Open thread Dec. 7, 2020 Dan Crawford | December 8, 2020 5:35 am Comments (15) | Digg Facebook Twitter |
The false positives from PCR tests used to detect Covid-19 are a serious issue. Apparently the Cycle threshold (Ct) used in these tests is not usually reported with the result of the test. And apparently most of these tests are done with a Ct of 40. The state of Florida is now requiring that the Ct be reported with the result of the test.
On 16 July 2020 Dr Fauci appeared on “This Week in Virology”. The discussion included the potential for false positives from PCR tests if the “Cycle threshold” (Ct) was over 34.
“What is now sort of evolving into a bit of a standard,” Fauci said, is that “if you get a cycle threshold of 35 or more … the chances of it being replication-confident are minuscule.”
“It’s very frustrating for the patients as well as for the physicians,” he continued, when “somebody comes in, and they repeat their PCR, and it’s like [a] 37 cycle threshold, but you almost never can culture virus from a 37 threshold cycle.”
“So, I think if somebody does come in with 37, 38, even 36, you got to say, you know, it’s just dead nucleotides, period.”
View at about 4:20: https://www.youtube.com/watch?v=a_Vy6fgaBPE&feature=emb_logo
Then on 29 August 2020 the New York Times ran an article titled “Your Coronavirus Test Is Positive. Maybe It Shouldn’t Be.”
“Officials at the Wadsworth Center, New York’s state lab, have access to C.T. values from tests they have processed, and analyzed their numbers at The Times’s request. In July, the lab identified 872 positive tests, based on a threshold of 40 cycles.
With a cutoff of 35, about 43 percent of those tests would no longer qualify as positive. About 63 percent would no longer be judged positive if the cycles were limited to 30.
In Massachusetts, from 85 to 90 percent of people who tested positive in July with a cycle threshold of 40 would have been deemed negative if the threshold were 30 cycles, Dr. Mina said. “I would say that none of those people should be contact-traced, not one,” he said.
Shouldn’t we be much more interested in those patients who test positive for live virus rather then dead nucleotides?
Is it remotely possible to do contact tracing with the huge number of new cases being reported daily? Would contract tracing be more effective if the number of false positives was reduced?
I guess the downside would be that you might be missing some infectious patients. But that seems like ‘the perfect being the enemy of the good’.
872 out of how many?
Run75441 wrote: “872 out of how many?”
Note that this 872 number is for the month of July at that Lab.
I suppose the correct answer is 872 out of 872 who tested positive with a Ct of 40.
The point of that sentence comes in the next paragraph in the article.
“With a cutoff of 35, about 43 percent of those tests would no longer qualify as positive. About 63 percent would no longer be judged positive if the cycles were limited to 30.”
So at a cutoff of Ct at 35 the positives would drop from 872 to 497. And at a cutoff of 30 Ct the positives would drop to 323.
I am going to assume you do not know for sure. You stated this: “With a cutoff of 35, about 43 percent of those tests would no longer qualify as positive. About 63 percent would no longer be judged positive if the cycles were limited to 30.”
Ok do we know the percentage for the 872?
since i couldn’t comment on Neera Tanden in the Dec. 1st Open thread; (in support of Anne) for reasons i still don’t understand, i’ll add the comment i intend then here now…
i have been wondering about Neera Tanden, too, but not on whether or not she could be confirmed…it seems this recent post by Matt Taibbi has nailed down my nebulous concern…
“With Tanden Choice, Democrats Stick it to Sanders Voters”
The Democratic Party is not known for its sense of humor, but news that Joe Biden will appoint longtime Center for American Progress chief Neera Tanden to his government qualifies as a rare, well-earned laugh line.
Tanden is famous for two things: having a puddle of DNC talking points in place of a cerebrum, and despising Bernie Sanders. She was #Resistance’s most visible anti-Sanders foil, spending awe-inspiring amounts of time on Twitter bludgeoning Sanders and his supporters as a deviant mob of Russian tools and covert “horseshoe theory” Trump-lovers. She has, to put it gently, an ardent social media following. Every prominent media figure with even a vague connection to Sanders learned in recent years to expect mud-drenched pushback from waves of “Neera trolls” after any public comment crossing DNC narratives. No name in blue politics is more associated with seething opposition to Sanders than Tanden.
Biden is making this person Director of the Office of Management and Budget. Sanders is the ranking member (and, perhaps, future chair) of the Senate Budget Committee. Every time Bernie even thinks about doing Committee business, he’ll be looking up at Neera Tanden. For a party whose normal idea of humor is ten thousand consecutive jokes about Trump being gay with Putin, that’s quite a creative “fuck you.”
I am not thrilled with Biden and I am damn sure not tickled pink to think of Sanders as the Pres. So for me this is a moot point. A constant parroting of this does not sit well with me especially when once again we have not gained what we were told we would gain in a national election much of which would not be any different with Sanders in office. We needed someone different than two old pieces of refuge left over from, the sixties, seventies, eighties and even the nineties. Once again, we did not achieve it and are sitting at the precipice waiting for another swipe by the shithead in the Senate who I wish would frickin pass on. He is as bad a trump.
