PCR test

Posted On 12/02/2021

This article is about the PCR test. What was this test developed for, what is it suitable for and how is it used? What are its advantages and disadvantages, also in comparison with other test options?

What is an infection?

An infection is the entry of microorganisms (for example viruses, fungi or bacteria) into an organism and their colonization and reproduction. In a broader sense, infectious diseases are also referred to inaccurately as “infections”.¹

Infections in persons with few symptoms are rare but possible. Cases have been described of less symptomatic/asymptomatic people who carry a high viral load and are infectious (superspreaders). However, exact numbers do not exist. Patient 1 in Germany, a business traveler from China, is now known to have suppressed her symptoms with medication.²

What does specificity mean?

Specificity indicates the probability that healthy people are also identified as healthy. Example: You have 100 really healthy people, one of them is tested false positive, which means that the specificity is 99%.

What does sensitivity mean?

The sensitivity indicates how many infected persons actually have a positive test result. The higher the sensitivity, the more reliably the test detects the presence of viral RNA.

What was the PCR test originally developed for?

The PCR test was developed by the American biochemist Kary Mullis in 1983 for laboratory purposes to identify the most minimal virus particles, but not to diagnose a disease.³

SARS-CoV2 PCR test and its development

In January 2020, the PCR test for SARS-CoV2 was created as a model based on 2003 SARS-CoV genome data at the Charité Berlin by Prof. Christian Drosten and his colleagues. However, without having examined a patient sample, i.e. without isolated SARS-Cov2 from 2019 as a template.⁴

As of February 2020, virus isolates were detected and taken for further test development.

What does PCR actually mean? And what is the CT value?

PCR stands for Polymerase Chain Reaction. The Polymerase is an enzyme by which any tiny genetic material (e.B. RNA fragments of viruses) is duplicated in order to detect the possible presence of these fragments. The chain reaction refers to the constant repetition of this multiplication. The multiplication causes an exponential doubling of the value. This means that the more cycles are performed, the test will be positive even when the virus load is originally the least clinically relevant. In other words, the higher the CT value (cycle threshold), the more likely a fragment can be found. The smaller the CT value (i.e. the threshold above which particles are detectable), the more likely a virus is to be. From a CT of 30, the cultivability of the virus decreases significantly. From a CT of 35, virtually no cultivable virus is detectable.⁵

PCR tests are therefore used to search for components of the genetic material of a virus and to demonstrate a possible presence. However, the test can be positive even if there are only virus fragments or inactive viruses. Different PCR tests search between one and three gene sequences. If only one gene sequence is used, the result is less accurate and the risk of a false positive test increases. The so-called Drosten test initially recommended by the WHO searched for one gene sequence. The tests used in Luxembourg measure up to three gene sequences.

The CT value is the number of repetitions (cycles) of the above-mentioned reproduction. In practical terms, it can be insinuated from this value how many genetic fragments were originally in the sample. The infectivity and severity of the disease depend, among other things, on the number of viruses present in the nose, mouth, throat, but also on the individual immune system of the affected person.

Infectious virus numbers strike at a CT value of 15-25. Here, someone is basically contagious. At 25 – 30, the risk of infection is lower, except with very close contact. With a CT between 30 – 35, there is a grey area in which it is statistically possible to be contagious, but this becomes increasingly unlikely. From a CT value of 35, infectious viruses are no longer present. However, due to the extreme accuracy of the test due to the reproductions, virus fragments can still be detected, even though they no longer have clinical relevance. The test is nevertheless positive.

On January 20th, 2021 the Corona test guidelines were updated by the WHO. The update states that a positive test result alone is no longer enough to diagnose an infection or disease. As early as December, the WHO warned against improper use of the PCR test and said that in order to determine the viral load, one should at least take the CT value into account and in some cases manually adjust the threshold at which a test is positive.

“WHO reminds IVD users that disease prevalence alters the predictive value of test results; as disease prevalence decreases, the risk of false-positive increases (2). This means that the probability that a person who has a positive result (SARS-CoV-2 detected) is truly infected with SARS-CoV-2 decreases as prevalence decreases, irrespective of the claimed specificity.” ⁶

How is testing done in Luxembourg?

As of mid-October 2020, one of the Luxembourg laboratories uses the Allplex test from Seegene^TM. Seegene^TMis a Korean company whose test received provisional approval in 2020, due to a sanitary emergency.

The Allplex test is qualitative, i.e. it can only tell whether fragments of SARS-Cov2 have been detected at a CT value between 10-40 RNA, but not at what exact value. Other laboratories work with tests that multiply up to 40 cycles.

