# Center for Viral Systems Biology- H5N1 Supplement

> **NIH NIH U19** · SCRIPPS RESEARCH INSTITUTE, THE · 2024 · $820,000

## Abstract

Summary
The spread of highly pathogenic H5N1 avian influenza clade 2.3.4.4b among dairy cattle in the United States
has raised concerns over the increased risk of major human outbreaks or even a pandemic. Thus, it is of critical
importance to monitor the ongoing transmission and evolution of the virus within cattle, humans, and other
infected animals residing in or near farms. Here, we propose to establish a real-time outbreak intelligence
framework to facilitate genomic surveillance of the virus at the host- and population-level using data from
individually infected hosts and aggregate samples from sources such as pooled milk. Our framework will
consist of three core components with automated workflows to process raw data from public sources such
as NCBI Sequence Read Archive, perform real-time phylogenetics, examine sequences for mutations of
potential antigenic or functional significance, and develop an early warning system with a real-time analytics
dashboard. We will also conduct real-time phylodynamic studies using Bayesian methods to understand the
emergence and spread of the virus among dairy cattle in the United States. Further, we will ensure that any
data newly collected through this work, and processed results from our framework are publicly available
through Github and whenever applicable through repositories such as NCBI GenBank and discoverable
through the NIAID Data Discovery Portal. Our proposed framework will provide critical insights into the
ongoing evolution of the virus and serve as an early warning system for the emergence of any phenotypes
with pandemic potential.

## Key facts

- **NIH application ID:** 11121682
- **Project number:** 3U19AI135995-07S2
- **Recipient organization:** SCRIPPS RESEARCH INSTITUTE, THE
- **Principal Investigator:** Kristian Graugaard Andersen
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $820,000
- **Award type:** 3
- **Project period:** 2024-07-01 → 2028-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11121682

## Citation

> US National Institutes of Health, RePORTER application 11121682, Center for Viral Systems Biology- H5N1 Supplement (3U19AI135995-07S2). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/11121682. Licensed CC0.

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