H5N1 Genotype D1.1 Spread Rapidly Across US Flyways in 2024

The D1.1 genotype of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b spread in a stepwise pattern among adjacent US flyways during fall 2024, according to a phylodynamic analysis combining targeted wild bird surveillance in Arizona with publicly available US sequence data.

The findings, published in Emerging Infectious Diseases, add detail to the timeline and spread pattern of a genotype that has caused severe human illness.^1,2 The effort was led by a group out of Arizona State University (ASU) and the Arizona Department of Fish and Wildlife, including Matthew Scotch, PhD, MPH, the senior associate dean of research, professor of biomedical informatics, and assistant director of the Biodesign Center for Environmental Health Engineering at ASU.

Phylodynamic analysis and Arizona wild bird surveillance trace fall 2024 dissemination pattern

H5N1 clade 2.3.4.4b has continued circulating in North America since its introduction, and its D1.1 genotype became the dominant lineage detected in birds in late 2024.¹ Although recent phylodynamic reconstructions have placed the emergence of D1.1 in mid-2024, they have differed on its inferred geographic origin and early spread pathways.¹ Researchers combined hemagglutinin sequence data from clade 2.3.4.4b detections across the United States with dedicated wild bird surveillance conducted in Arizona to refine estimates of when D1.1 emerged and how it moved among the 4 major US migratory flyways.¹

Phylodynamic analyses showed genotype transitions concentrated among adjacent flyway regions, a pattern consistent with stepwise dissemination during fall 2024 rather than simultaneous introduction across the country.¹ The analyses found limited support for long-distance exchange directly between the Pacific and Atlantic flyways, suggesting the virus more commonly moved through intermediate regions as it spread nationally.

As part of the targeted surveillance component, researchers tested 177 wild birds representing 38 species across 10 of 15 counties in Arizona between September 2023 and May 2025, identifying 10 birds, or 6%, positive for highly pathogenic avian influenza.¹ The Arizona data contributed additional geographic and temporal resolution to the broader flyway-level phylodynamic reconstruction.

D1.1 Genotype Carries Documented Risk to Humans and Livestock

Clade 2.3.4.4b, including the D1.1 genotype specifically, has caused severe and fatal human illness in North America, and D1.1 has also been detected in dairy cattle in multiple states following presumed bird-to-cattle transmission events, part of a broader One Health threat spanning wild birds, poultry, and mammals.² The genotype arose through reassortment between introduced Eurasian-lineage viruses and North American low pathogenicity avian influenza viruses circulating in wild birds.¹

The study authors said understanding how genotypes like D1.1 disseminate among flyways can help inform the geographic targeting of wild bird and poultry surveillance efforts as new H5N1 genotypes continue to emerge.¹ Continued genomic surveillance across flyway regions, rather than reliance on any single region's data, remains important given the virus's demonstrated capacity to reassort and spread across the country, including into Arizona dairy herds.¹

References

1. Scotch M, Faleye TOC, Urquidez-Negrete A, Varsani A, Fan A, Justice-Allen A. 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;32(8). Accessed July 31, 2026. https://wwwnc.cdc.gov/eid/article/32/8/26-0205_article

2. Centers for Disease Control and Prevention. H5 Bird Flu: Current Situation. Accessed July 31, 2026. https://www.cdc.gov/bird-flu/situation-summary/index.html