Research Project: Intervention Strategies to Control Endemic and New and Emerging Influenza A Virus Infections in Swine

Location: Virus and Prion Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

A 2018-2019 human seasonal H3N2 influenza A virus spillover into swine with demonstrated virus transmission in pigs - (Peer Reviewed Journal)

Experimental reproduction of viral replication and disease in dairy calves and lactating cows inoculated with highly pathogenic avian influenza H5N1 clade 2.3.4.4b - (Peer Reviewed Journal)

A single rare s70 variant establishes a unique gene expression pattern in the E. coli pathobiont LF82 - (Peer Reviewed Journal)
Arroyo - Mendoza, M., Proctor, A., Correa-Medina, A., Dewolf, S., Wymore Brand, M.J., Rosa, V., Lorenzi, H., Wannemuehler, M.J., Phillips, G.J., Hinton, D.M. 2024. A single rare s70 variant establishes a unique gene expression pattern in the E. coli pathobiont LF82. Nucleic Acids Research. https://doi.org/10.1093/nar/gkae773.

Phylogenetic-based methods for fine-scale classification of PRRSV-2 ORF5 sequences: a comparison of their robustness and reproducibility - (Peer Reviewed Journal)
Vanderwaal, K., Pamornchainvakul, N., Kikuti, M., Linhares, D.C., Trevisan, G., Zhang, J., Anderson, T.K., Zeller, M., Rossow, S., Holtkamp, D.J., Makau, D.N., Corzo, C.A., Paploski, I.A. 2024. Phylogenetic-based methods for fine-scale classification of PRRSV-2 ORF5 sequences: a comparison of their robustness and reproducibility. Frontiers in Virology. https://doi.org/10.3389/fviro.2024.1433931.

Reverse zoonosis of the 2022-2023 human seasonal H3N2 detected in swine - (Peer Reviewed Journal)
Zeller, M., Moraes, D., Ciacci Zanella, G., Souza, C.K., Anderson, T.K., Baker, A.L., Gauger, P.C. 2024. Reverse zoonosis of the 2022-2023 human seasonal H3N2 detected in swine. Viruses. https://doi.org/10.1038/s44298-024-00042-4.

Biomarkers associated with vaccine-associated enhanced respiratory disease following influenza A infection in swine - (Peer Reviewed Journal)
Wymore Brand, M.J., Souza, C.K., Gauger, P., Arruda, B.L., Baker, A.L. 2024. Biomarkers associated with vaccine-associated enhanced respiratory disease following influenza A infection in swine. Veterinary Immunology and Immunopathology. https://doi.org/10.1016/j.vetimm.2024.110787.

Potential pandemic risk of circulating swine H1N2 influenza viruses - (Peer Reviewed Journal)
Le Sage, V., Rockey, N.C., French, A.J., McBride, R., McCarthy, K.R., Rigatti, L.H., Shephard, M.J., Jones, J.E., Walter, S.G., Doyle, J.D., Xu, L., Barbeau, D.J., Wang, S., Frizzell, S.A., Myerburg, M.M., Paulson, J.C., McElroy, A.K., Anderson, T.K., Baker, A.L., Lakdawala, S.S. 2024. Potential pandemic risk of circulating swine H1N2 influenza viruses. Nature. https://doi.org/10.1038/s41467-024-49117-z.

Surveillance and detection of Haemaphysalis longicornis (Acari: Ixodidae) in protected areas from Georgia, USA - (Peer Reviewed Journal)
Fausett, E.N., Oscar, K.D., Bellman, S., Long, A., Roeske, I., Cheng, C., Piantadosi, A., Anderson, T.K., Vazquez-Prokopec, G.M. 2024. Surveillance and detection of Haemaphysalis longicornis (Acari: Ixodidae) in protected areas from Georgia, USA. Journal of Medical Entomology. https://doi.org/10.1093/jme/tjae051.

