Little Known COVID-19 Virus Variants Are Changing How Scientists Track the Pandemic

By Max Peterson

It’s official. Less than a month into the new year, a year quietly anticipated to be full of plentiful vaccines and bustling restaurants, 2021 was dubbed “the year of COVID-19 variants” by major science publications and public health specialists.

Already, the world has seen the rise of three especially troubling virus strains: The highly transmissible United Kingdom variant, the vaccine-resistant South African variant, and the Brazilian variant, which may be less detectable by people’s immune systems, according to the U.S. Centers for Disease Control and Prevention.

Outbreaks of these new virus strains resulted in sweeping changes to some governments’ containment policies and vaccine rollouts. In January, for example, South Africa halted its distribution of a vaccine made by AstraZeneca after it was found ineffective in preventing mild and moderate cases of the new variant that has overtaken the country.

To prevent future dangerous variants from spreading, a Swiss scientist is leading an effort combining genomics with traditional epidemiology to identify these viral upstarts long before they take over and upend governments’ attempts at control. At the annual American Association for the Advancement of Science (AAAS) meeting in February, Tanja Stadler, chair of the Data and Modeling team of the Swiss National COVID-19 Science Task Force, discussed her work reconstructing SARS-CoV-2 transmission links when contact tracing is unavailable or unreliable. SARS-CoV-2 is the virus behind COVID-19.

Viruses constantly mutate, making little typos in their genetic code as they replicate. Some mutate faster than others, but the SARS-CoV-2 mutation rate is average: About once every two weeks. Still, when this occurs in millions of infected people over a year, it’s a lot of variants.

Most of the SARS-CoV-2 mutations don’t make the variants more deadly, transmissible or resistant to vaccines. They simply make them unique, like a genetic fingerprint. Policy makers tend to only be interested in the nastier strains, but Stadler’s careful tracking of these unremarkable variants, in addition to those known to be worse, allows her team to build a sort of “family tree,” a map of the pandemic’s dynamics at a temporal and geographical resolution that that can’t be achieved with traditional epidemiological methods like contact tracing and hospitalization numbers.

“One genome doesn’t tell you much,” said Stadler, a professor at the Swiss Federal Institute of Technology in Zürich (ETH Zürich). What matters “is the context that it’s embedded in.”

By sequencing hundreds of virus samples from all over Switzerland on a weekly basis and comparing them to thousands more shared by scientists across the globe, Stadler and her team trace the spread of each unique variant, revealing trends from week to week that might be otherwise invisible.

Before the UK variant was discovered in fall 2020, scientists used her team’s genomic data to identify another variant that was spreading rapidly through Europe in the summer. But was this variant truly a greater threat, or were other factors in play?

“A key quantity in an epidemic is the so-called reproductive number,” Stadler explained. “This number quantifies how many people a single infected individual will infect, and it is influenced by two different characteristics -- the biological properties of the virus, including how easily it is transmitted, and our behavior.”

By comparing the constantly shifting reproductive numbers of the variant in locations across Europe, Stadler was able to discount the possibility that the variant was more transmissible. In some places, the variant became dominant, but in many others, it disappeared. Classical epidemiological methods confirmed this result many weeks later.

If scientists can determine which variants aren’t much of a threat, then they can likewise identify which variants need to be watched closely before a dangerous strain takes hold.

“Understanding where new infections occur allows [authorities] to design appropriate public health interventions to successfully contain the epidemic,” Stadler said in an ETH Zürich video.

Linfa Wang, director of the Programme in Emerging Infectious Diseases at Duke-NUS Medical School in Singapore and a speaker at the same AAAS session, agreed. “If we handle the first week or the first month [of an outbreak] as a global village, we don’t have to worry about how to distribute a vaccine.”

Max Peterson is a Science Writing MA student at Johns Hopkins University. After over a decade at the laboratory bench researching genetics and neuroscience, they have traded the pipette for the pen. Follow them on Twitter @MaxPeterson89 or email them at maxcp89@gmail.com.

This story was edited by NASW member Steven Benowitz, who served as Peterson's mentor during the NASW-AAAS Spring Virtual Mentoring Program.

Hero image by Pete Linforth from Pixabay

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