H5N1 2024 Influenza A Virus: HPAI Outbreak Reports¶

The BV-BRC HPAI H5N1 Outbreak Reports provide weekly summaries, statistics, and phylogenetics for the genomic data associated with H5N1. The reports also highlight our efforts to assemble and annotate sequences from SRA and news about the outbreak. The report is available as a PDF Summary Report, which highlights host and state differences detected.

In March 2024, several cases of highly pathogenic avian influenza A (HPAI) H5N1 virus were confirmed in dairy cattle in Texas, with cases spreading to at least eight other states. In addition, a human case of influenza from the same clade and genotype was also diagnosed in a dairy worker from Texas around the same time. As part of an effort to track this outbreak, the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) and the USDA National Veterinary Services Laboratories (NVSL) have been working to collect and sequence samples from additional cattle as well as avian species and other animals that also appeared to be infected with HPAI that might be related to the virus from the Texas dairy cattle. The genomic sequences of each virus isolate (consisting of the eight genomic segments sequenced for each individual isolate) are assembled from the sequenced short-read data and, after undergoing quality control, are submitted to the GenBank sequence repository, where they become publicly available. To enhance the ability of the USDA to rapidly submit sequences to GenBank, personnel from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) have been collaborating with USDA scientists to assist them with the submission of assembled HPAI genomic sequences to GenBank.

This report provides statistics on the public availability of HPAI H5N1 genomic sequences historically, especially from isolates collected in North America since 2024.

H5N1 2024 Influenza A Virus: HPAI Outbreak Reports¶

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