Lightweight multiscale early warning system for influenza A spillovers

2025/10/24 by Tommaso Alfonsi, Anna Bernasconi, Matteo Chiara +1 · 1 voice · 1 citation
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · Medicine · #Animal Disease Management and Epidemiology #Bacillus and Francisella bacterial research #Influenza Virus Research Studies

paper · pdf · doi:10.1126/sciadv.adz7312

openalex publication_date 2025/10/24 · openalex created_date 2025/10/25 · openalex updated_date 2026/08/01

Abstract

Spillovers of zoonotic Influenza A viruses (IAVs) into farmed animals and humans have the potential to trigger epidemics or even global pandemics. We introduce FluWarning, a highly efficient and elegant computational method based on anomaly detection of codon bias and dinucleotide composition for early identification of divergent viral HA segments. We applied FluWarning to the 2009 influenza pandemic as a test case. FluWarning successfully identified the emergence of pdm09, the virus that caused the pandemic, with warnings preceding the observed global spread. Applied to H5N1 specimens collected between 2019 and 2025, FluWarning flagged genotypes D1.1 and B3.13, both associated with recent spillovers in dairy cows in the United States. In summary, FluWarning is an effective, lightweight, multiscale warning system for IAVs, detecting spillovers with few available sequences.

Citations

• An evolutionary perspective on synonymous codon usage in unicellular organisms
• Origins of the 2009 H1N1 influenza pandemic in swine in Mexico
• The global H5N1 influenza panzootic in mammals
• Emergence of Antigenic Variants in Bovine H5N1 Influenza Viruses
• A codon usage-based approach for the stratification of Influenza A across recent spillovers
• Highly pathogenic avian influenza H5N1 in the United States: recent incursions and spillover to cattle
• Anomaly Detection in High Dimensional Data

Cited by

• Influenza A Virus H5N1 Subtype: Resurgent Interspecies and Intercontinental Transmission, and a New Host

Discussions

• #H5N1 #InfluenzaA #OneHealth - Alfonsi et al., 2025. doi.org/10.1126/scia... - Shimon, 2025. doi.org/10.1063/4.00... - Zhang et al., 2025. doi.org/10.1371/jour... 9/9 [bsky, 0 points, 0 comments]