The public has a right to know whether they can trust the COVID test results being used to destroy businesses and jobs, to curtail educational, community and religious activities and to exacerbate many of our already serious social ills, including substance abuse, domestic abuse, crime and suicides. An arrogant, “Because I say so,” is no longer acceptable. We are seeing public health officials and county commissioners finally speak against Governor Inslee’s arbitrary and unscientific dictates.

Citizens have the right to know how solid or flimsy is the testing data being used to extend lockdown orders now recognized as unfair and not based on sound science.

As explained in an article here by Annette Huenke, Jefferson Healthcare is using testing protocols that can return, in lay terms, practically meaningless positive COVID test results. We are not being told how many cycles were run on each reported positive “case.” Anything above 32-33 cycles or so is recognized as producing meaningless results (again, in lay terminology). Jefferson Healthcare employs a protocol that can run as many as 45 cycles on a sample until it gets a result or the cycles are completely run through, raising unanswered questions about how many of our “cases” were little more than meaningless test results.

It matters because people with only trace (again in lay terms–read the article for more precision) evidence of COVID, and with no symptoms or risk of transmission are being added to our numbers, Each additional “case” is used as justification to continue to inflict injury on our community and individuals with a senseless extension of the Governor’s ever-changing-but-never-expiring lock down order.

Private citizens have the right to ask these question. Disclosure of this information is routine in some states. It is mandatory in Florida. Stephen Schumacher is well qualified as an investigator of what should be a matter of public record. He understands data and knows the questions to ask. He graduated with honors in Mathematics from Harvard College and programmed funds transfer systems between Wall Street banks and the Federal Reserve before moving to Port Townsend in 1983. He has served as an officer for various community organizations such as the Food Co-op, Jefferson Land Trust, and the Northwest Nutritional Foods Association. He co-created The Port Townsend and Jefferson County Leader’s original online newspaper and programs shipboard stability software used by naval architects. He is a careful, rigorous researcher.

He has been asking important questions of Dr. Thomas Locke, Jefferson County Health Officer, for months, with no response at all. Recently, after publication of several articles here, Dr. Locke communicated with Mr. Schumacher, but still is not answering these questions. For that matter, neither is the Washington Department of Health. What we are getting is deflection and, at times, ad hominem jabs. This happened last year when Gov. Inslee was confronted with evidence that COVID death statistics included instances where people clearly died from other causes, such as being murdered. He deflected questions about these facts and insulted the research foundation that had uncovered this information in the DOH’s own records.

We are publishing the full exchange thus far of correspondence between Dr. Locke and Mr. Schumacher. The Board of County Commissioners has sometimes been in the middle of this exchange. The Clallam County Health Department has also been receiving the correspondence.

To fully grasp the importance of the details being discussed, we suggest reading Ms. Huenke’s article and Mr. Schumacher’s article published by Port Townsend Free Press, and the sources linked in each of those articles.

Mr. Schumacher to the Board of County Commissioners, a response and critique of Dr. Locke, 2/6/2021

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 the
percentage of cases exhibiting symptoms and the Ct associated with
positive tests.

Though the estimate of viral load provided by Ct may be imperfect, it
is far more helpful than a bare positive or negative test
result!  How could getting no information about viral load (or a wild
guess) be better than the rough estimate (or educated guess) provided
by a Ct value interpreted cautiously in a clinical context?  People
have a right to know and should be trusted to know.

Yours truly,
Stephen Schumacher

 

Dr. Locke’s immediately preceding correspondence to Mr. Schumacher, copied to BOCC and others, 2/2/2021 

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

Dr. Locke’s Correspondence to Mr. Schumacher, copied to BOCC and others, 2/1/2021

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

 

Stephen Schumacher to BOCC, 2/1/2021

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

Stephen Schumacher to BOCC, 1/31/2021

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