Publication - FOI/EIR release

Timeline for recording Cycle Threshold (Ct) values for positive COVID-19 Cases: FOI Review

Information request and response under the Freedom of Information (Scotland) Act 2002

Published:
9 Nov 2020
Timeline for recording Cycle Threshold (Ct) values for positive COVID-19 Cases: FOI Review
FOI reference: FOI/202000095265
Date received: 14 Sep 2020
Date responded: 6 Nov 2020
Information requested

On what date is it recorded that a minister/ministers of the Scottish Government directed/instructed real time reverse transcriptase polymerase chain reaction (rRT-PCR) Test Centres to associate the Cycle Threshold (Ct) values with the positive test results for "Covid-19" (specifically the putative virus SARS-CoV-2) that are provided to the Scottish Government (and thence released to the public)?

Response

In conducting my review, I have considered the circumstances of the case afresh, taking account of the points you raised in your request for review.  In accordance with review procedure, I have reviewed all of the documentation that falls within the scope of your request.

You requested a review because you felt the Scottish Government had not responded with the information that was asked for.  "On what date is it recorded that a minister/ministers of the Scottish Government directed/instructed real time reverse transcriptase polymerase chain reaction (rRT-PCR) Test Centres to associate the Cycle Threshold (Ct) values with the positive test results for "Covid-19" (specifically the putative virus SARS-CoV-2) that are provided to the Scottish Government (and thence released to the public)?"

I have reviewed the response to your FoI request and can confirm that you were not provided with the information you requested, for which I apologise.  The answer to your question is that Ministers haven't directed labs on associating Ct value with a positive test, so we do not have a date to provide you with.  It is up to the virologists at the diagnostic labs to interpret the result of the test that is reported, and where a test looks to be weak positive then there are protocols in place to retest.

Some further information which may be of interest to you is provided below.

Cycle threshold or Ct value is the number of PCR cycles that it takes before the virus (SARS-CoV-2) is first detected. The lower the Ct value the higher the amount of virus in the sample. There are a number of different versions of the RT-PCR test currently in use in Scotland.  All of these tests have been designed to detect at least one section of the SARS-CoV-2 genetic material (RNA) which is specific to the new virus.  These include the original assay developed in Public Health England’s (PHE) Colindale laboratory, as well as a number of commercially available assays, all of which have been validated by both PHE and the Scottish laboratory performing the assay.

No test is 100% accurate. The sensitivity of a test is the proportion of people who have the condition that is being tested for who actually have the disease. This gives the true positive rate and by extension defines the false negative rate (those who should have shown positive but the tests failed to see them as positive) Specificity is the opposite to sensitivity; it identifies the true negative rate and thus the false positive rate. Sensitivity and specificity define the accuracy of a test – how well does it rule in or rule out the diagnosis.

The type of tests being used for diagnosing covid-19 is one that detected the viral genetic sequence of the causative virus SARS-CoV-2 by a technique called real time PCR assays.  These tests are very sensitive and the gold standard for respiratory viruses. They are specific and shown not to detect other coronaviruses and have been tested on large panels of negative clinical samples.

 The current PCR tests in use in Scotland are effective at identifying people who have COVID-19 infection when they are symptomatic. As these tests only detect the presence of RNA from the SARS CoV-2 virus they cannot distinguish between live and inactivated virus. As a result  they cannot tell us if a person is currently infective. This means that testing cannot reliably tell us if someone who does not have symptoms currently has the disease, or has had it in the past and has inactivated virus in their sample.

Weak positive results can happen when the swab picks up fragments of the virus from an individual who is no longer infectious. Laboratories in Scotland have now implemented confirmation testing (or repeat testing) in certain circumstances to confirm whether weak positive test results are actually infectious cases.  Public Health Scotland have produced guidance for sampling and laboratory investigations:
https://www.hps.scot.nhs.uk/web-resources-container/covid-19-guidance-for-sampling-and-laboratory-investigations/

Public Health Scotland have published frequently asked questions about COVID-19 laboratory testing more information can be found at https://www.hps.scot.nhs.uk/web-resources-container/covid-19-laboratory-testing-frequently-asked-questions/

About FOI

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Contact

Please quote the FOI reference
Central Enquiry Unit
Email: ceu@gov.scot
Phone: 0300 244 4000

The Scottish Government
St Andrews House
Regent Road
Edinburgh
EH1 3DG