CURRENT PROJECTS

FLU Genomic EpidemiologY

Diversity and evolution of influenza in humans and birds

INFLUENZA VE

Part of the CDC's flu vaccine effectiveness network

Pandemic Surveillance

NSF-funded Center on pandemic preparedness 

DIGIAL EPIDEMIOLOGY

Host metadata enrichment and social media mining
KEY CONCEPTS
  • Molecular epidemiology
  • RT-qPCR
  • Library preparation
  • MinION long-read sequencing
  • Genomic epidemiology
COLLABORATORS
  • Anne Justice-Allen (AZGF)
  • Eric Murray (Wild At Heart)
  • ASU Student Health Clinic



MANUSCRIPTS
FUNDING
  • UA/AEGIS
  • ASU/KE
KEY CONCEPTS
  • Vaccine effectiveness
  • Test-negative design
  • Subtyping
  • RT-qPCR
COLLABORATORS
  • Vel Murugan (PI, ASU)
  • Joanna Kramer (PCH)
  • Lora Nordstrom (Valleywise)​
  • Brendan Flannery (CDC)
  • Jessie Chung (CDC)
  • And the rest of the Flu VE network!

MANUSCRIPTS
Chung et al. Influenza vaccine effectiveness against medically attended outpatient illness, United States, 2023–24 season. Clin Infect Dis. 2025 Jan 6:ciae658. doi: 10.1093/cid/ciae658.
FUNDING
KEY CONCEPTS
  • Wastewater-based epidemiology
  • High-throughput sequencing
  • Bioinformatics
  • Modeling
  • Community engagement
COLLABORATORS
  • Scott Berry (PI, U Kentucky)
  • James Keck (ANTHC/U Alaska Anc)
  • Sarah Olson (Wildlife Cons. Soc.)
  • Aarvind Varsani (ASU)
  • Kerry Hamilton (ASU)
  • Qiyun Zhu (ASU)
MANUSCRIPTS
Strike W, et al. Implementing Wastewater-Based Epidemiology for Long-Read Metagenomic Sequencing of Antimicrobial Resistance in Kampala, Uganda. Under Review.
FUNDING
KEY CONCEPTS
  • Natural language processing
  • Pathogen sequence databases
  • Metadata enrichment
  • Genomic epidemiology
  • Social media mining
  • Vaccine effectiveness
COLLABORATORS
  • Graciela Gonzalez-Hernandez (MPI, Cedars)
  • Ebbing Lautenbach (UPenn)
MANUSCRIPTS
  • O'Connor et al. Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis. Accepted by JMIR Research Protocols.
FUNDING