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PCR Cycle threshold of Covid cases

P McKenna made this Official Information request to Ministry of Health

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From: P McKenna

Dear Ministry of Health,

Can you please supply the following Information
1. A 'communinty case' of Covid 19 identified in Auckland on 17/8/21.Please supply the Polymerase Chain Reaction (PCR) Cycle Threshold (Ct) for this particular case. (ie: the Ct value at which viral matter was detected- otherwise know as the Ct value)
2. The PCR Ct value (as above) for all cases identified in NZ in the last 6 months

Yours faithfully,

P McKenna

Link to this

From: OIA Requests

Kia ora
Thank you for your email.
Information regarding the cycle threshold (CT) values of individuals is
withheld under section 9(2)(a) of the Official information Act (the Act)
to protect the privacy of natural persons. The Ministry is satisfied that
in the circumstances of this case, the withholding of the information is
not outweighed by other considerations which render it desirable in the
public interest to make the information available. 
Please refer to the following link for a previously published response
regarding CT values which may be useful to you:
[1]https://www.health.govt.nz/system/files/....
Under section 28(3) of the Act you have the right to ask the Ombudsman to
review any decisions made under this request. The Ombudsman may be
contacted by email at: [email address] or by calling 0800 802
602.
Ngā mihi
OIA Services
Government Services
Office of the Director-General
Ministry of Health
E: [email address]

--------------------------------------------------------------------------

From: P McKenna <[FOI #16428 email]>
Sent: Tuesday, 17 August 2021 16:28
To: OIA Requests <[email address]>
Subject: Official Information request - PCR Cycle threshold of Covid cases
 
Dear Ministry of Health,

Can you please supply the following Information
1.  A 'communinty case' of Covid 19 identified in Auckland on
17/8/21.Please supply the Polymerase Chain Reaction (PCR) Cycle Threshold
(Ct) for this particular case. (ie: the Ct value at which viral matter was
detected- otherwise know as the Ct value)
2. The PCR Ct value (as above) for all cases identified in NZ in the last
6 months

Yours faithfully,

P McKenna

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From: P McKenna

Dear OIA Requests,

Thank you for your prompt reply.
You state that; 1) Ct rates are not divulged to protect an individual's privacy, and; 2) that the MOH has determined that witholding Ct values does not outweigh other considerations that render it a matter of public interest.

In relation to the first assertion, please explain how the divulging of a PCR cycle rate can risk exposure of personal details any more than divulging said person is a PCR positive 'case'.

In relation to the second assertion, I am sure you are aware that the Ct value of 'cases' bares significantly on establishing whether or not 'cases' are actual infections and a threat to the public health. A Ct of 26 represents only a 53% chance an actual infection (see: https://academic.oup.com/cid/article/72/...). A Ct of 36 or higher represents an almost impossible chance of the result being an actual infection (see: https://www.youtube.com/watch?v=A867t1Jb...). In NZ PCRs are being run to at least 40 cycles meaning many so called 'cases' may well be false positives. Indeed, the MOH sent 200 samples of confirmed cases to ESR for culture and was not able to culture 120 of them indicating than up to 60% were not actual infections capable of transmitting the disease, but were instead dead viral matter from historic infections, or plain old false positives.

It is in the public's interest to know what Ct values are, so that we may have confidence in the decisions being made by the director General of Health and the Prime Minister.

