Design Specific and Sensitive PCR Assays For The New Covid-19 UK Variant

DNA Software and PanelPlex-Consensus has been used for the design COVID-19 molecular diagnostics by greater than 20 organizations globally. Additionally, DNA Software (DNAS) has worked directly with its customers to provide multiplex panels which include COVID, FLUA, FLUB and other relevant respiratory pathogens.

With COVID-19 variants are circulating globally, DNAS has worked with its partners to directly provide designs for the (UK) variant B.1.1.7. DNAS customers continue to rely and trust PanelPlex as they leverage DNAS solutions to design UK variant B1.1.7 and the South Africa variant 1.351 which shares some mutations with the UK variant. In addition, another COVID-19 variant P.1 has been identified from Brazil and PanelPlex-Consensus can be leveraged to provide “consensus” designs, designs which cover all COVID-19 variants, ( UK B.1.1.7, South Africa 1.351 and Brazil P.1 ) with the same set of primers.

Click here to Download the paper from the “Stakeholders Panel on Agent Detection Assays” (SPADA) with best-practices for designing PCR assays for pathogens such as SARS-CoV-2.

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Why can PanelPlex™-Consensus help build uniquely sensitive and specific PCR assays to detect SARS-CoV-2 (Coronavirus), including all variants?

  • PanelPlex™-Consensus has been rigorously validated for the detection of thousands of bacteria, viruses and human targets.
  • PanelPlex™-Consensus provides consensus designs PCR assays to detect all sequence variants of a given virus. Often, this is accomplished with a single primer pair (i.e. singleplex reaction) while in other cases with high sequence diversity a small multiplex reaction is required (typically 1 to 5 plex is required).  For example, we have made singleplex assays for pandemic 2009 H1N1 FluA, and 7-plex assay for the highly divergent Lassa virus.  PanelPlex™-Consensus is fully capable of designing a new assay to address the (COVID-19) Coronavirus.
  • PanelPlex™-Consensus allows the user to input panels of GenBank accessions to form inclusivity, exclusivity (i.e. phylogenetically near neighbor sequences), and background lists.
  • PanelPlex™-Consensus uses our proprietary ThermoBLAST and TargAn (target analysis) algorithms so that the assays are designed with maximum coverage of sequence variants with minimum false positives and false negatives.
  • PanelPlex™-Consensus saves over six months on average of iterative experimental trial-and-error optimization.
  PanelPlexTM-Consensus Traditional Design
First pass of multiplex primer design 80-90% >50% *
Second pass of multiplex primer design 98-99% <70%
Time to functional design <2 days >6 months

* Based on personal communication with PCR specialist at Roche and Sr. Scientist at a Boston based Biotech company


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Dna Software provides its customers direct access to its software solutions as well as performing custom assay designs on a contact basis.
Panelplex-Consensus as been recognized as in 2019 by Frost and Sullivan as best in class in the industry.