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News & Press: COVID-19


Thursday, March 26, 2020   (1 Comments)

Dear Colleagues,

As you know, we are in a very serious coronavirus pandemic at this time and the laboratories at the Vaccine Research Center (NIAID/ NIH) are involved in the research and efficacy of the current vaccine in the clinical trial now beginning in Seattle. Some of our laboratories will be involved in the measurement of neutralizing antibodies and the flow cytometry core lab will be responsible for a large part of this effort by cell sorting antigen specific B cells.  These isolated cells are an important key to understanding the biology of protection and for genetic studies to isolate neutralizing antibodies to further characterize the efficacy of this vaccine.  Furthermore, complex phenotypes of these cells and others can aid in developing tools to best monitor patients for protection. Therefore, it is critical and timely that we have established procedures of infectious cell sorting and understanding of risk assessment.
Our procedure, now posted on the ISAC website, was recently approved by the NIH- Institutional Biosafety Committee (IBC) for CoV-2 cell sorting. It is important to note that the protections and guidelines required to do these sorts properly and safely highlight the importance of the risk assessment and the involvement of your local biosafety office and/or IBC. In our case, COVID-19 patient samples (PCR negative) can safely be sorted in a BSL-2 laboratory with certain BSL-3 level practices in place during the sort BSL-2/3).

Two factors are critical among these practices: (1) the use of an aerosol management system (AMS), (2) respiratory protection for the operator at times when the cell sorting chamber must be opened, and (3) an SOP detailing procedure in the event of a nozzle clog.
In our facility, the CDC has approved sorting of PBMCs from TB infected patients with these additional procedures at BSL-2/3. Here, the infectious agent is considered a lower risk in these blood samples, which permits this analogous level of operation to be used for the sorting of these samples.  In samples where the infectious agent is definitely present or present at higher concentrations (e.g. bronchial lavages, etc.) a risk assessment must be performed to determine if a procedure may best be performed within a BSL-3 laboratory, or at a minimum with the sorter operational and certified within its own biosafety cabinet or other chamber within a BSL-2 laboratory.

This decision to increase the safety parameters (and likely the cost) is made to even further lower the risk of potential exposure to personnel during the sort. For instance, TB infected bronchial lavage samples where the agent is at higher concentrations requires sorting to be performed at the BSL-3 level containment. This example demonstrates the importance for a risk assessment as described in the 2014 ISAC Cell Sorter Biosafety Standards.
Recommendations* under the BSL-2/3 level as defined in the recent SARS-CoV-2 procedures:

  1. Reviewing a risk assessment plan with your biosafety representative, such as the Institutional Biosafety Officer (BSO), and/or the IBC.
  2. Testing of containment pre-sort using the Cyclex-d procedure to validate instrument containment of aerosols while sorting.
  3. Performing the sorting on a unit with an operational and HEPA filtered aerosol management system.
  4. Required use of PPE: Tyvek full body suit, gloves and shroud with HEPA filtered PAPR to be used at particular times during the sorting procedure.
  5. Measurement check for negative room air flow.**
  6. Clean surfaces before and after sort with 70% Ethanol or 10% hypochlorite.
  7. Record of containment measurement and safety checklist.

*Please refer to the full procedure for all other recommendations and details.
**It is critical to ensure that the cell sorting facilities are operated under negative pressure with respect to surrounding spaces, with exhaust air that is directly exhausted to the outside without recirculation to other spaces.  Work with your Facilities Office to verify the room pressurization.
With great science and tools available to us we will defeat SARS-CoV-2 and maintain a high level of public safety through vaccine development and deployment.


Stephen P. Perfetto
Chair, ISAC Biosafety Committee
Vaccine Research Center
Ben Fontes
Co-Chair, ISAC Biosafety Committee
Yale University


Cynthia Guidos says...
Posted Wednesday, May 20, 2020
Hi Steve and Ben - Can you please clarify your guidelines for sorting PBMC from subjects with active COVID-19 - ie who tested positive by PCR of nasal swab? Your message only mentions that it is safe to sort COVID-19 patient samples that are PCR negative - so I presume you mean samples from patients who have recovered and no longer have detectable virus? Did your committee identify safe procedures for sorting PBMC from patients with active disease, short of full BSL3?