Yours sincerely,

P McKenna

Link to this

From: OIA Requests

Kia ora Paul,
Thank you for your email. 
When considering whether clinical information (such as CT values) should
be released, the Ministry of Health (the Ministry) weighs up the risk of
identification against the public interest in knowing the information.
Given the small number of people contracting COVID-19 the Ministry
considers that the risk of identification is higher than the public
interest in knowing the CT values of any given case.
CT values will vary according to the variety of tests done and are often
repeated using different platforms to establish any trend. The CT value is
useful during the case investigation stages but must be considered as part
of a suite of other personal health information. Thus, a standalone CT
value without clinical context and appropriate clinical interpretation is
not necessarily helpful and could be interpreted incorrectly.
Under section 28(3) of the Act, you have the right to ask the Ombudsman to
review any decisions made under this request.
Ngā mihi
OIA Services
Government Services
Office of the Director-General
Ministry of Health
E: [email address]

--------------------------------------------------------------------------

From: P McKenna <[FYI request #16428 email]>
Sent: Thursday, 19 August 2021 09:57
To: OIA Requests <[email address]>
Subject: Re: Official Information request - PCR Cycle threshold of Covid
cases
 
Dear OIA Requests,

Thank you for your prompt reply.
You state that; 1) Ct rates are not divulged to protect an individual's
privacy, and; 2)  that the MOH has determined that witholding Ct values
does not outweigh other considerations that render it a matter of public
interest.

In relation to the first assertion, please explain how the divulging of a
PCR cycle rate can risk exposure of personal details any more than
divulging said person is a PCR positive 'case'.

In relation to the second assertion, I am sure you are aware that the Ct
value of 'cases' bares significantly on  establishing whether or not
'cases' are actual infections and a threat to the public health. A Ct of
26 represents only a 53% chance an actual infection (see:
[1]https://scanmail.trustwave.com/?c=15517&...
A Ct of 36 or higher represents an almost impossible chance of the result
being an actual infection (see:
[2]https://scanmail.trustwave.com/?c=15517&...
In NZ PCRs are being run to at least 40 cycles meaning many so called
'cases' may well be false positives. Indeed, the MOH sent 200 samples of
confirmed cases to ESR for culture and was not able to culture 120 of them
indicating than up to 60% were not actual infections capable of
transmitting the disease, but were instead dead viral matter from historic
infections,  or plain old false positives.

It is in the public's interest to know what Ct values are, so that we may
have confidence in the decisions being made by the director General of
Health and the Prime Minister.

Yours sincerely,

P McKenna

show quoted sections

Link to this

From: P McKenna

Dear OIA Requests,

Thankyou again for your prompt reply.

You have published this individual's sex, age, where he lives (enough to enable the media to decern what street he lives on), his job, and everywhere he visited over the weekend. It is not plausible that the Ct rate of his PCR test is going to diminish his privacy any more than you already have by the information you have given out.

Whatever other clinical information MOH considers important, it does not alter the fact (well grounded in science) that any Ct value over 30 is unlikely to be infectious, and a Ct of 36 or above is guarenteed to be not infectious. Yet we know that this individual could have a Ct as high as 40 since this appears to be the upper limit of the NZ testing programme. A PCR + result is itself completely meaningless without knowledge of the Ct value (among other things).

The desision to decide whether or not this individual is a covid case or not, is not one that effects this individual alone. It affects the entire nation in a dramatic way. Therefore, I believe, the public has a right to know all information relating to that decision.

In relation to the second item of my original request, if you insist that privacy is an issue, then send me Ct values only, in a randomised order so they can not be identified, or in any way related back to the case number.

Yours sincerely,

P McKenna

Link to this

Carli Botes left an annotation ()

Note: In this request [ https://fyi.org.nz/request/15541-current... ] there was a response from Jill Vintiner (Signed Joint General Manager Health and Environment Group – Health, ESR) on 2 June 2021.

She stated in her response that the current cycle threshold value used to perform the PCR test for COVID19 was 40, and that ESR have no intention of changing their cycle threshold value cut-offs.

Hope this helps!

Link to this

From: OIA Requests

Kia ora Paul,
Thank you for your email. The Ministry has nothing further to add
regarding your request. If you are unsatisfied with your response, please
feel free to contact the ombudsman. 
The Ombudsman may be contacted by email at: [email address]
or by calling 0800 802 602.
 Ngā mihi
OIA Services
Government Services
Office of the Director-General
Ministry of Health
E: [email address]

--------------------------------------------------------------------------

From: P McKenna <[FOI #16428 email]>
Sent: Thursday, 19 August 2021 14:48
To: OIA Requests <[email address]>
Subject: Re: Official Information request - PCR Cycle threshold of Covid
cases
 
Dear OIA Requests,

Thankyou again for your prompt reply.

