In the Eye of the Storm: Researching COVID-19

Two years ago, University of Vermont Cellular, Molecular, & Biomedical Sciences Ph.D. student Hannah Despres was working in the Botten Lab and primary focused on research of lymphocytic choriomeningitis virus (LCMV)—a largely understudied tropical virus that causes meningitis/encephalitis. Then, SARS-CoV-2 began its first deadly journey around the globe and, like many researchers, Despres’s research shifted quickly.

Now, Despres works in the lab of Assistant Professor of Microbiology & Molecular Genetics Emily Bruce, Ph.D.

Alpha, Delta, Omicron—Despres’s research in the Bruce Lab has followed the trajectory of the virus, from one variant-of-concern to the next.

Below, we asked her about her research and what it’s like to work with SARS-CoV-2 samples all day, and then walk out of her the lab and into a world still very much in the midst of its battle against the virus.

(Left) Hannah Despres collects phosphate buffered saline (PBS) in a container. (Middle) Despres uses a multi-channel pipettor to put a colormetric developing reagent into the cells of the viral focus assay plate. (Right) Despres and UVM Master of Public Health student Madaline Schmidt look at fully developed plates for blue dots – which indicate the presence of infected cells.

Before the Pandemic

What were you working on prior to the COVID-19 pandemic?

I was researching a different virus called lymphocytic choriomeningitis virus (LCMV)—a tropical virus—and how post translational protein modifications might impact its growth. LCMV is known for making “dummy” virions (ones that aren’t infectious), called, “defective interfering particles.” The scientific community has not yet been able to determine exactly how these virions are made—a biological feature that could prove significantly impactful in approaches to possible prevention and treatment of Lassa fever, the hemorrhagic fever caused by Lassa mammarenavirus (LASV).

Lassa fever is endemic in West Africa and makes up roughly 12 percent of hospitalizations for the region. 20 percent of people infected with Lassa experience hemorrhaging, respiratory distress, and neurological problems, and 30 percent develop deafness.

Lassa is difficult to study because it is a biosafety level four (BSL-4) agent, which requires the highest level of containment a pathogen can have. There are fewer than 10 of these labs in the United States and the training required to work with BSL-4 pathogens is extensive.

Due to the difficulties and dangers posed by working with Lassa, our research utilized LCMV as a model virus, because it is similar to Lassa, but only a BSL-2 pathogen.

Pivoting to COVID-19

When did your research pivot from LCMV and Lassa to SARS-CoV-2, the virus that causes COVID-19?

The Botten Lab, which I was a member of, pivoted to focus on SARS-CoV-2 in March 2020. Much of our early work was focused on helping improve or simplify diagnostic testing.

In spring of 2021, the Bruce Lab officially opened its doors and I began to work on SARS-CoV-2 research with Dr. Bruce in July 2021. Initially, our research centered on polymerase chain reaction (PCR) testing. With a traditional PCR test, before COVID-19 can be detected in a nasal swab sample, the RNA has to be extracted from the sample first. In the early days of the pandemic, this posed a significant hurdle to testing initiatives, when there was a massive shortage in the chemicals necessary to complete RNA extraction.

To address the complications posed by this shortage, researchers at the University of Vermont (UVM), UVM Larner College of Medicine, and University of Washington teamed up to figure out how to detect SARS-CoV-2 in nasal swab samples without extracting RNA first. Their findings were published in a peer-reviewed paper in PLOS Bio in October 2020.

How did your prior knowledge and research of viral hemorrhagic fever viruses (VHFs) help in your transition to researching SARS-CoV-2?

Viruses vary in size, shape, how they replicate themselves, and more! I already had a solid base in virology, and more specifically, enveloped RNA viruses (which SARS-CoV-2 is), so I already knew how to do a lot of the essential skills required to work with these types of viruses.

I was already confident in my basic laboratory skills, which is important when you’re working with infectious pathogens. However, SARS-CoV-2 is a BSL-3 virus, and I had only ever worked with BSL-2 and BSL-1 pathogens before. Before I was able to work with the virus, I had to be specifically trained how to do high containment work.

This video, published on Aug 6, 2021 (before the emergence of the Omicron variant) from the Centers for Disease Control and Prevention (CDC) explains how viruses mutate and virus variants emerge.

From Diagnostics to Variants-of-Concern

Eventually, the research you were working on in the Bruce Lab regarding diagnostics transitioned to comparing different SARS-CoV-2 variants-of-concern. What is a “variant-of-concern?”

A SARS-CoV-2 variant is any version of the virus which contains mutation(s), or changes in the genetic code. A variant is classified as “of concern” when there is scientific evidence to show that it is more transmissible, makes people sicker, or previous preventive measures and treatment are significantly reduced (this includes vaccines, treatments, and general testing).

