COVID-19: What’s the Difference Between Lateral Flow Tests (LFT) and PCR?


Lateral flow tests are more accurate than previously reported and cannot be compared directly to how PCR tests work, finds a new paper led by UCL researchers.

The peer-reviewed paper, published today in Clinical Epidemiology, uses a new formula to show that lateral flow tests (LFTs) are likely more than 80% effective at detecting any level of COVID-19 infection and likely more than 90% effective at detecting those who are most infectious when using the test.

This level of accuracy is much higher than some previous studies have suggested and the authors say the tests are a reliable public health tool in stopping the spread of the virus.

The researchers from UCL, Liverpool University, Harvard University and the University of Bath highlight that LFTs work in a very different way to polymerase chain reaction (PCR) tests and cannot be compared “like for like.”

LFTs detect material from the surface proteins of the virus and are very likely to give a positive result when someone is infectious whereas PCR tests detect the virus’ genetic material, which can be present for weeks after a person is no longer infectious.

Lead author, Professor Irene Petersen (UCL Institute of Epidemiology and Health Care), explained: “Previous studies comparing the reliability of lateral flow tests and PCR tests could be potentially misleading because a PCR test is a marker of having been infected at some point within a certain window of time and does not necessarily mean someone is infectious when testing positive.

“In most validation studies, individuals were tested simultaneously with LFTs and PCR tests, with PCRs being used as a gold standard to say someone is ‘positive or negative.’

The sensitivity of the LFTs was therefore evaluated by their ability to identify the same cases that the PCRs picked up. However, this is like comparing apples and oranges.”

The paper presents a formula for calibrating the sensitivity of LFTs and gives an illustrative example from a study in Liverpool. In the Liverpool study a head-to-head validation suggested the sensitivity of LFT was only 40%.

However, after taking into account the differences between the tests and the biology of COVID-19 the UCL-led team suggests that, in reality, the sensitivity of the typical LFT in being able to identity someone who is likely to be infectious, is above 80%.

Professor Michael Mina (Harvard School of Public Health) said: “There is a spectrum of infectious amounts of the COVID-19 virus and we show that LFTs are likely to detect cases 90–95% of the time when people are at their most infectious. The tests could achieve even 100% sensitivity when viral loads are at their peak and therefore catch nearly everyone who is currently a serious risk to public health.

“It is most likely that if someone’s LFT is negative but their PCR is positive then this is because they are not at peak transmissible stage.”

Professor Petersen added: “As LFTs are becoming widely used in schools, workplaces and for admittance to venues such as those used for large events, it is important that health professionals and the public have clear information about the operating characteristics of the tests. We have demonstrated that the absolute sensitivity to detect SARS-CoV-2 antigens is likely high with LFTs.

“To improve our understanding of their characteristics, longitudinal studies where individuals, and ideally contacts of cases, are tested daily by LFTs and PCR tests would help to further understand false negatives (and false positives) and, importantly, the time differences of between turning PCR positive, LFT positive, and symptom onset.”

The authors acknowledge that the sensitivity of the LFTs is, of course, dependent on sampling errors and experience of the person performing the sampling and the test and that these uncertainties are not taken into account in their formula calibrations.

The use of rapid lateral flow antigen testing (LFT) for SARS-CoV-2 has been questioned1, 2, 3 with uncorroborated4 reports of poor LFT sensitivity. The debate surrounding the use of the Innova Lateral Flow SARS-CoV-2 Antigen Test in the UK risks confusing policy makers internationally and potentially stalling deployment of LFTs in other countries.5

As scientists and health professionals evaluating some of the world’s largest pilots of LFT, we wish to challenge those interpretations and clarify the evidence on how such testing might be used to detect SARS-CoV-2 in minutes and improve COVID-19 control measures.

Testing for SARS-CoV-2 is central to COVID-19 management and has relied on quantitative reverse transcriptase polymerase chain reaction (PCR) technology. PCR seeks the genetic code of the virus from nose or throat swabs and amplifies it over 30–40 cycles, doubling each cycle, enabling even miniscule, potentially single, copies to be detected.

PCR is thus a powerful clinical test, specifically when a patient is, or was recently, infected with SARS-CoV-2. Fragments of RNA can linger for weeks after infectious virus has been cleared,6 often in people without symptoms or known exposures.7

However, for public health measures, another approach is needed. Testing to help slow the spread of SARS-CoV-2 asks not whether someone has RNA in their nose from earlier infection, but whether they are infectious today. It is a net loss to the health, social, and economic wellbeing of communities if post-infectious individuals test positive and isolate for 10 days.