You have published this individual's  sex, age, where he lives (enough to
enable the media to decern what street he lives on), his job, and
everywhere he visited over the weekend. It is not plausible that the Ct
rate of his PCR test is going to diminish his privacy any more than you
already have by the information you have given out.

Whatever other clinical information MOH considers important, it does not
alter the fact (well grounded in science) that any Ct value over 30 is
unlikely to be infectious, and a Ct of 36 or above is guarenteed to be not
infectious. Yet we know that this individual could have a Ct as high as 40
since this appears to be the upper limit of the NZ testing programme. A
PCR + result is itself completely meaningless without knowledge of the Ct
value (among other things).

The desision to decide whether or not this individual is a covid case or
not, is not one that effects this individual alone. It affects the entire
nation in a dramatic way. Therefore, I believe, the public has a right to
know all information relating to that decision.

In relation to the second item of my original request, if you insist that
privacy is an issue, then send me Ct values only, in a randomised order so
they can not be identified, or in any way related back to the case number.

Yours sincerely,

P McKenna

show quoted sections

Link to this

From: P McKenna

Dear OIA Requests,

Are you prepared to give the Ct values requested, in a randomised way, to protect identities?

I am prepared to accept this as a compromise.

Yours sincerely,

Paul

Link to this

From: OIA Requests

Kia ora Paul,
The Ministry of Health (the Ministry) is also unable to release CT values
in bulk under section 9(2)(a) of the Act, to protect the privacy of
natural persons.
Thank you for your email. The Ministry has nothing further to add
 regarding your request. If you are unsatisfied with your response, please
feel free to contact the ombudsman. The Ombudsman may be contacted by
email at: [email address] or by calling 0800 802 602.
Ngā mihi
OIA Services
Government Services
Office of the Director-General
Ministry of Health
E: [email address]

--------------------------------------------------------------------------

From: P McKenna <[FOI #16428 email]>
Sent: Saturday, 21 August 2021 14:58
To: OIA Requests <[email address]>
Subject: Re: Official Information request - PCR Cycle threshold of Covid
cases
 
Dear OIA Requests,

Are you prepared to give the Ct values requested,  in a randomised way, 
to protect identities?

I am prepared to accept this as a compromise.

Yours sincerely,

Paul

show quoted sections

Link to this

From: P McKenna

Dear OIA Requests,

Which 'Act' are you referring to?
Section 9 of the Health act has been repealed.
Section 9 of the Covid response Act, and section 9 the Privacy Act have nothing to do with this.

Please clarify.

Yours sincerely,

P McKenna

Link to this

From: OIA Requests

Kia ora Paul,
The Official Information Act 1982
Ngā mihi
OIA Services
Government Services
Office of the Director-General
Ministry of Health
E: [email address]

--------------------------------------------------------------------------

From: P McKenna <[FOI #16428 email]>
Sent: Monday, 23 August 2021 16:01
To: OIA Requests <[email address]>
Subject: Re: Official Information request - PCR Cycle threshold of Covid
cases
 
Dear OIA Requests,

Which 'Act' are you referring to?
Section 9 of the Health act has been repealed.
Section 9 of the Covid response Act, and section 9 the Privacy Act have
nothing to do with this.

Please clarify.

Yours sincerely,

P McKenna

show quoted sections

Link to this

From: P McKenna

Dear OIA Requests,

You have reasoned yourself in a full circle!

I am willing to make another concession:

Supply the average, mode, median, and range of Ct values for all cases from 24/2/21 to 24/8/21. Ct values can be calculated using whole numbers.

There should be no privacy issues with that.

