Phlebotomy Top Gun: Safe Handling of Laboratory Specimens During the COVID-19 Pandemic

Hot Topic

Expires: February 28, 2025



Photo of Brad Karon, M.D., Ph.D.

Brad Karon, M.D., Ph.D.

Professor of Laboratory Medicine and Pathology
Mayo Clinic College of Medicine and Science
Division of Clinical Core Laboratory Services
Mayo Clinic, Rochester, Minnesota



Hello, I’m Brad Karon, chair of the Division of Clinic Core Laboratory Services at the Mayo Clinic in Rochester, Minnesota. I have been a conference organizer and presenter at our annual phlebotomy conference for more years than I care to remember, and I’m also co-director for our Laboratory Services, or Phlebotomy group, here at Mayo Clinic Rochester. 

For those of you who have not attended our phlebotomy conference, either in person here in Rochester, or last year virtually, the title of my "Hot Topic" video today, “Phlebotomy Top Gun,” may seem a little odd, but I hope I’ll be able to explain to you what is “Phlebotomy Top Gun” and what we try to do at our annual phlebotomy conference. Today’s "Hot Topic" video presentation will address the safe handling of laboratory specimens submitted during the COVID-19 pandemic.


I have no disclosures relevant to today’s presentation.  

The following specimens, uncapped or aliquoted during the COVID-19 pandemic, should be handled in a biosafety cabinet or if not available, chemical fume hood.

Every year at the Mayo Clinic Laboratories phlebotomy conference, I present a talk that’s always called “Phlebotomy Top Gun.” The format of “Phlebotomy Top Gun” is a case-based presentation. I solicit from you, the attendees, the cases, issues, or questions that you would like to hear about. I present these as case-based scenarios, and using an audience response voting mechanism, the attendees of the conference vote on the action or answer they feel is appropriate to the case. I then present the collective experience from our practice, and the evidence, guidelines, and published data that I can find related to the topic. At the end of the case the attendees vote again. For each case I can see whether I’ve been able to change anyone’s mind on the question at issue by presenting the data and information relevant to this topic. This is an actual case from a “Phlebotomy Top Gun” presentation at last year’s virtual phlebotomy conference. In this case the question was, “The following specimens, uncapped or aliquoted during the COVID-19 pandemic, should be handled in a biosafety cabinet or if not available, a chemical fume hood.” 

  1. Blood, CSF and pleural fluid.
  2. Stool, urine and blood.  
  3. Pleural fluids, oropharyngeal swabs, and saliva.
  4. Buccal swabs, nasopharyngeal swabs, and tracheal aspirates.
  5. Answers 3 and 4 are both correct.
  6. All of the above answers are correct.

So in this case I’ve given you perhaps too many answers, but it’s an example of how we do the “Phlebotomy Top Gun” case scenarios. At this point during the live conference or virtual conference, attendees using an audience response system would vote for the answer they thought was most appropriate, and we would get to see in real time the distribution of results that our audience felt was correct among these answers.  

Sample handling precautions for COVID-19

During the COVID-19 pandemic, all health care workers have been reminded of the importance of universal personal protective equipment and the need to consider all biological specimens as potentially infectious. We cannot rely upon testing or symptoms to identify patients infected with SARS-CoV-2, so laboratory safety procedures have been developed around identifying the types of specimens most likely to transmit virus from specimen to person and the types of laboratory activities most likely to generate aerosols, and therefore, most likely to expose laboratory workers to infectious viral particles.

Of course, we must use universal personal protective equipment (PPE) such as coats, gloves, and eye protection whenever we collect, handle, or manipulate biological specimens. In situations where a splash of a body fluid or biological specimen is possible, we must add face protection for laboratory staff, including phlebotomists. Face protection for laboratory staff might include a face shield, a bench shield, or a biological safety cabinet or chemical fume hood, depending upon the situation and environment where biological fluids are being manipulated and the risk of a splash. In most situations where there is a need for splash protection, but the laboratory or area is not handling high-risk specimens for respiratory virus transmission, either a face shield or bench shield would be used to mitigate the risk of disease transmission from specimen to health care worker. Beyond universal PPE including face protection when a splash is possible, we also need to consider high-risk specimens for COVID-19 disease transmission, and high-risk activities where health care workers have greater risk of exposure and infection with respiratory viruses. For laboratory or any other health care worker performing high-risk activities with high-risk specimens, additional precautions beyond the universal PPE will be necessary.   

Let’s first cover the types of biological specimens that are high-risk for transmission of respiratory viruses — including SARS-COV-2, the virus that causes COVID-19. Many respiratory viruses, and this is certainly true of SARS-CoV-2, are transmitted either as aerosols or respiratory droplets. Therefore, high-risk activities for SARS-CoV-2 transmission, and this would also be true for influenza and other respiratory viruses, are those activities most likely to generate aerosols or droplets. You can see on this slide a list of common laboratory activities that are known to generate aerosols and therefore are considered high-risk activities when handling respiratory specimens. Many of these are performed mainly within the testing laboratories and would not be things that a phlebotomist would do, but practices and duties vary by location, so it is important to be aware of these high-risk activities. Phlebotomists may be asked to perform some of these duties if they are involved in collecting or testing for COVID-19 at the point of care, as one example. 

