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What is the baseline test to find out if I am infected with SARS-CoV-2?

Text updated on 2020-04-30


To find out if I am infected with coronavirus, we can look for the presence of genetic material specific to this virus. The standard test validated by the WHO is based on the RT-qPCR method to detect the genetic sequence of the virus SARS-CoV-2. The reference PCR test should: 1) be done early to limit false negatives, 2) be done regardless of the severity of symptoms - this reflects a public health strategy and not an individual one, 3) if the clinical suspicion is strong, it is recommended to isolate even if the test is negative. Other tests are now emerging for screening. See the question "What approaches could accelerate large-scale screening? ».

A distinction must be made between tests that detect the virus from oral or nasopharyngeal specimens to see whether you are currently infected with the virus (see "What is the reference test to find out if I am infected with SARS-CoV-2 ? ") from serological tests that tell you that you have been infected with the virus by detecting your immune response in your blood (see "What are the tests to find out if I've ever had COVID-19?").

Virus detection tests can be very sensitive thanks to a process of amplification of the virus (classic method called Reverse Transcription Quantitative PCR or "RT-qPCR" or recent Reverse Transcription Loop-mediated isothermal AMPlification or "RT-LAMP" method), or less sensitive if the virus is detected without amplification (these are the so-called "antigenic" tests).

When to test for the virus? The PCR test indicates the presence of viral material only during infection. A person who has been infected in the past and subsequently recovered will test negative for RT-qPCR sometimes days or weeks after symptoms. A person who has been infected in the past and subsequently recovered will be negative for the RT-qPCR test, sometimes several days or weeks after symptoms appear, but may become positive for the serological test that shows antibodies to the virus. How to identify a COVID-19 case with certainty  and identify contact cases? If there are symptoms: the RT-qPCR test should therefore be performed early, regardless of severity. If there are no symptoms: it is recommended to wait about 5 days after contact. See question " How many days after a contact to do a COVID test ?».

What is being sampled for the virus? Current reference tests are typically performed on nasopharyngeal swabs using a swab inserted quite deeply into the nasal cavity. However, salivary sputum contains a lot of viral particles and because the swab is self-contained and low-risk, it is used in several countries such as Japan or the United States. Authorized at the end of September by the French National Authority for Health for symptomatic patients only, this sampling method is, unfortunately, not yet routinely used in France.

What technique is used to test for COVID-19 ? The reference tests are based on the technique of detecting the genetic material of the virus by PCR, known in the jargon as "RT-qPCR".

What are the steps to detect the virus? The processing of samples, whether nasopharyngeal or buccal, begins with the inactivation of the virus, before the extraction of the genetic material of the virus, the RNA. Then, for the analysis of saliva, the samples must be fluidized. In France, the reference protocol for the detection of virus RNA is then based on a one-step RT-qPCR amplification developed at the national reference centre of the Institut Pasteur and the World Health Organization. The RT-qPCR amplification targets two specific regions of the virus and, for some tests, a genomic region specific to the patient's cells. This human sequence makes it possible to validate both the origin of the sample and the quality of the samples and to standardize them with respect to each other. False-negative errors due to incorrect sampling are thus avoided. A standard range of synthetic viral RNA allows the number of RNA molecules in the samples to be quantified from SARS-CoV-2. However, it is rarely used and the results do not give the real viral load. This protocol takes at least 3 - 4 hours from the start of sample processing until the test result is obtained in the laboratory.

Where do the false negatives come from? If the sample is taken incorrectly, it is possible that the test result is negative even though the person is infected: these errors are called "false negatives". This can happen if the sample was taken incorrectly, but it can also happen with a good sample. Indeed, in some COVID-19, patients, the virus is not detected in nasal or pharyngeal secretions, whereas it is detected in lung fluid. The many reasons leading to false negatives indicate that great caution is required. Even if the test is negative, clinical signs may lead to the suspicion of COVID-19 and the imposition of self-confinement before any further tests are performed.


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Sources

First kinetics of the amount of SARS-CoV-2 in hospitalized patients in Munich, Germany (April 1, 2020) reveal that infectious viral particles are easily isolated from throat or lung specimens, but not from stool - despite high concentrations of viral RNA. Analysis of blood and urine samples has never revealed any virus.

Wölfel, R., Corman, V. M., Guggemos, W., Seilmaier, M., Zange, S., Müller, M. A., ... & Hoelscher, M. (2020). Virological assessment of hospitalized patients with COVID-2019. Nature, 1-10.

The transmission analysis of the COVID-19 reveals that many infections occur before or at the onset of symptoms, that the incubation period is short, and that many PCR tests have resulted in false negatives when an infected person is not detected.

Böhmer, M. M., Buchholz, U., Corman, V. M., Hoch, M., Katz, K., Marosevic, D. V., Böhm, S., Woudenberg, T., Ackermann, N., Konrad, R., Eberle, U., Treis, B., Dangel, A., Bengs, K., Fingerle, V., Berger, A., Hörmansdorfer, S., Ippisch, S., Wicklein, B., Grahl, A., ... Zapf, A. (2020). Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series. The Lancet. Infectious diseases, 20(8), 920-928.

An analysis comparing the results of more than 50 laboratories in Austria using the same inactivated virus samples shows that while the results of the reference PCR test are consistent for samples with high virus presence, this is not the case for samples with low virus abundance:

Görzer, I., Buchta, C., Chiba, P., Benka, B., Camp, J. V., Holzmann, H., Puchhammer-Stöckl, E., & Aberle, S. W. (2020). First results of a national external quality assessment scheme for the detection of SARS-CoV-2 genome sequences. Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology, 129, 104537.

RNA from SARS-CoV-2 is not found in the blood of asymptomatic and minimally symptomatic patients, making the risk of transfusion contamination negligible.

Corman, V. M., Rabenau, H. F., Adams, O., Oberle, D., Funk, M. B., Keller-Stanislawski, B., Timm, J., Drosten, C., & Ciesek, S. (2020). SARS-CoV-2 asymptomatic and symptomatic patients and risk for transfusion transmission. Transfusion, 60(6), 1119-1122.

German study of 49 children aged 0-10 years, 78 people aged 11-20 years, and more than 3,000 adults of all ages, all tested positive for the SARS-CoV-2 coronavirus between January and April 2020. Analysis of viral load according to patient age reveals similar values for young and asymptomatic people as for older and symptomatic people:

Jones, TC, Mühlemann, B, Veith, T, Biele, G, Zuchowski, M, Hoffmann, J, Stein, A, Edelmann, A, Max Corman, V, Drosten, C. An analysis of SARS-CoV-2 viral load by patient age. medRxiv 2020.06.08.20125484.

Further reading

What sample to test for COVID-19: nasopharyngeal or buccal?

What are the different types of serological tests?

Grouping tests ("pooling", "pools"): why and for what purpose?

What are the tests to find out if I've ever had COVID-19?

False positives, false negatives, sensitivity, specificity of COVID tests: what are we talking about?

What strategies to detect contagious people at the entrance of a bar or an airplane?

What approaches could accelerate large-scale screening?