Application of whole genome sequencing to the ORCHARDS household influenza surveillance project.
Kelsey Florek, MPH, PhD
2019 Wisconsin Virology Conference
May 21, 2019
Slides available at:
www.k-florek.net/talks
disease transmission and population dynamics
disease transmission and population dynamics
Oregon Child Absenteeism due to Respiratory Disease Study (ORCHARDS)
Relationship between school absenteeism and influenza in the community
What is the genetic diversity of influenza in the ORCHARDS study?
How does the genetic diversity of influenza in this community change over the season?
What is the likelihood a linked infection is a transmission event?
2017-2018 influenza season
day 0 and day 7 post-absence
pharyngeal swabs collected from children who reported absent
family members of household conducted self-swabs
criteria for sequencing
linked infection: child was positive for influenza and at least one household member was positive on day 0 or day 7
total: 149
influenza A: 109
H1N1: 14
H3N2: 93
influenza B: 40
Sequencing influenza
directly from sample
PCR to confirm
short read, large depth sequencing
thenativeantigencompany.com
What is the genetic diversity of influenza in the ORCHARDS study?
How does the genetic diversity of influenza in this community change over the season?
What is the likelihood a linked infection is a transmission event?
genetic diversity appears to increase over time
What is the genetic diversity of influenza in the ORCHARDS study?
How does the genetic diversity of influenza in this community change over the season?
What is the likelihood a linked infection is a transmission event?
Household transmission is likely
46 total household pairs
34 passing sequencing quality control
1 pair had a discrepant subtype
Next Steps
What does this tell us about influenza
how generalizable statements from large scale surveillance
effectiveness of interventions at the community level
defining how changes at the community level affect global evolution
Acknowledgements
HTML Presentation Framework
Wisconsin State Laboratory of Hygiene
Dr. Peter Shult
Dr. Allen Bateman
Erik Reisdorf
Richard Griesser
Tonya Danz
Orchards Study group
Dr. Jonathan Temte
Shari Barlow
Maureen Goss
Emily Temte
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Application of whole genome sequencing to the ORCHARDS household influenza surveillance project. Kelsey Florek, MPH, PhD 2019 Wisconsin Virology Conference May 21, 2019 Slides available at: www.k-florek.net/talks