Examining the Workflow of a Cutting-edge COVID-19 Diagnostic Lab

Authors: Patrick de Boer, Arvind Kothandaraman, Paul Jeffrey

In early 2020, the Netherlands identified its first COVID-19 cases. Facilitating test capacity for all symptomatic individuals resulted in extensive pressure on diagnostics labs making it challenging for non- symptomatic individuals such as travelers, teachers and professional athletes to get tested.

In April 2020, CoronaLab, a business unit of Microbe&Lab B.V., began providing cutting-edge SARS-CoV-2 RT-PCR testing for non-symptomatic people using a test approved by the RIVM (Dutch Health Organization). CoronaLab is a test clinic in the Netherlands, with a fast, same day, sample-to-result service, including a physician-approved digital report of the outcome.

In order to facilitate this fast turnaround time of high-quality data, CoronaLab collaborated with PerkinElmer to implement a state-of-the-art robotic workflow with the capacity to process up to 37.000 tests per week.

Automated Sample Preparation: Incoming biological samples from nasopharyngeal, oropharyngeal, and anterior nasal swabs are aliquoted into destination labware supporting viral RNA extraction. For this step the JANUS^® G3 primary sample reformatter is used for safe and traceable barcode scanning and sample preparation of up to 192 samples in just 30 minutes.

Viral RNA Extraction: The chemagic™ 360 system is used to extract viral RNA from 96 samples per run in only 31 minutes. For this Coronalab is using multiple chemagic™ 360 systems resulting in high yield RNA aliquots for PCR analysis. Then the JANUS^® PCR workstation prepares PCR plates easily and efficiently.

PCR Analysis: The key step in our COVID-19 testing workflow is reliable and robust PCR chemistry for accurate diagnosis and screening. As an RNA-virus, SARS-CoV-2 mutates easily, resulting in multiple variants. These include the United Kingdom variant (VUI 202012/01 (linage B.1.1.7)) which the world is watching closely. Initial analyses suggest a strong correlation between this new mutation and an increasing number of COVID-19 cases in the affected geographical regions^1,2. The UK variant, South African variant (501.V2 (B.1.351 lineage)), and the P.1 variant from Brazil are all characterized by multiple mutations in the spike glycoprotein’s S-gene³.

CoronaLab is using the PerkinElmer SARS-CoV-2 RT-PCR assay which was designed specifically to identify SARS-CoV-2 highly conserved ORF1ab and N genes and therefore is not affected by S-gene variants.  The kit comes with internal human DNA controls, in order to check for proper sample collection of each sample.

“With multiple SARS-CoV-2 variants in the population we wanted to have a kit with highly conserved genomic loci probes and at least 2 targets in order to give our clients to most reliable reports.”
Patrick de Boer co-founder CoronaLab

Future: Operation Warp Speed by the US Department of Defense⁴ opened the door for multiple vaccine releases at the end of 2020 and a growing group of individuals are exposed to the SARS-CoV-2 virus. Serological studies will be the next step in monitoring the pandemic and vaccine effectivity. CoronaLab is using the PerkinElmer SuperFlex™ Immunoassay CE-IVD system for accurate and rapid serological antibody testing.

“Coronalab is proud to keep on supporting individuals and companies with fast and up-to-date COVID-19 tests.”
Patrick de Boer co-founder CoronaLab

References

1. European Center for Disease Prevention and Control (2020) Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom. https://www.ecdc.europa.eu/en/publications-data/threat-assessment-brief-rapid-increase-sars-cov-2-variant-united-kingdom
2. Rambaut, A., et al. (Dec 20, 2020) Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations: COVID-19 genomics UK consortium. https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563.
3. “Emerging SARS-CoV-2 Variants”. Centers for Disease Control and Prevention. 15 January 2021 https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html
4. US Department of defense. January 2021. https://www.defense.gov/Explore/Spotlight/Coronavirus/Operation-Warp-Speed/