In our view, current PCR testing is therefore not the appropriate gold standard for evaluating a SARS-CoV-2 public health test.

Most people infected with SARS-CoV-2 are contagious for 4–8 days.7 Specimens are generally not found to contain culture-positive (potentially contagious) virus beyond day 9 after the onset of symptoms, with most transmission occurring before day 5.7, 8

This timing fits with the observed patterns of virus transmission (usually 2 days before to 5 days after symptom onset), which led public health agencies to recommend a 10-day isolation period.9 The short window of transmissibility contrasts with a median 22–33 days of PCR positivity (longer with severe infections and somewhat shorter among asymptomatic individuals).10

This suggests that 50–75% of the time an individual is PCR positive, they are likely to be post-infectious.11, 12

Once SARS-CoV-2 replication has been controlled by the immune system, RNA levels detectable by PCR on respiratory secretions fall to very low levels when individuals are much less likely to infect others.13, 14, 15

The remaining RNA copies can take weeks, or occasionally months,16, 17 to clear, during which time PCR remains positive.7

A public health test for detecting someone who might be contagious is, by logical deduction, expected to have a sensitivity of around 30–40% versus PCR when testing a random sample of asymptomatic people in a steady-state outbreak.18 Furthermore, the asymmetry of RNA reflecting more infectiousness nearer to the time of exposure, means that the sensitivity of the ideal test of infectiousness when measured against PCR may vary across the epidemic curve, from as high as 50–60% when an outbreak is surging to 20–30% or less as infections decline.19

LFT and the UK testing programme have been criticised1, 2, 3, 5 for poor sensitivity in people without symptoms. In our view, these criticisms misinterpreted data from the interim report on the pilot of community testing in Liverpool, UK.20, 21 When paired LFT and PCR testing was done in Liverpool, the epidemic curve was declining.20

At this point, a priori one should expect a public health test that is highly sensitive for detecting infectious virus to show low overall sensitivity relative to PCR in people without symptoms or known exposures.

Further confusion reigns over PCR cycle threshold (Ct) values, viral loads, and infectiousness. In the Liverpool pilot, Innova LFT picked up 19 of 24 (79%) samples with Ct below 20 and ten of 11 (91%) samples with Ct below 18.20 The 66% sensitivity in the Liverpool interim report20 was based cautiously on Ct below or equal to 25 indicating viable virus.

For the laboratory processing of the Liverpool samples, Ct values of 21–18 most likely reflect the 100 000 to 1 million RNA copies per mL, quantities below which virus cultures usually become negative and transmission risks are low.22, 23, 24

Other laboratories place this threshold at a Ct of 30.24 There is no international standardisation between laboratories and assays, leaving Ct calibration with viral load poorly reported and easy to misunderstand.

Early findings, widely reported,3 from a study by Ferguson and colleagues,25 suggested that LFT had only 3% sensitivity for detecting SARS-CoV-2 among PCR-positive students at Birmingham University. Test underperformance was implied to explain finding only two positive results among 7189 individuals tested with Innova LFT.25

In that study,25 in a random sample of 710 (10%) LFT-negative individuals there were six PCR-positive results. That finding was extrapolated to 60 cases in the whole cohort, giving an extrapolated sensitivity of two of 62 (3·2%). The Ct values from the six PCR-positive samples were projected to Ct values for the 60 cases (54 unobserved plus six observed); in all six observed cases, viral loads were very low (Ct ≥29 reflecting around <1000 RNA copies per mL in the laboratory used) – when LFT should be negative.

By comparison, the Liverpool pilot saw virus levels 1000 to 1 million times higher.20 In our view, the Birmingham study showed that PCR-positive asymptomatic students at a time of falling COVID-19 incidence had low viral loads compared with symptomatic members of the public attending testing centres and that LFT was working as expected.26

We wholeheartedly support healthy scientific debate to inform policies promptly. The COVID-19 road ahead looks challenging; therefore, we need big, bold actions across science and society, such as the Liverpool community testing pilot. The prompt evidence from such pilots can inform policies and help maintain public confidence in the public health responses needed to navigate this pandemic’s onward path

reference link :

More information: Irene Petersen et al, Recalibrating SARS-CoV-2 Antigen Rapid Lateral Flow Test Relative Sensitivity from Validation Studies to Absolute Sensitivity for Indicating Individuals Shedding Transmissible Virus, Clinical Epidemiology (2021). DOI: 10.2147/CLEP.S311977


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