The pristine X-ray crystallography data gathered by Rosalind Franklin played a crucial role in the discovery of DNA’s structure. Yet when the discovery was recognized by the Nobel Committee in 1962, the winners of the Nobel Prize did not include Franklin, who had died in 1958. Only recently has Franklin received some of the recognition that she deserves for her essential contribution to one of the biggest discoveries of the past century.
“We still have a lot of work to do, unfortunately,” notes Akiko Iwasaki, PhD, an immunologist at Yale School of Medicine and a fierce advocate for women in science. “Things have definitely gotten better since [Franklin’s] days” she tells GEN. But we still have a huge disparity in women representation—especially at the senior level. Iwasaki adds that we have to address what she thinks is the root cause of the problem—the academic culture and the unconscious (or conscious) bias against women and people of color that prevents these brilliant people from moving up the academic ladder.
To mark the centenary of Franklin’s birth, GEN sought to highlight scientists at the forefront of COVID-19 research—some of the most influential research currently being conducted—who are women. In this article, GEN speaks with researchers who are leading efforts to track SARS-CoV-2 genomes, to uncover host factors influencing COVID-19 progression, to develop saliva-based COVID-19 tests, and more.
Host factor finding
Working as a pediatrician in China, Qian Zhang, MD, wanted to understand why some children are more susceptible to infections than others. “Children are exposed to hundreds of pathogens every day,” Zhang tells GEN, “but only a very small proportion get really severe infections.” Zhang has been researching differences in susceptibility for the past decade. Notably, she performed postdoctoral work at the National Institute of Allergy and Infectious Diseases (NIAID) with Helen Su, MD, PhD. Afterward, Zhang became a postdoctoral fellow at the Rockefeller University, in the laboratory of Jean-Laurent Casanova, MD, PhD.
Working with patient samples, researchers in the Casanova laboratory look for rare, deleterious mutations that might govern susceptibility to infection. In particular, they look for monogenic variants, where a single defect makes an individual far more susceptible to infection. Zhang’s hypothesis for COVID-19 is that patients who are susceptible to less virulent respiratory pathogens will also be susceptible to COVID-19. By taking an unbiased approach, Zhang and colleagues may find genetic factors that have never been identified before.
Normally, Zhang analyzes children because it is in childhood that people usually experience infection for the first time. But COVID-19 is different, she notes, because “this infection is the first time for everyone.”
Zhang previously led the influenza team in the Casanova laboratory. So, taking on COVID-19 is a natural shift. She adds that many commonalities between the two lung infections have been established, and that many tools developed for flu research can be used in COVID-19 work. Besides, there simply aren’t any more flu patients coming in.
Zhang asserts that her group, like others, has adapted its work to the pandemic. Investigators normally work on well-defined infections. COVID-19, however, isn’t so well defined. Too little about it is known. For example, without key pieces of data such as a fatality rate, investigators who look for genetic lesions may be unaware of the lesions’ prevalence. “We have to change our analysis while the data are coming in,” Zhang explains.
How much hesitation did Akiko Iwasaki, PhD, have in moving into COVID-19 research? “None,” she says. “I knew the importance of speed and urgency.” She notes that she had learned the value of these attributes from her experience jumping into Zika.
Iwasaki, a professor of immunobiology and molecular, cellular, and developmental biology at the Yale School of Medicine and an investigator at the Howard Hughes Medical Institute, has spent the past few months trying to understand the immune response of COVID-19 patients. Iwasaki’s laboratory is working to develop real-time analyses of immune markers and cytokines that could sharpen patient assessments and even inform treatment
The biggest surprise, so far, has been “the role of interferon (IFN) in this disease,” asserts Iwasaki. For other viruses, such as influenza and rhinovirus, type 1 IFN has a protective role for the host. But SARS-CoV-2 seems different. Studies in a mouse model have shown that IFN contributes to the inflammatory response without shutting down viral replication. According to Iwasaki, this is unusual. In other viral infections, IFN can shut down the virus. But Iwasaki thinks that the IFN here is being induced “a little bit too late or in too small of an amount.”
