Accelerate SARS-CoV-2 research and surveillance
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Leveraging our extensive experience and knowledge in genomics, we built the SOPHiA GENETICS SARS-CoV-2 analytical solutions to enable a rapid and precise identification of circulating and emerging variants.

The combination of the SOPHiA DDM™ platform with the amplicon-based Paragon Genomics SARS-CoV-2 Panels offers coverage of the whole viral genome and sensitive variant detection through a streamlined, end-to-end workflow (from sample to surveillance report). The resulting solutions accelerate surveillance and evolution studies of SARS-CoV-2.

Future-proof strain identification including*:
‘Alpha’ (B.1.1.7)
‘Beta’ (B.1.351)
‘Gamma’ (P.1)
‘Epsilon’ (B.1.429)
‘Iota’ (B.1.526)

‘Kappa’ (B.1.617)

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  • Ultra-sensitive and fast SARS-CoV-2 whole genome analysis with tailored quality assessment
  • Optimized identification and filtering for current and emerging variants
  • Integrated access to public databases and secure knowledge sharing in peer networks
  • SARS-CoV-2 Surveillance Report for real-time reporting of SARS-CoV-2 data

Generate high-quality viral genome data

The Paragon Genomics highly multiplexed target enrichment panels, CleanPlex® SARS-CoV-2 and SARS-CoV-2 FLEX, generate a sequencing-ready library in just 5.5 hours. Both solutions generate high-quality NGS libraries to reach 99% coverage of the viral genome for a more robust and confident variant calling, even as the virus mutates. In fact, the SARS-CoV-2 FLEX panel includes degenerate primers and additional internal library preparation control for consistent coverage to withstand mutations and more confident negative calls.

Applications/Intent CleanPlex® FLEX®
SARS-CoV-2 Detection & Full Genome Coverage +++ +++
Surveillance and Monitoring ++ +++
Variant Typing + ++
Human RNA Control
New Variant Research + ++
Control Primer
Spike in Optimization
Degenerate Primers

+ = Good confidence, ++ = More sensitive/robust, +++ = Top performance
All versions can deliver reliable and robust performance for varying sequencing strategies.

The top graph shows trends of emerging circulating variants collected from nearly 10,000 viral profiles across SOPHiA GENETICS’ decentralized community of 71 institutions in 15 countries. The graph shows that SOPHiA DDM™ reflects global dynamics found in the public database.

Identify new and emerging variants with confidence

SOPHiA GENETICS has developed a fast, highly sensitive and analytically accurate detection workflow to surveil circulating, emerging SARS-CoV-2 variants at a global scale. The overall clade distribution in the SOPHiA DDM™ platform is similar to that of global datasets that require manual upload and analyses. With the SOPHiA DDM™ platform, data quality is controlled and analyses can be automated, and data screened in real time.

Real-time reporting of SARS-CoV-2 data with our SARS-CoV-2 Surveillance Report

The SOPHiA DDM™ platform offers at-a-glance reporting to help streamline the interpretation process of variants of concern (VOC), including valuable insights such as:

  • Lineages associated with spike mutations
  • Variant classification (VOC, VOI/VUI, VOHC, Monitoring) consistent with WHO/CDC and Public Health England
  • Real-time tracking of known circulating variants by geography
  • Hotspot identification by variant
  • Key spike protein mutational monitoring
  • New mutation and new mutation combination spotlights
  • Insights enhanced with published scholarly data
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Find Out More


End-to-end workflow to boost laboratory efficiency and enable retrospective analyses
Discover how the University Hospital of Sassari adopted SOPHiA DDM™ for SARS-CoV-2 to analyze thousands of COVID-19 samples and maintain public health surveillance.


Mutational hotspot in the SARS-CoV-2 Spike protein N-terminal domain conferring immune escape potential
Learn about a reported mutational hotspot from our researchers: a striking increase in the frequency of recruitment of diverse substitutions at a critical residue, W152, positioned in the N-terminal domain (NTD) of the Spike protein.


Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples
Read what our team, in collaboration with international centers, developed and published – in-line with WHO guidance – for the accurate genotyping of SARS-CoV-2.

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Robust CNV detection using whole exome sequencing for complex cases
SARS-CoV-2 Spike protein variant surveillance modelled in real time using the SOPHiA DDM™ platform

SOPHiA GENETICS has demonstrated a proof of concept for real-time global variant surveillance of spike protein mutations through the SOPHiA GENETICS community secured peer-network and compared findings to the GISAID timeline.

Robust CNV detection using whole exome sequencing for complex cases
SARS-CoV-2: How to Make the Most of Your Samples
In this brief presentation, our expert will share insights on the different approaches to monitor viral genome sequences and how your data can help fuel surveillance efforts.
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Read More


A straightforward molecular strategy to retrospectively investigate the spread of SARS-CoV-2 VOC202012/01 B.1.1.7 variant


First reported cases of SARS-CoV-2 sub-lineage B.1.617.2 in Brazil: an outbreak in a ship and alert for spread

*Data on file. Results may vary.
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