We currently track BioProjects associated with the outbreak of H5N1 clade 2.3.4.4b in dairy cattle, peridomestic animals, and other wildlife. We also track BioProjects associated with the surveillance of retail milk samples.
| BioProject | Description |
| PRJNA1102327 | U.S. H5N1 clade 2.3.4.4b genotype B3.13 immediate releases related to emergence and spread in dairy cattle. |
| PRJNA1122849 | U.S. H5N1 clade 2.3.4.4b immediate releases related to peridomestic animals. |
| PRJNA1134696 | Viral sequencing of US dairy milk. |
| PRJNA1219588 | U.S. H5N1 clade 2.3.4.4b genotype D1.1 immediate releases related to emergence in dairy cattle. |
| PRJNA1207547 | U.S. Influenza A Surveillance in Wildlife. |
| PRJNA980729 | US HPAI Sequencing. |
These BioProjects are monitored every 24 hours with processed genomes, intrahost variants, and associated metadata deposited on the repository. We also provide genotypes for each genome using GenoFLU, and for aggregate samples isolated from sources such as “Bulk milk tanks” we provide estimates of the abundance of lineages within each sample. Please see the README in the repository for details on the methods and the folder structure of the processed data. The genomes from this repository are also incorporated into NextStrain and UShER.