Iwasaki’s main goal is to understand what type of immune response confers protective immunity versus the types that lead to disease. Because patients have diverse responses to SARS-CoV-2, the researchers are working to build disease trajectories that reflect patient-specific aspects of the immune response—cytokine or antibody production, T-cell response, viral load, etc. By conducting longitudinal sampling and following patients’ trajectories, the researchers hope to predict how patients will fare when they are admitted to the hospital. Ideally, she envisions a panel that could be ordered by a physician that would allow patients to be treated with a more personalized medicine approach, based on their immune profiles.
This analysis has never been done so extensively for an infectious disease, Iwasaki asserts, because “we never had the urgency to do this for other viral pathogens.” In 2020, thankfully, the technology exists to do this type of analysis in real time.
Another area Iwasaki has recently explored is sex differences in SARS-CoV-2 infection. By studying male and female immune responses, her group found one clue as to why males are reportedly more susceptible to COVID-19. In a preprint posted in medRxiv, Iwasaki and colleagues described how they investigated sex differences in viral loads, antibody titers, and cytokines in COVID-19 patients, and how they found that T-cell activation was significantly more robust in women than in men. Men who don’t develop a good T-cell response have worse disease outcomes.
Genome chasing in Basel
Emma B. Hodcroft, PhD, a postdoctoral researcher at the University of Basel, recalls agreeing to keep her supervisor’s project going while he traveled. She was to take charge in early February. Continuity was important because they had just started uploading sequences of SARS-CoV-2 into the online genomics engine Nextstrain—a collaboration started in 2014 to track flu virus diversity and help predict the next flu strain.
Because Nextstrain has hubs in Europe and the United States, the absence of data uploads at the University of Basel would hamper runs during the European daytime. She has, in her own words, “never looked back.”
The pipeline analysis that Nextstrain runs makes phylogeny from viral genome mutations. “Phylogenetics is a field full of limitations,” Hodcroft notes. She adds that the field is “particularly troublesome because it’s beautifully dangerous”—the picture that is drawn is always less certain than it looks. While it is tempting to start telling stories about these sequences, she says, one must be cautious. The roughly 40,000 cases currently in the system is a drop in the bucket compared to the number of COVID-19 cases. “There is much more likelihood that we haven’t sampled someone than we have,” she admits.
As borders reopen and travel resumes, continued genomic analysis, Hodcroft tells GEN, could uncover details about virus transmission, including transmission routes. She will be keeping a close watch while cautiously communicating new findings. These data are of interest to a large and growing audience, and members of this audience may misinterpret (intentionally or not) what they hear. Deciphering the uncertainty that surrounds the field of phylogenetics requires expertise—something not all scientists who have ventured into the world of COVID-19 phylogenetics possess.
Hodcroft gets upset when misinterpreted data spark a storyline that needs to be debunked. “I don’t think that telling these false stories that panic the public helps anybody,” she declares. “There is plenty to be worried about with this virus.”
COVID-19 is the second SARS epidemic Rachel Graham, PhD, has worked on since she started her graduate work in a coronavirus lab in 2002. Currently working in a large coronavirus laboratory at University of North Carolina (UNC) led by Ralph S. Baric, PhD, she says that Baric’s group has scaled up “from what was a busy program to an extremely busy program.”
Graham uses large sequence sets to study how the virus’ transcriptional program contributes to replication and virulence. As the virus mutates, its subgenomic RNAs are produced in different ways, indicating that the transcription itself may be a virulence factor. She says that as the population acquires more herd immunity, researchers “may see a lot of transcriptional differences in the virus,” and these differences could result in changes in virulence. SARS-CoV-2 will be the first virus where this relatively new idea in virology will be examined in detail.
Lisa Gralinski, PhD, assistant professor of epidemiology at UNC, has been studying coronaviruses for 12 years. Her current work centers around virus host interactions, specifically in animal models such as the humanized ACE2 transgenic mouse. The mouse was developed at UNC in the mid-2000s after the first SARS outbreak. Researchers had even started the paperwork to cryopreserve the mouse just before COVID-19 struck. Quickly adjusting to COVID-19, they changed course and started as many breeding pairs as possible.
