HomeMy WebLinkAbout02022021_Schumacher_PCR Testing_ResponseFrom:Tom Locke
To:Stephen Schumacher
Cc:Board of Health; Allison Berry, Clallam County Health Officer
Subject:RE: New hope for "negative cases" before Feb. 14
Date:Tuesday, February 2, 2021 3:09:44 PM
Mr. Schumacher,
Hopefully, the bulk of your concerns were addressed in my response to your long list of questions yesterday. Yournotion that Jefferson County case rates might somehow be reduced by applying a new definition to PCR positivity isfanciful, at best, and delusional, at worst. CT values are only one of many factors used to interpret PCR test results. CT is merely a measure of the degree of amplification of the viral genetic material present in the clinical specimen. As previously mentioned, many factors can affect the amount of virus on a swab. Additionally, labs vary in terms ofprotocols and testing equipment and CT values can vary from lab to lab, even on identical specimens. Far moreimportant, from a standpoint of separating "true positives" from "false positives" is the pretest probability ofinfection. Most diagnostic tests will yield false positive if done on people with very low risk of having the conditionbeing tested for (low pretest probability). The converse is true as well, if performed on people with high pretestprobability of infection, the positive predictive value of a positive test result is much higher. This is why we focusPCR testing on people who are symptomatic with COVID-like illness and/or have close contact exposure to knowncases of infection. These are the Jefferson County cases you are speculating might be erased by redefining CTthresholds -- people who are acutally symptomatic for COVID-19 or are household/workplace contacts of activecases.
The group that is more likely to have false positive results are those who are being screened prior to surgicalprocedures or travel. This is especially true if the person is asymptomatic and has no exposure risk factors. Since20-40% of COVID infection can be asymptomatic and infection can be spread in the presymptomatic phase ofillness, preprocedure testing has its values but it does run the risk of generating false positive results. This iscompletely independent of the CT value you seem very interested in. When we suspect a false positive result, wegenerally need to do two additional negative tests to establish that diagnosis.
Your apparent belief that there is an epidemic of false positive COVID tests is not supported by the facts. Ifanything, confirmed tests dramatically underestimate the true COVID disease burden in a community (by a factor of5 to 10X in most studies). The reason that CT values are not routinely reported by labs is that they add little ofvalue to the purpose of the test -- the diagnosis of active SARS-CoV-2 infection. They are more reflective ofspecimen quality, viral load, and variations in lab technology. If you would like the Washington State Departmentof Health or the FDA to revise their PCR testing protocols you should take that up with them. Jefferson CountyPublic Health cannot serve as your intermediary in this process. We have far more urgent duties to perform.
Sincerely,
Thomas Locke, MD, MPHJefferson County Health Officer________________________________________From: Stephen Schumacher [solmaker@olympus.net]Sent: Monday, February 1, 2021 12:33 PMCc: Board of Health; Tom Locke; Allison Berry, Clallam County Health OfficerSubject: New hope for "negative cases" before Feb. 14
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Dear Jefferson County Commissioners,
Watching the Zoom of this morning's BoCC meeting, I noted that Dr.Locke did not answer or even address any of my questions at bottom,
so they are all still on the table. I'm mystified by his
mischaracterization of well-documented concerns over 90% false
positive rates at high cycle counts as "nitpicky" and hiseasily-refuted opinion that PCR tests are "highly accurate".
Philip Morley observed that Jefferson Healthcare handles only a smallpercentage of our county's PCR testing, with most conducted by UW andothers. If so, that raises the additional question:
7) What Cycle Threshold is used by each organization performing PCRtesting in our county, and approximately what percentage of testingis done by each organization?
Because of the critical importance of the cycle count in evaluatingthe significance of a positive PCR test result, both pieces ofinformation need to be reported to individuals as well as in overallcounty statistics.
Dr. Locke's report began by warning about a tripling of cases with 26new ones last week if I heard correctly. But what are the cyclecounts of these new cases? It makes a huge difference whether theywere found positive after 20 amplification cycles or after 45 cycles.
My interest is getting at the truth, not politics. But today'smeeting seemed concerned about county cases showing percentageimprovements before a Feb. 14 deadline One way to achieve that in ahurry might be to re-examine recent cases and reclassify any thatwere incorrectly counted due to amplification cycles higher than 33,then continue using that rule for new cases. Not only would that bethe right thing to do, it might achieve the "negative cases" Gregruefully joked are needed!
Yours truly,Stephen Schumacher2023 E. Sims Way #200Port Townsend, WA 98368(360) 821-9509
--- Pubic Comment sent 8:28 PM 1/31/2021 ---
Dear Jefferson County Commissioners,
On September 2, 2020, I sent the following Public Comment to theJefferson County Board of Health and Health Officer Dr. Tom Locke:
"Per the August 29 New York Times report [of 90% false positives at40-cycle threshold], I'm concerned about the criteria used todetermine confirmed cases of COVID-19 in Jefferson County. Do allthese cases exhibit symptoms, or are "cases" being equated topositive test results? If the latter, what percentage of casesexhibit symptoms? Are positive test results being recorded using PCRtests, and if so, what is the Cycle Threshold value used for these tests?"
I never received any answers to these questions nor have seen themaddressed by Dr. Locke in the press.
Last week the Port Townsend Free Press reported that Jefferson
Healthcare is "using a PCR assay with a 45-cycle threshold, well
beyond the outer limits of reliability."
https://www.porttownsendfreepress.com/2021/01/25/is-jefferson-county-health-department-overstating-covid-case-numbers/
This revelation raises various accountability issues, including:
1) Why did our county have to wait nearly 4 months to learn about its45-cycle threshold from a fortuitous Public Records Request?
2) Since Dr. Locke was also Clallam Health Officer until recently, isthis same unreliable 45 Ct test also in use throughout Clallam County?
3) Was the choice to use this 45 Ct test ever discussed and approvedby the Jefferson County Board of Health or County Commissioners? Ifnot, was it ever even reported and its significance explained to them?
4) Does Dr. Locke or anybody else keep statistical track ofcumulative cycle counts for positive tests and resulting cases in ourcounty, or is this info unavailable or being ignored? Could thisinformation be regularly published in the media, or at least be madeavailable upon request?
5) Does our county always order a second test following a positivePCR result, and if not, how often and on what basis? Are allpositive tests treated as COVID-19 cases regardless of symptoms, andif not, how often has high cycle count been used to discard extremelyweak positive test results?
6) How many county residents have been reported as cases,quarantined, and contact-traced based on cycle counts above 33, whenthe CDC shows "it is extremely difficult to detect any live virus ina sample above a threshold of 33 cycles"?
Yours truly,Stephen Schumacher2023 E. Sims Way #200Port Townsend, WA 98368