What is difference between Nasopharyngeal Swab and Throat Swab?

Posted on  October 29, 2020, Edited by Jason, Category  

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Nasopharyngeal swab and throat swab are very important component in diagnosis of infectious disease. Now it’s the key role during covid testing. The noval coronavirus pneumonia is a sudden, endangering global public health events. The elderly and people with underlying diseases have a high prevalence and a high proportion of critically ill patients. The disease is highly contagious, droplets, contact and aerosol can be the transmission route of the disease. Therefore, timely and accurate diagnosis of the disease is essential to control its outbreak and protect people's lives.

In clinical practice, due to the large number of patients in the early stage of the outbreak and the lack of viral nucleic acid detection capabilities, experts have proposed to use chest CT as the main indicator for the diagnosis of the disease. But as we all know, for infectious diseases, pathogenic diagnosis is the gold standard. Therefore, whether it is domestic or international, the diagnosis standard is still based on the positive nucleic acid of the new coronavirus isolated from the patient's body fluid sample. At present, various documents have proposed to collect patients' sputum, bronchoalveolar lavage fluid, and stool for nucleic acid testing. However, whether it is a nasal swab or a throat swab for viral nucleic acid detection, it is still the easiest and most popular method, which is also the respiratory tract. An effective method for rapid diagnosis of virus infection or carrier status.

How to select Nasopharyngeal swab and throat swab (Oropharyngeal swab)

In the guideline of USA CDC “Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Patients Under Investigation (PUIs) for 2019 Novel Coronavirus (2019-nCoV)” indicate clearly: Use only synthetic fiber swabs with plastic or wire shafts. Do not use calcium alginate swabs or swabs with wooden shafts, as they may contain substances that inactivate some viruses and may inhibit molecular tests.


Only allow to use nasopharyngeal swab and throat swab that made by synthetic fiber. Why? The nylon flocked swab can increase the surface area of the swab in contact with the physical evidence, which can maximize the transfer of cells to the surface of the swab, and fully release the adherent cells during DNA extraction, thereby obtaining a higher concentration of template DNA. Research by Daley [2] et al. showed that the efficiency of nylon flock swabs in transferring microorganisms on the surface of objects is 20% to 60% higher than other swabs. A study by forensic workers in my country also confirmed that nylon flocking swabs are better than cotton swabs for blood stain testing, and the advantages are more obvious in micro blood stain testing. Therefore, when the nasopharyngeal virus is less in the late stage of the virus infection, this kind of swab has a higher probability of retaining the viral nucleic acid. However, some studies [4] believe that the test results of the two swabs are not significantly different.

Pros and Cons of Nasopharyngeal Swab and Throat Swab

Nasopharyngeal Swab


  1. It can stay in the pharynx for a longer period in order to obtain more sufficient samples. This is why the positive rate is higher than that of oropharyngeal swabs reported in literature.
  2. The skilled nurse can basically take samples without anesthesia after proficient operation; if new nurse, at the beginning, surface anesthesia and contraction of the nasal mucosa can be performed.
  3. The exposure risk of the sampler is lower than oropharyngeal swab, because we can operate the sampler from the back of the patient during collecting, and the patient is required to pull down the mask to expose only the nostrils and cover the oral cavity without looking directly at the patient’s oral cavity. In addition, there is basically no pharyngeal reflex. A few patients may have sneeze reflex after sampling. The patient can be covered by elbows or tissues, and because the sampler is not in front of the patient, the exposure risk is quite lower, so the psychological pressure of the sampler will not be so great.


Compared with oropharyngeal swabs, patients may be more difficult to tolerate. If the patients tolerate well, they can basically take samples without anesthesia after proficient operation. However, new nurse can perform surface anesthesia and contraction of the nasal mucosa at the beginning

Throat Swab


Since the oropharyngeal swab can be operated just only opening the mouth, it is very simple and commonly used clinically


The risk of exposure of the sampler is higher, and the operator often needs to face the patient’s mouth. During the sampling process, the patient is prone to irritating dry cough, vomiting and other symptoms, exposing the collector to the aerosol containing the virus.

How to use nasopharyngeal swab to collect samples from covid 19 suspicious case?

  1. The sampler holds the swab with his right hand (plastic swab with polypropylene fiber head), and presses the top of the subject's head with his left hand to fix it.
  2. Make the swab with the tip slightly bent down from the anterior nostril, and go deep along the bottom of the lower nasal passage. {Because the nasal passage is curved, the movement should be gentle and slow, and must not use excessive force to avoid traumatic bleeding}.
  3. When the tip of the swab reaches the back wall of the nasopharyngeal cavity (with a feeling of touching the wall), leave the swab for a while (about 3 seconds), and then gently rotate it one week to slowly take out the swab.
  4. You can take another plastic rod swab with polypropylene fiber head to collect the other nostril in the same way, immerse the above two swabs into the same tube containing 3ml virus sampling solution, discard the tail, and tighten the tube cap
  5. After being packaged according to biosafety requirements, it should be transported to CDC laboratories at all levels for viral nucleic acid testing as soon as possible.

Precautions for Sample Colletion

Whether collecting nasopharyngeal swabs or oropharyngeal swabs, the depth of collection is the key. The collected nasopharyngeal swabs are not collected deep into the nasal cavity. Most of the cells collected are virus-free cells, which may cause "False negative".

Precautions for Covid Testing

To avoid vomiting, please refrain from eating 2 hours before sampling;

To avoid affecting the test results, please refrain from smoking, drinking and chewing gum 30 minutes before sampling;

In order to reduce the risk of cross-infection in the hospital, all need to wear a mask and prepare a spare mask;

All person waiting for inspection must keep a social distancing more than 1 meter and avoid talking;



In summary, in clinical practice, priority should be given to nasopharyngeal swabs for virus nucleic acid detection specimen sampling. This can further reduce missed diagnosis and reduce the possible exposure of medical staff to the virus. Of course, if the nucleic acid of other body fluids of the patient can be detected at the same time, the diagnosis of new coronavirus pneumonia patients and the monitoring of discharged patients will be more advantageous.


  1. Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19)
  2. Daley P, Castriciano S, Chernesky M, et al. Comparison of flocked and rayon swabs for collection of respiratory epithelial cells from uninfected volunteers and symptomatic patients. J Clin Microbiol, 2006, 44(6): 2265-2267
  3. Dalmaso G, Bini M, Paroni R, et al. Qualification of high-recovery, flocked swabs as compared to traditional rayon swabs for microbiological environmental monitoring of surfaces. PDA J Pharm Sci Technol, 2008, 62(3): 191-199.
  4. Brownlow RJ, Dagnall KE, Ames CE. A comparison of DNA collection and retrieval from two swab types (cotton and nylon flocked swab) when processed using three QIAGEN extraction methods. J Forensic Sci, 2012, 57(3): 713-717

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