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Selecting the Right Swab: Comparing Different COVID Testing Methods

Written by Yidan Gao, Edited by Edward Chen and LisaMichelle Pecaro

So far, an estimated 300 million polymerase chain reaction (PCR) tests for COVID-19 have been conducted in the US. Over 1.8 million tests are administered daily. Among those tested, more than 100,000 people test positive for COVID on a daily basis. As more and more testing methods become available, it is worth reviewing how each method differs in terms of accuracy, comfort level, and turnaround time.

In order to understand the goals of the different testing methods, it is beneficial to learn about the several ways scientists test for the presence of SARS-CoV-2. The three major COVID-19 tests are the molecular test, antigen test, and antibody test. To break it down, the molecular test looks for genetic material of the virus which, in the case of SARS-CoV-2, is RNA. The detection of RNA is often performed in a lab using PCR, which amplifies the RNA present in a sample. On the other hand, the antigen test looks directly for the presence of viral particles, such as viral surface proteins, with flow immunoassays. The third test, the antibody test is a bit more complicated since it assesses the host immune response against the virus. When an individual is exposed to SARS-CoV-2, their immune system produces antibodies that halt viral infection. By using an assay called ELISA (which stands for enzyme-linked immunosorbent assay), researchers detect specific antibodies against the virus and may conclude that the patient was once infected. We will focus on the first two themes for the purpose of this blog. For more specific information about antibody testing and mechanisms, please refer to our previous blog on testing for COVID-19.

Let’s start with the molecular test, which detects RNA. Swabbing is the main way to generate samples for this test. This includes nasal, nasopharyngeal, throat/oropharyngeal, and even anal swabs. Some of these procedures can take place at home. When performing a nasal swab, one uses a long cotton swab with a specialized absorbent tip and inserts the tip into the nostril. The tip is swirled around the nasal wall at least 4 times for about 15 seconds. The swab is then placed in a sterile tube and shipped to a lab for analysis. Nasal swabbing is very popular due to its convenience in administration. For LabCorp, a major COVID testing provider, the time it takes to get results is around 2-4 days from the date of specimen submission. Some companies, such as Lucira, developed rapid testing mechanisms that shorten the wait to under an hour.

The remaining methods are a bit more invasive and complicated, requiring sample collection by trained healthcare providers. The nasal epithelium and the oral cavity are the two major entry points for SARS-CoV-2. After an initial infection, the spike protein of the virus binds to the ACE2 receptor on epithelial cells to gain access into host cells. In this case, obtaining samples from the upper respiratory tract with nasopharyngeal or throat swabs is very efficient for accurate detection of viruses. Although considered to be the most sensitive and common method, nasopharyngeal swabbing is rather uncomfortable because the long cotton swab must be inserted 8-10 cm (3-4 inches) deep into the nasal cavity. Throat swabbing is similar in that the swab extends to the base of the tongue and reaches for the oropharynx. Some might gag during the process, but the discomfort only lasts for seconds. As an individual who went through both tests myself, I concede that the time during which the swab remains in the nose feels like the longest few seconds in my life. The time it takes to generate results varies depending on the facility's capabilities, so it can range from less than an hour to a few days.

Another interesting way of testing is via an anal/rectal swab, which is now applied in some countries, including China. The benefit for this test is that it provides an accurate measure for recovered COVID-19 patients, who may otherwise incorrectly test negative using the nasopharyngeal swab. According to a case study, two out of four COVID-19 patients confirmed to be positive by chest CT scans tested positive by anal swabbing but negative by throat swabbing. The same phenomenon was also observed by another research group, who found that six out of seven COVID patients had positive rectal swab results but negative upper respiratory swabs. In another study, live virus could be isolated from fecal samples in 3 out of 11 COVID-19 patients, suggesting that recovered COVID-19 patients may still need further quarantine before being discharged.

The second major testing method is an antigen test, which utilizes methods somewhat similar to molecular testing. In this case, a nasal swab is collected in order to look for the presence of viral particles. BinaxNOW and Ellume’s COVID-19 home test are both products that enable rapid testing for viral antigens. Both work with similar mechanisms and take only 15-20 minutes. Taking BinaxNOW as an example, by running the sample down the antigen card or analyzer, one can simply determine if he/she is infected by counting the number of bands. A positive result is indicated by 2 bands, comparable to a pregnancy test. Although antigen tests are very specific for the coronavirus and its particles, its sensitivity is lower than molecular testing. Sensitivity refers to how accurately the test can identify positive individuals, so a lower sensitivity means more false negative results. Put into the context of COVID-19, a false negative result happens when the test result is negative even though the patient is actually infected with COVID-19.

In 2020, we learned much about the epidemiology and mechanisms of viral infection thanks to many great researchers. And we learned that flattening the curve, through testing for COVID-19, is vital. As more and more people receive regular tests and follow self-quarantine guidelines, new cases will hopefully be extensively reduced.


Results from ongoing research and the current understanding of COVID-19 are constantly evolving. This post contains information that was last updated on February 2, 2021.


Edward Chen is a master's student studying immunology. He's also the national president of Students vs. Pandemics. @EdwrdChen

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