S FR E P O RTE R .CO M / TH E I N TE R FAC E
New LANL research provides methods for early assessment of COVID-19 variants
BY JULIA GOLDBERG @votergirl
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n the early days of the pandemic in the spring of 2020, news of a mutation to the SARS-CoV-2 virus that causes COVID-19 made headlines and stirred controversy. Bette Korber, a theoretical biologist at Los Alamos National Laboratory, had first identified the D614G mutation, named for the amino acid mutation in the virus’s spike protein, and co-authored a pre-print paper alerting the world to a new and possibly more transmissible strain. Pushback came swiftly, with many scientists questioning both the study and the reporting about its claims—the original article’s metrics indicate more than 7,000 tweets, some quite outraged. Fellow LANL scientist Ethan RomeroSeverson, a computational epidemiologist in the lab’s Theoretical Division, first heard Korber’s observation about the D614G mutation during an internal talk at the lab and it gave him an idea. “I heard this and I was thinking, ‘I bet we can use this data to actually estimate exactly how much more contagious these things are,” Romero-Severson tells SFR. His thinking proved apt. RomeroSeverson is the senior author of a peer-reviewed paper published last month in Nature Communications that puts forth methods for quantifying the transmissibility of new COVID-19 variants.
den anywhere. Anyone can download it and look at it and anyone can download the data and look at that too.” That sort of collaborative approach, Romero-Severson notes, has emerged as a dominant theme among scientists during the pandemic. “I have never seen anything like this in my career,” he says. “Scientists are just like people…they tend to want to protect their own research. The amount of open Doing so, he says, takes advantage of the collaboration and cooperation going on in global nature of the data in service of prothe scientific community has been unprecviding new modeling tools to rapidly assess edented. We are actively coming up with a variant’s transmissibility and risk. Those ways to better understand and document assessments, in turn, can help guide vaccihow COVID is spreading and how to prenation and public health policies. vent it.” ICYMI, Korber’s observations turned The work Romero-Severson and his colout to be correct: The variant with the leagues have done, he says, is a “little sliver,” D614G mutation became the dominant in the service of helping quantify variants’ strain of the virus around the world. But risks. More broadly: “What we want to fathat did not become evident immediately. cilitate here is knowledge and we want that “It’s very important to remember that knowledge to be public and disseminated.” people were very dismissive of [Korber’s] Currently, of course, New Mexico—and idea initially,” Romero-Severson says. everywhere else—is grappling with the “Bette faced a lot of pushback…people ramifications of the highly transmissible didn’t want to believe the virus was evolvOmicron variant and the glimmer of hope it ing in real time and adapting to humans, might be more mild than previous variants. but she was absolutely right. We wanted to The model Romero-Severson’s really put the things Bette was seeteam has devised looks to dising to a really rigorous test and that tinguish between some of the was our motivation in doing this different factors that play into work.” analyzing a variant’s impact Korber had seen the mutation and tease apart its innate conthrough intensive study of the tagiousness versus, for examSARS-CoV-2 genomes being upple, a mass gathering that might loaded to the international GISAID cause it to spread more widely. database. “We try to be as conservative “With COVID, we have a massive as possible,” he says. “We want collection of COVID sequence data,” to avoid falsely claiming someRomero-Severson notes. “And thing is going to be a concern; there’s a huge global effort to share that’s a big concern for us.” COVID sequence data, and it’s been At the same time, he caugrowing exponentially…our method tions about drawing conclufocuses on: How do we use that type sions too quickly that Omicron, of data?” for instance, might be less of a Specifically, he and his colleagues threat to public health. developed three methods for ana“There’s a lot of confoundlyzing global SARS-CoV-2 sequence ing factors to think about here,” data and applied them to four forhe says, such as the possibility mer variants. that Omicron’s capacity to inThey found they were able to find fect already vaccinated people evidence that a variant was more could play a role in its seemingcontagious than a previous strain ly more mild attributes. even when the frequency of the variBut a few things are ant was fairly low. “Understanding certain: “the virus has been contagiousness is really importadapting consistently over ant,” he says. “This research funtime.” And “the data is really nels into [providing] information to clear that three shots, full people who are doing modeling on Ethan Romero-Severson, a computational epidemiologist in Los vaccination plus a booster, vaccine efficacy and public health Alamos National Laboratory’s Theoretical Division, is the senior does provide protection interventions.” author of a recently published paper that demonstrates modeling against Omicron. That is clear While the new paper doesn’t exmethods to quantify the transmissibility of new COVID-19 variants. and unambiguous.” amine either the Delta or Omicron variants, forthcoming research does, using the population-genetic model the scientists devised, which they describe as providing “a reasonable balance between computability and accuracy.” The computability element is important to Romero-Severson, who has a background working with public health departments. “We were really, really sensitive to this,” he says. “We wanted something that could be run in a really low computational environment. One of the things that is really easy for a scientist like myself to get wrong is we come up with these super sophisticated things that take a 200-core computer, 100 hours to run and it’s really hard to do.” Avoiding that outcome was “one the reasons in this paper that we have these three methods is we wanted something that a person could run on a reasonable laptop… doesn’t require specialized resources or libraries or anything like that.” In addition to computational accessibility, the scientists also make their methods available. “All of our code and our papers is 100% publicly available,” he says. “It’s not hid-
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