ABCDEFGHIJLMNOPQRSTUV
1
#FOI IdentifierRespondentFOI linkQueryCategory of FOIDate of FOIDate of responseResponse typeResponse
2
1O'Hooley (1)Department of Health and Social CareLinkFor Pillar One PCR swab tests for antigens for SARS-CoV-2, please provide detail of the threshold cycle (CT) values that are used as a cut off for a positive recorded test result.Cycle Threshold20-Oct-20209-Apr-2021Doesn't hold infoThe DHSC does not hold the information you requested
3
O'Hooley (2)Department of Health and Social CareLinkFor Pillar Two PCR swab tests for antigens for SARS-CoV-2, please provide detail of the threshold cycle (CT) values that are used as a cut off for a positive recorded test result.Cycle Threshold20-Oct-20209-Apr-2021BoilerplateA typical RT-PCR assay will have a maximum of 40 thermal cycles. Furthermore, the ongoing ONS infection survey has not found any sample which has been positive with a CT Value above 37, with the exception of one. More information on cycle threshold in positive cases has been published by the University of Oxford and is accessible here: Viral load in community SARS-CoV-2 cases varies widely and temporally (medrxiv.org)
4
O'Hooley (3)Department of Health and Social CareLinkFor Pillar Four PCR swab tests for antigens for SARS-CoV-2, please provide detail of the threshold cycle (CT) values that are used as a cut off for a positive recorded test result.Cycle Threshold20-Oct-20209-Apr-2021Doesn't hold infoThe DHSC does not hold the information you requested.
5
O'Hooley (4)Department of Health and Social CareLinkFor Pillars One, Two and Four, please give a percentage for positive test results for antigens for SARS-CoV-2, for threshold cycle (CT) values from 1-20, from 21-30, from 31-36, from 37-39, and 40 and above cycles.Cycle Threshold20-Oct-20209-Apr-2021RedirectThe ONS datasets contains the percentage and Cycle threshold (Ct) values of COVID-19 cases in the UK from 21 September 2020 to 13 March 2021 which can be accessed here: https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/datasets/coronaviruscovid19infectionsurveydata
6
O'Hooley (5)Department of Health and Social CareLinkPlease give the current official UK Governmental policy for threshold cycle values regarding PCR testing for antigens for SARS-CoV-2, including specific policy for CT values above 35 cycles, any changes with regard to this policy for 2020 to date and any scientific guidance that has been used to provide said policies.Cycle Threshold20-Oct-20209-Apr-2021Doesn't hold infoThe DHSC does not hold this information.
7
O'Hooley (6)Department of Health and Social CareLinkPlease provide official UK Governmental policy for the recording of ambiguous PCR test results for SARS-CoV-2 antigens for 2020 to date.PCR Other Info20-Oct-20209-Apr-2021AnswerThe DHSC informs the patient and on a case by case advices the patient on whether to take another test.
8
2Misty (1)Public Health WalesLinkCan you tell me the distribution of cycle thresholds used to provide a positive PCR test? In other words, what percentage of positive tests came at what cycle threshold value?Ct Values4-Nov-202011-Dec-2020AnswerCt % of Range Tests in October:
11-20 - 17.6%
21 - 30 -58.1%
31 - 40 - 23.8%
41-45 - 0.5%
9
Misty (2)Public Health WalesLinkHave you undertaken any viral culture to cross reference with cycle threshold values? If so, what are the results? Additionally, if you have any information about the proportion of culturable samples by cycle threshold can you please provide those.Viral Culture4-Nov-202011-Dec-2020Doesn't hold infoWe have not undertaken viral culture in Welsh NHS laboratories.
10
Misty (3)Public Health WalesLinkCan you please the approximate false positive and false negative rates for your PCR test? Does this vary with cycle threhold?PCR Other Info4-Nov-202011-Dec-2020Non-answerThe false positive and false negative rates are determined by the sensitivity and specificity of the test, but also the prevalence of the condition within the test population that is being tested for. The sensitivity and specificity do change with cycle threshold; generally the sensitivity increases and specificity decreases as the Ct values decreases.
11
3Roper (1)Department of Health and Social CareLinkIs the PCR cycle threshold required to be recorded with every PCR test in England?Cycle Threshold7-Dec-20208-Jan-2021Black BoxCt values are not provided for all SARS-CoV-2 molecular detection methods. Some commercial RT-PCR techniques are closed 'black box' systems whereby the operator cannot observe the reaction in real-time and the result is interpreted by software into a qualitative non-interrogatable positive or negative result
12
Roper (2)Department of Health and Social CareLinkTo date, what is the proportion of positive covid tests in England with a PCR cycle threshold greater than 25?Cycle Threshold7-Dec-20208-Jan-2021Doesn't hold infoDHSC does not hold information relevant to your request. We are not recording PCR cycle thresholds systematically unless as part of a surveillance study such as the Office for National Statistics (ONS).
13
4McCann (A1)Southern Health and Social Care TrustLinkCan you tell me the distribution of cycle thresholds used to provide a positive PCR test? In other words, what percentage of positive tests came at what cycle threshold value?Ct Values26-Feb-202118-Mar-2021Answer0 -10 0.00%
11- 20 8.80%
21-30 52.81%
31-40 37.83%
41-45 0.57%
14
McCann (A2)Southern Health and Social Care TrustLinkAlso specifically what percentage of the total positives tests were carried out at a CT value between 30-45?Ct Values26-Feb-202118-Mar-2021Answer38.40%
15
McCann (A3)Southern Health and Social Care TrustLinkHave you or or any other labs you have outsourced to undertaken any viral culture to cross reference with cycle threshold values? If so, what are the results? Additionally, if you have any information about the proportion of culturable samples by cycle threshold can you please provide those.Cycle Threshold26-Feb-202118-Mar-2021Doesn't hold infoWe do not do viral culture, and we are unaware if this has been performed by any laboratory to which we forward samples.
