HomeMy WebLinkAbout02062021_Schumacher_PCR Testing.3From:Stephen Schumacher
Cc:Board of Health; Tom Locke; Allison Berry, Clallam County Health Officer; news@ptleader.com; PT Free Press
Subject:Response about High Cycle Threshold PCR Testing
Date:Saturday, February 6, 2021 10:15:23 AM
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Dear Jefferson County Commissioners,
I received the following emails from Dr. Locke responding to my
questions to you about PCR tests with high Cycle Thresholds.
Dr. Locke says the county doesn't set "standards for what is
considered a positive PCR test" so "if you have an issue with Ct
values you should take it up with Washington DoH or the FDA."
This passes the buck while ignoring things the county CAN do, such as
(1) direct Jefferson Healthcare to look for a PCR test with Ct cutoff
below 35 cycles instead of 45; (2) obtain the Ct value for each
positive test through PCR labs' customer support when Ct is not
routinely reported as Florida DoH requires; (3) include Ct values
with case statistic reports, so our county can know how many cases
occurred at each Ct level.
Dr. Locke says Cts "add little of value to ... the diagnosis of
active SARS-CoV-2 infection [since] they are more reflective of
specimen quality, viral load, and variations of lab technology."
But "viral load" is directly relevant to infection diagnosis! The
hundred million virus copies per microliter at low Ct are far more
indicative of a true positive diagnosis than the trace viral debris
identified at Ct of 45. Even if the negligible quantity was due to
"specimen quality", high Ct indicates a re-test is needed before
counting a positive test result as a COVID case.
Dr. Locke says "false positive tests ... appear to be quite
infrequent with PCR testing, especially when a person has a
COVID-like illness".
This may be true when Ct is low, but consider that "in three sets of
testing data that include cycle thresholds, compiled by officials in
Massachusetts, New York and Nevada, up to 90% of people testing
positive carried barely any virus... from 85 to 90% of people who
tested positive in July with a cycle threshold of 40 would have been
deemed negative if the threshold were 30 cycles".
https://www.nytimes.com/2020/08/29/health/coronavirus-testing.html
Dr. Locke says false positives are infrequent because "we focus PCR
testing on people who are symptomatic". But where is the data
showing most of our nearly 18,000 tests to date were on people having
relevant symptoms? Many asymptomatic county residents have sought
tests out of fear, and every hospital patient is required to be
tested even if their issues are not COVID-related.
It may also be that our county case count is as high as it is because
routine testing of many asymptomatic people has led to many high Ct
positive tests. The only way to know for sure is by reporting thepercentage of cases exhibiting symptoms and the Ct associated withpositive tests.
Though the estimate of viral load provided by Ct may be imperfect, itis far more helpful than a bare positive or negative testresult! How could getting no information about viral load (or a wildguess) be better than the rough estimate (or educated guess) providedby a Ct value interpreted cautiously in a clinical context? Peoplehave a right to know and should be trusted to know.
