Specimen collection for molecular tests

Significance of the specimen collection area for the virus molecular test (nucleic acid amplification tests (NAAT), such as RT-PCR) is apparent.

According to the World Health Organization (WHO):

At minimum, respiratory material should be collected:

upper respiratory specimens: nasopharyngeal and oropharyngeal swab or wash in ambulatory patients;

• and/or lower respiratory specimens: sputum (if produced) and/or endotracheal aspirate or bronchoalveolar lavage in patients with more severe respiratory disease.

Nasopharyngeal and oropharyngeal swabs are the commonly accepted standard. However, it is technically difficult procedure which require professional training. It is more easily present on the diagram than in a real situation (see both diagrams).

Diagram of the nasopharyngeal test specimen collection

Anatomical conditions of nasopharyngeal specimen collection for COVID-19 molecular test. Red arrow- collection swab in, green arrow- swab out.

Collection a nasopharyngeal swab specimen is invasive. Following of the anatomical structure (conches), which is very much individual, require some training, skill and even instruments. Actually, this is a medical procedure. How far the swabs can reach in every collection? Are the swab’s handles calibrated for approximate depth of penetration?  Many technical details can influence the test’s result.

The solution was found for the “testing, testing, testing” mantra.

Remove preference for NP (nasopharyngeal) swabs” is among “Excerpts from CDC Summary of Recent Changes. Revisions were made on April 29, 2020 to reflect the following”.

And now:

In the list of acceptable specimens for initial diagnostic testing for SARS-CoV-2, CDC recommends:

An anterior naris (nasal swab) specimen collected by a healthcare professional or by onsite or home self-collection (using a flocked or spun polyester swab)”.

 The technical difficulty to obtain the specimen for molecular test from the most representative areas was substituted by simple nostril area. This substitution opens the gates to mass testing everywhere.

Drive-through screening centers have been designed and implemented in South Korea (Drive-Through Screening Center for COVID-19: A Safe and Efficient Screening System against Massive Community Outbreak. J Korean Med Sci. Published online Mar 16, 2020.  https://doi.org/10.3346/jkms 2020 Mar 23;35(11). According to the article, this procedure increased testing capacity over 100 tests per day.

The real drive- through when a tested person opens the car’s window and a swab is poked in the nostril. You can see this procedure on the TV screen how.

The U.S. Food and Drug Administration (FDA) authorized option for the Laboratory Corporation of America (LabCorp) COVID-19 RT-PCR Test to permit testing of samples self-collected by patients at home using LabCorp’s Pixel by LabCorp COVID-19 Test home collection kit. A sample collected from the patient’s nose in saline is mailed to a LabCorp lab for testing. According to FDA Commissioner Stephen M. Hahn, M.D. the data demonstrated from at-home patient sample collection is as safe and accurate as sample collection at a doctor’s office, hospital or other testing site. 30 participants (?!) were enrolled in a self-collection study by LabCorp.

This post will explore only nares specimen collection for COVID-19 RT-PCR test from the nostril’s anatomy, histology, and pathophysiology aspect leaving aside clinical, epidemiological, and medical statistic aspects and other details of this type of specimen collection. These issues require a special post.

Nostrils as part of the nasal cavity are initially a continuation of the skin lined with squamous epithelium and different size of hair. Their protective role is in preventing dust entering the respiratory tract, but it serves also of stopping infections materials, especially droplet containing airborne microorganisms. In this regard, droplet nuclei containing SARS-CoV-2 virus are “hanging” on the hair even without touching the surface of the nostril. Squamous epithelium lining of the anterior nares is followed by ciliated epithelium whose cilia form a carpet on which dust settles, as well as droplet nuclei might be engulfed by mucus. The virus, if it is there became the target of first line of immunology defense through intensive mucus production and tool of cellular  (macrophages , T-lymphocyte cells). All these popular biology data are presented here just to show the place where the collection swabs is operating.

By the way, this operation is not completely innocent.  During this collection manipulations, the droplet nuclei might be taken off the defense line provided by nostrils hair and pushed further into nose cavity which would not be right.

Every specimen collection has some uncertainty. Deviation of the standard bring additional confusing data. Is the method of collection reflected in the at the requisition form documents? As an extraordinary exception with the mark.


Positive SARS-CoV-2 virus molecular test is only evidence of virus presence in the nose’s content when the virus hasn’t even interacted with a person ‘s first line of innate immunity defense response.

The nares collection area for the SARS-CoV-2 virus molecular test can be done only as an extraordinary exception with the special mark.  The clinical and epidemiological interpretation of the result should take into account the nares collection area.

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