So, if these activities shown on the last slide are high-risk activities, what then are the samples we need to be concerned about when performing these high-risk activities? The answer is any sample from the respiratory tract, unless that sample has been treated with something that will inactivate respiratory viruses. Bronchoalveolar lavage, sputum, nasopharyngeal swabs, oropharyngeal swabs, nasal swabs, nasal tissue, oral tissue, lung tissue, and tracheal aspirates are the highest risk samples. These samples are likely to contain the highest concentration of viral particles in a patient infected with SARS-CoV-2, influenza, and several other respiratory viruses. Pleural fluids are also considered high-risk specimens as well, but probably not as high-risk as the first group. Finally, samples such as saliva, spit, salivary glands, and buccal swabs are also respiratory specimens and should only be manipulated in a biological safety cabinet or, if one is not available, in a chemical fume hood.  

Fortunately, some of the most common specimens collected and manipulated by the laboratory staff are considered low risk for transmission of SARS-CoV-2 and other respiratory viruses. SARS-CoV-2 RNA has been detected in blood, but blood is generally not considered an infectious sample for SARS-CoV-2 transmission. Similarly, CSF, urine, and any respiratory tissue fixed in formalin are not considered infectious and thus no special handling of these samples is necessary. Early on in the COVID-19 pandemic there was a lot of concern about laboratory staff that handled stool specimens. RNA is detected in stool samples from patients infected with SARS-CoV-2, often at fairly high levels. There have been some reports that SARS-CoV-2 RNA is so easy to detect in stool samples that anal swabs can be used as an alternative sample type to test for SARS-CoV-2 infection. I think we can all agree that this may not be the ideal way to test for COVID-19, but it appears to work fairly well. However, the RNA present in stool does not appear to be intact virus, and so far, no one has cultured SARS-CoV virus from these specimens. Currently stool is not considered to be a high-risk specimen that would require manipulation in a biological safety cabinet or chemical fume hood to reduce the risk of SARS-CoV-2 transmission, though there may be other reasons to manipulate stool in a safety cabinet or fume hood if possible.  

Finally, a word about safe handling of specimens used to perform point of care testing for SARS-CoV-2. Here at Mayo Clinic Rochester, our outpatient laboratory service techs, or outpatient phlebotomists, do perform point of care testing for SARS-CoV-2 RNA using a point of care molecular test. Point of care antigen tests are also becoming increasingly common as a tool to address the ongoing COVID-19 pandemic. Given the “all hands on deck” approach needed within health care systems to address COVID-19, it would not surprise me to learn that in other systems phlebotomists are performing point of care testing for COVID-19 or collecting or manipulating these specimens. Most point of care COVID-19 tests require collection of a nasal or nasopharyngeal swab, and some manipulation of that swab to detect either viral RNA or viral antigen. Quite often a nasal or nasopharyngeal swab is collected and then immersed in a viral transport media tube (for RNA testing) or an extraction buffer (for antigen testing). The viral transport media (VTM) or antigen extraction buffer sample is mixed, uncapped, then the viral transport media or extraction buffer is applied to a test to detect either viral RNA or antigen. Mixing of transport media or extraction buffer, and uncapping that mixture, is an aerosol generating activity, and thus many point of care tests for COVID-19 do put some risk on testing personnel who are performing these tasks. The ideal practice would be to perform sample manipulation, the mixing of viral transport media or extraction buffer, the uncapping of that mixture and dosing of the device in a biological safety cabinet, but this is not a practical workflow for many point of care situations. 

There are two solutions to reducing the risk for testing personnel in this context that do not involve the use of a biological safety cabinet or chemical fume hood. One is to choose a test that has a viral inactivation buffer prior to manipulation of swabs. In these tests the swab is collected and placed in a buffer or transport media that inactivates SARS-CoV-2 virus, and therefore further manipulation of the sample is not risky for testing personnel. Antigen tests that use viral inactivation buffer are available today, and point of care molecular tests that use a viral inactivation buffer rather than transport media are under development. The second solution is to use a direct dosing device, an antigen or molecular test that allows a swab to be placed directly into a closed system that completes the test without any need to manipulate the samples. These devices do exist and allow the user to place a nasal swab, once collected, directly into a sealed cartridge or disposable unit so that mixing and uncapping of a solution with potentially infectious virus is not necessary.  

The following specimens, uncapped or aliquoted during the COVID-19 pandemic, should be handled in a biosafety cabinet or, if not available, chemical fume hood.

At this point during the phlebotomy conference, I would return to the original question that I polled the audience on. The attendees of the conference would use the audience response system to respond again, and I would share with the audience what I believe to be the correct or intended response. Based upon available data, guidelines, and our experience here at Mayo Clinic, my opinion is the single best answer to this question would be answer number 5, that both answers 3 and 4 are correct. Answers 3 and 4 are the respiratory specimens I mentioned as being high-risk sample types, and these should be manipulated in a biological safety cabinet or, if not available, in a chemical fume hood to reduce the risk of transmission of SARS-CoV-2 to laboratory staff while manipulating these samples in any way that might generate aerosols or droplets.   

Thank you

Thank you for your time and attention today. If you liked today’s presentation, or even if you didn’t, please consider attending our next virtual phlebotomy conference on April 21st and 22nd, 2022: "Performance, public health and people in a post-COVID world." Our conference titles are always based upon the themes of our learning sessions, so please also check out the conference agenda now posted online at the Mayo Clinic Laboratories website (no longer available). Learning at the conference takes place via both large group didactic sessions, and small group break-out sessions that allow more interaction with conference speakers. Virtual tours of Mayo Clinic facilities are also offered during the conference. Thank you for listening today and have a wonderful day.  


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