Yours truly,Stephen Schumacher2023 E. Sims Way #200Port Townsend, WA 98368
>________________________________________ >--- At 03:09 PM 2/2/2021, Dr. Thomas Locke wrote: >Mr. Schumacher, > >Hopefully, the bulk of your concerns were addressed in my response to >your long list of questions yesterday. Your notion that Jefferson >County case rates might somehow be reduced by applying a new >definition to PCR positivity is fanciful, 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 of protocols and testing >equipment and CT values can vary from lab to lab, even on identical >specimens. Far more important, from a standpoint of separating "true >positives" from "false positives" is the pretest probability of >infection. Most diagnostic tests will yield false positive if done on >people with very low risk of having the condition being tested for >(low pretest probability). The converse is true as well, if performed >on people with high pretest probability of infection, the positive >predictive value of a positive test result is much higher. This is >why we focus PCR testing on people who are symptomatic with COVID-like >illness and/or have close contact exposure to known cases of >infection. These are the Jefferson County cases you are speculating >might be erased by redefining CT thresholds -- people who are acutally >symptomatic for COVID-19 or are household/workplace contacts of active cases. > >The group that is more likely to have false positive results are those >who are being screened prior to surgical procedures or travel. This >is especially true if the person is asymptomatic and has no exposure >risk factors. Since 20-40% of COVID infection can be asymptomatic and >infection can be spread in the presymptomatic phase of illness, >preprocedure testing has its values but it does run the risk of >generating false positive results. This is completely independent of >the CT value you seem very interested in. When we suspect a false >positive result, we generally 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. If anything, confirmed tests
>dramatically underestimate the true COVID disease burden in a
>community (by a factor of 5 to 10X in most studies). The reason that >CT values are not routinely reported by labs is that they add little >of value to the purpose of the test -- the diagnosis of active >SARS-CoV-2 infection. They are more reflective of specimen quality, >viral load, and variations in lab technology. If you would like the >Washington State Department of Health or the FDA to revise their PCR >testing protocols you should take that up with them. Jefferson >County Public Health cannot serve as your intermediary in this >process. We have far more urgent duties to perform. > >Sincerely, > >Thomas Locke, MD, MPH >Jefferson County Health Officer > >________________________________________ >--- At 03:50 PM 2/1/2021, Dr. Thomas Locke wrote: >Mr. Schumacher, > >Cycle threshold values on PCR tests performed to detect SARS-CoV-2 are >not routinely reported by laboratories to health departments or the >person ordering the test. The Washington State Department of Health >establishes standards for what is considered a positive PCR test and >is reportable as a notifiable condition. The local health officer has >nothing to do with establishing CT parameters or any other diagnostic >lab parameter. If you have an issue with CT values you should take it >up with Washington DOH or the FDA. Jefferson County Public Health >does case investigations and contact tracing of all positive tests >reported to Washington State and available to us through a >confidential on-line registry known as WEDSS. > >The fact that a thermal cycler can perform up to 45 amplification >cycles does not mean that ALL tests are amplified to that degree. >Samples are cycled until a signal is detected or they have undergone >the maximum amplification of the testing protocol. Samples can have >high CT values for many reasons -- poor sample quality, degradation of >the sample during transport, low viral levels in the person being >tested, and testing late in illness when fragments of non-replicating >virus can be detected. And it is certainly true that high CT values >correlate with lower transmission risk (assuming adequate sample >collection and specimen transport). Setting standards for FDA >approved diagnostic tests is a federal regulatory function. States >set standards for notifiable conditions such as SARS-CoV-2 infection. >County health officers, local boards of health, county boards of >commissioners, and public hospital district commissioners have nothing >to do with these decisions. > >Again, if you have grave concerns that the Washington State Department >of Health is using scientifically indefensible criteria for >determining which COVID-19 PCR tests are positive, please share your >expertise and concerns with them. These criteria are not set by >county health officers or local hospital districts. Nor do we >manufacture or license the PCR machines that are used to test >diagnostic specimens for SARS-CoV-2. We rely on these tools along >with our case investigations (looking at exposure risk, symptom onset,
>and other risk factors) in assessing cases. False positive tests can
>occur with any diagnostic technology. They appear to be quite
