What is Genomic Epidemiology?
Before the pandemic, many of us had never heard of an epidemiologist, let alone a genomic epidemiologist. Some may still be scratching their heads. Well, worry not! We are here to help decode the work of these vital disease detectives.
Let’s start with epidemiology. Epidemiologists study the patterns and causes of diseases like COVID-19. Genomic epidemiologists zoom in a bit further, studying the genomes of the pathogens that cause disease. Normally, when we hear the word “genome,” we think of our own DNA instructions that make us who we are. We think of hair color, eye color, and all of the traits that make us unique. However, we are not the only ones with a genome. Just as our DNA provides our bodies with the blueprint needed to function, viruses have genetic material as well. It can be in the form of DNA, or in the case of SARS-CoV-2, the virus that causes COVID-19, a similar nucleic acid called RNA. The genetic instructions of a virus not only make it a virus, but contain the information to build more copies of itself inside a host.
So, what do genomic epidemiologists do with the genetic instruction book of a virus? What information does it hold that can help these scientists track a pandemic, for example? Well, they can use one key characteristic of genomes to their advantage–they change.
Time for an activity break. Ready for a game of telephone? Let’s imagine that the DNA of a virus is written as the following sentence: “The small orange cat played with a blue ball of yarn.” Now, let’s play! Whisper that sentence to the person next to you. Then, have them pass the message along to someone else. Repeat with as many people as you can, and remember, you can use an actual telephone to include friends and family that might be farther apart right now. Now for the moment of truth. Ask the last person to repeat the sentence to the person who started it all. Did the sentence stay the same? If not, what changed?
We tried this out with some of our staff here at the Connecticut Science Center and somewhere along the way, we made a few mistakes. What started out as, “the small orange cat played with a blue ball of yarn” became, “the tall orange bat played with a blue doll at the farm.” Take a moment and conjure that image up in your mind. There are definitely some differences. What do you think happened? Do you think all of the mistakes happened at once?
It would be extremely unlikely for all of those changes to happen at once, unless someone really let their imagination get away from them! More likely, they accumulated over time. One person might have heard bat instead of cat, while another heard farm instead of yarn. Let’s call these changes in the sentence mutations. For a disease detective, these are vital pieces of evidence. Just as changes occurred as we passed the sentence from one person to the next, as a virus replicates and spreads, changes add up in its genetic instructions. Genomes are copied over and over again, inevitably resulting in some errors. Think about typing on a computer. If you type the same sentence over and over, you would eventually make a mistake, or a change. These mutations, or changes in a genetic sequence happen naturally all the time as DNA is copied. Genomic epidemiologists can track these mutations to trace the path of a virus, see how long it has been circulating in an area, or even work backwards to the strain that started it all.
The Use of Genomic Epidemiology in the Fight Against COVID-19
Today, genomic epidemiologists are working on a larger scale than ever before to combat COVID-19. By looking at the genomes of SARS-CoV-2 that have been isolated from patients around the globe and counting the number of mutations, they have been able to make some amazing conclusions. While SARS-CoV-2 is a little more careful when copying its genetic code than the flu, which develops mutations at a faster rate, it still accumulates about 2 changes every month. The location of these changes are important. For example, a change in the instructions to build the spike protein the virus uses to attach to and get inside our cells would matter more than others. Would a change here make the virus better able to cause an infection? Well, that is just what genomic epidemiologists, along with the help of some graduate students, studied.
These students at the University of Illinois tracked mutations in SARS-CoV-2, starting with the first genome published in January. They ended their study in May, more than 15,300 genomes later. They found several changes that were particularly illuminating. According to researcher Tre Tomaszewski, the virus’ spike protein “was a completely different protein at the very beginning than it is now.” It is essentially a combination of random mutations and natural selection occurring before our very eyes. One particular mutation in the spike protein spread widely during March and April. Though this is still being studied, scientists hypothesized that in order for the mutation to establish itself in the viral population so successfully, it might help the virus in terms of its ability to infect a host. Two other mutations seem to have gone hand in hand, and are pretty prevalent in the viral genomes we currently see. According to Gustavo Caetano-Anolles, professor of bioinformatics at Illinois, “all three mutations seem to be coordinated with each other. They are in different molecules, but they are following the same evolutionary process.”
So we have seen the wealth of information a genome possesses and how disease detectives can use it to solve scientific mysteries, but how can scientists visualize all of this information? They use phylogenetic trees. This is a diagram, or a branching “tree” that displays the evolutionary relationships between different organisms. In the tree below, adapted from Nextstrain and featured in the article below from the American Chemical Society, samples “A” through “E” are all viral genome sequences. The colored circles represent mutations the virus has accumulated over time. Genomic epidemiologists construct and use these trees to see how the virus has changed over time, with the leftmost branch being the oldest version.
One thing is for certain–these amazing disease detectives are working tirelessly to continue to study SARS-CoV-2 as it changes, as well as other pathogens. Perhaps one day you will join their ranks as the newest genomic epidemiologist.
“How genomic epidemiology is tracking the spread of COVID-19 locally and globally”
“Tracking evolution of SARS-CoV-2 virus mutations” https://www.sciencedaily.com/releases/2020/10/201026114157.htm
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