Why are PCR tests done with nose samples if the virus is spread by saliva?

On these days, a message in which the author questions his or herself the PCR nasopharyngeal diagnosis is circulating in WhatsApp, in which a nasal sample is extracted to check whether the patient has covid-19. In the message, it is asked why this method is used when “a single drop of saliva is supposed to infect half the world”. We investigate the reasons for which nasopharyngeal PCR tests are more generalised and which is their reliability in comparison to PCR with saliva samples.

"Sometimes I can’t explain myself: why do a swab with a so long stick, at the back of the nose to find the “virus”, when a single drop of saliva is supposedly able to infect half the world? All this is strange, don’t you wonder?"

The author of the message is probably not the first person to wonder why PCR tests us with a swab that is introduced in the nose if the population is required to always wear a mask to avoid the contagion by aerosols. Would it not be enough to take samples directly from saliva?

Indeed, several research centres have already started measuring how sensitive a diagnostic test which sample is saliva is. “Several studies prove that saliva can be used to detect, not only the presence of the virus, but also antibodies against it”, points Adelaida Sarukhan, immunologist and scientific writer at ISGlobal, to Verificat. In these studies, she continues, it has been observed that “the amplification of the genetic material from saliva can have the same specificity and sensitivity than nasopharyngeal samples”, that is, that the studies indicate that, at least in terms of the capacity of detecting the virus, is quite similar to the nose swab PCR test.

And in the real world?

However, the experts consulted insist that one thing is the taking of samples in the laboratory, through controlled clinical trials, and another one is to do the same in the real world: “Saliva is quite a complex sample. First, because when one says ‘saliva’ you don’t know exactly what you mean: gingival secretion, what the kids called a ‘spit’, a sputum…”, Tomàs Pumarola, head of the Microbiology Services at “Hospital Universitario Vall d’Hebron”, and spokesman of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC in Spanish), told to Verificat. In addition to the difficulty of knowing which is the right sampling way, there is also the question of when is the best time to take it: “Do you need to be fasting beforehand or not? Do you have to take it during the morning, afternoon or evening? Do you have to rinse your mouth first? There are lots of factors when collecting saliva, it is not as easy as people think”, concludes the physician.

For the moment, the experts are also unclear about the performance of saliva samples in the real world: “In the proved study situation the sensitivity probably is very similar to the rhinopharyngeal, but is real life situations it may be lower, because there are a lot of sample types and very different conditions”, reasons the scientist.

In that sense the National Spanish Research Council (CSIC in Spanish) has assessed the PCR test as “a vital tool to determine the extent of the covid-19 pandemic”, because it offers the "highest reliability".