16
5Hemmings (A1)Department of Health and Social CareLinka) The cycle threshold currently used for COVID-19 PCR tests.Cycle Threshold1-Jul-202121-Jul-2021BoilerplateA typical RT-PCR assay will have a maximum of 40 thermal cycles. The lower the CT value the higher the quantity of viral genetic material in the sample (as an approximate proxy for viral load). CT values obtained in this way are semi-quantitative and are able to distinguish between high and low viral load.
17
Hemmings (A2Department of Health and Social CareLinkb) If the cycle threshold has been changed any time since January 2020, when was it changed and what values were used.Ct Change1-Jul-202121-Jul-2021AnswerThere have been no changes to the CT value as there is no one set CT value to measure against.
18
Hemmings (A3)Department of Health and Social CareLinkc) Highlight any differences in testing regimes (frequency, timing, PCR CTs) between vaccinated and unvaccinated people.PCR Other Info1-Jul-202121-Jul-2021AnswerEqually, no changes to the testing regime have been made as result of vaccinations for this reason.
19
Hemmings (A4)Department of Health and Social CareLinkd) A distribution of positive tests by CTs, for each month from January 2020 to the present (most recent data available)Other1-Jul-202121-Jul-2021Doesn't hold infoDHSC does not hold information relevant to your request. While labs do record CT values for analysed test samples, a data collection exercise of this nature is not viable currently.
20
6Shaw (A1)UK Health Security AgencyLinkA plot of the number of PCR tests taken against the number of positive results for Covid, by month, for 2021, and then an adjusted graph to take into account the additional testing and remove the skew of additional positive results simply caused by more testing.Case Defn.7-Sep-202128-Oct-2021RedirectPHE can confirm that it holds the information as specified in your request. This information is exempt under Section 21 of the Act because it is reasonably accessible by other means, and the terms of the exemption mean that we do not have to consider whether or not it would be in the public interest for you to have the information.
21
Shaw (A2)UK Health Security AgencyLinkThe average PCR amplification cycles month by month for the year of 2021 that generated a positive resultCycle Threshold7-Sep-202128-Oct-2021Doesn't hold infoUKHSA can confirm that it does not hold the information as specified in your request.
22
7Shaw (B1)Public Health EnglandLinkA plot of the number of PCR tests taken against the number of positive results for Covid, by month, for 2021, and then an adjusted graph to take into account the additional testing and remove the skew of additional positive results simply caused by more testing.Case Defn.1-Nov-202129-Nov-2021RedirectPHE can confirm that it holds the information as specified in your request. This information is exempt under Section 21 of the Act because it is reasonably accessible by other means, and the terms of the exemption mean that we do not have to consider whether or not it would be in the public interest for you to have the information.
23
Shaw (B2)Public Health EnglandLinkThe average PCR amplification cycles month by month for the year of 2021 that generated a positive result.Cycle Threshold1-Nov-202129-Nov-2021BoilerplateThere are multiple tests being used and every kit will have its own interpretative criteria and thresholds, as recommended by the manufacturer. There are at least 80 different platforms in use, configured in various ways in different laboratories. Some tests provide cycle threshold (Ct) values, some do not.
24
8Mackay (1)NHS Western IslesLinkI would like to now how many cycles you are currently running on the PCR testsCycle Threshold19-Sep-202115-Oct-2021Non-answerThe analysers in use at WIH have cycle lengths set by the manufacturer as part of the method installation. The exact cycle length is not disclosed in the method literature and is not user definable.
25
Mackay (2)NHS Western IslesLinkhas this changed over the time you have been doing them, and if so, how?Ct Change19-Sep-202115-Oct-2021AnswerThere have been no changes to the cycle lengths in the time we have been testing for SARS-CoV-2.
26
Mackay (3)NHS Western IslesLinkAfter Appeal: I would like to now how many cycles you are currently running on the PCR testsCycle Threshold19-Sep-202130-Nov-2021Non-answerAfter appeal and review: The exact number of cycles used by each analysis platform used at NHS Western Isles is not available as it is not disclosed in the assay instructions for use. It would be possible to provide a rough estimate of the number of cycles, but not an accurate response. The number of PCR cycles a sample goes through will vary based on if the sample is negative or positive and if positive, the amount of viral material in the sample.
27
9Whicker (A1)Bedfordshire Hospitals NHS Foundation TrustLinkI would like to find out the number of cycles you are using for your RT PCR tests to diagnose Covid 19Cycle Threshold10-Aug-202125-Nov-2021Non-answerWe use commercial assays and follow manufacturer instructions.
28
Whicker (A2)Bedfordshire Hospitals NHS Foundation TrustLinkHas the cycle threshold changed since March 2020Ct Change10-Aug-202125-Nov-2021No responseNo response
29
10McCann (B1)Belfast Health and Social Care Trust (Northern Ireland)LinkI would like a breakdown of the CT cycles and at what percentage that were used in your trust from the following dates separately: 27th December 2020 to 10th January?Cycle Threshold1-Jul-202117-Nov-2021Doesn't hold infoAfter appeal clarification and review: Information not available.

