False Positive Equation laid out in this blog – looks to be GP in UK who is generally a skeptic so bear that in mind – https://drmalcolmkendrick.org/2020/09/28/false-positive-tests/amp/?
The numbers he is using is based UK figures – “test test” may have been a good mantra in the beginning but the test itself perhaps needs a test?
“The specificity of a test is defined by the equation:
SP = TN / (TN + FP)
Where SP = specificity, TN = number of true negatives, FP = number of false positives. TN + FP = the total number of tests carried out.
Now the latest Government figures from Monday 7th September state that 350,100 tests were carried out and 2,948 people tested positive 2. So, if we apply the above equation to our PCR test and the Government’s figures, we get:
0.956 = TN / 350,100
Therefore, the number of true negatives is:
TN = 350,100 * 0.956 = 334696
Therefore, the number of false positives, FP we would expect from 350,100 tests is:
FP = 350,100 – 334,696 = 15,404
This is more than five times the number of positive tests reported, which means we cannot have any confidence that any one of those positive tests represents a genuine case.
What these figures show is that it is totally inappropriate to use RT-PCR as a screening test for a virus in an asymptomatic population when the prevalence of the infection is very low.
Even if there were a test with 99% specificity, you would still expect to get 3500 false positives from performing 350,000 tests – which is still greater than the number of “cases” reported. When the number of “cases” is lower than your rate of false positives, then a positive result on its own is virtually meaningless.
The PCR test is best utilized as a diagnostic test to confirm the diagnosis of an infection based on clinical signs and symptoms. It certainly should not be used as a screening test when there is low prevalence of disease and should NEVER be used as the sole determinant in the diagnosis of a case. One source of false positives is the persistence of fragments of viral RNA long after a patient may have recovered and is no longer infective. These fragments will be amplified by PCR and will give a positive result that is indistinguishable from a genuine case. We’ve had a patient whose swabs have been testing positive in our lab every week for over 3 months!”
As noted in the other article on PCR (https://covid19mathblog.com/2020/09/covid-9-28-20/) solution proposed was a cell culture test after the positivity test to test for infection – currently long time line for results and limited lab capabilities but I am sure there is some genius out there that can solve this process issue – its not a science issue.
Remember the HCQ scandal – well here is a well written timeline of events and the debacle and some of the ramifications from allowing this paper to make the rounds – at some point perhaps it can be made into a movie – https://www.the-scientist.com/features/the-surgisphere-scandal-what-went-wrong–67955?
“It sounds absurd that an obscure US company with a hastily constructed website could have driven international health policy and brought major clinical trials to a halt within the span of a few weeks. Yet that’s what happened earlier this year, when Illinois-based Surgisphere Corporation began a publishing spree that would trigger one of the largest scientific scandals of the COVID-19 pandemic to date. At the heart of the deception was a paper published in The Lancet on May 22 that suggested hydroxychloroquine, an antimalarial drug promoted by US President Donald Trump and others as a therapy for COVID-19, was associated with an increased risk of death in patients hospitalized with the disease. ”
“The study was a medical and political bombshell. News outlets analyzed the implications for what they referred to as the “drug touted by Trump.” Within days, public health bodies including the World Health Organization (WHO) and the UK Medicines and Healthcare products Regulatory Agency (MHRA) instructed organizers of clinical trials of hydroxychloroquine as a COVID-19 treatment or prophylaxis to suspend recruitment, while the French government reversed an earlier decree allowing the drug to be prescribed to patients hospitalized with the virus.”
“Desai’s astonishing influence on COVID-19 policy was dependent on multiple parties, Cooper notes, from the institutions that employed him to the coauthors on his research studies, the journals that published the work, and the organizations that issued public health decisions based on his research.”
“An investigation by The Scientist points to a series of missed opportunities to halt Surgisphere’s progress—in some cases stemming from people’s failure to check implausible claims made by Desai or from a pattern of ignoring warnings of problematic data or behavior. While a few parties have since accepted some responsibility and outlined plans to avoid similar situations in the future, the majority have not.”
US continues to be under 1K – but we have a new leader in deaths out of nowhere Argentina reports 3351 deaths – this type of batch reporting makes time series data almost useless.
“Argentina’s coronavirus death toll leapt above 20,000 on Thursday as a large number of previously untallied fatalities were added to the total, emphasizing how the country has gone from regional role model to one of the worst-hit in the world.
The South American nation, which slowed the spread of the virus with a strict lockdown in March, reported 14,001 new COVID-19 cases to take the total confirmed infections to 765,002, one of the 10 highest in the world.”
“Argentina’s rolling 7-day average of daily cases and fatalities has continued to rise, even as other countries in the region have seen the spread of the virus slow in recent weeks as governments look to reopen their battered economies.”
Lockdowns don’t work or do they? What is the metric to say they work?
FL leads the US in deaths at 127
This time the leading county is LA at 34. Deaths in FL seems dispersed vs. the usual Miami-Dade. Wake NC reported 17666 but at the same time some negatives in other counties – looks like a data revision occurring in NC as the overall state numbers seem reasonable.
After the data revisions and all Harris county back to being one of the best fatality rates at under 2% (1.82%).
Interestingly Argentina never observed a lull in confirms or deaths – they have been steadily rising throughout the year and now with the data update a spike.
