flu-crew datasets used in manuscripts, tutorials, and other work.
Data and files for: Celeste A. Snyder, Garrett M. Janzen, Giovana Ciacci Zanella, Daniel C. A. Moraes, Gustavo S. Silva, Jefferson J. S. Santos, Elizabeth M. Drapeau, Nancy H. L. Leung, Scott E. Hensley, Benjamin J. Cowling, Tavis K. Anderson, Phillip C. Gauger, and Amy L. Baker. Occupationally exposed and general population antibody profiles to influenza A viruses circulating in swine as an indication of zoonotic risk; 2021-22.
We are grateful to the OFFLU Swine Group for their expertise and for sharing data.OFFLU network.
Phylogenetic analysis files for: Le Sage, V., Souza, C.K., Rockey, N.C., Shepard, M., Zanella, G.C., Arruda, B., Wang, S., Drapeau, E., Doyle, J.D., Xu, ., Barbeau, D.J., Paulson, J.C., McElroy, A.K., Hensley, S.E., Anderson, T.K., Baker, A.L., and Lakdawala, S.S. Eurasian 1C swine influenza A virus exhibits high pandemic risk traits. Emerging Microbes & Infections. 2025 Apr 11:2492210..
Powell JD, Thomas MN, Anderson TK, Zeller MA, Gauger PC, Vincent Baker AL. 2018-2019 human seasonal H3N2 influenza A virus spillovers into swine with demonstrated virus transmission in pigs were not sustained in the pig population. Journal of Virology. 2024 Dec 17;98(12):e00087-24. DOI: 10.1128/jvi.00087-24.
We gratefully acknowledge all data contributors, i.e., the Authors and their Originating laboratories responsible for obtaining the specimens, and their Submitting laboratories for generating the genetic sequence and metadata and sharing via the GISAID Initiative, on which components of this research is based. The GISAID acknowledgment table is provided in this repo.
Arruda B, Baker AL, Buckley A, Anderson TK, Torchetti M, Bergeson NH, Killian ML, Lantz K. Divergent pathogenesis and transmission of highly pathogenic avian influenza A (H5N1) in swine. Emerging Infectious Diseases. 2024 Apr;30(4):738. DOI: 10.3201/eid3004.231141.
Raw FASTQ files are available by emailing tavis.anderson@usda.gov
The consensus genomes for the four strains are provided at NCBI Genbank or are hosted at GISAID. We gratefully acknowledge all data contributors, i.e., the Authors and their Originating laboratories responsible for obtaining the specimens, and their Submitting laboratories for generating the genetic sequence and metadata and sharing via the GISAID Initiative, on which components of this research is based. The GISAID acknowledgment table is provided in this repo.
A/red fox/Michigan/22-018712-001-original/2022 = EPI_ISL_15078253
A/raccoon/Washington/22-018406-002-original/2022 = EPI_ISL_15078252
A/turkey/Minnesota/22-010654-002-original/2022 = EPI_ISL_16555202
A/bald eagle/Florida/W22-134-CL/2022 = OP470733-OP470740
A/bald eagle/Florida/W22-134-OP/2022 = OP377436-OP377443
Tree files and data for:
Le Sage, V., Rockey, N.C., McCarthy, K.R., French, A.J., Shephard, M.J.,Jones, J.E., Walter, S.G., Doyle, J.D., Xu, L., Barbeau, D.J., Frizzell, S.A., Myerburg, M.M., McElroy, A.K., Anderson, T.K., Vincent Baker, A.L., Lakdawala, S.S. Potential pandemic risk of circulating swine H1N2 influenza viruses. Nature Communications. 2024 Jun 13;15(1):5025. DOI: 10.1038/s41467-024-49117-z.
Tree files and data for:
Kimble, J.B.; Souza, C.K.; Anderson, T.K.; Arendsee, Z.W.; Hufnagel, D.E.; Young, K.M.; Lewis, N.S.; Davis, C.T.; Thor, S.; Vincent Baker, A.L. Interspecies Transmission from Pigs to Ferrets of Antigenically Distinct Swine H1 Influenza A Viruses with Reduced Reactivity to Candidate Vaccine Virus Antisera as Measures of Relative Zoonotic Risk. Viruses 2022, 14(11), 2398. DOI: 10.3390/v14112398.
Figures and data for:
Thomas, M.N.; Zanella, G.C.; Cowan, B.; Caceres C.J.; Rajao, D.S.; Perez, D.R.; Gauger, P.C.; Baker, A.L.; Anderson, T.K. Nucleoprotein reassortment enhanced transmissability of H3 1990.4.a clade influenza A virus in swine. Journal of Virology. 2024 Mar 19;98(3):e01703-23. DOI: 10.1128/jvi.01703-23.
Tree files and data for:
Souza, C.K., Kimble, J.B., Anderson, T.K., Arendsee, Z.W., Hufnagel, D.E., Young, K.M., Gauger, P.C., Lewis, N.S., Davis, C.T., Thor, S., Vincent Baker, A.L. Transmission from swine-to-ferret of antigenically drifted contemporary swine H3N2 influenza A virus as indications of zoonotic risk to humans. Viruses 2023, 15(2), 331. DOI: 10.3390/v15020331.
Tree files and data for:
Goulart, D.N., Souza C.K., Zanella, G.C., Snyder, C., Zanella, J.C., Markin, A., Arruda, B., Anderson, T.K., Baker, A.L. Pathogenesis and transmission of a reassorted H1 influenza A virus detected in North American swine. In preparation.