Emergence of D1.1 #reassortant #H5N1 avian #influenza viruses in North #America

 

Abstract

Since 2021, highly pathogenic avian influenza viruses (HPAIV) belonging to H5N1 clade 2.3.4.4b have caused high mortality in North American wild birds and poultry. In 2025, a new D1.1 genotype caused two human deaths and host-switched to dairy cattle. However, the evolutionary origins and dynamics of D1.1 have not been fully characterized. Here, our phylogenetic analysis of 17,516 H5N1 genome sequences uncovers how D1.1 introduced a major shift in the antigenic diversity and ecology of the H5N1 epizootic in North America. D1.1 is the first major H5N1 genotype to (a) emerge in the Pacific flyway and spread west-to-east faster than any prior genotype; (b) antigenically shift via reassortment with the North American N1 segment, displacing the previously fixed Eurasian N1; and (c) transmit to a broader range of host species than any H5N1 genotype to date, introducing mammalian adaptations.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Research Foundation - Flanders, https://ror.org/03qtxy027, G098321N, G0E1420N

European Union Horizon 2023 RIA project LEAPS, 101094685

DURABLE EU4Health project 02/2023-01/2027, 101102733

Fonds National de la Recherche Scientifique, F.4515.22

European Union Horizon 2020 project MOOD, 874850

Source: 

Link: https://www.biorxiv.org/content/10.64898/2025.12.19.695329v1

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The spatial and temporal #spread of highly pathogenic avian #influenza in North #America: Newton's Cradle hypothesis

 

Abstract

The recent emergence of highly pathogenic H5N1- especially clade 2.3.4.4b has led to widespread mortality in poultry and wild birds and has raised significant concerns for the dairy industry and human health. Migratory waterfowl are considered the main source of infection, and we used publicly available surveillance data and bird observation data from continental North America to show clear seasonal signals correlated with waterfowl movement, both on the continental scale and in three of the four flyways. In early 2024, the virus expanded its host range, and we observed a phase transition with the loss of the seasonal signal coupled with a concomitant increase in the proportion of mammalian cases. We also identified a second harmonic, with a regional east-to-west movement with infections spreading between regional flyways, followed by local viral amplification. We likened this to the movement of balls in a Newton's Cradle with an analogy between potential and viral energy. We used bird data to identify bird species associated with viral cases and identified specific waterfowl species and highlighted the importance of predatory and scavenging birds, specifically raptors and gulls, in local amplification. These findings will help to focus surveillance strategies both at local and regional levels.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

United States Department of Agriculture, AP23OA000000C025

Center for Poultry and Livestock Excellence, CPLE23-11

Source: 

Link: https://www.biorxiv.org/content/10.64898/2025.12.19.695483v1

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Distinctive viral #genome #signatures are linked to repeated #mammalian #spillovers of #H5N1 in North #America

 

Abstract

Highly pathogenic avian influenza H5N1 rarely infects mammals. In 2024-2025, however, genotypes B3.13 and D1.1 caused two independent spillovers into U.S. dairy cattle. By analysing 26,930 complete H5N1 genomes from global surveillance, we identified 73 major viral groups, most of which show continent-specific distribution in Europe, Asia, Africa, and North America. North American viruses exhibit higher genetic diversity in specific viral segments, including variants potentially associated with mammalian adaptation. Both dairy-cattle-associated B3.13 and D1.1 genotypes originate from the same geographic macro-area, suggesting a possible regional hotspot where avian-mammalian interfaces may facilitate viral adaptation. Our findings place the U.S. outbreaks in a global framework and indicate that North American H5N1 may be predisposed to cross-species transmission.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

NextGenerationEU, PRIN PNRR 2022 (Italian Ministry of University and Research), P2022CNN2J

Source: 

Link: https://www.biorxiv.org/content/10.64898/2025.12.09.693147v1

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Overview of high pathogenicity avian #influenza #H5N1 clade 2.3.4.4b in #wildlife from Central and South #America, October 2022 - September 2025

 

Abstract

Between 2022 and 2025, high pathogenicity avian influenza (HPAI) H5N1 clade 2.3.4.4b was detected in poultry and wildlife across most countries in Central and South America. The epizootic peaked in 2023, subsided in 2024, and resurged in 2025. In Central America, outbreaks in wildlife were few and small, and mostly affected pelicans. In contrast, South America experienced unprecedented mass mortality in colonial seabirds and pinnipeds, including endangered and endemic species. Notably, viral adaptation enabled mammal-to-mammal transmission in pinnipeds and rapid viral spread across multiple countries along the Pacific and Atlantic coasts. Subsequent introductions to subantarctic islands and Antarctica stemmed from South American viruses. In February 2025, a novel reassortant virus emerged, recombining HPAI H5N1 B3.2 genotype with South American low pathogenicity avian influenza viruses. In May 2025, HPAI H5N1 viruses re-emerged in Brazil, causing a series of outbreaks in poultry and wild birds. The ongoing circulation and evolution of HPAI H5N1 in this region underscores the need for strengthened surveillance, expanded genomic monitoring, and enhanced integration of wildlife conservation and environmental sectors in regional response frameworks.

Source: Canadian Journal of Microbiology, https://cdnsciencepub.com/doi/10.1139/cjm-2025-0189

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