Belfast Trust has not been able to answer your question as stated above. As previously advised, there are a number of different assays, kits and platforms currently in use for SARS-CoV2 testing. The numerous PCR based assays for SARS-CoV2 used by the Regional Virus Laboratory in Belfast Trust employ Taqman technology and the number of PCR cycles for this technology is generally 40 to 45 cycles - that is stated in the manufacturer’s instructions and is not altered by Belfast Trust’s laboratory. We have not, and do not adjust the number of cycles that the SARS-COV-2 PCR assays are run. The Trust considers that the cost of retrieving the information would be above the ‘Appropriate Limit’ as defined by the FOI Act under Section 12. Section 12
30
McCann (B2)Belfast Health and Social Care Trust (Northern Ireland)Link25th January 2021 to the 15th May 2021?Cycle Threshold1-Jul-202117-Nov-2021Doesn't hold infoAfter appeal clarification and review: Information not available
31
McCann (B3)Belfast Health and Social Care Trust (Northern Ireland)Link7th June to 1st July?Cycle Threshold1-Jul-202117-Nov-2021Doesn't hold infoAfter appeal clarification and review: Information not available
32
McCann (B4)Belfast Health and Social Care Trust (Northern Ireland)LinkHow you determine a positive other than the result of the PCR test, since as given in the manufacturers instruction, it cannot detect if someone is infectious or not.Cycle Threshold1-Jul-202117-Nov-2021AnswerAfter appeal clarification and review: As the regional virology reference lab, we process at least 10 times the number of samples as the other Trust you requested this information from. No CT values have been altered. As stated previously, samples crossing the threshold at < ct 37 are reported as positive and between >=ct 37 to <ct 40 results are reported as indeterminate and a repeat sample requested.
33
McCann (B5)Belfast Health and Social Care Trust (Northern Ireland)LinkHave you cultured in a lab or outsourced to see if they were true positives for what you are testing for? If so I would like breakdown of the positives that were able to be cultured at what ct cycle?Viral Culture1-Jul-202117-Nov-2021AnswerWe do not culture for SARS-COV-2 in the Regional Virus Laboratory in Belfast Trust.
34
11Hill (A1)University Hospitals Coventry and Warwickshire NHS TrustLinkThe number to deaths whereby Covid is the sole cause of death listed , there were no other pre existing conditions or comorbidities noted on the death certificate, covering the period from March 2020 until present day. If there answer is any, are you able to provide me with the average age of the deceased?C19 Deaths25-Jun-20219-Nov-2021Doesn't hold infoInformation not held.
35
Hill (A2)University Hospitals Coventry and Warwickshire NHS TrustLinkI would also like the number of cycles you run your PCR tests on normally as well as the the number of cycles that you are running for PCR tests where the patient/recipiant is known to have been vaccinated with one of the available Covid jabs.Cycle Threshold25-Jun-20219-Nov-2021BoilerplateCoventry and Warwickshire Pathology Services use assays from multiple manufacturers for COVID-19 testing, and assay cycling conditions vary according to manufacturer’s instructions; there is no single maximum number of cycles used for all tests. Depending on assay manufacturer, the maximum number of amplification cycles used ranges between 40 and 45. All samples collected from patients for SARS-CoV-2 PCR testing are subject to the same cycling conditions, including total number of cycles.

All samples collected from patients for SARS-CoV-2 PCR testing are subject to the same cycling conditions, including total number of cycles. Samples collected from vaccinated and unvaccinated individuals are not treated any differently; the methodology used is identical irrespective of vaccination status.
36
12Stronge (1)Department of Health (Northern Ireland)LinkI formally request the cycle threshold used for pillar 1 and pillar 2 rtPCR testing for the sars-cov-2 virus. If the CT has varied over the course of testing, this should be forthcoming.Cycle Threshold8-Jan-20213-Nov-2021BoilerplatePlease be advised that, as per manufacturer instructions, PCR assays are ran as 40-45 cycles, and the Ct cut off for determining a positive versus negative result is determined individually for every different SARS- CoV-2 assay run in laboratories. This is based on extensive validation before an assay is put into service. In very general terms, most of these tests will have a Ct cut off of between Ct35-40 depending on the data and the assay.
37
Stronge (2)Department of Health (Northern Ireland)LinkIf the CT has varied over the course of testing, this should be forthcoming.Ct Change8-Jan-20213-Nov-2021No responseNo response
38
Stronge (3)Department of Health (Northern Ireland)LinkWhat daily checks, if any, are carried out to identify and compensate for the false positive rate of PCR testing? What is the daily false positive rate? Are any checks carried out between test facilities each day to check for false positivesOther8-Jan-20213-Nov-2021No responseNo response
39
13McGuigan (1)Department of Health (Northern Ireland)LinkPlease supply the current PCR cycle threshold being used in Northern Ireland when testing individuals for the SARS-Cov-2 virus, who a/ are greater than 14 days post full vaccination against Covid-19Cycle Threshold27-Sep-202125-Oct-2021Doesn't hold infoEach laboratory test will have recommendations from the manufacturer specifically around how a test should be run and a guide to interpretation. However, it is best and standard practice to assess locally the exact performance of all tests. This includes establishing a cut off cycle threshold for PCR tests that contribute to the interpretation of a result as positive or negative. Each PCR test, be it for bacteria, virus or fungi, will undergo rigorous local assessment to establish individual cut off threshold cycle and limit of detection. For SARS-CoV-2 (the virus that causes COVID-19) testing, there are multiple platforms and kits in use in Northern Ireland; each one of those has been assessed individually with its own cycle threshold cut off. No one cut off cycle threshold can be applied to multiple systems.

From a laboratory perspective the Ct (cycle threshold) value is only one of a number of criteria that is considered when interpreting test results. Other criteria may include, for example, multiple SARS-CoV-2 gene targets detection, fluorescence levels, sigmoidal shape of amplification curves, and confirmatory testing using assays with alternative specificity profiles, where required. This is in line with good laboratory practice and the World Health Organisation (WHO) papers on PCR testing for SARS-CoV-2 detection. You may also wish to read the Public Health England publication ‘Understanding cycle threshold (Ct) in SARS-CoV-2 RT-PCR’ which is available at the following link: Understanding cycle threshold (Ct) in SARS-CoV-2 RT-PCR (publishing.service.gov.uk)
40
McGuigan (2)Department of Health (Northern Ireland)LinkPlease supply the current PCR cycle threshold being used in Northern Ireland when testing individuals for the SARS-Cov-2 virus, who b/ are less than 14 days post full vaccination against Covid-19Cycle Threshold27-Sep-202125-Oct-2021AnswerThe number of PCR cycles that are done to test for SARS-CoV-2 remains the same regardless of patient interventions. Diagnostic testing must ensure that all samples follow the same diagnostic pathway. This is the same for all PCR tests that diagnose viruses and bacteria where preventative vaccinations programs are in place. Cycle threshold (Ct) cutoffs are based on analytical data, not patient status.
