On Sunday, April 21st, 2024, “in the interest of public transparency and ensuring the scientific community has access to this information as quickly as possible to encourage disease research and development to benefit the U.S. dairy industry”, the National Veterinary Services Laboratories (NVSL) of the Animal and Plant Health Inspection Service (APHIS) of the U.S. Department of Agriculture (USDA) shared H5N1 sequence reads from 239 Biosamples related to the ongoing H5N1 clade 2.3.4.4b influenza A virus outbreak in U.S. cattle and other species [1]. As they noted, “the sequences were made available with appreciation to the state animal health authorities and National Animal Health Laboratories conducting testing”.
These data were shared as BioProject PRJNA1102327 on the Sequence Read Archive (SRA) of the National Institute of Health’s National Library of Medicine, National Center for Biotechnology Information (NCBI). Sequences posted were from cattle (n=202), cats (9), chickens (18), skunk (1), raccoon (1), grackle (3), blackbird (2), canada goose (1), peregrine falcon (1), and goose (1). APHIS announced that they would continue making additional raw genetic sequences available on a rolling basis at Home - SRA - NCBI (nih.gov ) by searching for “WGS of H5N1” [2].
In order to provide the wider scientific community with consensus sequences required for evolutionary, phylodynamic, molecular, virologic, diagnostic, therapeutic, and other studies, as well as to conduct our own research into the H5N1 outbreak in cattle and other species, we rapidly generated high-quality genome assemblies of each of the eight H5N1 viral genome segments for each of the 239 sets of raw sequencing reads made available by APHIS. We initially shared these consensus genomes in a public GitHub repository [3] on April 22nd, 2024 and have continued to update the repository as new data and metadata become available…
The consensus genome sequences for the eight segments were generated with EPI_ISL_19032063 (GISAID [4]) as a reference, using iVar v1.4.2 [5], a computational package that contains functions broadly useful for viral amplicon-based sequencing. Minimum depth was set at 1, minimum quality at 20, and the minimum frequency to call consensus was set at 50%. Consensus genome sequences, metadata from SRA, and alignments of each genome segment of the 239 viruses are available in this repository
We created an initial table of the metadata associated with the sequencing reads shared in the SRA by APHIS, including host species, which are available in the SRA files [6]. These files do not include information on when (other than year) or where (other than the US) the samples were collected. Dates and locations for a subset of the samples were included in a presentation by Dr. Rosemary Sifford, DVM, Deputy Administrator Veterinary Services, and Chief Veterinary Officer, APHIS, given at a virtual symposium hosted by The Association of State and Territorial Health Officials to facilitate a discussion between public health leaders and scientists driving the U.S. Government’s response to Highly Pathogenic Avian Influenza (HPAI) [7]. We thus updated our table with dates (to day) of sampling and US state of provenance for 152 of the 239 samples [6].
We hope the H5N1 genome sequences we have assembled from sequence read data generously shared publicly by USDA/APHIS will assist in the USDA’s goal of enabling timely outbreak responses and infectious disease research. We, in turn, encourage researchers globally to use these sequences to support biomedical research, public health, animal health and welfare, and safe and secure food production within the U.S. dairy industry and beyond.
Karthik Gangavarapu, Jonathan Pekar, Florence Débarre, Kristian Andersen, Gytis Dudas, Daniel Goldhill, Joseph Hughes, Xiang Ji, Jeffrey Joy, Moritz Kraemer, Philippe Lemey, Louise Moncla, Martha Nelson, Stuart Neil, Tom Peacock, Oliver Pybus, Andrew Rambaut, Angela Rasmussen, Christopher Ruis, Lorena Mariana Malpica Serrano, Marc Suchard, Joel Wertheim, Michael Worobey
References
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USDA Publishes H5N1 Influenza A Virus Genetic Sequences on publicly available site. [cited 27 Apr 2024]. Available: https://www.aphis.usda.gov/livestock-poultry-disease/avian/avian-influenza/usda-publishes-h5n1-influenza-virus-genetic
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Home - SRA - NCBI. [cited 27 Apr 2024]. Available: https://www.ncbi.nlm.nih.gov/sra
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GitHub - andersen-lab/avian-influenza: Consensus sequences for U.S. H5N1 clade 2.3.4.4b. In: GitHub [Internet]. [cited 27 Apr 2024]. Available: https://github.com/andersen-lab/avian-influenza
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avian-influenza/acknowledgements/gisaid_acknowledge_table_assemby_reference_sequences.xls at master · andersen-lab/avian-influenza. In: GitHub [Internet]. [cited 27 Apr 2024]. Available: https://github.com/andersen-lab/avian-influenza/blob/master/acknowledgements/gisaid_acknowledge_table_assemby_reference_sequences.xls
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GitHub - andersen-lab/ivar: iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. In: GitHub [Internet]. [cited 27 Apr 2024]. Available: https://github.com/andersen-lab/ivar
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Website. Available: https://github.com/andersen-lab/avian-influenza/blob/f016919bfb0ef2367fd5e78b98d294523b3207e0/metadata/PRJNA1102327_metadata.csv
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Highly Pathogenic Avian Influenza Scientific Symposium. 2024. Available: https://www.youtube.com/watch?v=aTizSNagjFI