Sanders is a big boy and he will figure it out. Biden is old enough to figure out where the logjams might be too. Neither of the two are acceptable to Repubs and we do not control the Senate and may not in 2021. I would hope someone would clue Sanders in that his version is not Single Payer when he is using ACOs like they did in Vermont and di not set budgets for hospitals. That to me is a far better goal which would have a huge payoff for the country.
vårt mektigste hekseri er kvantitativt.
in the best-case scenario the Earth will reflect some of the photons from the Sun before they are absorbed, converted to heat. In the best-case scene Earth’s black body radiation will radiate energy into outer space.
in the worst case scenario Earth will keep all the energy. How long will this worst case require to raise the temperature of the Earth by 1 Kelvin?
Assume that the aggregate specific heat of Earth is 1000 joules/kg. Assume that the total mass of Earth is 5.97237×10^24 kg. Thus 5.97237×10^27 joules will raise the temperature of Earth by one Kelvin.
Now assume that the radius of the Earth is 6,367 kilometers. Thus the area of Earth facing the Sun is π * 6,367^2 or π * 40,538,689 or 127,356,047 square kilometers. Assume TSI, total solar irradiance is 1.365 kilowatts per square meter (kW/m²), and 1,365,000 kilowatts/square kilometer. Thus Earth receives 127,356,047 * 1,365,000 kilowatts or 1.73841×10¹⁴ kW. from the sun, 1.73841×10¹⁴ kWh each hour. Assume that one kWh = 3.6 megajoules. Thus each hour we get 6.25827615×10²⁰ joules from the Sun each hour, 5.97237×10^27 joules every 9,542,563 hours, the time required to heat us all up by 1 Kelvin. Assuming 8765 hours / year, thus 9,542,563 hours is merely 1,088 years. The best case Étude will take longer. Will significant AGW require more than one Kelvin?
In the meantime acid rain by its increased osmolarity lowers the freezing point of water, melts the glaciers.
Matt Taibbi jumped the shark quite awhile ago. Following in the footsteps of Glen Greenwald.
Neither should be paid any attention to,
Run75441 wrote “Ok do we know the percentage for the 872?”
This is why I cite sources. In this case the source was a NY Times reporter.
The reporter did not report the percentage which you want. He reported that “In July, the lab identified 872 positive tests, based on a threshold of 40 cycles.
But whether there were additional tests using some other Ct is irrelevant to the point of his article.
Dr Fauci and that reporter are pointing out that using a Ct over 34 is going to over report the number of positive cases.
In other words, using a Ct over 34 is going to report false positives and not by just a few!
And to compound the error, laboratories have not been reporting the Ct with their results. This denied health care professionals the information needed to interpret the validity of the test.
The state of Florida is now requiring that the Ct be reported with the result of the test.
I have been scratching my head trying to figure out what your questions were about.
An obvious question is whether using a Ct over 34 was still happening at later dates? And the answer is yes.
Here is something from MIT dated 2 November 2020.
“But might PCR tests be too good at finding traces of the virus? That’s a question scientists are starting to investigate.
The PCR test analyzes samples by amplifying viral RNA in cycles. Most tests, like the Broad Institute test used by MIT, use a 40-cycle protocol. If the virus isn’t detected within 40 amplification cycles, the test result is negative. If viral RNA is detected in 40 cycles or less, the PCR machine stops running, and the test is positive. Because you received a positive result, we know that the test detected the virus in your sample by the time it reached its 40-cycle limit.”
On the PCR thread, it seems to me that the best response is if you get a positive test and have no symptoms, get another test to confirm.
It is essential to recall that the PCR test (really real time RT-PCR) doesn’t test for virus, it tests for the viral genomic RNA. As Fauci said, it could be “dead” virus. But culturing virus is much slower and much more expensive, so the PCR test is a proxy. Cycle threshold would be useful to know, and the people doing the test will know it. They should report it.
From the director of a clinical testing lab in the midwest:
“we use 37, and positives are usually below 35. We scrutinize all curves for positives by eye. We also test for three viral targets, and typically all three amplify in a positive sample.”
So three separate amplicons have to fulfill the sensitivity threshold. This should reduce the false positive rate.
You also assumed that the temperature of the Earth is uniform though its radius. If that were true we would already have been cooked by the molten core.
It will be a great day for the US when this person is no longer in government. Can’t come soon enough.
” Tulsi Gabbard Introduces Anti-Transgender Bill After Claiming To Be LGBTQ-Friendly
The Hawaii Democrat has drafted a bill to bar schools from receiving federal funds if they allow transgender girls and women to compete in women’s sports.”
Of course trump leaving office will be great for the country, but there are others.
Like this thing.
“Tulsi Gabbard Introduces Anti-Transgender Bill After Claiming To Be LGBTQ-Friendly
The Hawaii Democrat has drafted a billto bar schools from receiving federal funds if they allow transgender girls and women to compete in women’s sports.”