they also do like to gloat over difficulties in the west, not unlike what the BBC does here. The answer is to be selective in what information you get from which site.
                            There are a number of scientists who have great achievements in one field who go rogue and pontificate in other fields, often leading others astray. A case in point is the discoverer of the PCR who won a Nobel science prize but then turned climate and HIV skeptic, using his previous fame and knowledge to mislead others.

                            #61859
                            Steph

                              It is not what I’m ‘advocating’ at all and I rather resent that remark. I am merely suggesting that, to use this as a specific instance, just because it is Delingpole that has seized an opportunity to publisize a viewpoint that helps support his own agenda, does not automatically mean that Mike Yeadon is wrong. I would imagine that Mike Yeadon is glad of any opportunity he can get to broadcast his beliefs to a wider audience. He’s certainly not going to get that opportunity in msm is he?
                              If I do not reply to something it is because I don’t have time. I only occasionally comment, and that is because I don’t really have much time to idle away in what is, after all, a rather fruitless hobby! I like to read Craig’s blogs and the comments but it is not really my life’s work!

                              #61860
                              Steph

                                SA – Indeed, always listen to the message not the messenger.

                                #61869
                                Clark

                                  “I would imagine that Mike Yeadon is glad of any opportunity he can get to broadcast his beliefs to a wider audience.”

                                  Why? If he’s interested in science and determining facts, he would do much better publishing in the scientific domain, where people with appropriate expertise and many years experience congregate precisely to discuss such matters, to further refine their own and each other’s understanding.

                                  If, however, Yeadon’s concern is for maximising profit, he may wish to influence public attitudes against social restrictions, in which case it may be his intention that the public reach a particular conclusion by not fully understanding.

                                  – “He’s certainly not going to get that opportunity in msm is he?”

                                  Delingpole is “MSM”, which properly should be called the corporate media; he’s a regular columnist for the Telegraph. The corporate media is primarily funded by selling audiences to advertisers, so of course it is dedicated to maximising profits. And indeed, the corporate media has been far more critical of social restrictions than is the epidemiological community.

                                  #61870
                                  Clark

                                    “It is not what I’m ‘advocating’ at all and I rather resent that remark”

                                    And what I rather resent is that you repeatedly throw your ill-informed two-penneth in, accuse me and others of bias, and then clear off. That’s not the way it’s done in scientific matters.

                                    SARS-CoV-2 is showing many signs of being an extremely serious virus which leaves devastating long term damage upon those infected, yet your arguments are always for letting it run riot through the population of which I and those I love are members.

                                    The following translated quotes are from Étienne Decroly, Director of research at CNRS in the Architecture and Functions of Biological Macromolecules Laboratory (CNRS / Aix-Marseille University), member of the French Society of Virology. CNRS is the largest fundamental science institute in Europe:

                                    “It was discovered that the gene encoding the Spike protein contains four insertions of short sequences which are not found in the human CoVs closest genetically. These insertions probably confer remarkable properties on the Spike protein of SARS-CoV-2. Structural studies indicate that the first three insertions are localized to exposed domains of the S protein and therefore probably play a role in the escape of the virus to the host immune system.”

                                    See that? The virus can infect the human immune system. That’s what HIV does. Airborne AIDS anyone? Encourage transmission of it?

                                    “The fourth insertion is more recent and reveals a site sensitive to furins, protease enzymes produced by the host’s cells. It is now clearly demonstrated that the cleavage of Spike by furins induces a change of conformation favoring the recognition of the cellular receptor ACE2.”

                                    ie. it has a feature that encourages human cells to infect themselves with it, via the ACE2 receptor which is present in organs all over the body, not just the respiratory system. This thing can infect everything from your kidneys to your brain.

                                    #61873
                                    SA

                                      Clark
                                      There are a couple of expressions in the statement from Etienne Declory which are a bit strange. This may be due to translation. Could you please post a link?

                                      #61877
                                      Steph

                                        Clark

                                        ‘And what I rather resent is that you repeatedly throw your ill-informed two-penneth in, accuse me and others of bias, and then clear off. That’s not the way it’s done in scientific matters.’

                                        Firstly, this is a forum open for general comments. It is not a specific platform for scientists. Or a specific platform for your own opinion.

