Recent updates to

primer-monitor.neb.com

Date

Brad Langhorst

 Brad Langhorst, Matt Campbell, Caiden Kumar

Talk Plan

  • Review primer-monitor.neb.com
  • 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!

https://medium.com/@Naturalish/gremlins-three-rules-an-evolutionary-analysis-de4c4fae2785

Other people probably need this too... FDA guidance

What can we do???

Shine some light

Aligned Sequences AY.1

https://github.com/cov-lineages/pango-designation/issues/95

Lineage Variants

Other Variants Matter for Diagnostics

Data, well-organized, is light

Nightly Download

Genome Alignment

Variant Calling

RelationalDatabase

Matt Campbell, Caiden Kumar

https://www.nature.com/articles/d41586-023-01517-9

Visualization - simple

Visualization - multiplex PCR

Challenges

  • 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!

Thanks!

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)