COVID-19 DIAGNOSTIC LAB WORKFLOW

Coronalab.eu Travel Clinic

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.

asymptomatic COVID Testing Automation

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.

Viral RNA isolation for asymptomatic COVID testing

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 regions1,2,3. 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-gene4.

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. It is reported as the most sensitive commercial kit in the market by the FDA5.

“With multiple SARS-CoV-2 variants in the population we wanted to have a kit with highly conserved genomics 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 Defense6 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. COVID-19 Genomics UK Consortium. COG-UK update on SARS-CoV-2 Spike mutations of special interest: Report 1 (December 19, 2020). https://www.cogconsortium.uk/wp-content/uploads/2020/12/Report-1_COG-UK_19-December-2020_SARS-CoV-2-Mutations.pdf.
  2. 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
  3. 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.
  4. “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
  5. FDA Reference Panel Comparative Data. Oct. 2, 2020. https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-reference-panel-comparative-data
  6. US Department of defense. January 2021. https://www.defense.gov/Explore/Spotlight/Coronavirus/Operation-Warp-Speed/

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