Genome sequencing is getting cheaper and faster. That’s been nearly a mantra for years from articles in science journals, as well as publications for a wider range of readers. In particular, whole genome sequencing (WGS) keeps getting easier to do. As a result, scientists use this technique more than ever, especially in 2020 as the world deals with the pandemic driven by the SARS-CoV-2 virus that causes COVID-19.
Within a couple of months from the initial reports of health crisis in Wuhan, China, scientists had published the genome of SAR-CoV-2. As a result, the value of sequencing to monitor the molecular aspects of the virus and how it might change was quickly realized. As an example, the U.S. Centers for Disease Control and Prevention (CDC) created SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES). The CDC describes SPHERES as a “new national genomics consortium to coordinate SARS-CoV-2 sequencing across the United States.” Among other objectives, the CDC created SPHERES to “advance public health research in the areas of transmission dynamics, host response, and evolution of the virus.”
As experts around the world are showing, WGS of SARS-CoV-2 provides crucial insight into the structure of this virus, how it’s evolving, and what can be done to keep the health consequences as low as possible.
Tracking origins in Belgium
In collaboration with Simon Dellicour from the Université Libre de Bruxelles and the group of Piet Maes at KU Leuven, geneticist Keith Durkin—a post-doctoral researcher at the University of Liège in Belgium—determined sequences of SARS-CoV-2, for use in two primary ways. “Firstly, Dr. Dellicour has used the data to investigate the introduction of SARS-CoV-2 in Belgium, the effect lockdown had on its spreads, and its ongoing circulation,” Durkin says. The scientists described this application in a preprint. Second, Durkin notes that he and his colleagues at the University of Liège “have used the data to ensure that diagnostic tests are not negatively impacted by mutations that arise in SARS-CoV-2.”
From this work, these scientists found about 330 separate introductions of this virus in Belgium. “The data also showed that while the lockdown did reduce the level of viral transmission, it had a relatively moderate impact on its ability to spread within Belgium,” Durkin explains. “Second, we found a mutation that had arisen in SARS-CoV-2 that interfered with one of the SARS-CoV-2 diagnostic tests.” Moreover, the researchers found other examples of this mutation arising around the world. “This observation highlighted that it is important to monitor mutations in SARS-CoV-2 to ensure that they don’t interfere with testing,” Durkin says.
That means that scientists must continue to study this virus, especially through ongoing sequencing. Consequently, Durkin and his colleagues are still sequencing SARS-CoV-2 samples. “We are hoping this will help us better understand the dynamics of viral spread within Belgium, identify clusters of infection, and ensure that the testing remains accurate,” he explains.
Explorations down under
Other scientists also apply sequencing of SARS-CoV-2 to local samples for epidemiological information. For example, a team of scientists in Australia sequenced samples from more than 1,000 people with COVID-19 in Victoria.
These scientists reported: “Laboratory and bioinformatic workflows were developed to support large-scale rapid processing of samples, enabling genomic sequencing and bioinformatic analysis of 96 samples in an approximately 45-hour time period.”
This work revealed one crucial aspect of how scientific information could be used to develop public health guidelines. As this team of researchers stated: “Prior to the implementation of enhanced (stage 3) restrictions in Victoria, we identified a large genomic cluster (the largest in our dataset, comprising 75 cases) associated with several social venues in metropolitan Melbourne. This finding demonstrates the propensity for chains of SARS-CoV-2 transmission throughout urban areas associated with leisure activities and provides additional justification for the unprecedented population-level social restrictions in our setting.”
Other studies also show the value of WGS in determining the best pathways in public health. Scientists who used WGS to study the spread of COVID-19 in The Netherlands stated: “We show that WGS in combination with epidemiological data strengthened the evidence base for public health decision-making in the Netherlands as it enabled a more precise understanding of the transmission patterns in various initial phases of the outbreaks.”
Keep sequencing
If one thing is true about viruses, it’s that they change. Scientists already see mutations in SARS-CoV-2, and that’s not going to stop. So, the sequencing must continue. Plus, gathering data globally will provide an increasingly detailed picture of just what this virus is doing and how.
Given the devastating impact of COVID-19, every second seems to count in studying this virus—all focused on the desire to defeat it. We have all benefitted from the fact that WGS gained speed in advance of this pandemic. Otherwise, scientists and public health officials would have started even further behind in handling this disease.
The world of medicine today, though, watches two ends of the public health spectrum working as one. From the 1918 flu to the COVID-19 pandemic, some of the simplest tactics—masks and social distancing—remain crucial and valuable tools, despite a century of advances in science and medicine. To develop treatments and vaccines, though, experts rely on some of the most advanced tools in today’s box, such as WGS.
Even with the speed of modern WGS, it cannot instantly create a cure for COVID-19. Instead, advanced tools must be balanced with the simple ones, the ones that can be applied instantly. So from masks and maintaining distance to advanced epidemiology and sequencing, healthcare leaders must find ways to optimize the easy tools until the complex ones can catch up. By jumping on the sequence of SARS-CoV-2 so quickly, the global healthcare system hopes for an emerging collection of therapeutics and vaccines. Until then, keep it simple: Wear a mask.
Hero image: Transmission electron micrograph of SARS-CoV-2 virus particles, isolated from a patient. Image captured and color-enhanced at the NIAID Integrated Research Facility in Fort Detrick, Maryland. Image courtesy of National Institute of Allergy and Infectious Diseases, NIH.