Deadly bird flu establishes a foothold in North America

Stokstad, Erik

doi:10.1126/science.ade5542

Cited by 11 publications

(8 citation statements)

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“…Other European colony breeding species affected by HPAI in the breeding season 2022 are the Eurasian spoonbill ( Platalea leucorodia ) in the Netherlands and, in other parts of northwest Europe, common guillemots ( Uria aalge ). This development turned out to be embedded in a larger scale expansion of HPAIVs of the gs/GD lineage of Southeast Asian origin into the Northern Atlantic and onward to North America [7, 8]. In early May 2022, AI was detected in a sandwich tern colony on the German Baltic coast (Langenwerder).…”

Section: Introductionmentioning

confidence: 99%

Mass mortality among colony-breeding seabirds in the German Wadden Sea in 2022 due to distinct genotypes of HPAIV H5N1 clade 2.3.4.4b

Pohlmann

Stejskal

King

et al. 2023

Journal of General Virology

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Mass mortality was observed among colony-breeding seabirds in the German Wadden Sea area of the North Sea during the summer months of 2022. Several species’ colonies were affected, most notably sandwich terns (Thalasseus sandvicensis), common terns (Sterna hirundo) and Germany’s only northern gannet (Morus bassanus) colony on the island of Heligoland. Mortality in some tern colonies reached 40%, while other colonies were almost spared. In all cases, infections with the high-pathogenicity avian influenza virus (HPAIV) subtype H5N1 of clade 2.3.4.4b were identified to have caused the epidemic. Phylogenetic analysis of whole-genome sequences revealed that the outbreaks were dominated by two genotypes, Ger-10–21 N1.2 and Ger-10–21 N1.5, previously identified in Germany. Spatiotemporal analyses of phylogenetic data suggested that these viruses could have entered the continental North Sea coastal region via the British Isles. A close linkage of viruses from tern colonies in the German Wadden Sea was evident with further connections to breeding colonies in Belgium and the Netherlands, and further spread to Denmark and Poland. Several of the affected species are endangered, such that negative effects of epizootic HPAIV infections on populations are feared, with uncertain long-term consequences.

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Section: Introductionmentioning

confidence: 99%

Mass mortality among colony-breeding seabirds in the German Wadden Sea in 2022 due to distinct genotypes of HPAIV H5N1 clade 2.3.4.4b

Pohlmann

Stejskal

King

et al. 2023

Journal of General Virology

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“…In contrast, we were able to replicate these findings using only existing short-read whole genome sequencing data and pangenome methods. We expect that our pangenome, and future pangenomes using telomere-to-telomere genome assemblies, which exist for increasing numbers of species [54][55][56][57][58] but not yet chickens, will enable discoveries about complex structural variation at important immune loci such as the major histocompatibility complex (MHC) and T cell receptor gene (TCR), providing insight into the genetic diversity necessary to fight evolving pathogen threats in this major worldwide source of protein, which also threaten wildlife with increasing frequency [59].…”

Section: Discussionmentioning

confidence: 99%

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Rice¹,

Alberdi²,

Alfieri³

et al. 2023

Preprint

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Background. The red junglefowl, the wild progenitor of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. Results. We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K ‘feathering’ locus using short reads, which would not be possible using a linear reference. Conclusions. We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.

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“…H5N1 has now reached the remote islands of Galapagos and threatens endemic bird species. Also, sea lions and fur seals have been hit hard in South America (Stokstad, 2023). In contrast to earlier HPAI H5 clades which primarily circulated regionally in domesticated birds, the new H5 clade (2.3.4.4b) showed longer persistence in wild than domesticated birds.…”

Section: H5n1 Infectionsmentioning

confidence: 99%

Avian influenza virus cross‐infections as test case for pandemic preparedness: From epidemiological hazard models to sequence‐based early viral warning systems

Brüssow

2024

Microbial Biotechnology

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Pandemic preparedness starts with an early warning system of viruses with a pandemic potential. Based on information collected in a multitude of surveys, hazard models were developed identifying influenza viruses presenting a pandemic threat. Scores are attributed for 10 viral traits by expert panels which identified avian influenza viruses (AIV) belonging to subtypes H7N9 and H5N1 as representing the greatest pandemic risk. In 2013, more than 100 human cases infected with AIV H7N9 were observed in China. Case fatality rate (CFR) was high (27%), but the human‐to‐human transmission rate was low and by serological evidence H7N9 did not spread widely. Nevertheless, until 2019 more than 1500 H7N9 patients were identified characterized by a high CFR of 39%. Serology demonstrated that mild infections with H7N9 were widespread. In 2003, more than 400 people experienced AIV H7N7 cross‐infection causing mainly conjunctivitis during a large poultry epidemic in The Netherlands. Between 1996 and 2019, a total of 881 human infections with avian H5N1 viruses were documented showing a CFR of 52%. Outbreaks were centred on South East Asia and showed close associations with epizootics in poultry. Mutations predisposing to human cross‐infections were identified in the haemagglutinin (HA) and the RNA polymerase subunit PB2 of human H7N9 isolates. Human H5N1 isolates showed mutations in the receptor binding domain of HA and transmission in mammals could be obtained by as few as four additional aa changes introduced experimentally. Researchers have defined viral point mutations in HA, PB2 and the nucleoprotein NP that allowed AIV to cross the species barrier to mammals with respect to receptor recognition, RNA replication and escape from innate immunity respectively. Based on this insight a sequence‐based early warning system for AIV preadapted to human transmission could be envisioned. Mink farms and live poultry markets are prime targets for such sequencing efforts.

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Deadly bird flu establishes a foothold in North America

Abstract: H5N1 has continued to kill wild birds and poultry this summer. The fall migration could bring it back in force

Cited by 11 publications

References 0 publications

Mass mortality among colony-breeding seabirds in the German Wadden Sea in 2022 due to distinct genotypes of HPAIV H5N1 clade 2.3.4.4b

Mass mortality among colony-breeding seabirds in the German Wadden Sea in 2022 due to distinct genotypes of HPAIV H5N1 clade 2.3.4.4b

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Avian influenza virus cross‐infections as test case for pandemic preparedness: From epidemiological hazard models to sequence‐based early viral warning systems

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