                                        Secondly, your posts re Mike Yeadon have yet to demonstrate that what he asserts is untrue, only that you personally view him as a profiteering charlatan. He claims that what he is saying is ‘basic textbook’ stuff. As just one instance, by no means the only one, he says that there are other elements to the immune system which fight off viruses before antibodies are created and that therefore testing for the presence of antibodies is not particularly helpful in determining whether a person has or has not already had the disease. Thus many more than known may have been infected. Is that wrong? I don’t know, I’m a garden designer, my knowledge of viruses extends as far as verticillium wilt. But you have yet to explain why it, or any of the other assertions he makes, is incorrect, you’ve only said that he is an attention-seeking prat. That’s hardly very ‘scientific’ either. I have not accused anyone of bias, I have no idea why you say that. I have simply highlighted the Mike Yeadon interview, and expressed the opinion that very often people dismiss contrary arguments with nothing more than character assignation.
                                        I’m sorry if I annoy you, but perhaps you should ask yourself why you spend so much time in an activity which makes you so cross with other people, it can’t be good for you.

                                        #61878
                                        SA

                                          The false positive rate for PVR for SARS cov2 is not known. A recent article in the BMJ
                                          addresses this issue and allows an interactive calculation on assumed results according to the prevalence of the infection. The problem is that in low prevalence areas, a specificity of the PCR of 99%, although it sounds small could lead to a large error in estimation of positive cases and a poor predictive value for negative cases. Although no official figures for the specificity of the PCR in field setting are available, some indirect deductions can be made. In China, after a small outbreak of the virus in Qingdao, the authorities tested the whole population of the town, 10.2 million people, and found no positive results.
                                          Another way of inferring the specificity of the testing in the field can be deduced from daily published figures, for example from this website, World meters

                                          I extracted the figures from this website of countries with less than 5000 reported cases, and with a population of over 3 million and with data available of total number of tests performed.
                                          There were 17 countries that fell into this group:
                                          World Country Cases Tests Pos/test FP1% FP 0.1% FP0.01%
                                          207 Laos 24 65,305 3.2 -6 653 65 6
                                          188 Cambodia 291 180,378 0.00160 1,804 180 18
                                          187 Mongolia 340 88,230 0.00380 823 82 8
                                          177 Taiwan 553 101,218 0.00540 1,012 100 10
                                          176 Burundi 560 49,642 0.01120 496 49 5
                                          174 PNG 589 29,254 0.02010 293 29 3
                                          165 Vietnam 1,177 1,246,480 0.00094 1,246 125 13
                                          164 Niger 1,219 37,027 0.03290 370 37 4
                                          163 Liberia 1,426 30,332 0.04700 303 30 3
                                          160 NZ 1,950 1,090,702 0.00179 10,907 1,091 109
                                          158 Togo 2,296 117,117 0.01960 1,171 117 12
                                          154 Benin 2,643 238,105 0.01110 2,381 238 24
                                          153 S.Sudan 2,903 12,044 0.24103 102 10 1
                                          152 Uruguay 3,044 314,820 0.00966 3,148 315 32
                                          150 Mali 3,537 73,365 0.04820 734 73 7
                                          147 Thai 3,775 977,854 0.00386 9,778 977 97
                                          138 CAR 4,863 32,711 0.14866 327 33 3

                                          Number on left is world rating total cases, next column name of country, total number of cases, total number of tests performed, percentage positive tests/test performed, Exp 1%= expected number of false positive tests at 99% specificity, Exp. 0.1%=expected number of false tests if 99.9% specificity and exp 0.01%= expected false positives if specificity 99.99%.
                                          The sample was further reduced to countries with less than 1% positive cases/ test performed. The purpose was to look at the problem of false positives in the context of low incidence:
                                          Country Cases Pos/tested 1%FP 0.1%FP 0.01%FP
                                          Cambodia 291 0.16% 1804 180 18
                                          Taiwan 553 0.38% 1012 101 10
                                          Vietnam 1177 0.09% 1246 125 13
                                          New Zealand 1950 0.18% 10907 1090 109
                                          Uruguay 3044 0.97% 3148 315 32
                                          Thailand 3775 0.39% 9778 978 98

                                          In all 6 countries the number of false positives would exceed the number of observed cases, sometimes as in the case of New Zealand of x5 and in Thailand by x3 If the FP rate was 1%. The numbers of possible false positives still remain a high proportion of cases at 99.9% specificity also in the case of these two countries. It is obviously not possible to determine the exact figure for specificity, and in turn, the likelihood of false positives from these figures, but it would be a fair assumption that the figure lies more in the region between 0.1% and 0.01% rather than 1%.

