SARS-CoV-2 genome surveillance, powered by Biosero workcells


The COVID-19 pandemic has been fueled by the effects of more transmissible variants, including well-known variants initially identified in the UK, South Africa, and Brazil. These variants have underscored the need for genome surveillance efforts.

Unlike individual PCR tests designed to detect the presence of viral material, genome surveillance requires sequencing the entire viral genome to help scientists spot mutations as the SARS-CoV-2 pathogen continues to evolve.

Recently, sequencing leader Illumina established a high-throughput facility to generate genome surveillance data by sequencing viral isolates collected from patients. The ambitious effort is being managed with Biosero workcells enabled by Green Button Go® Scheduler, streamlining sample preparation and processing.

Learn more about how the Biosero solutions enabling genome surveillance at scale for the COVID-19 pandemic.

Isolation of SARS-CoV-2 viral RNA

This workcell manages the extraction and purification of viral genomic content from patient samples needed for the Illumina COVIDSeq Test.

Viral material is bound to magnetic beads and subsequently isolated using the Thermo Fisher Scientific KingFisher Presto. Magnetic rods on the Presto instrument bind the magnetic beads containing the SARS-CoV-2 nucleic acid, followed by buffers and cleaning steps. After the viral material is purified, it is then eluted or released into a microtiter plate that will proceed to the next preparation step.

RNA to cDNA conversion + amplification

Once the viral genetic material purification is completed by the extraction system, samples can be immediately transferred into a Pre-PCR Workcell where the RNA of the SARS-CoV-2 virus is annealed and then converted to a more stable cDNA form. Through partnership with SPT Labtech, the cDNA material is partitioned, and the necessary reagents dispensed (master mixes for each directional strand template) to accomplish this conversion using the Mosquito liquid handler and Dragonfly liquid dispenser. Once in cDNA form, the sample material can then be amplified by thermal cyclers.

Amplicon Tagmentation

After cDNA is amplified in a PCR step, the samples are introduced to the next Biosero automation workcell. This Post-PCR workcell will recombine the amplified material and tag the PCR amplicons with adapter sequences that will allow subsequent detection.

In a step after the Post-PCR workcell, the tagmented amplicons are amplified in a PCR program. This PCR reaction step also attaches multiple index adapters and sequences that will generate clusters for use in sequencing and analysis.

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