41
McGuigan (3)Department of Health (Northern Ireland)LinkPlease supply the current PCR cycle threshold being used in Northern Ireland when testing individuals for the SARS-Cov-2 virus, who c/ have received one dose of a vaccination against Covid-19Cycle Threshold27-Sep-202125-Oct-2021AnswerThe number of PCR cycles that are done to test for SARS-CoV-2 remains the same regardless of patient interventions. Diagnostic testing must ensure that all samples follow the same diagnostic pathway. This is the same for all PCR tests that diagnose viruses and bacteria where preventative vaccinations programs are in place. Cycle threshold (Ct) cutoffs are based on analytical data, not patient status.
42
McGuigan (4)Department of Health (Northern Ireland)LinkPlease supply the current PCR cycle threshold being used in Northern Ireland when testing individuals for the SARS-Cov-2 virus, who d/ have not received any vaccination against Covid-19.Cycle Threshold27-Sep-202125-Oct-2021AnswerThe number of PCR cycles that are done to test for SARS-CoV-2 remains the same regardless of patient interventions. Diagnostic testing must ensure that all samples follow the same diagnostic pathway. This is the same for all PCR tests that diagnose viruses and bacteria where preventative vaccinations programs are in place. Cycle threshold (Ct) cutoffs are based on analytical data, not patient status.
43
14GroveOffice for National StatisticsLinkWhat is the recorded date when the Office of National Statistics (ONS) started recording the Cycle Threshold (Ct) values that are associated with the positive test results (i.e. “cases”) in the polymerase chain reaction (PCR) test that is used to detect “COVID-19" and/or infection with the SARS-CoV-2 virus?Cycle Threshold10-Sep-20218-Oct-2021RedirectThe COVID-19 infection survey has recorded Ct values since the survey began on 26 April 2020. We began publishing the Ct values of positive tests from the 21 September 2020. In the [1]technical dataset accompanying our [2]latest bulletin, you can find the percentages of positive cases by Ct value in the UK on tab 1a. For further information and an overview of data about the coronavirus (COVID-19) pandemic from the ONS and other sources, please check our [3]Latest Insights Tool. (Links provided)
44
15Hodgskiss (1)Department of Health and Social CareLinkWho is responsible for calculating the official COVID-19 testing, cases, healthcare and death statistics (as shown at https://coronavirus.data.gov.uk/ )?Case Defn.28-Oct-202030-Sep-2021Doesn't hold infoDHSC does not hold the information you have requested. The coronavirus dashboard is produced by Public Health England (PHE), an executive agency of DHSC. From October 2021, it will be produced by the UK Health Security Agency (UKHSA), the successor organisation to PHE. More details can be found on this link.
45
Hodgskiss (2)Department of Health and Social CareLinkWhy was RT-PCR chosen for Pillar 2 testing, who chose it and when?PCR Other Info28-Oct-202030-Sep-2021Doesn't hold infoUnder Section 8(1) of the FOIA, the department is not required to give opinions to answer your request.
46
Hodgskiss (3)Department of Health and Social CareLinkHow many amplification cycles are currently used in your RT-PCR testing? If this number has been subject to change over time, please also provide the historical values (along with the dates they pertain to).”Ct Change28-Oct-202030-Sep-2021RedirectRefer you to the published source in the Understanding cycle threshold (Ct) in SARS-CoV-2 RT-PCR. You will find the answers to your question on amplification cycles on Pages 3, 5 & 6.
47
16EdwardsUniversity Hospitals Coventry and Warwickshire NHS TrustLinkI would like to know the number of cycles you have been using on the PCR (Polymerase Chain Reaction) test as standard and if that number has ever been changed at anytime for whatever reason.Cycle Threshold21-Jun-202128-Sep-2021BoilerplateDepending on assay manufacturer, the maximum number of amplification cycles used ranges between 40 and 45. All samples collected from patients for SARS-CoV-2 PCR testing are subject to the same cycling conditions, including total number of cycles.
48
17McGuiganPublic Health Agency for Northern IrelandLink[See FOI 13]
Public Health Agency for Northern Ireland did not have the information requested, but the Q was "Please supply the current PCR cycle threshold being used in Northern Ireland when testing individuals for the SARS-Cov-2 virus, who..."		Cycle Threshold27-Sep-202129-Oct-2021Doesn't hold infoPublic Health Agency does not hold the information which you request.

Supplied links to FOI offices: https://www.whatdotheyknow.com/request/795497/response/1905877/attach/html/2/Appendix%201%20Trust%20FOI%20Contact%20details%20Feb%202021..pdf.html
49
18GroveScottish GovernmentLinkTherefore please provide the Cycle Threshold (Ct) values that define a positive test result for all of the recorded tests that are being used to create the 8% positive test cases figure released by the First Minister.Cycle Threshold9-Jul-202121-Jul-2021Doesn't hold infoWhile our aim is to provide information whenever possible, in this instance the Scottish Government does not have the information you have requested.
50
19FrancesDepartment of Health (Northern Ireland)LinkPlease provide the rate of amplification used in UK for all Pcr tests since March 2020.Cycle Threshold11-Apr-202117-Sep-2021BoilerplateEach laboratory test will have recommendations from the manufacturer specifically around how a test should be run and a guide to interpretation. However, it is best and standard practice to assess locally the exact performance of all tests.

