What is the test to find out if I am infected with SARS-CoV-2?
Text updated on 2020-04-30
To find out if one is infected with the SARS-CoV-2 virus, we can look for the presence of genetic material specific to this virus. Since the genetic sequence of the SARS-CoV-2 virus is known, so-called RT-qPCR tests have been developed and validated by the WHO. However, they do not detect 100% of the cases of infection. Saliva tests are promising because they are more sensitive and easy to use. The 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 presumption is strong, it is recommended to isolate even if the test is negative.
COVID-19 tests are based on a technique to detect the genetic material of the SARS-CoV-2 virus by Polymerase Chain Reaction (PCR).
What is taken to detect the virus? Current tests are typically performed on nasopharyngeal swabs using a swab inserted quite deeply into the nasal cavity. The virus is also present in the feces but in small amounts. Recently, tests based on saliva have become more sensitive because the viral load is high. Since the associated samples are very easy to collect, sputum tests are very promising for rapidly testing a large part of the population. In addition, combining samples from several people in the same household in a single test could optimize the detection of infected outbreaks in the population.
How do we detect the virus? The processing of samples, whether nasopharyngeal, salivary, or fecal, begins with inactivation of the virus before the extraction of the genetic material of the virus, the RNA. For saliva analysis, the samples are fluidized. In France, the virus RNA detection protocol is then based on a one-step RT-qPCR type 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 a genomic region specific to the patient's cells in a "housekeeper gene". 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. This avoids having numerous false negatives linked to a bad sample. A standard range of synthetic viral RNA allows researchers to quantify samples for the number of RNA molecules of SARS-CoV-2. In total, it takes about 4 hours from the start of sample processing to providing the test results from the laboratory.
The test indicates the presence of viral material only during infection. A person who has been infected in the past and subsequently recovered will be negative for the RT-qPCR test. However, he or she may be positive for another test, the serological test. The RT-qPCR test should therefore be done early, regardless of the severity of symptoms.
False negatives. Note that the virus in some patients COVID-19 has sometimes not been detected in nasopharyngeal secretions while it was present in lung fluids. These cases of false negatives indicate that the virus may remain in the body without necessarily being present in the nasal or oral secretions used for testing. In addition, if the sample is taken incorrectly, it is possible that the sample may be negative even though the person is infected. Thus, even if the test is negative, the clinical signs may lead to the conclusion that isolation is COVID-19 necessary.
First measurements of the amount of virus in COVID-19 hospitalized patients (April 1, 2020).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.
One of the first studies indicating the reliability of saliva tests.Azzi, L., Carcano, G., Gianfagna, F., Grossi, P., Dalla Gasperina, D., Genoni, A., ... & Maurino, V. (2020). Saliva is a reliable tool to detect SARS-CoV-2. Journal of Infection.
One of the first studies indicating the reliability of saliva tests.Williams, E., Bond, K., Zhang, B., Putland, M., Williamson, D.A. (2020) Saliva as a non-invasive specimen for detection of SARS-CoV-2. J Clin Microbiol. pii: JCM.00776-20.
Saliva measurements are more sensitive than nasopharyngeal tests.Wyllie, A. L., Fournier, J., Casanovas-Massana, A., Campbell, M., Tokuyama, M., Vijayakumar, P., ... & Petrone, M. E. (2020). Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. medRxiv.
Pooling the samples within a household could optimize the detection of infected outbreaks in the population.Hogan, C. A., Sahoo, M. K., & Pinsky, B. A. (2020). Sample Pooling as a Strategy to Detect Community Transmission of SARS-CoV-2. JAMA.