Impact of PCR false positive results during periods of low prevalence

Charlotte Johnson made this Freedom of Information request to Public Health England

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Charlotte Johnson

Dear Public Health England,

A government guidance document for laboratories, highlighting this issue & providing recommendations, was published on September 7th and last updated on 16th October. SARS-CoV-2 RNA testing: assurance of positive results during periods of low prevalence (https://www.gov.uk/government/publicatio...).
It recommended that
All laboratories should determine the threshold for a positive result at the limit of detection based on the in-use assay.
It also recommended specific actions to be taken for a positive result at the limit of detection for pillar 1 and pillar 2 laboratories:

· Pillar 1 - Retest existing sample in the same or an alternate nucleic acid amplification assay of equivalent sensitivity and specificity. If necessary, request a repeat sample. Subjects should be advised to self isolate pending the results of the repeat or retested sample.

· Pillar 2 - Request a repeat sample and advise self isolation pending the results of the second sample.

The above recommendations come into effect during periods of “low prevalence”. The guidance states:

Laboratories should make an assessment of the disease prevalence threshold at which they stop/start confirmatory testing. Two possible strategies are proposed:

1. Use publicly available population prevalence estimates, such as from the Office for National Statistics (ONS) or Imperial College REACT1 study. A threshold of <0.5% population prevalence is suggested as indicative of a period of low prevalence. A caveat of use of these data is that variation in prevalence by region is not captured.

2. Implement a threshold based on local laboratory data indicating the proportion of positive tests. Once positive tests within the laboratory exceed 5% to 8% of total tests performed, low prevalence assurance strategies may be discontinued.

Please can you answer the following questions on the implementation of this guidance in all laboratories:

1. Has the recommendation that All laboratories should determine the threshold for a positive result at the limit of detection based on the in-use assay been implemented? If so, please publish the list of laboratories and the thresholds each has adopted.

2. Is the threshold dependent on a particular type of test? If so, please provide the thresholds for each test type.

3. Has each laboratory implemented the guideline to retest a sample or to request a repeat sample? Assuming the answer has to be yes, please provide data for each laboratory for the number of positive tests at the limit of detection, the number of retests or repeat samples requested, and the outcome of the retest/ test on a repeat sample. The ONS prevalence estimate was lower than 0.5% until the latest report on 16th October, so it is reasonable to assume that laboratories were implementing the low prevalence guidelines at least up until the 9th October, and possibly later.

4. Please provide details of PHE monitoring to ensure that laboratories are adhering to this guidance and to ensure that the limits set by the laboratories are evidence based and will achieve the aims set out by the guidance.

Yours faithfully,
Charlotte Johnson

Charlotte Johnson

Dear Public Health England,
Please can you acknowledge receipt of this FOI request

Yours faithfully,

Charlotte Johnson

FOI, Public Health England

OFFICIAL
Dear Charlotte Johnson,

We acknowledge receipt of your email and request for information of 27th October, which will be treated as a request for information under statutory access legislation.

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Public Accountability Unit
Public Health England
[Public Health England request email]
Tel: 020 8327 6920
www.gov.uk/phe Follow us on Twitter @PHE uk

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Dear FOI,

By law you should have normally responded promptly and by 24th November.

Please can you respond to my request

Yours sincerely,

Charlotte Johnson

FOI, Public Health England

Dear Charlotte Johnson,

Thank you for your email and patience whilst we work on your request. We apologise for the delay in providing our response. Due to the pandemic we are dealing with a high volume of requests at this time. We hope to provide you with our response at the very latest by 23 December 2020.

Thank you once again for your patience.

Yours sincerely,

FOI Team
Public Accountability Unit
Public Health England
[Public Health England request email]
Tel: 020 8327 6920
www.gov.uk/phe Follow us on Twitter @PHE uk

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FOI, Public Health England

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OFFICIAL
Dear Charlotte Johnson,

Please find attached Public Health England's response to your request.

FOI Team
Public Accountability Unit
Public Health England
[Public Health England request email]
Tel: 020 8327 6920
www.gov.uk/phe Follow us on Twitter @PHE uk

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