The Impact of SARS-CoV-2 on Research & Flow Cytometry

Two researchers wearing face masks in a UCLA laboratory

Dr. Francisco Ibarrondo and Leila Zamani in their UCLA lab.

Coronavirus pushed researchers across the world to respond to the COVID-19 pandemic. Francisco Ibarrondo, Ph.D., studies immune cell response to chronic viral infections. During our discussion with Ibarrondo, he shared how he shifted research topics and the way he works in reaction to SARS-CoV-2.

How did you get involved with SARS-CoV-2 research?

On March 11, the university (UCLA) asked for volunteers from researchers, nurses, clinicians, for a large project about studying the effects from SARS-CoV-2. As a lab, we sat down and discussed our thoughts, and we said yes to working on the group project. Everything was started from scratch, from creating a testing site to a site for sample collection to designing and executing the basic science experiments around the disease and virus. There was not much in the beginning for SARS-CoV-2 research, so we purified proteins and created antibody panels for flow cytometry. We also got an additional flow cytometry analyzer, the Attune NxT Flow Cytometer, to analyze all the blood samples.

What were you working on before SARS-CoV-2?

I was working on the role of immune cell exhaustion and senescence in HIV infection and aging. HIV causes chronic infection and therefore drives immunosenescence. It was a basic science research project as compared to the clinical nature of our current COVID-19 project.

Can you describe your response to studying SARS-CoV-2?

I shifted my research and hypothesized that a population infected with SARS-CoV-2 and exhausted and senescent cells will respond poorly. The senescent B cells may give a more explosive response since it produces less tuned antibodies and may be more inflammatory.

How are you conducting your experiments?

We use the Attune NxT Flow Cytometry analyzer to see immune cells populations and response from samples with SARS-CoV-2. Samples with a larger viral load correspond to those with a greater immune response as determined by their IgM and IgG levels and those levels will deteriorate over a period of time [1]. For this study, we will use blood that is collected in a cohort of volunteers from healthy to sick. We are especially interested in those infected with SARS-CoV-2 over a time course.

Can you describe how you create your immune cell panels?

Instead of a large, multi-color panel, I have broken down my panel into three 13-color panels to look at innate cells, T cells, and B cell responses. I optimized my panel for two months to have compensation values under 45%. This gives me clear plotted data (the data should be a circle that if you draw a quadrant through, it would form perfect 90 degree angles and this shows well compensated data) that is standardized and reproducible. I also look at these populations on gated live cells.

Is it difficult to perform your work? Has SARS-CoV-2 changed the way you work in the lab?

No, it is not difficult to work. We maintain social distancing and use precautions. There is now one person per aisle and we always wear a mask. We take turns in the tissue culture room so there is only one person in there, unless we are processing blood, then there are two. Large group meetings are now online. When we have lab meetings, the six of us are in a large conference room. We are so spread apart it is difficult to hear each other. Also, lunch is no longer in the cafeteria but now catered and eaten separately, and I must drive my car to work instead of taking the bus!

Has the pandemic impacted your work? Stay prepared like Dr. Ibarrondo with a lab minifridge so that you can go with the flow.

SARS-CoV-2 is requiring researchers to be ready for anything while maintaining social distancing. One solution is to have mini-supply center in your lab next to your Attune NxT Flow Cytometer. What should you keep in your 4°C fridge?

Attune NxT flow cytometer buffers—keep your flow cytometer going through the pandemic and the night by having buffers in stock.
Performance Tracking beads—run these daily to understand your flow cytometer performance.
Compensation beads including UltraComp eBeads Plus—identifying immune cells can require many single-color controls. Having these beads on hand can save experiments if there are not enough cells for controls.
Invitrogen antibodies that are commonly used in your lab—why wait? Keep the antibodies you need to identify the immune cells in your experiment close at hand.
Fixation and Permeabilization buffers, including Foxp3 Transcription Buffer Set—want to minimize labmates from touching the same bottle? Stow a few bottles when possible and keep your bottle pristine.
Gibco cell culture media and Dynabeads or MagniSort beads—when you don’t have enough cells, stimulate and culture to collect enough events.