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Using genomic sequencing to predict COVID’s next move

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Brittany Niccum, Beckman Coulter Life Sciences, shares how genomic sequencing and laboratory automation can monitor new variants of COVID and potentially nip them in the bud, before they transform into future pandemics.

Key highlights:

Since 2019, SARS-CoV-2 has been attacking humans. The virus’ survival depends on its ability to copy its genome enough times that an infected person can spread it to someone else. But mistakes occur when any organism copies its genetic material, and RNA viruses like coronaviruses are especially error prone. These inaccuracies, however, provide the raw material upon which natural selection and evolution can act. For COVID-19, this has resulted in a series of new variants that are more transmissible and/or better able to evade immune defenses from vaccines and previous infections.

Until now, the scientific community has responded to new variants like Delta and Omicron only after they appeared on the public health radar. By the time a new variant is detected, it’s generally too late to stop it from rapidly spreading around the world. It’s why scientists have been pushing for methods that would enable them to predict what types of variants are the most important to watch via routine genomic surveillance. Any effort, however, would require sequencing—a lot of sequencing.

With public health budgets already stretched thin, performing additional genomic analyses may seem impossible. Thanks to the latest cutting-edge technology, laboratories can increase their throughput by automating time-consuming or repetitive tasks that will allow them to capture more viral genomes and get data to scientists more quickly.

Increasing throughput

Scientists rely on genomic sequencing not just to diagnose an infection and track its spread, but also as part of disease surveillance. Unlike sequencing for diagnosis, in which labs need to determine whether each sample contains the SARS-CoV-2 virus, sequencing for surveillance casts a wider net. What counts in surveillance is capturing as many genomes as possible, even if they’re not always 100% complete. In this case, quantity matters more than quality.

Human lab technicians, however, can sequence only a limited number of samples per day. Pipetting by hand takes time, and asking someone to repeat these tasks, day in and day out, puts them at risk for repetitive use injuries such as carpal tunnel syndrome. Even the best technicians also have natural variability in their skills, both from day to day and from technician to technician. It’s why the lab of Dr. Eric Chow, a geneticist at the University of California, San Francisco, relied on automation technology like the Echo liquid handler from Beckman Coulter Life Sciences, which uses acoustic waves to transfer liquid droplets between plates.

Dr. Chow’s lab first transitioned to performing PCR tests to assist local health departments in northern California in March 2020. By early 2021, however, the lab hit its stride when staff began sequencing samples positive for SARS-CoV-2 for the California Department of Public Health as part of the state’s disease surveillance program.

“As the first variants began to appear, it became clear that if you wanted early warning for things like this, you needed better surveillance,” Dr. Chow said.

The lab depends on the Echo liquid handler and other automation to allow them to sequence 768 samples per run, and to do so with consistency and precision. Their lab hasn’t identified any new variants, but Dr. Chow says that efforts like this - repeated around the world - will help detect any that do occur as early as possible.

Other labs have begun pooling their samples to maximise the number of genomes they can sequence per run. Because only a tiny fraction of samples will reveal variations of interest and concern, researchers can screen more viruses at low depth, and focus their more time-consuming, high-coverage sequencing on those few samples that reveal something worthwhile.

Speeding up sequencing

While automated liquid handlers and pooling samples can increase throughput, other parts of sequencing, such as library prep, remain time-consuming. It’s why some researchers have begun tweaking the typical protocols, which usually use overlapping PCR amplicons to make copies of viral cDNA, followed by traditional library prep to build a barcoded sequence library. But some scientists have developed a strategy that foregoes the use of amplicons.

Instead of amplicons, geneticists created small adapter molecules that they can add to the ends of all the primers. Then, after they run the first multiplex PCR to amplify the cDNA, they directly follow that with a second PCR that adds barcodes to the adapters. Eliminating the traditional library prep step not only saves time, but it also reduces consumables usage. This last feature has been especially useful when supply chain disruptions left items like pipette tips in short supply.

However, amplicon-free sequencing does have its drawbacks. The process means that labs need to be able to sequence snippets of DNA that are 400 base pairs in length. Very few machines can do this, so unless a lab has a long-read sequencer, this approach isn’t very useful. But by tweaking the process further, Dr. Chow’s lab has been able to shorten the sequencing length to 275 base pairs, which can be run on nearly any machine. The process is also quicker and can be completed in a day instead of two.

Global collaborations

The combination of automation, pooling, and streamlined sequencing protocols not only enabled scientists to identify the Omicron variant shortly after it started circulating, but it also allowed public health officials to track new Omicron sub-variants, including the “stealth” variant known as BA.2. This sub-variant emerged in the wake of Omicron and has now overtaken its parent strain as the dominant version of SARS-CoV-2 currently circulating in many parts of the world.

While the pandemic has generated an unprecedented level of genomic sequencing and data sharing, a recent analysis of global sequencing efforts showed a lopsided distribution of percentage of positive samples that were sequenced and data that was made publicly available in repositories. Low- and middle-income countries lagged markedly behind Europe, the U.S. and the U.K.

Many public health officials predict that COVID-19 will likely become an endemic virus. As a result of its continued spread and the virus’ need to evade immune responses, new variants will almost inevitably occur. Genomic surveillance offers the world its best chance at identifying these variants of concern when they begin circulating, which provides officials with the best opportunity to stem their spread before they sweep across the world.

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