                                          #61879
                                          SA

                                            Sorry table garbled.

                                            #61880
                                            SA

                                              Steph
                                              Not wishing to speak for Clarks, but what I understand from what he says, is that both the choice of forum, to expound scientific theories, and his manner, are not appropriate to someone addressing a scientific question. He rubbishes others and so others feel free to rubbish him.
                                              He is also selective: Why is Ioannides antibody test so marvelous and accurate, whilst that of the NHS so insenitive? Why on the one hand say that antibody tests are not reliable as a test of immunity, but then relies on only one set of figures. This is just one of internal inconsistencies he makes. He also proposes a theory, that about 30% of people have an innate immunity to the virus, purely by extrapolation of unconnected findings, all coated with a sheen of plausibility. Unfortunately he targets people like you (no offence to you) who seek wider knowledge and want to explore alternatives, but without the necessary knowledge to understand his methods and errors. This type of scientist can be dangerous for exactly this reason.

                                              #61881
                                              Clark
                                                #61882
                                                Steph

                                                  SA – Thank you for your post. Are antibody tests a reliable indicator of previous infection or not? Is the statement ‘other elements of the immune sytem which do not produce antibodies may fight off a virus’ correct or incorrect? etc etc?
                                                  I accept what you are saying about those such as myself having insufficient knowledge to ascertain the veracity of any given statement, but in my own particular case I am not concerned if Yeadon, or anybody else, is being selective. I am not holding him up as the definitive authority, only as a voice. The only thing I am interested in is are his particular ‘selections’ correct according to the known and accepted ‘text book’ definitions or not?
                                                  Obviously Yeadon is an admirer of Iaonnidis, as am I, I have to say, although I fully accept that my opinion is entirely subjective, based upon nothing but an intuitive feeling that he is an honest and decent person. Most unscientific I know but, as a non-specialist, how could it be otherwise? Now, Iaonnidis plods patiently on with his work aggregating the work of many other scientists and researchers, regularly releasing his findings. Here is, I believe, the latest.
                                                  https://www.who.int/bulletin/online_first/BLT.20.265892.pdf
                                                  As far as I am able to see, much of his conclusions concur with some of Yeadons own, presumeably that is why Yeadon quotes him. He finds that fatality rates vary hugely between populations and that therefore an overall rate is very misleading. If an overall rate must be given, then it appears that it is actually very low. Please read the paper and tell me what is wrong with it. Perhaps you feel Iaonnidis is being selective too, but then maybe the NHS data is also selective! How can you tell!

                                                  #61883
                                                  Clark

                                                    Steph, science is about evidence and testing of theory. Do you propose that Yeadon’s theory be tested by letting SARS-CoV-2 infect the general population without restriction? Because as a member of that population, I have major ethical objections to that.

                                                    You are making me angry. I am not your lab rat.

                                                    #61884
                                                    Clark

                                                      “Most unscientific I know but, as a non-specialist, how could it be otherwise?”

                                                      By inspecting evidence.

                                                      If Yeadon were right, infection numbers and mortality could not be rising rapidly now, but they are. There are dozens of examples; look at all the US states that “opened up” only to lock down again shortly thereafter. Wherever social restrictions have been lifted too much, infections have begun to increase.

                                                      “my opinion is entirely subjective, based upon nothing but an intuitive feeling that he (Ioannidis) is an honest and decent person”

                                                      In practical terms it makes no difference whether some theory is an honest mistake or a malicious lie. But if someone bypasses the scientific forums and presents directly to the public – especially someone like Yeadon, who has worked among scientists for years and must have seen many scientific misapprehensions corrected during scientific discussion – it’s a fair sign that they’re insulating their assertions from critical scrutiny.

                                                      Anyone can reason scientifically. You see a coffee flask but you’re not sure how much coffee is in it, so you pick it up and shake it a bit to find out – that’s an experiment. We all do experiments every day.

                                                      How long have you been an “admirer of Ioannidis”? I’d never heard of him before SARS-CoV-2. Now, I wouldn’t be able to miss him. That suggests a massive increase in media exposure. That in turn adds weight to my theory that the major motivator of the media is to promote the making of profit.

                                                      Media Lens

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