Tracking the spread of SARS-CoV-2 variants in Wisconsin

Wisconsin State Laboratory of Hygiene
Kelsey Florek, PhD, MPH
June 24, 2021

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Sequencing has become a key tool in understanding the transmission dynamics of disease outbreaks

SARS-CoV-2 Sequencing Approach

ARTIC Tiled Amplicon Sequencing Approach

Where we started in 2020

Illumina MiSeq

Oxford Nanopore MinION

Where we are in 2021

Illumina NextSeq 2000

Oxford Nanopore GridION

SARS-CoV-2 Sequence Analysis

Generating actionable data visualizations from complex genomics data.

  • What is the current total of SARS-CoV-2 sequences?
  • How many sequences are being generated each week?
  • What proportion of sequences are variants of concern?
  • How many B.1.1.7s are there?
  • How many variants of concern are in my health jurisdiction?
  • What about X,Y, or Z variant?

Wisconsin SARS-CoV-2 Genomic Dashboard

Cumulative SARS-CoV-2 Sequences in WI

SARS-CoV-2 Sequences by WI County

SARS-CoV-2 Variants in WI

Regional distribution of SARS-CoV-2 Variants


  • SARS-CoV-2 genomics is a powerful tool that can help us better understand the pandemic
  • WSLH has increased sequencing capacity to address outbreaks and provide surveillance
  • Continuing development of data infrastructure


  • Wisconsin State Laboratory of Hygiene
    • Abigail Shockey
    • Sara Wagner
    • Alicia Mooney
    • Mike Mamerow
    • Rich Griesser
    • Tonya Danz
    • Erika Hanson
    • Tracy Heidke
    • Tim Davis
  • Special Thanks