Detection and characterization of influenza A virus endemic circulation in suckling and nursery pigs originating from vaccinated farms in the same production system - (Peer Reviewed Journal)
Silva Dias, A., Baker, A.L., Baker, R.B., Zhang, J., Zeller, M.A., Kitikoon, P., Gauger, P.C. 2024. Detection and characterization of influenza A virus endemic circulation in suckling and nursery pigs originating from vaccinated farms in the same production system. Viruses. https://doi.org/10.3390/v16040626.

Divergent pathogenesis and transmission among avian and mammalian isolates of highly pathogenic avian influenza A (H5N1) in swine - (Proceedings)

Divergent pathogenesis and transmission of highly pathogenic avian influenza A(H5N1) in swine - (Peer Reviewed Journal)
Arruda, B.L., Baker, A.L., Buckley, A.C., Anderson, T.K., Torchetti, M., Hines Bergeson, N., Killian, M.L., Lantz, K. 2024. Divergent pathogenesis and transmission of highly pathogenic avian influenza A(H5N1) in swine. Emerging Infectious Diseases. https://doi.org/10.3201/eid3004.231141.

Amino acid 138 in the HA of a H3N2 subtype influenza A virus increases affinity for the lower respiratory tract and alveolar macrophages in pigs - (Peer Reviewed Journal)
Cardenas, M., Seibert, B., Cowan, B., Fraiha, A.S., Carnaccini, S., Gay, C.L., Faccin, F., Caceres, J.C., Anderson, T.K., Baker, A.L., Perez, D.R., Rajao, D.S. 2024. Amino acid 138 in the HA of a H3N2 subtype influenza A virus increases affinity for the lower respiratory tract and alveolar macrophages in pigs. PLoS Pathogens. https://doi.org/10.1371/journal.ppat.1012026.

Nucleoprotein reassortment enhanced transmissibility of H3 1990.4.a clade influenza A virus in swine - (Peer Reviewed Journal)
Thomas, M.N., Ciacci Zanella, G., Cowan, B., Caceres, J.C., Rajao, D.S., Perez, D.R., Gauger, P.C., Baker, A.L., Anderson, T.K. 2024. Nucleoprotein reassortment enhanced transmissibility of H3 1990.4.a clade influenza A virus in swine. Journal of Virology. https://doi.org/10.1128/jvi.01703-23.

The evolution of SARS-CoV-2 and influenza A virus at the human-animal interface - (Book / Chapter)
Anderson, T.K., Medina, R., Nelson, M.I. 2024. The evolution of SARS-CoV-2 and influenza A virus at the human-animal interface. Book Chapter. https://doi.org/10.1016/B978-0-443-28818-0.00016-1.

Asymmetric cluster-based measures for comparative phylogenetics - (Peer Reviewed Journal)
Wagle, S., Markin, A., Gorecki, P., Anderson, T.K., Eulenstein, O. 2024. Asymmetric cluster-based measures for comparative phylogenetics. Journal of Computational Biology. https://doi.org/10.1089/cmb.2023.0338.

Pigs lacking TMPRSS2 displayed fewer lung lesions and reduced inflammatory response when infected with influenza A virus - (Peer Reviewed Journal)
Ciacci Zanella, G., Snyder, C.A., Arruda, B.L., Whitworth, K., Green, E., Poonooru, R.R., Telugu, B.P., Baker, A.L. 2024. Pigs lacking TMPRSS2 displayed fewer lung lesions and reduced inflammatory response when infected with influenza A virus. Frontiers in Genome Editing. https://doi.org/10.3389/fgeed.2023.1320180.