Yours sincerely,

Paul McKenna

Link to this

From: OIA Requests


Attachment image001.png
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Kia ora Paul,

 

Thank you for your request for official information received on 24 August
2021 for:

 

"Supply the average, mode, median, and range of Ct values for all cases
from 24/2/21 to 24/8/21. Ct values can be calculated using whole numbers.”

 

The Ministry's reference number for your request is: H202112337.

 

As required under the Official Information Act 1982, the Ministry will
endeavour to respond to your request no later than 21 September 2021,
being 20 working days after the day your request was received.

 

Due to the COVID-19 global pandemic response, the Ministry is experiencing
significantly higher volumes of queries and requests for information. If
we are unable to respond to your request within this time frame, we will
notify you of an extension of that time frame.

 

If you have any queries related to this request, please do not hesitate to
get in touch.

 

Ngâ mihi

 

OIA Services

Government Services

Office of the Director-General

Ministry of Health

E: [1][email address]

 

 

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From: OIA Requests


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Attachment CT Values.csv.txt
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Kia ora Paul,

 

Please find attached a response to your official information act request

 

Ngā mihi 

 

OIA Services

Government Services

Office of the Director-General

Ministry of Health

E: [1][email address]

 

 

 

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From: P McKenna

Dear OIA Service,
Thankyou for your response and the data supplied.
May I request some clarifications:
1. Does each row in the CSV file supplied relate to one 'case'? one test result deemed positive? or something else? Please clarify (Some rows have one test result, others have up to 6).
2. I understand that each positve test result is validated by repeat analysis, yet many rows have only one Ct value. Is this the highest, lowest or average value out of 2? Or was there no repeat anaylisis? If not why would this occur?
3. Some rows have multiple sets of 2 results (up to 3 sets). Does this reflect; multiple tests obtained at various times throughout infection? 2-3 separate cases? or something else?
4. Many Cts are very high and would not normally be considered positive. What protocol is used to determine these to be actual SARS-CoV-2 infections?
5. Many postive test results use an Envelope (E) gene assay. Since E-gene assays have been shown to lack specificity, particularly in relation to other coronaviruses, what measure have been used to ensure these are not false positives?

Yours sincerely,

Paul

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From: OIA Requests


Attachment image001.jpg
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Kia ora Paul

 

Thank you for your request for official information received 27 September
2021 for:

 

" 1. Does each row in the CSV file supplied relate to one 'case'? one test
result deemed positive? or something else? Please clarify (Some rows have
one test result, others have up to 6).

2. I understand that each positve test result is validated by repeat
analysis, yet many rows have only one Ct value. Is this the highest,
lowest or average value out of 2? Or was there no repeat anaylisis? If not
why would this occur?

3. Some rows have multiple sets of 2 results (up to 3 sets). Does this
reflect; multiple tests obtained at various times throughout infection?
2-3 separate cases? or something else?

4. Many Cts are very high and would not normally be considered positive.
What protocol is used to determine these to be actual SARS-CoV-2
infections?

5. Many postive test results use an Envelope (E) gene assay. Since E-gene
assays have been shown to lack specificity, particularly in relation to
other coronaviruses, what measure have been used to ensure these are not
false positives?"

 

The Ministry's reference number for your request is: H202113156.

 

As required under the Official Information Act 1982 we will endeavour to
respond to your request no later than 26 October 2021, being 20 working
days after the day your request was received.  

 

If we are unable to respond to your request within this time frame, we
will notify you of an extension of that time frame.

 

If you have any queries related to this request, please do not hesitate to
get in touch.

 

Ngā mihi

 

OIA Services

Government Services

Office of the Director-General

Ministry of Health

E: [1][email address]

 

 

 

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From: OIA Requests


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Attachment H202113156 Response.pdf
286K Download View as HTML


Kia ora Paul,

 

Please find attached a response to your official information act request

 

Ngā mihi 

 

OIA Services

Government Services

Office of the Director-General

Ministry of Health

E: [1][email address]

 

 

 

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