A-Z Index × Submit A-Z Index × Submit A-Z Index Search Dropdown × Submit Facebook Twitter LinkedIn Syndicate Emerging Infectious Disease journal ISSN: 1080-6059 Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released.
Highly pathogenic avian influenza clade 2.3.4.4b virus continues to circulate in North America and has caused severe human disease. That clade includes genotype D1.1, which became dominant in birds in late 2024. Recent phylodynamic reconstructions place D1.1 emergence in mid-2024 but differ on its inferred origin and early dissemination pathways. We combined targeted surveillance of wild birds in Arizona with publicly available US clade 2.3.4.4b hemagglutinin sequences to estimate when D1.1 genotype emerged and to infer its diffusion among the 4 major US flyways. Phylodynamic analyses showed transitions concentrated among adjacent flyways regions, consistent with stepwise dissemination during fall 2024 and limited support for long-distance Pacific–Atlantic exchange. The Pacific Flyway showed patterns consistent with an early source and the Central Flyway with a secondary hub linked to onward spread. Our findings support coordinated genomic surveillance across adjacent flyways to reduce detection delays and improve situational awareness during rapid viral expansion.
Highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b virus was first detected in North America in December 2021 in the Atlantic Flyway ( 1 , 2 ). The virus has extensively infected wild birds ( 3 ), poultry flocks ( 4 ), cattle ( 5 ), and numerous mammalian species ( 6 ). Among various emerging genotypes, D1.1 rapidly became dominant after its detection in the Pacific Flyway in fall 2024. Predominantly found in avian hosts, the D1.1 genotype remained the most abundant lineage for much of 2025 ( 7 ), accounting for most 2.3.4.4b infections in wild birds and domestic poultry. In addition, D1.1 genotype has exhibited substantial zoonotic potential, evidenced by several confirmed human infections in the United States, including a fatal case in Louisiana ( 8 ).
Recent phylodynamic reconstructions have begun to resolve the timing of D1.1 virus emergence ( 9 ; A. Crespo-Bellido et al., unpub. data, https://www.biorxiv.org/content/10.64898/2025.12.19.695329v2 ), but its early diffusion across the 4 North American Flyway regions remains unresolved. To address that gap, we combined targeted wild bird surveillance in Arizona, within the Pacific Flyway, with phylodynamic analyses of newly generated and publicly available clade 2.3.4.4b hemagglutinin (HA) sequences to reconstruct the timing of early D1.1 virus expansion and infer flyway-scale diffusion patterns.
Beginning in September 2023, Arizona Game and Fish Department (AZGFD) staff collected cloacal and oropharyngeal swab samples from sick or dead birds as part of routine surveillance and diagnostic testing. We screened for H5 virus via quantitative reverse transcription PCR, performed long-read sequencing, and assembled raw reads via a bioinformatics pipeline ( Appendix ).
We estimated evolutionary rates and the timing of D1.1 expansion from 660 US avian influenza A(H5N1) clade 2.3.4.4b D1.1 virus genomes by using concatenated whole genomes and individual HA sequences available from GISAID on June 25, 2025 ( 7 ). We leveraged ModelTest-NG version 0.1.7 ( 10 , 11 ), which selected general…