What we have learned about SARS-CoV-2 through genomics

Wisconsin State Laboratory of Hygiene
Kelsey Florek, PhD, MPH
December 10, 2020

Application of Next-generation sequencing

• 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.

Use genomics to better understand the transmission and evolution of the SARS-CoV-2 virus.

Inform public health interventions and outbreak investigations.

SARS-CoV-2

ARTIC Tiled Amplicon Sequencing Approach

Sequencing Instrumentation

Illumina MiSeq

Oxford Nanopore MinION

WSLH SARS-CoV-2

By County

D614G Variant

• There is growing evidence that the G variant increases infectivity in vitro and may have been selected for increased transmission in humans
  • Korber et al.
  • Zhang et al.
  • Yurkovetskiy et al.
  • Daniloski et al.
  • Volz et al.
• It has also been suggested that this mutation increases the virus' suceptibility to neutralizing antibodies
  • Weissman et al.

D614G Variant

D614G Variant

Brown County

Seneca Foods

• Food processing and distribution – 10 locations in WI
• Workers tested at start of season in June
• First positive case on July 19th
• 28 cases were identified by July 27th
• After mass testing 34 additional cases were identified between July 31st and August 24th
• Sequencing performed on 9 samples but only 6 met quality requirements

Seneca Foods

Key Takeaways

SARS-CoV-2 in Mink

• November 5th – Ministry of Environment and Food of Denmark announced Denmark would cull their mink population
  • 17 million animals
• Danish National Institute of Public Health
  • Reports of Mink to human transmission events
  • Mutations in the SARS-CoV-2 Spike protein
    • Preliminary reports suggested these mutations could affect Antibody neutralization
    • WHO review concluded these mink-associated mutations are not a higher risk to humans

SARS-CoV-2 in Mink

SARS-CoV-2 in Mink – H69/V70 deletion (yellow)

SARS-CoV-2 in Mink – Y453F (yellow)

SARS-CoV-2 in Mink – I692V (yellow)

SARS-CoV-2 in Mink – M1229I (yellow)

Key Takeaways

• Evidence of Mink / human transmission in WI
• The mutations associated with the Denmark mink outbreak do not appear to increase the risk to humans
• The combination of mutations do not appear in any samples sequenced so far

Wisconsin Correctional Facilities

• As of December 9th the Wisconsin Department of Corrections reports:
• more than 9,400 positive cases
• 8 facilities with more than 500 cases
• 4 facilities with more than 100 active cases
• WSLH has completed sequencing on more than 200 samples

Wisconsin Correctional Facilities

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
• If you have a sample/s that are of interest please let us know we would be happy to work with you to get them sequenced

Questions