The cycle threshold (Ct) number refers to the number of rounds of repeated heating and cooling (also known as a ‘cycle’) a PCR undergoes before the genetic material of the virus is first detected; the lower the Ct value, the greater the quantity of viral genetic material in the original sample. The maximum number of amplification cycles used for each real-time PCR (RT-PCR) test is set according to the recommendations of the test manufacturer. It should be noted that the maximum number of cycles a PCR reaction undergoes should not be confused with the cycle threshold value Ct). Coventry and Warwickshire Pathology Services use assays from multiple manufacturers for COVID-19 testing, and assay cycling conditions vary according to manufacturer’s instructions; there is no single maximum number of cycles used for all tests. Depending on assay manufacturer, the maximum number of amplification cycles used ranges between 40 and 45. All samples collected from patients for SARS-CoV-2 PCR testing are subject to the same cycling conditions, including total number of cycles.
51
20WhickerNorthumbria Healthcare NHS Foundation TrustLinkI would like to know if the trust uses different RT PCR test cycle thresholds for Covid vaccinated indivuals and unvaccinated individuals when performing analysis of the PCR test. If so, please provide the cycle threshold used for -
1. vaccinated individuals
2. unvaccinated individuals.		Cycle Threshold15-Sep-202116-Sep-2021AnswerThere is no differentiation in RT PCR Test Cycle Thresholds used by Northumbria NHS Foundation Trust between vaccinated and unvaccinated individuals.
52
21DayMid and South Essex NHS Foundation TrustLinkI would like to know the Cycle Theshold (CT) you are using for your PCR tests as at 8th August 2021 to diagnose Covid 19 and if the cycle threshold has changed since March 2020? [NOTE: a couple of subsidary Qs that don't appear relevant]Cycle Threshold10-Aug-202115-Sep-2021Answer45 cycle threshold used as standard in 2020 and 2021. There has been no change.
53
22GroveScottish GovernmentLinkWill the Scottish Government (Scottish Ministers) release all of the recorded mean, median and mode statistical data for the Cycle Threshold (Ct) values of “positive COVID cases” in RT-PCR testsCycle Threshold4-Sep-202113-Sep-2021Doesn't hold infoWhile our aim is to provide information whenever possible, in this instance the Scottish Government does not have the information you have requested.
54
23Moffett (1)Public Health EnglandLinkCan you please tell me the cycle threshold that is used in the UK for the PCR test.Cycle Threshold22-Jan-202116-Feb-2021BoilerplateIn the case of the CE-IVD tests the thresholds used for result interpretation will be defined by the manufacturer of the assay. Currently there are over 80 different testing platforms in use across the various networks of laboratories and the thresholds for result interpretation will be configured in each case by the manufacturers of the assays and the instrumentation. Each laboratory will regularly assess the performance of their assays within their local quality management system. The results are monitored in accordance with defined quality control procedures. Whilst each laboratory has a statutory duty to report positive cases to Public Health England, additional information such as Ct values in the case of PCR tests, is not submitted
55
Moffett (2)Public Health EnglandLinkIf it has varied at different times during the 'pandemic' can you specify the range.Ct Change22-Jan-202116-Feb-2021No responseNo response
56
Moffett (3)Public Health EnglandLinkCan you also please define how many people have been tested at the various cycle thresholds ie how many at 30, how many at 40 etc.Cycle Threshold22-Jan-202116-Feb-2021No responseNo response
57
24Newton (1)Public Health EnglandLinkThe validation study for each of the RT-PCR and Rapid Lateral Flow tests currently in use on or in England.PCR Other Info18-Jul-202113-Sep-2021BoilerplateAfter review: RT-PCR test: There are over 85 different SARS-CoV-2 RT-PCR assays/platforms in use across the UK. Most tests used in England are commercial. Each test/platform comes with its own standardised interpretation and have a slightly different limit of detection (LoD) – the lowest concentration of virus that can be reliably and consistently detected by the assay and will be configured according to local arrangements.

Each testing kit manufacturer includes the criteria for interpretation in the Information for Use (IFU) leaflets provided with their kits. All testing centres are required to follow the manufacturer’s interpretation. Validation is performed by the manufacturer; all labs are expected to test the kits in house to determine limit of detection and use this for interpretation.

PHE has performed some assessments of PCR – see https://www.gov.uk/government/publications/covid-19-phe-laboratory-assessments-of-molecular-tests

Also see publication of report: https://www.ox.ac.uk/sites/files/oxford/media_wysiwyg/UK%20evaluation_PHE%20Porton%20Down%20%20University%20of%20Oxford_final.pdf
58
Newton (2)Public Health EnglandLinkThe known error/accuracy ratePCR Other Info18-Jul-202113-Sep-2021AnswerAfter review: RT-PCR test: The RT-PCR assays used for the UK’s COVID-19 testing programme have been verified by PHE. RT-PCR tests are highly sensitive and highly specific, but can show, as every diagnostic test, low rates of false negative and false positive results. These false negative and false positive results cannot be entirely eliminated. A test result is called ‘false positive’ when it gives a positive result for a person who is not infected with the infectious agent the test is designed for.

RT-PCR test show over 95% sensitivity and specificity. This means that under laboratory conditions, these RT-PCR tests should never show more than 5% false positives or 5% false negatives. Also see publication of report: https://www.ox.ac.uk/sites/files/oxford/media_wysiwyg/UK%20evaluation_PHE%20P
orton%20Down%20%20University%20of%20Oxford_final.pdf
59
Newton (3)Public Health EnglandLinkInformation demonstrating that the RT-PCR and Rapid Lateral Flow tests are diagnostic instruments contrary to manufacturer literature.PCR Other Info18-Jul-202113-Sep-2021Doesn't hold infoAfter review: PHE do not hold this information. Questions regarding manufacturing and production need to be directed to the commercial manufacturers. PHE does not mandate what each lab needs to do – we provide guidance – the assessment of quality is performed by UKAS (UK accreditation service).
