Questions concerning PCR testing in Scotland : FOI release

Information requested

1. Who manufactures, and supplies the PCR Testing kits in use in Scotland?
2. What is their country of origin of the PCR tests?
3. What is the sensitivity (cycle threshold) of the PCR tests conducted in Scotland?
4. What analysis of the sensitivity (cycle threshold) has been undertaken to ensure that it is correct?
5. What is the accuracy of the PCR tests in percentage?
6. What data is available or used to measure the PCR test accuracy?
7. How is the accuracy of the PCR tests monitored?
8. Who conducts quality control on the PCR test results?
9. What reports, data, information is used for quality control of PCR test results?
10. How many false positives have the PCR tests returned?
11. How many false negatives have the PCR tests returned?

Response

1, 2, 4. While our aim is to provide information whenever possible, under section 17 of FOISA and in this instance the Scottish Government does not have all of the information you have requested. However, you may wish to contact Public Health Scotland, who may be able to help you with questions 1, 2, 4.

3. The Cycle Threshold, or CT value, is the number of PCR cycles that it takes before the virus is first detected; the lower the CT value the higher the level of virus in the original sample.

Each manufacturer of the PCR test will recommend a differing maximum amplification cycle number to determine presence of SARS CoV-2 when interpreting results, but a maximum of around 40 amplification cycles is normally used.

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/

5. Based on Local data published, PCR is 98% accurate for those with symptoms.

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.

6, 7, 8, 9. The information you have requested in points 6, 7, 8 & 9 are available from COVID-19 Laboratory testing Frequently Asked Questions (windows.net). Under section 25(1) of FOISA, we do not have to give you information which is already reasonably accessible to you. If, however, you do not have internet access to obtain this information from the website(s) listed, then please contact me again and I will send you a paper copy.

10, 11. While our aim is to provide information whenever possible, under section 17 of FOISA and in this instance the Scottish Government does not have the information you have requested relating to how many false positives/negatives the PCR tests have returned.

However it is important to note that development of polices in response to managing the spread of COVID-19 by The Scottish Government is supported by guidance from a range of experts in their relevant fields, as well as direction from UK GOV and World Health Organisation.

The likelihood of false positives arising is dependent on a number of factors such as the overall prevalence of infection in the population, the clinical presentation of disease in the person sampled, and quality of the sampling method. It is very difficult to exactly measure the false positive rate of any testing system. NHS Scotland Laboratories have a number of quality procedures in place to minimise false positives results.

NHS Scotland Laboratories have a protocol in place to carry out confirmation testing (or repeat testing) in certain circumstances to confirm whether low positive test results should be reported as positive or negative. Public Health Scotland have produced guidance for sampling and laboratory investigations to minimise reporting of false positives occurring: HPS Website - COVID-19 - guidance for sampling and laboratory investigations (scot.nhs.uk)

UK Government Laboratories (Lighthouse) also have similar quality procedure systems in place to minimise false positives but are unable to repeat test low positive results.

In terms of how false positives are dealt with in our published statistics:

In the case of weakly detected positive results (i.e. not true current infection), the sample is reprocessed and if, when more detailed virology analysis has been undertaken, it is assessed that there is no current infection or infectivity present, then the original test will be taken as a false positive, de-notified, and removed from the confirmed case tally. However, where it is not possible to reprocess the test or carry out more detailed analysis, then the original test cannot be de-notified and the weak positive will remain recorded in the case tally.

This process is undertaken in relation to statistics published for daily and weekly tests carried out through both the NHS and the UK Government Extended Testing Programme in Scotland here:Coronavirus (COVID-19): daily data for Scotland - gov.scot (www.gov.scot)

 

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