Last year Luxembourg laboratories generally do not indicate at what CT value the test is positive, but this would be important to exclude infectivity. This is also the case with many laboratories in Germany. The German laboratory Gärtner points out the importance of the CT value in an information letter.⁷

However, since January 2021, Luxembourg laboratories such as Laboratoire national de Santé (LNS) have started to communicate the CT values on the test results.

Example of a test result:

SARS-CoV-2 positiv 1

CT-Werte E-gene: 20.14 , N-gene: 20.78, MOP/S-gene: 20.85

This means that there are 3 genome sequences tested and the CT value of the PCR tests is currently around 20.

Rapid antigen tests are currently not carried out in Luxembourg because the Ministry of Health considers them to be too imprecise. To be sure, you would still have to do a PCR test as a control.

The quality of the test samples

Important for the highest possible accuracy of the test result is the method of Swab sampling, the location (nose, mouth, lungs) – for example, the specificity of the Allplex-test is nose/mouth at 94.8% and lungs at 97.87% – e.g. of 10,000 tests, there are still 213 false-positive results -, the time of collection (presymptomatic, symptomatic or after infection), and whether training, certainly not contaminated healthcare professionals take the sample. The quantity of sample material and the correct transport from the sampling site to the laboratory are also important. The enormous amount of data due to the variety of tests and the associated overload of the laboratories can also generate errors. ^{8, 9}

And so even the minimum cross-contamination is sufficient to contaminate samples, which leads to increase positive tests, which then turn out to be negative when retested. Prof. Drosten points out this problem in his podcast.¹⁰

This was shown in a case, among others, of a clinic in Taufkirchen in Bavaria (Germany), where 58 out of 60 tests were falsely positive.¹¹

Problems with the PCR-Tests

In addition to the difficult quality of sampling, another problem is that no asymptomatic people should have priority for testing. Both the Robert Koch Institute and the Johns Hopkins Center for Health Security point that out.

“At the time of publication, individuals who are asymptomatic and are not in hig- risk environments are not a priority for testing.“¹²

“Untargeted testing of asymptomatic individuals is generally advised against due to the unclear significance of a negative result (snapshot only).“ ¹³

The more asymptomatic people are tested, the higher is the risk of a false-positive or even false negative test result. This also explains why people who are negatively tested can exhibit typical COVID-19 symptoms or whether those who have tested positive do not develop symptoms at all. PCR tests should therefore only be used to confirm a suspected diagnosis. Currently, however, most tested are asymptomatic, whether they have accepted an invitation for Large Scale Testing or if a negative test is needed for work, school, or travel.

In the CHL (Center Hospitalier Luxembourg), 20% of the patients (mid-October 2020) who had corona pneumonia detected by a lung scanner were nevertheless tested negative. This was likely because the virus was in the lungs, not the nasopharynx (where the swap was taken). This means that in 20% of the corona patients who tested negative, an infection can occur through coughing. However, these patients have severe symptoms and cannot be described as asymptomatic.

There are no official numbers on the false positives. Due to the now very high number of tests and thus the increased number of positively tested, systematic follow-up by the state is hardly possible anymore. It is now requested that the positively tested take care of the follow-up themselves.¹⁴

In addition, the laboratories (in terms of procedures, test kits…) are not standardized, i.e. in one laboratory the CT value of 30 says something different than the CT value of 30 in another laboratory, according to Prof. Drosten.¹⁵

Another point is that symptoms can also be caused by other viruses, such as influenza or rhinoviruses. The PCR test finds RNA fragments that could indicate a SARS-CoV2 infection. In the end, it has not been clarified whether these are also influenza or rhinoviruses, because these viruses are not specifically searched for. Establishing SARS-CoV-2 alone as the cause of the disease is therefore uncertain in this regard and so-called differential diagnostics should be carried out (test for other pathogens). If a patient tests positive for SARS-CoV-2 for the second time and develops symptoms of the disease, other pathogens should also be tested in this case. The differential diagnosis can rule out infection with other viruses.

Also, PCR tests are not suitable to detect a past infection or immunity. This means that the test can still strike positively because particles of the virus can still be detected, although there are no more active viruses or acute cell infestations by viruses (as in the case of an illness).

There is also the question of data security and what happens to the DNA samples of the people tested and the results in the long term.

With regard to the counting of so-called new infections, it is also not clear whether someone is counted more than once if they have two or three positive tests within two weeks, but only got sick once.

What if you have already tested negative after a proven infection and the subsequent test is positive again?