60
Newton (4)Public Health EnglandLinkThe Cycle threshold for the RT-PCR test in laboratories under the superintendence of Public Health England.Cycle Threshold18-Jul-202113-Sep-2021BoilerplateAfter review: PHE have not set a specific Cycle threshold (Ct) that should be used. Ct cut offs for COVID-19 PCR tests are subjected to a standardised laboratory algorithm and this informs interpretation of positive or negative results. The algorithm is based on evaluating the limit of detection for each test using known positive control material and will differ depending on the assay used. Further information on understanding cycle threshold (Ct) in SARS-CoV-2 RT-PCR can be found at the following link: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attach
ment_data/file/926410/Understanding_Cycle_Threshold__Ct__in_SARS-CoV-2_RT-
PCR_.pdf
61
Newton (5)Public Health EnglandLinkThe genetic sequence UNIQUE to SARS-CoV-2 and not the sequence currently used which show up 93 times in the Human genome and 91 times in Bacteria and Fungi (microbe) genomesOther18-Jul-202113-Sep-2021RedirectAfter review: PHE does not hold the information as specified in your request. However, you may be interested in the following information on the COVID-19 variants: https://github.com/phe-genomics/variant_definitions PHE’s virology teams use the term “virus isolation” to mean culture of SARS-CoV-2 in the laboratory. This specialised technique involves adding patient samples to cell cultures and looking for virus growth. It is time consuming and highly specialised work. For this reason, the SARS-CoV-2 virus is identified most often by looking for its unique genetic material in a clinical sample and further identification is refined and confirmed by whole genome sequencing.
62
Newton (6)Public Health EnglandLinkIn isolating and purifying SARS-CoV-2 from a COVID-19 patient sample, please provide a copy of the negative control experiments to rule out other possibilities of disease causation such as toxicity, trauma and malnutrition etc.Other18-Jul-202113-Sep-2021AnswerAfter review: The SARS-CoV-2 virus has been isolated in the PHE Viral Reference Lab by culturing clinical material from patients who have tested positive for the virus. The virus isolation is reported in a publication from Singanayagam et al: https://www.eurosurveillance.org/content/10.2807/1560-
7917.ES.2020.25.32.2001483.
63
25Doran (1)North Cumbria Integrated Care NHS Foundation TrustLinkPlease could you tell me what the current cycle threshold is set to on the PCR test?Cycle Threshold1-Jul-20219-Sep-2021BoilerplateThe cycle threshold (Ct) for a real-time PCR assay is the thermal cycle number when the signal in the assay exceeds the background signal and the test is reported as positive. Typically a real-time PCR test will run for a maximum of around 40 thermal cycles. We do not use a Ct cut-off to determinate whether a real-time PCR assay is positive or not – a real-time PCR assay is reported as positive when the signal in the assay exceeds the background signal within the maximum number of thermal cycles (specific to each assay/analyser).
64
Doran (2)North Cumbria Integrated Care NHS Foundation TrustLinkCould you also clarify if there is a different cycle threshold for the vaccinated and the unvaccinatedCycle Threshold31-Jul-20219-Sep-2021AnswerWe do not differentiate between the vaccinated and un-vaccinated.
65
26Cox (1)Mid and South Essex NHS Foundation TrustLinkHow many patients at Basildom (sic) hospital have died as a direct result of systematic Covid19. That's means not with but because of covid.C19 Deaths24-Jun-202126-Jul-2021RedirectThe death and cause of death statistics are published nationally by the Office for National Statistics (ONS), the Department of Health and Social Care (DHSC) and NHS England (NHSE), as the publishing authorities. In line with national guidance, deaths occurring in hospitals are uploaded to the NHS England COVID-19 Patient Notification System (CPNS).
66
Cox (2)Mid and South Essex NHS Foundation TrustLinkHow many patients have test positive of covid19 after initially being tested negative.Case Defn.24-Jun-202126-Jul-2021No responseNo response
67
Cox (3)Mid and South Essex NHS Foundation TrustLinkHow many beds have been occupied with patients by week for last 3 years.Other24-Jun-202126-Jul-2021RedirectInformation not held (Links provided)
68
Cox (4)Mid and South Essex NHS Foundation TrustLinkAge breakdown of covid deaths with systematic covid.C19 Deaths24-Jun-202126-Jul-2021RedirectInformation not held (Links provided)
69
Cox (5)Mid and South Essex NHS Foundation TrustLinkHow many DNR orders have been issued per year for last 5 years.Other24-Jun-202126-Jul-2021No responseNo response
70
Cox (6)Mid and South Essex NHS Foundation TrustLinkWhat is the cycle threshold (CT) used to confirm a positive PCR result.Cycle Threshold24-Jun-202126-Jul-2021Answer45 cycles used as standard in 2020 and 2021.
71
27EmmersonYork and Scarborough Teaching Hospital NHS Foundation TrustLinkcan you Let Me Know How Many Cycles You Use With The Pcr TestsCycle Threshold27-Aug-20213-Sep-2021AnswerWe can confirm that our cycle threshold used with PCR tests is 30 – 35.
72
28JonesPublic Health WalesLinkWhat limits on amplication on the PCR test does Wales use and/or recommend?Cycle Threshold17-Dec-202025-Apr-2021BoilerplateThe number of amplification cycles can vary with different platforms used. Most platform use threshold cycles that range from 27 to 43. The threshold cycle is determined by the platform used and is not something that the laboratory services has control over.
73
29ThompsonBlackpool Teaching Hospitals NHS Foundation TrustLinkThe cycle threshold you have been using for the RT-PCR test?Cycle Threshold7-Aug-202124-Aug-2021AnswerManufacturer/assay and remains constant, as we cannot amend the software, however confirmation of positive results is performed where the sample Ct threshold is >38 on Cepheid Genexpert and >34 Neumodx analysers.
