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

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

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

• 2014-2016 West African Ebola Outbreak Quick et al.
• 2015-2016 Americas Zika Outbreak Faria et al.
• African and South American Yellow Fever Faria et al.

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

Summary

• 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

Acknowledgments