So-called “relapses” are possible with SARS-CoV2 as with any other pathogen, if the patient was already symptom-free and virus fragments are detected again due to contamination in the nasal-throat area. These viruses do not cause the disease to recur in recovered patients. However, if the patient develops symptoms again, then one should definitely look for other pathogens or causes of illness.

So a PCR test can be positive even though a previous test after an infection was negative.¹⁶

This is generally the problem of false-positive and false-negative test results. In addition, the conditions for the tests are not standardized and may vary from laboratory to laboratory and from test kit to test kit. This is also the statement of Prof. Drosten who said that a CT value of 30 in one laboratory can say something different in another laboratory. ¹⁷

Alternatives to PCR testing respectively complementary methods

As an alternative to the PCR test, antigen and antibody tests also exist.

Antigen tests are among the rapid tests. The WHO says about the antigen tests:

“A new technology for COVID-19 detection has become available that is much easier and faster to perform than the currently recommended nucleic acid amplification (NAAT) tests, such as PCR, for example. This method is based on the direct detection of SARS-CoV-2 virus proteins in nasal swabs and other respiratory secretions using a lateral flow immunoassay (also called RDT), which provides results in < 30 minutes. Although these antigen detection RDTs (Ag-RDTs) are much less sensitive than NAAT, they offer the possibility of rapid, cost-effective and early detection of the most infectious COVID-19 cases under appropriate conditions.“ ¹⁸

Antibody tests are able to detect a past or end of infection or immunity to a virus, but not whether someone is infectious at the moment.

Comparison PCR test, antigen test, and antibody test ¹⁹

	PCR test	Antigen test	Antikörper test
What is verified?	Genetic virus material	Protein fragments of the virus	Antibodies against the virus
👉	Direct pathogen detection	Direct pathogen detection	Immune response of the patient
At what stage of the infection does the test shows results?	During an acute infection (relevance only in case of symptoms, may also strike at the lowest viral load)	During an acute infection (with high virus load)	In the final phase of the infection or if the infection is already through
Which sample material is required?	Nose / throat swab, bronchial secretion, urine, stool	Nose / throat swab, bronchial swab	Blood sample
Where is the test performed?	In a lab	At the point-of-care (e.g. directly in the doctor’s office, in the hospital or outpatient department)	At the point-of-care (e.g. directly in the doctor’s office, in the hospital or outpatient department)
How long does it take for the result to be available?	About 24 – 48 hours (including transport to the lab)	About 15 – 30 minutes (only rapid test, not in the lab)	About 10 – 20 minutes (rapid test or in the lab)
What is the purpose of the test?	To confirm a suspected diagnosis	For symptoms, to monitor contacts and to identify infected people with no symptoms that can be highly contagious	To detect a previous infection
Costs	Luxembourg laboratories charge approx. 60 EUR / PCR test *	Currently not available in Lux.	About 10-30 EUR

Comparison of the various test options

*In PCR Large Scale Testing (primarily asymptomatic people), however, there are additional costs in the millions (logistics, follow-up, correspondence, manpower, etc.).

Our summary: A positive PCR test does not necessarily mean that you have to fall ill easily or even seriously or at all. In addition, no test in the world is 100% safe.

References:

[1] https://flexikon.doccheck.com/de/Infektion

[2] https://www.sciencemag.org/news/2020/02/paper-non-symptomatic-patient-transmitting-coronavirus-wrong

[3] https://www.youtube.com/watch?v=Xc0Kysti6Kc https://www.bitchute.com/video/wOSeTz57xrCF/

[4] https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf?sfvrsn=a9ef618c_2

[5] https://doi.org/10.1002/3527600418.bipcrbasicd0016

[6 https://www.who.int/news/item/20-01-2021-who-information-notice-for-ivd-users-2020-05

[7] https://www.labor-gaertner.de/uploads/media/LaborwissenKonrekt_SARS-CoV-2_Ct-Wert.pdf

[7] https://www.aerzteblatt.de/archiv/214370/PCR-Tests-auf-SARS-CoV-2-Ergebnisse-richtig-interpretieren

[9] https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Vorl_Testung_nCoV.html

[10] https://www.ndr.de/nachrichten/info/40-Coronavirus-Update-Jetzt-ist-Alltagsverstand-gefragt,podcastcoronavirus208.html

[11] https://www.idowa.de/inhalt.nach-labor-panne-in-augsburg-was-hat-es-mit-falsch-positiven-corona-tests-auf-sich.be509670-1074-41a5-88ea-876c50cd22f8.html