Graham and Gralinski may be new to the UNC faculty, but they are veterans in a rapidly growing field. Gralinski notes that six months ago, “few people worked in coronavirus.” Unlike SARS, SARS-CoV-2 is not currently a “select agent”—which means that more people are free to work on it. Both Graham and Gralinski welcome more hands on deck, but they’ve been alarmed by some of the ways that people are working with SARS-CoV-2 in their Biological Safety Level 3 (BSL3) labs. SARS-CoV-2 requires special precautions and security due to the high titers used in experiments.
Spitting it out
In early March, Anne L. Wyllie, PhD, an associate research scientist in epidemiology at Yale, was chatting with her colleague, Nathan D. Grubaugh, PhD, an assistant professor of epidemiology. He was lamenting the level of SARS-CoV-2 RNA detection in patient samples. Wyllie drew his attention to a method she had been using to detect Streptococcus pneumoniae from saliva samples of asymptomatic carriers.
Her method, which used Thermo Fisher’s MagMAX Kit for Nucleic Acid Extraction, had worked so well for Wyllie that she suggested that Grubaugh use it to test for SARS-CoV-2. Wyllie recalls that when Grubaugh and colleagues compared the methods, Wyllie’s method “blew the other one out of the water.” Ultimately, the MagMAX Kit and the King Fisher platform (which happens to be named “Frankie” in the lab, in honor of Rosalind Franklin) became the Grubaugh laboratory’s method of choice. Wyllie is now co-lead on the COVID-19 project with Grubaugh.
Wyllie was the lead author on a preprint uploaded to medRxiv showing that saliva samples offer a more sensitive and consistent alternative to nasopharyngeal swabs for COVID-19 testing. Saliva samples, the paper argued, should be considered a viable alternative to nasopharyngeal swabs to alleviate COVID-19 testing demands. This could be key to meeting public testing demands.
Ready and waiting
“We knew a pandemic would come … and we knew we would have to be ready,” says Viviana Simon, MD, PhD, professor of microbiology at Mount Sinai School of Medicine. A decade after starting her virology laboratory in 2006, Simon and her colleagues built the Virology Initiative in 2017, which allowed real-time access to samples from patients with viral infections. The goal, she explains, was to study emerging viruses in New York City—viruses such as Zika, chikungunya, and dengue. Having the initiative established allowed the laboratory to “spring into action” when the pandemic hit. Simon notes that a virology infrastructure capable of such responsiveness would not be easy to build in the middle of a pandemic.
Simon remarks that there was never any doubt that there would be a pandemic: “We thought that it would be a respiratory virus and figured that it would be an avian influenza strain.” Any pandemic would almost certainly come through New York City, which serves as a gateway not just for people, but for viruses from all over, she says.
Simon tells GEN that her team heard rumors about a new virus in December and began preparing. The moment the first sequences were released in mid-January, she recalls, “We ordered primers.” And then? Simon and colleagues “waited and waited,” she says, for the first case to show up. The first COVID-19 case was diagnosed at Mount Sinai on February 29. Only then could the Simon team grow the virus and sequence it.
Simon’s team has analyzed the genetic diversity of SARS-CoV-2 circulation in New York City and how the virus was introduced. The team is also interested in assessing the durability of antibodies and determining the degree to which antibodies are protective.
The size of Simon’s laboratory has doubled, primarily due to a temporary influx of postdoctoral researchers and technicians, volunteers that come from laboratories shut down by COVID-19. This “COVID task force” jumped in to support the COVID-19 research being done at Mount Sinai. Simon remarks that when temporary personnel start returning to their own laboratories, she will be busy “hiring more people.”
The dedicated researchers highlighted in this article have been working almost nonstop for months, motivated by a shared passion to beat back a virus that has taken over the world. These researchers represent different scientific backgrounds, and they are tackling different facets of the virus. But they would no doubt recognize common elements in their professional development. For example, the challenges that come with being women in male-dominated fields. Hopefully, it will not take decades to recognize and celebrate the contributions of some of these outstanding scientists.