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

• Ann Fan (AZGF)
• Eric Murray (Wild At Heart)
• ASU Student Health Clinic

MANUSCRIPTS

• Scotch et al. Campus-based genomic surveillance uncovers early emergence of a future dominant A(H3N2) influenza clade. iScience. 2025 Nov 4;28(12):113941.
• Yeh et al. Three things we can do now to reduce the risk of avian influenza spillovers. PNAS. 2025 Aug 5;122(31):e2503565122.

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

• Scotch et al. Influenza A(H3N2) subclade K (J.2.4.1) viruses associated with a surge at a university health clinic, Arizona, the United States, November to early December 2025. Euro Surveill. 2026 Feb;31(7). 
• Chung et al. Influenza vaccine effectiveness against medically attended outpatient illness, United States, 2023–24 season. Clin Infect Dis. 2025 Jan 6:ciae658.

FUNDING

• CDC

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

• Scotch M, et al. Rapid Expansion of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Genotype D1.1 Virus across Flyway Regions, North America, Fall 2024. Emerg Infect Dis. 2026 Aug;32(8):1241-1250. doi: 10.3201/eid3208.260205. Epub 2026 Jul 13.
• Kraberger S, et al. Divergent poxvirus identified in a non-native black rat from Madagascar. Virology. 2026 Oct;623:111021. doi: 10.1016/j.virol.2026.111021. Epub 2026 Jun 30.
• Strike W, et al. Implementing Wastewater-Based Epidemiology for Long-Read Metagenomic Sequencing of Antimicrobial Resistance in Kampala, Uganda. Microorganisms. 2025 May 28;13(6):1240.

FUNDING

• NSF/BIO

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

• Xu et al. Mining Social Media Data for Influenza Vaccine Effectiveness Using a Large Language Model and Chain-of-Thought Prompting. AMIA Annu Symp Proc. 2025 May 22;2024:1404-1413. eCollection 2024.
• O'Connor et al. Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis. JMIR Res Protoc. 2025 Apr 22;14:e58567.

FUNDING

• NIH/NIAID
• NIH/NLM