The Science Behind Studying Viruses
What Tools Do Scientists Use To Study Viruses? – Visual Description Transcript
[Animated image of a man in 17th century dress and a large wig next to an early microscope—a device involving mirrors and candles.]
NARRATOR: In the late 17th century, Robert Hooke was trying to get an ant to hold still.
[A close-up inset view of an animated ant pops up next to Hooke. It scuttles out of frame.]
NARRATOR: Hooke was an early user of a new tool called the compound microscope and was seeing some of humanity’s first glimpses into tiny worlds.
He looked at everything from bread mold to his own urine to insects, like the ant.
[Inset views show archival etchings depicting close up views of mold, snowflake-looking crystals of urine, and finally, the animated ant.]
NARRATOR: But when recording his observations, the ant—perhaps unsurprisingly—refused to stay put.
[The animated ant sits in an easy chair, reading a book entitled Micrographia, while a large human hand serves it a drink.]
NARRATOR: Hooke managed to temporarily knock it out with a few drops of brandy and immortalized it in the pages of a book called Micrographia.
[The scene transitions back to Hooke’s compound microscope. Its interior dissolves into a view of an underground ant colony and the camera zooms in.]
NARRATOR: Sometimes, tools like Hooke’s microscope open entirely new fields of science to explore.
[A microscope lens clicks into place, as we have an even closer view of an ant. The lens clicks again, and we see dozens of animated viruses of many different shapes and sizes.]
NARRATOR: And that’s just what’s happening right now when it comes to viruses—new tools and technologies let us peer into worlds that would have been impossible to see even a few decades ago.
[The microscope lens clicks again and the virus virions now appear even larger and more detailed.]
NARRATOR: These tools let us view things on different scales, each a window into how a virus works.
Essentially, a virus is just a piece of genetic material wrapped inside a shell.
[The camera pushes into the center of a Herpes virion, and the microscope lens clicks again. An uncoiling spiral of DNA appears.]
NARRATOR: So, let’s start at the level of DNA with a technique called genomic sequencing.
[The word “GENOME” floats above an animated strand of DNA.]
NARRATOR: A genome is all the genetic material inside an organism—the set of DNA or RNA instructions for how it looks, works, and grows.
Humans have a genome. Ants have a genome. Even viruses have a genome.
[An illustrated human, ant, and cartoon virus (with arms and legs) jauntily walk along the DNA strand, holding up tiny pieces of DNA or RNA.]
NARRATOR: And genomic sequencing lets us decode all that information.
[A strand of RNA spits out a line of A, U, C, and G letters.]
NARRATOR: This is what a decoded genome looks like—a string of letters.
[The screen fills with dozens of As, Us, Cs, and Gs.]
NARRATOR: You may be thinking, “Hmm, that still looks like…code.” And you’re not wrong.
[The letters begin scrolling up the screen. Some sections change to a different color.]
[DIGITAL COMPUTER CALCULATING SOUNDS]
NARRATOR: All the combinations of letters still have to be analyzed to understand what we’re seeing.
But over the last few decades, we’ve gotten pretty good at doing that and doing it quickly.
[The scrolling letters rapidly speed up and wipe off the screen, revealing another field of hundreds of letters. The scene pulls out farther and farther away, showing thousands of As, Cs, Gs, and Us.]
NARRATOR: This is the genome of SARS-CoV-2, which causes COVID-19: about 30,000 letters.
[Hands quickly sweep around the face of a clock dial.]
NARRATOR: It took less than 48 hours to decode.
[A woman sneezes and the camera follows the trajectory of her sneeze, passing silhouettes of people walking, talking, and sitting together. As the scene moves by, the silhouettes fill up with letters representing genetic code and each figure has a short sequence of letters in a different color.]
NARRATOR: Using genomic sequencing, we can now track a virus’ evolution almost in real time—as we have during the pandemic. We can understand how it spreads and raise alarms when dangerous variants arise.
[The highlighted sequence of letters inside one silhouette is different than all the others. Short, agitated lines surround the figure.]
[LOW, PULSING ALARM]
NARRATOR: Understanding a virus’ genome is key to understanding how it works and necessary for making diagnostic tests and vaccines for threats like COVID-19.
[The screen again fills with letters. Certain lines are highlighted and inset images shoot out: computer models of tiny viral proteins of different shapes. They are labeled NSP1 Protein, ORF3a Protein, and Spike Protein.]
NARRATOR: Ok, so we can read a virus’ code.