74
30Munroe (5)Department of Health and Social CareLinkWhat cycle threshold rate have you been using for your tests?Cycle Threshold5-Aug-202125-Aug-2021BoilerplateA typical RT-PCR assay will have a maximum of 40 thermal cycles. The lower the Ct value the higher the quantity of viral genetic material in the sample (as an approximate proxy for viral load). Ct values obtained in this way are semi-quantitative and are able to distinguish between high and low viral load.

Ct values cannot be directly compared between assays of different types due to variation in the sensitivity (limit of detection), chemistry of reagents, gene targets, cycle parameters, analytical interpretive methods, sample preparation and extraction techniques.
75
Munroe (6)Department of Health and Social CareLinkDid you lower the threshold cycle rate in line with the recomendation by the WHO, and if so at what date was this adjustment made and what was the new cycle rate.Ct Change5-Aug-202125-Aug-2021No responseNo response
76
31Hemmings (B1)University Hospital Southampton NHS Foundation TrustLinkThe cycle threshold currently used for COVID-19 PCR tests.Cycle Threshold29-Jun-202124-Aug-2021Non-answerWe use four different methods, only one is based on cycle thresholds accessible to the user. We do not use a static threshold value for this method.
77
Hemmings (B2)University Hospital Southampton NHS Foundation TrustLinkIf the cycle threshold has been changed any time since January 2020, when was it changed and what values were used.Ct Change29-Jun-202124-Aug-2021AnswerOn 17th February 2021 we re-introduced a passive reference dye which allowed our instruments to automatically set baseline and threshold values for each run to simplify analysis but still no static threshold is used.
78
Hemmings (B3)University Hospital Southampton NHS Foundation TrustLinkA distribution of positive tests by CTs, for each month from January 2020 to the presentCycle Threshold29-Jun-202124-Aug-2021Too much effortThis data range would involve looking at hundreds of thousands of individual results. We are unable to produce this data due to the amount of hours it would take for our data systems to generate (and so block its usage for clinical need) plus the many hours it would take to manually manipulate the data into the below categories.
79
32Jones (A1)Greater London AuthorityLinkPlease send me any recorded information that GLA has for the number of cycle thresholds for the PCR testCycle Threshold19-Dec-202021-Jan-2021Doesn't hold infoThe GLA does not hold information in relation to part 2 and 3 of your request. You should resubmit your request to either the Department of Health and Social Care who oversee the Government testing programme, or the Medicines and Healthcare products Regulatory Agency, who would have been involved in specificity testing.
80
Jones (A2)Greater London AuthorityLinkHow many cycle thresholds is any data based on that the Mayor is making statements on.Cycle Threshold19-Dec-202021-Jan-2021Doesn't hold infoThe GLA does not hold information in relation to part 2 and 3 of your request. You should resubmit your request to either the Department of Health and Social Care who oversee the Government testing programme, or the Medicines and Healthcare products Regulatory Agency, who would have been involved in specificity testing.
81
33AdelePublic Health EnglandLinkWhat has the ct threshold been set at in the various pillar 2 labs?Cycle Threshold14-Oct-20212-Nov-2021Doesn't hold infoPHE can confirm it does not hold the information you have specified.
82
34PricePublic Health EnglandLinkThe CDC changed the requirement for the cycle threshold count (CT) those that are vaccinated, <28 CT, COVID positive. For the non-vaccinated <40 CT, COVID positive.
Is this the case in the UK?		Cycle Threshold17-Jul-202112-Aug-2021BoilerplateThere are multiple tests being used and every kit will have its own interpretative criteria and thresholds, as recommended by the manufacturer. There are at least 80 different platforms in use, configured in various ways in different laboratories. Some test provides Ct values some does not. Range, mean, median for thresholds will be dependent on the operating arrangements in each laboratory and relate to each kit/assay being used. These laboratories have a statutory duty to report positive cases to PHE, but they are not obliged to advise PHE which tests they are using nor submit CT values used to PHE.
83
35ReidLondon North West University Healthcare NHS TrustLinkI would be obliged if you could tell me under the Freedom of Information act how many cycles are run as standard in the PCR test?Cycle Threshold11-Jul-202111-Aug-2021Non-answerOne of the methods we use (SAMBA) does not cycle different temperatures. Instead, it uses a method called Nucleic Acid Sequence Based Amplification (NASBA) which is an isothermal method. As a result, we are unable to give cycle threshold values as the temperature remains the same throughout amplification. Our LOD of 250cp/ml equates to around 34/35 Ct but this is just a marker.
84
36Hemmings (C1)Hampshire Hospitals NHS Foundation TrustLinkThe cycle threshold currently used for COVID-19 PCR tests.Cycle Threshold29-Jun-202111-Aug-2021AnswerOf the primary assays that report a CT value we report a positive result <38 CT. This is set by the manufacturer.
85
Hemmings (C2)Hampshire Hospitals NHS Foundation TrustLinkIf the cycle threshold has been changed any time since January 2020, when was it changed and what values were used.Ct Change29-Jun-202111-Aug-2021AnswerN/A as this has not changed.
86
Hemmings (C3)Hampshire Hospitals NHS Foundation TrustLinkA distribution of positive tests by CTs, for each month from January 2020 to the presentPCR Other Info29-Jun-202111-Aug-2021Too much effortHampshire Hospitals is unable to identify the cycle threshold in each case as this would require a manual search of records, which the Trust estimates would exceed the appropriate time and cost limit to undertake such a detailed investigation (Section 12(1)).
87
37GomezDepartment of Health and Social CareLinkIf PCR testing has been used for the above then how many cycles are used in the PCR tests historically and now?Cycle Threshold28-Jun-20219-Aug-2021BoilerplateAn explanation of Ct values (also known as Cq values) can be found here: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/
926410/Understanding_Cycle_Threshold__Ct__in_SARS-CoV-2_RT-PCR_.pdf
88
38King (A1)NHS EnglandLinkPlease would you kindly inform me the cycle threshold that you are running the PCR tests at as of 26.07.2021?Cycle Threshold26-Jul-20219-Aug-2021Doesn't hold infoNHS England does not hold information in relation to your request.

