The HSE has adopted RNA PCR as the gold standard test for diagnosing Covid-19. This is consistent with international best practice.
The World Health Organization (WHO) and the European Centre for Disease Prevention and Control (ECDC) recommend that nucleic acid amplification tests, such as RT-PCR, should be used to detect suspected, active SARS-CoV-2 infection. The advice of the WHO and the ECDC is available on their websites. For example, in its Technical Report “Options for the use of rapid antigen tests for COVID-19 in the EU/EEA and the UK”, published on 19 November 2020, the ECDC confirmed that “To date, testing for SARS-CoV-2 infection mostly relies on reverse transcription polymerase chain reaction (RT-PCR) performed on a nasopharyngeal specimen. This testing method remains the gold standard for detecting SARS-CoV-2 and is characterised by both high sensitivity and specificity in detecting viral ribonucleic acid (RNA).”
SARS-CoV-2 PCR assays in Ireland are operated in accordance with the manufacturers' instructions, and the CE marking for the assay. It is the manufacturer that decides the optimal number of cycles for the assay, not the testing laboratory. For commercial assays, the manufacturer chooses the PCR parameters including the amplification cycles. Intentionally moving away from the manufacturer's instruction would invalidate the CE mark.
This position remains unchanged and the WHO Information Notice simply reminds the professionals involved in the analysis of samples using the rRT-PCR to follow manufacturer instructions. SARS-CoV-2 PCR assays in Ireland in use by the HSE and laboratories operating on behalf of the HSE are operated in accordance with the manufacturers' instructions and the CE marking for the assay.
Higher Cycle threshold values typically indicate a lower amount of virus in the sample. However, the CT value alone does not indicate whether the virus load is increasing or decreasing, it does not indicate whether the individual is infectious or not, and it does not provide an indication of the specimen quality (i.e. how closely the specimen mirrors what is actually happening in the patient's respiratory tract).
In the Irish context, specificity (or false positive) data are not collated centrally. However, based on the data we do have available, and based on our growing level of experience with the SARS-CoV-2 assays in use in Ireland, the false positive rate is estimated to be somewhere between 0.1% and 0.2% (suggesting a specificity of around 99.8-99.9%). This does mean that for every 10,000 tests performed, there will potentially be 10-20 false positives, although this number can be reduced by repeat testing of some low level (or weak) positives. However, it is often not possible to distinguish between true positives and false positives.
Considerable work has been undertaken to date to evaluate the use of Antigen Detection Tests (ADTs) in an Irish context and this will continue on an ongoing basis due to the role they can have in the national testing strategy. In particular, further setting-specific ADT validation work continues to be undertaken by the HSE. Antigen testing will not, however, replace the requirement for large scale PCR testing which remains the gold standard for community testing
The HSE continues to monitor the evidence for other testing types in conjunction with other public bodies, such as the Health and Information Quality Authority (HIQA), and having regard to best international evidence and advice. On an ongoing basis, the National Public Health Emergency Team considers and reviews, based on public health risk assessments, how best to target testing to detect, and mitigate the impact of, the virus across the population. This includes keeping Ireland’s national testing policy under continuing review.