Providing Efficiency and Accuracy for Labs to Process COVID-19 Samples

As part of the battle to lower the cases of COVID-19 and its effect on the human population, many researchers are beginning to process specimens from COVID-19 patients to better understand how the virus operates and monitor the spread of the infection throughout the population.  One key component in processing samples is to ensure results are linked back to the correct patient.  Manual handling of samples can lead to errors that can impact your end results and findings.    

Illumina understands the importance of tracking samples through your COVID-19 workflows and being able to quickly setup to process those samples to help fight the COVID-19 battle with accurate results and interpretation.  We are playing our part in this battle by offering labs that are processing COVID-19 samples with a free, 1 year BaseSpace Clarity LIMS subscription to help with efficiency and accuracy in processing COVID-19 samples.  Your BaseSpace Clarity LIMS includes 2 new COVID-19 workflows to help you get setup quickly to process your COVID-19 samples.  You will also have access to our 30+ preset protocols and all of our Illumina instrument integrations to ensure you can support any additional workflows required in your lab. 

COVID-19 Workflows  

BaseSpace Clarity LIMS COVID-19 workflows are available with: 

  • Automated calculation of sample and buffer volumes. 
  • Automated calculation or display of reagents at every step in the protocol. 
  • Automatic step transition when required. 
  • Automatic placement of samples when necessary. 
  • Automated assignment of QC Pass/Fail, based on user-selected threshold values. 
  • Full integration to Illumina Sequencers for easy run planning and to perform QC on primary metrics prior to data analysis. 

During onboarding, we will work with your lab to optimize these workflows for your needs. 

CDC COVID-19 RT-PCR Workflow  

The CDC COVID-19 RT-PCR workflow (Figure 1) is designed based on the CDC recommended protocol for processing COVID-19 samples.  This workflow supports multiple RNA extraction and cDNA synthesis kits to provide your lab with the flexibility you need to process your COVID-19 samples. 

Supported RNA Extraction Kits/Instruments 

  • Qiagen QIAamp DSP Viral RNA Mini Kit or QIAamp Viral RNA Mini Kit 
  • Qiagen EZ1 Advanced XL 
  • Roche MagNA PURE LC 
  • Roche MagNA Pure Compact 
  • Roche MagNA Pure 96 
  • bioMerieux EMAG instrument 

Supported cDNA Synthesis Kits 

  • Thermofisher TaqPath 1-Step RT-qPCR 
  • Promega GoTaq Probe 1-Step RT qPCR 
  • Quantbio qScript XLT One-Step RT-qPCR Tough Mix 
  • Quantabio UltraPlex 1-Step ToughMix 
Figure 1. CDC COVID-19 RT-PCR workflow using Qiagen QIAmp RNA extraction kit. 

Respiratory Virus Panel workflow  

The Respiratory Virus Panel v1.0 workflow (Figure 2) is designed based on Illumina’s application note Enrichment workflow for detecting coronavirus using Illumina NGS systems.  This workflow supports multiple DNA/RNA extraction and cDNA synthesis kits to provide your lab with the flexibility you need to process your COVID-19 samples. 

Supported RNA Extraction Kits/Instruments 

  • QIAamp Viral RNA Mini Kit 
  • AllPrep PowerViral DNA/RNA Kit 

Supported cDNA Synthesis Kits 

  • Maxima H Minus Double-Stranded cDNA Synthesis Kit 
  • NEBNext Ultra II First Strand Synthesis Module 
  • NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module 
  • SuperScript Double-Stranded cDNA Synthesis Kit 
Figure 2.  Respiratory Virus Panel workflow using Qiagen QIAmp RNA extraction kit and Maxima H Minus Double-Stranded cDNA Synthesis Kit. 

To learn more about accessing a free year of BaseSpace Clarity LIMS, please contact your Illumina representative. 

For more information on how Illumina is supporting researchers with COVID-19, please visit Illumina Technology and COVID-19

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