Recent updates to


Brad Langhorst

 Brad Langhorst, Matt Campbell, Caiden Kumar

Talk Plan

  • Review
  • Recent enhancements
  • Demostration (Caiden)
  • Next steps / Discussion

Why does NEB Care About SARS-CoV-2 Variants?

 We want be sure that our LAMP, qPCR and sequencing SARS-CoV2 kits can be updated as new variants arise


They don't like sunlight

Don't get them wet

Don't feed them after midnight!

Other people probably need this too... FDA guidance

What can we do???

Shine some light

Aligned Sequences AY.1

Lineage Variants

Other Variants Matter for Diagnostics

Data, well-organized, is light

Nightly Download

Genome Alignment

Variant Calling


Matt Campbell, Caiden Kumar

Visualization - simple

Visualization - multiplex PCR


  • not interactive enough
  • can't fit multiplex PCR (too many primers)
  • not auto-updating (manual publishing needed)
  • does not visualize geography (map based?)
  • dense data (SARS-CoV-2) vs. sparse data (all others)
  • variant frequency vs time is not visible

Take it away Caiden

Planned Features

  • More geographic detail ✅
  • Fully automated intake/update ✅
  • Automated visualization updates ✅ (almost)
  • Automated notification ✅
  • Primer set scores ✅
    • View primer set as a whole ✅
    • mulitplex PCR visualizations
  • Add data sources for RSV, influenza, HPV, ...?
  • Variants by time 
  • Suggestions welcome!


Caiden Kumar

Matt Campbell

NEB Leadership

Discussion/ Questions

Possible Topics:

  • Can we achieve good coverage with 1.4 kb amplicons in typical clinical samples? Ct limitations?
    • Initial results from collaborators with clinical samples show good performance even at higher Ct (27-32)

Primer Monitor Update - 2023-08

By Brad Langhorst

Primer Monitor Update - 2023-08

  • 138