>infrequent with PCR testing, especially when a person has a COVID-like >illness or a recent exposure to a confirmed case. If your goal is to >support the pandemic denialism that Ms. Huenke promotes in the "Port >Townsend Free Press" article you reference, I could not disagree more. > With the spread of more transmissible variants of SARS-CoV-2, the >social cost of pandemic denialism is increasing. If sizeable numbers >of people indulge in the wishful thinking that attempts to control >COVID-19 transmission are unnecessary, it is only a matter of time >before variant strains become predominant. We still have time to >avert this future or at least slow it enough to allow widespread >vaccine deployment. I urge you to join the community fight against >COVID-19 and stop attacking those who are working long hours trying to >protect their community from the worst public health emergency in the >last 100 years. > >Sincerely, > >Thomas Locke, MD, MPH >Jefferson County Health Officer > >________________________________________ >From: Stephen Schumacher [solmaker@olympus.net] >Sent: Monday, February 1, 2021 12:33 PM >Cc: Board of Health; Tom Locke; Allison Berry, Clallam County Health Officer >Subject: New hope for "negative cases" before Feb. 14 >> >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 his >easily-refuted opinion that PCR tests are "highly accurate". > >Philip Morley observed that Jefferson Healthcare handles only a small >percentage of our county's PCR testing, with most conducted by UW and >others. If so, that raises the additional question: > >7) What Cycle Threshold is used by each organization performing PCR >testing in our county, and approximately what percentage of testing >is done by each organization? > >Because of the critical importance of the cycle count in evaluating >the significance of a positive PCR test result, both pieces of >information need to be reported to individuals as well as in overall >county statistics. > >Dr. Locke's report began by warning about a tripling of cases with 26 >new ones last week if I heard correctly. But what are the cycle >counts of these new cases? It makes a huge difference whether they >were found positive after 20 amplification cycles or after 45 cycles. > >My interest is getting at the truth, not politics. But today's >meeting seemed concerned about county cases showing percentage
>improvements before a Feb. 14 deadline One way to achieve that in a
>hurry might be to re-examine recent cases and reclassify any that
>were incorrectly counted due to amplification cycles higher than 33, >then continue using that rule for new cases. Not only would that be >the right thing to do, it might achieve the "negative cases" >[Commissioner] Greg [Brotherton] ruefully joked are needed! > >Yours truly, >Stephen Schumacher >2023 E. Sims Way #200 >Port Townsend, WA 98368 > >________________________________________ >--- Pubic Comment sent 8:28 PM 1/31/2021 --- > >From: Stephen Schumacher <solmaker@olympus.net> >Sent: Sunday, January 31, 2021 8:28 PM >Cc: Board of Health; Tom Locke; Allison Berry, Clallam County Health >Officer; news@ptleader.com; PT Free Press >Subject: Accountability for Jeffco's 45-Cycle Threshold PCR Test > >Dear Jefferson County Commissioners, > >On September 2, 2020, I sent the following Public Comment to the >Jefferson County Board of Health and Health Officer Dr. Tom Locke: > >"Per the August 29 New York Times report [of 90% false positives at >40-cycle threshold], I'm concerned about the criteria used to >determine confirmed cases of COVID-19 in Jefferson County. Do all >these cases exhibit symptoms, or are "cases" being equated to >positive test results? If the latter, what percentage of cases >exhibit symptoms? Are positive test results being recorded using PCR >tests, and if so, what is the Cycle Threshold value used for these tests?" > >I never received any answers to these questions nor have seen them >addressed 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-h >ealth-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 its >45-cycle threshold from a fortuitous Public Records Request? > >2) Since Dr. Locke was also Clallam Health Officer until recently, is >this same unreliable 45 Ct test also in use throughout Clallam County? > >3) Was the choice to use this 45 Ct test ever discussed and approved >by the Jefferson County Board of Health or County Commissioners? If >not, was it ever even reported and its significance explained to them? > >4) Does Dr. Locke or anybody else keep statistical track of >cumulative cycle counts for positive tests and resulting cases in our
>county, or is this info unavailable or being ignored? Could this
>information be regularly published in the media, or at least be made
>available upon request? > >5) Does our county always order a second test following a positive >PCR result, and if not, how often and on what basis? Are all >positive tests treated as COVID-19 cases regardless of symptoms, and >if not, how often has high cycle count been used to discard extremely >weak positive test results? > >6) How many county residents have been reported as cases, >quarantined, and contact-traced based on cycle counts above 33, when >the CDC shows "it is extremely difficult to detect any live virus in >a sample above a threshold of 33 cycles"? > >Yours truly, >Stephen Schumacher >2023 E. Sims Way #200 >Port Townsend, WA 98368