[Scene transitions to an illustration of the SARS-CoV-2 virion—a sphere with spiky, cauliflower-like protrusions emerging from its surface.]
NARRATOR: Let’s zoom out to the next level: understanding its structure.
[The microscope lens clicks by and a smaller version SARS-CoV-2 sphere floats above the outstretched hand of a researcher wearing a mask.]
NARRATOR: Figuring out how a virus’ structure allows it to infect cells can help researchers develop defenses against it—things like vaccines and antiviral drugs.
[A thought bubble pops out from the researcher’s head. Inside are illustrations of a syringe and pill capsules.]
NARRATOR: But viruses are small. Too small for a conventional microscope.
[The floating virion shrinks down in size until it can no longer be seen. We cut to a researcher looking through the eyepiece of a tabletop microscope.]
NARRATOR: So, one way we peer into their minuscule worlds is with a technique called x-ray crystallography.
[The researcher at the microscope morphs into an abstract form that rotates and becomes an “X.” The words “X-Ray Crystallography” appear.]
NARRATOR: Scientists create crystals from a virus’ proteins, fire x-rays at them, and measure how the x-rays scatter.
[A cube is labeled “Virus Protein.” Wavy lines representing x-rays bombard the cube and bounce off. Points of impact create what looks like an abstract pattern, but their points resolve into the shape of a viral spike protein.]
NARRATOR: Those measurements can reveal detail on an atomic level.
Zoom out again.
[The microscope lens clicks into place and the scene changes to a researcher working in front of a monitor, with two large machines behind her. On the monitor, two SARS-CoV-2 virions appear.]
NARRATOR: Another imaging tool is the electron microscope.
Electron microscopes bounce a beam of subatomic particles off a sample’s surface to magnify objects up to 50 million times, giving us a look at the shape of the overall virus.
[We zoom into the electron microscope and photo archival images of different viruses appear: Polio, H1N1 Influenza, Rabies, Ebola. Their shapes and textures are diverse.]
NARRATOR: It's a view into the microscopic world that’s a million times better than Robert Hooke ever saw.
[The microscope lens clicks again and we see an electron microscopic image of an ant’s head. A small circle with Robert Hooke bounces in from the side.]
NARRATOR: So, that’s the micro level, but we can zoom out even further—to a macro scale, understanding how human populations are infected by viruses.
[The microscope lens clicks by, taking us wider and wider in scale. We begin with a close up of an ant running on a blanket. We zoom out to see two people sitting on the blanket. And zoom out again to an overhead view showing their blanket as one of many in a park.]
NARRATOR: Mathematical modeling lets us look at big trends as they unfold, and gives us a window into possible futures. How might a disease spread? How will a virus mutate?
[The picnic blankets and people morph into abstract forms. The forms are connected by networks of lines and wavy shapes.]
NARRATOR: Using estimates for things like the total number of infections in a city, or the percentage of people wearing masks, researchers run their disease models many times to determine likely outcomes.
[Researchers stand beside a giant, fantastical machine. Numbers and percentages flicker on various screens, duct pipes connect various modules, and workers input data through slots. At the end of the machine, sheets of paper print out into a person’s waiting hands. A group of people talk in a board room, pointing at a board displaying networked abstract forms.]
NARRATOR: These models can help public health experts manage the spread of a disease.
But new diseases bring many unknowns and humans can be hard to predict.
[A group of researchers compare notes and look at papers. Above their heads, thought bubbles contain a SARS-CoV-2 virions, a surgical mask, and question marks.]
NARRATOR: So, as we’re tested for COVID-19 and get our shots, researchers continually refine their models.
[The camera again pans across the fantastical machine. This time, one module connects to a giant funnel labeled “NEW DATA” where numbers trickle down into the pipes.]
NARRATOR: Rather than just predicting likelihoods, researchers can use data collected by front-line health care providers to get a better picture of what’s actually unfolding.
[The scene transitions back to the researcher with the SARS-CoV-2 virion floating above her hand. This time, her thought bubble features a differently colored version of the virion.]
NARRATOR: Moving forward, we may use another type of predictive modeling to help protect against different strains of viruses like SARS-CoV-2.
We already do this for the annual flu shot.
[A nurse wearing a surgical mask vaccinates a masked patient.]
NARRATOR: Using genomic sequencing, researchers track flu infections all over the world, noting how different strains are evolving and which vaccines have worked most effectively against them.