When new variants began being identified, we pivoted to comparing how each variant behaves. We can look at things like how well they grow or how they do at certain temperatures. If there is a trend between certain markers (genetic changes and the effect they have on our tests in the lab) and the potential risks of different variants, our research can be used as a potential predictive tool for future variants.

(Left) A photo of a SARS-CoV-2 viral focus assay (a test used to determine how much virus is in each sample). In the photo, each distinct blue dot within the individual wells represents one SARS-CoV-2 virion. (Right) A close-up view of an individual well depicting a sample from a PCR test with SARS-CoV virions present in it.

The Rise of More Infectious Variants

Eventually, you began researching the infectivity of the dominant variants of COVID-19 – Alpha versus that of the Delta variant which became the dominant variant of concern in August 2021. How did you go about doing so?

We study the variants using clinical patient samples. When a person infected with SARS-CoV-2 gets a nasal swab PCR test, we can use the leftover sample to grow the variant of the virus which they were infected with. Since people have been getting PCR tests throughout the entire pandemic, this has allowed us to collect samples from a variety of SARS-CoV-2 variants.

Once we identify which variant the patient has, we confirm the variant using Next Generation Sequencing (NGS). NGS is a way of identifying all the genetic material within a sample, the string of nucleotide ‘letters’ that make up the information that is the viral genome. In our case, we’re talking about ‘reading’ all the genetic material within a virus. NGS lets us know which variant we have, and if it has any unusual mutations for that particular variant.

We can also use these patient samples to study the properties of the virus coming directly out of patients (ex: how much virus is in the sample).

In our variant research, we sought to determine the relationships between levels of viral RNA and infectivity for the SARS-CoV-2 Alpha, Delta, and Epsilon variants. In other words, was the increased infectivity of Delta in relation to Alpha and Epsilon due to higher levels of viral RNA present in hosts (SARS-CoV-2 patients)?

What did your research find?

Our findings were recently published in a peer-reviewed paper in Proceedings of the National Academy of Sciences of the United States of America (PNAS), and put succinctly, what we saw was that people infected with Delta had almost six times more virus in their nasal swab samples than people infected with Alpha.

Essentially it means that people infected with Delta have more virus within their noses than people infected with Alpha. This makes a lot of sense since we saw the Delta variant overtake the Alpha variant this past summer.

How are these findings useful for the medical and research community as we continue to face this pandemic?

A lot of the efforts towards SARS-CoV-2 so far has been to monitor spread, new variants, and how this information impacts the success of the vaccines. All this information is essential but does not provide a lot of details about how the new variants are outcompeting the original SARS-CoV-2.

Our research group trying to figure out important questions like “what features about the Delta variant allowed for it to beat out the Alpha variant?” By understanding what biological features of the variants give them their traits, we can assess new variants for infectiousness and severity of disease more quickly when they inevitably show up.

Now that Omicron is becoming the dominant variant-of-concern, will your research focus on Omicron?

Yes, we’ve already added Omicron to our repertoire and are comparing it to wild-type, Alpha, and Delta, specifically in terms of characteristics related to infectivitiy.

Hannah Despres poses for a photo in the Bruce Lab at the UVM Larner College of Medicine. The photo was taken in early August 2021, before emergence of the Omicron variant and updated guidelines regarding use of KN95 masks rather than cloth masks.

Researching SARS-CoV-2 While Living Amidst It

What has it been like to be on the frontlines of the pandemic as a graduate student? We often hear about medical professionals treating patients as being on the frontlines, but scientists and researchers are too – albeit, a bit more behind-the-scenes.

It’s been an experience distinct from any other. Research moves at wildfire pace and the variables you’re working with are constantly changing. I enjoy doing my part in the pandemic and find the day-to-day variability enthralling. There is so much research going on globally it can be difficult to keep up to date!

On the other hand, it sometimes is exhausting to have COVID-19 be the focus of my workplace and my personal life as well.

What are some of the questions you get asked regularly about COVID-19 and the pandemic by family and friends and how do you answer them?

Most of the questions I get are about public health measures. Things like, “How well do the rapid tests work?” or, “Okay, so how worried should we be about Omicron?” and, “What is the safest way to do a holiday gathering?”

I answer the questions as completely as I can. Most of the time I look up the appropriate data in journal databases such as PubMed, and go from there. Unfortunately, some of the time the answer is, “We don’t have a lot of data on that right now”- this is especially true when a new variant is first detected.

Do you have any recommendations for how the public might seek valid, trusted, peer-reviewed data to answer these types of questions for themselves? What are some of the pitfalls of people doing “their own research” about the virus?

The most reliable findings are those which are found by multiple groups or organizations. Corroborating information from multiple reliable sources is a good way to ensure the validity. This can come in the form of peer-reviewed journal articles or public health organizations (ex: CDC, WHO, etc.).

People start to run into issues when the information is only coming from a single source and other experts in the field can’t back up the information with similar findings.