The New York Times is out with a bombshell, and we do mean bombshell, of an article on COVID-19 that suggests we’ve been doing testing all wrong and up to 90% of the people who test positive for the virus might have viral loads so low that they “are no longer contagious and don’t need to isolate”
NEW: All these months into the pandemic, we may have been testing the wrong way. Data from some state labs suggest up to 90% (!!) of people who get a positive result are no longer contagious and don’t need to isolate.
Strap in, this is important. 1/xhttps://t.co/rR4aBDK4Xl
— Apoorva Mandavilli (@apoorva_nyc) August 29, 2020
The reporter, Apoorva Mandavilli, tweets, “It turns out that the PCR, that old reliable workhorse, is both too slow and too sensitive for what we need”:
It turns out that the PCR, that old reliable workhorse, is both too slow and too sensitive for what we need. And it all hinges on a metric called the “cycle threshold.” Here’s a handy explanation of what the CT value is and why it matters. 2/xhttps://t.co/ejOY7JQ9Kp
— Apoorva Mandavilli (@apoorva_nyc) August 29, 2020
In a nutshell, the PCR test is run in cycles and the more cycles it takes to get a positive result, the less virus you have in your system:
Essentially, the PCR test amplifies genetic matter from the virus in cycles; the fewer cycles required, the greater the amount of virus, or viral load, in the sample. The greater the viral load, the more likely the patient is to be contagious. 3/x
— Apoorva Mandavilli (@apoorva_nyc) August 29, 2020
In the U.S., the machines are calibrated at between 37 to 40 cycles, which, according to this report, is way too sensitive:
Here’s where it gets truly shocking. Most PCR machines at state labs are set to a cutoff of 40 or 37, meaning it takes that many cycles to get a signal. But acc to most virologists, at that level, you are amplifying so little virus that it might almost be an artifact. 4/x
— Apoorva Mandavilli (@apoorva_nyc) August 29, 2020
Note: We don’t have the numbers for every country, but India’s threshold is only 35:
Re: this fascinating thread, it appears that India doesn't have the same issue with overly sensitive tests. @ICMRDELHI protocols say RT-PCR tests are deemed positive if they cross a threshold within 35 cycles (not 37 or 40, as in some labs in the US): https://t.co/wgv6QallHX https://t.co/jnNEvj4IoW
— Joanna Slater (@jslaternyc) August 30, 2020
A reasonable cycle threshold should be around 30:
If you adjust that down to a more reasonable CT threshold of 30, anywhere form 40%-90% of state lab results are *no longer positive.* The rest are well past the point of contagiousness. 5/x
— Apoorva Mandavilli (@apoorva_nyc) August 29, 2020
The implications of this are massive:
Think about that for a minute. Think of the thousands of people being asked to isolate, refrain from work and submit to contact tracing. But also, think of the needless bottlenecks, and all the people who aren’t getting tested and isolated *when* they need to be. 6/x
— Apoorva Mandavilli (@apoorva_nyc) August 29, 2020
We’re figuratively (and quite possibly literally) letting our neighborhoods burn down:
Imagine a neighborhood on fire. Here, the firefighters have defined even dying embers as a “fire” and are so busy putting those out that they are missing entire homes that are burning down and setting others ablaze. 7/x
— Apoorva Mandavilli (@apoorva_nyc) August 29, 2020
The argument here is we need the FDA to approve “rapid, less sensitive tests”:
Let’s be very clear: this is not an argument for testing less. It’s an argument for testing MORE and testing more OFTEN. With rapid, less sensitive tests that tell you what you actually need to know from a public health perspective: whether you are contagious. 8/x
— Apoorva Mandavilli (@apoorva_nyc) August 29, 2020
What’s worse is that these labs aren’t even reporting back the number of cycles it takes to get a positive test, only yes or no:
Apart from the mind-blowing public health implications of these numbers, we are also losing valuable scientific intel about the virus and disease trajectory by not paying attention to CT values and delivering just yes-no answers (per FDA authorizations). 9/x
— Apoorva Mandavilli (@apoorva_nyc) August 29, 2020
You can read the entire piece here:
Massive thanks to @michaelmina_lab who alerted me to this, and to @JumoDr @angie_rasmussen @ashishkjha @scottjbecker and many others, incl at state labs. –/10https://t.co/rR4aBDK4Xl
— Apoorva Mandavilli (@apoorva_nyc) August 29, 2020
Some excerpts:
"In three sets of testing data that include cycle thresholds, compiled by officials in Massachusetts, New York and Nevada, up to 90 percent of people testing positive carried barely any virus, a review by The Times found."
— Phil Kerpen (@kerpen) August 29, 2020
"On Thursday, the United States recorded 45,604 new coronavirus cases… If the rates of contagiousness in Massachusetts and New York were to apply nationwide, then perhaps only 4,500 of those people may actually need to isolate and submit to contact tracing."
— Phil Kerpen (@kerpen) August 29, 2020
"Any test with a cycle threshold above 35 is too sensitive, agreed Juliet Morrison, a virologist at the University of California, Riverside. 'I’m shocked that people would think that 40 could represent a positive,' she said."
— Phil Kerpen (@kerpen) August 29, 2020
"Dr. Mina said he would set the figure at 30, or even less. Those changes would mean the amount of genetic material in a patient’s sample would have to be 100-fold to 1,000-fold higher than the current standard for the test to return a positive result."
— Phil Kerpen (@kerpen) August 29, 2020
"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."
— Phil Kerpen (@kerpen) August 29, 2020
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