The Cycle Threshold, or CT value, is the number of PCR (Polymerase Chain Reaction) 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.
89
King (A2)NHS EnglandLinkWould you also inform me if this number has changed recently?Ct Change26-Jul-20219-Aug-2021No responseNo response
90
39EmmettWirral University Teaching Hospital NHS Foundation TrustLinkI would like details of the PCR testing, specifically the cycle threshold (CT) that is used in the lab and also if this cycle threshold number has changed within the last 18 months.Cycle Threshold7-Aug-2021N/ANo responseNo response
91
40ReidGreater Glasgow NHS BoardLinkI would be obliged if you could tell me under the Freedom of Information act how many cycles are run as standard in the PCR test?Ct Values11-Jul-20219-Aug-2021AnswerAmplification cycles in PCR test for COVID
Glasgow Royal Infirmary Applied Biosystems, 7500 Real-Time PCR System 40
Abbott Alinity M 40
Roche Cobas 6800 45
Seegene CFX96 45
Cepheid GeneXpert 45 Abbott M2000 40
Roche Liat 45
QEUH Roche Liat 45
Hologic, Panther n/a**
Thermo Fisher Scientific Amplitude 40
Each manufacturer of the RT-PCR test will recommend a differing maximum amplification cycle number to determine presence of SARS CoV-2 when interpreting results.
92
41MeierGovernment Office for ScienceLinkWhy did you use it and why if it’s only useful at 24 cycles do you use 44 cycles making it 97% false positives. Creating fear.Cycle Threshold13-Jul-20213-Aug-2021RedirectFor your second question, please note that Public Health England (PHE) is the body responsible for providing information and guidance to health protection teams regarding PCR testing and cycle thresholds. This information is publicly available, and may answer your questions here: https://www.gov.uk/government/publications/cycle-threshold-ct-in-sars-cov-2-rt-pcr
93
42MarshnHampshire Hospitals NHS Foundation TrustLinkAt what CT value is the PCR test conducted at? And is this individualised to the Trust or set nationally?Cycle Threshold14-Apr-202130-Jul-2021Doesn't hold infoHampshire Hospitals is unable to provide an answer to this question as a polymerase chain reaction test (PCR) is not conducted with a cycle threshold (CT) value.
94
43Whicker (B1)Northumbria Healthcare NHS Foundation TrustLinkI would like to know the cycle threshold you are currently using for the RT PCR testing for Covid 19 [NOTE: see row 43, same person, same trust - different dates/requestsCycle Threshold27-Jul-2021N/ANo responseNo response
95
Whicker (B2)Northumbria Healthcare NHS Foundation TrustLink
I would also like to know if this threshold has changed since the beginning of the Covid 19 pandemic last year when you began using this test as a diagnostic tool.
Ct Change27-Jul-2021N/ANo responseNo response
96
44PayneDepartment of Health and Social CareLinkI would like to know the PCR amplification cycles used in corona virus tests over the period 1st June 2021 to 28th June 2021 inclusive.Cycle Threshold28-Jun-202126-Jul-2021BoilerplateA typical RT-PCR assay will have a maximum of 40 thermal cycles. The lower the Ct value the higher the quantity of viral genetic material in the sample (as an approximate proxy for viral load). Ct values obtained in this way are semi-quantitative and are able to distinguish between high and low viral load. Ct values cannot be directly compared between assays of different types due to variation in the sensitivity (limit of detection), chemistry of reagents, gene targets, cycle parameters, analytical interpretive methods, sample preparation and extraction techniques (Gov.UK). More information on PCR CT values is available here - Cycle threshold (Ct) in SARS-CoV-2 RT-PCR - GOV.UK (www.gov.uk)
97
45Hemmings (D1)University College London Hospitals NHS Foundation TrustLinkThe cycle threshold currently used for COVID-19 PCR tests.Cycle Threshold29-Jun-202126-Jul-2021BoilerplateWe have followed manufacturers’ guidelines for PCR cycle thresholds (Ct) interpretation where they are given. In practice, we don’t have hard cycle thresholds limits. We correlate results with the clinical picture, previous COVID-19 results etc.
98
Hemmings (D2)University College London Hospitals NHS Foundation TrustLinkIf the cycle threshold has been changed any time since January 2020, when was it changed and what values were used.Ct Change29-Jun-202126-Jul-2021AnswerNo changes have been made to the Ct cycle during this period.
99
Hemmings (D3)University College London Hospitals NHS Foundation TrustLinkA distribution of positive tests by CTs, for each month from January 2020 to the present (most recent data available)PCR Other Info29-Jun-202126-Jul-2021Too much effortUnfortunately the Trust is unable to provide the requested information. The data is not held in a manner that would allow us to easily extract the information. Due to the size and the hours of work involved in formatting the data it is estimated that this would exceed the limits (currently 18 hours/£450) under the Freedom of Information Act 2000, and as such, is exempt under Section 12 [Appropriate limit and fees].
100
46ThorburnNHS National Services ScotlandLinkPlease provide full details and information on the PCR cycle threshold settings being used for coronavirus 19 testing in June 2021. Please provide minimum and maximum cycle threshold settings used.Cycle Threshold29-Jun-202126-Jul-2021Doesn't hold infoI can advise that National Services Division (NSD) of NHS National Services Scotland (NSS) does not actually provide PCR testing for NHS Scotland, although the Scottish National Blood Transfusion Service (SNBTS) does carry out some but only on blood samples not respiratory swabs. NSD however includes the National Managed Diagnostic Networks within its’ service offering for NHS Scotland.