[A globe rotates in front of a field of genomic code. The outlines of the continents are filled with genomic sequence letters, virions, and syringes.]
NARRATOR: That modeling, which incorporates on-the-ground data collection, helps determine the make-up of our annual flu shot and can steer resources to where they’re most needed.
[A pipe emerges from the side of the globe and the “NEW DATA” funnel feeds numbers into it. As the camera pans right, it reveals that the pipe is the body of a syringe. An elderly man seated near a pregnant woman receives a vaccine.]
NARRATOR: We may see something similar with COVID-19 or other diseases in future years.
[The scene of people shrinks in size to become a small screen on the side of the fantastical modeling machine. Again, we pan across—this time the machine has different, futuristic modules.]
NARRATOR: Meanwhile, researchers are making our existing tools faster and stronger.
And completely new technologies are on the horizon.
[The scene returns to an aerial view of people sitting on picnic blankets, enjoying the park. The camera pulls further and further back.]
NARRATOR: Who knows what discoveries lie ahead?
[Credits roll.]
Profile: Jude Kong, Disease Modeler
Dr. Jude Kong has spent the COVID-19 pandemic building models. Not the physical kind—the kind that run on computers.
During the COVID-19 pandemic, these models are saving lives. Epidemiologists use them to monitor the spread of the pandemic, to evaluate efforts to control it, and to guide policymakers as they make decisions about measures like vaccination, school closing, and allocating healthcare resources.
Kong, an assistant professor in the Mathematics and Statistics Department at York University in Toronto, Canada, grew up in Cameroon, the third of five children of a single mother, a subsistence farmer. As a little boy he would finish his math homework quickly, then help his friends with theirs. He worked his way through college as a secondary-school math teacher.
The year he graduated, he attended a workshop on disease modeling, something he didn’t know much about. But he had plenty of firsthand experience with infectious diseases—malaria in particular, which had taken the lives of his aunt and several of his cousins.
“People were dying a lot. People I knew, loved ones. I wanted to prevent that from repeating itself, within my community, anymore,” he says. Here were mathematicians working to figure out how diseases spread—and how to stop them. He knew this was what he had to do.
“A model is a representation of a system that can be used to explore its behavior,” says Kong. Kong and his colleagues build models and use them to make recommendations to policymakers.
The models themselves are key, of course. But to work, they need the right data—and plenty of it. Without locally relevant data, says Kong, the models will not produce useful results. That’s why it’s vital for modelers to collaborate with community leaders.
“You ask what they need in their communities. As a scientist, as a modeler, you have the tools, but you don't know the problem," says Kong. "[The community leaders] describe the problem to you. You work with them and present the tools. Then you tell them what data to collect. They get that data, it goes into your model, and it ends up informing policies in the right direction, because the data was informed by the community. And there's a feedback into the community, too.”
Kong and his colleagues used this approach to study the effects of what he calls self-medication on the spread of COVID-19. By self-medication, he means unproven treatments that some people believe will cure or prevent the disease, which they rely on instead of on proven treatment.
In the United States, for example, some people self-medicated with ginger, hydroxychloroquine, or Ivermectin. In Ghana, some believed a particular kind of green tea would keep them safe or cure them. In Cameroon, it was a certain very strong alcoholic drink, or local traditional medicines.
“You need to respect that people will believe in things because that’s what defines them, what makes them unique. But you need to take that into your model and account for that,” says Kong.
He and his colleagues built a model that incorporated self-medication, something previous models had not done. They took their results to policymakers there, who worked with community leaders to address the issue. “Those community leaders will know how to discourage such practices within their communities,” he says. “They can use local relationships, local radio stations, and so on. It's very important that local community leaders are involved in the entire process.”
It's very important that local community leaders are involved in the entire process.
Information from local communities is especially important because differences in communities’ history translate into disparities in health outcomes. That’s particularly true during a pandemic. COVID-19 is spreading differently between different racial and ethnic groups based on their susceptibility, says Kong, due to historical factors such as crowded, segregated housing.
“If you assume that one size fits all the country,” he says, “you will not be able to capture the dynamic, because you are ill-informed through the data that you have.”
Kong stresses that disease modeling is a dynamic process. As a pandemic spreads, its course will change. Interventions, treatments, public messaging, public behavior, vaccination rates—all change. Even the disease itself will change, as new variants arise.
“If you keep working with community leaders, they will inform you, ‘Oh, things are changing in this direction. How do we address this?’ And then you come in and you adjust your model,” says Kong. “That is the right way to go.”
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