Detection and disease diagnosis trends (2017-2022) for Streptococcus suis, Glaesserella parasuis, Mycoplasma hyorhinis, Actinobacillus suis and Mycoplasma hyosynoviae at Iowa state university veterinary diagnostic laboratory - (Peer Reviewed Journal)
Poeta Silva, A.S., Almeida, M., Michael, A., Rahe, M.C., Siepker, C., Magstadt, D.R., Pineyro, P., Arruda, B.L., Macedo, N.R., Sahin, O., Gauger, P., Krueger, K., Mugabi, R., Streauslin, J.S., Trevisan, G., Linhares, D., Silva, G.S., Fano, E., Main, R., Schwartz, K.J., Burrough, E.R., Derscheid, R.J., Sitthicharoenchai, P., Clavijo, M.J. 2023. Detection and disease diagnosis trends (2017-2022) for Streptococcus suis, Glaesserella parasuis, Mycoplasma hyorhinis, Actinobacillus suis and Mycoplasma hyosynoviae at Iowa state university veterinary diagnostic laboratory. BMC Veterinary Research. https://doi.org/10.1186/s12917-023-03807-w.

classLog: Logistic regression for the classification of genetic sequences - (Peer Reviewed Journal)
Zeller, M.A., Arendsee, Z.W., Smith, G.J., Anderson, T.K. 2023. classLog: Logistic regression for the classification of genetic sequences. Frontiers in Virology. https://doi.org/10.3389/fviro.2023.1215012.

Refining PRRSV-2 genetic classification based on global ORF5 sequences and investigation of their geographic distributions and temporal changes - (Peer Reviewed Journal)
Yim-Im, W., Anderson, T.K., Paploski, I.A., Vanderwaal, K., Gauger, P.C., Krueger, K., Shi, M., Main, R., Zhang, J. 2023. Refining PRRSV-2 genetic classification based on global ORF5 sequences and investigation of their geographic distributions and temporal changes. Microbiology Spectrum. https://doi.org/10.1128/spectrum.02916-23.

Salmonella enterica induces biogeography-specific changes in the gut microbiome of pigs - (Peer Reviewed Journal)
Gomes-Neto, J., Pavlovikj, N., Korth, N., Naberhaus, S.A., Arruda, B.L., Benson, A.K., Kreuder, A.J. 2023. Salmonella enterica induces biogeography-specific changes in the gut microbiome of pigs. Frontiers in Veterinary Science. https://doi.org/10.3389/fvets.2023.1186554.

Human-to-swine introductions and onward transmission of 2009 H1N1 pandemic influenza viruses in Brazil - (Peer Reviewed Journal)
Junqueira, D.M., Tochetto, C., Anderson, T.K., Gava, D., Haach, V., Cantao, M.E., Baker, A.L., Schaefer, R. 2023. Human-to-swine introductions and onward transmission of 2009 H1N1 pandemic influenza viruses in Brazil. Frontiers in Microbiology. 14. https://doi.org/10.3389/fmicb.2023.1243567.

Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential - (Peer Reviewed Journal)
Markin, A., Ciacci Zanella, G., Arendsee, Z.W., Zhang, J., Krueger, K.M., Gauger, P.C., Baker, A.L., Anderson, T.K. 2023. Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential. PLoS Pathogens. 19(7). Article e1011476. https://doi.org/10.1371/journal.ppat.1011476.

Mucin 4 is a cellular biomarker of necrotizing bronchiolitis in influenza A virus infection - (Peer Reviewed Journal)
Arruda, B.L., Kanefsky, R.A., Hau, S.J., Janzen, G.M., Anderson, T.K., Baker, A.L. 2023. Mucin 4 is a cellular biomarker of necrotizing bronchiolitis in influenza A virus infection. Microbes and Infection. e105169. https://doi.org/10.1016/j.micinf.2023.105169.

PARNAS: Objectively selecting the most representative taxa on a phylogeny - (Peer Reviewed Journal)
Markin, A., Wagle, S., Grover, S., Baker, A.L., Eulenstein, O., Anderson, T.K. 2023. PARNAS: Objectively selecting the most representative taxa on a phylogeny. Systematic Biology. esyad028. https://doi.org/10.1093/sysbio/syad028.

Phylogenetic diversity statistics for all clades in a phylogeny - (Peer Reviewed Journal)
Grover, S., Markin, A., Anderson, T.K., Eulenstein, O. 2023. Phylogenetic diversity statistics for all clades in a phylogeny. Bioinformatics. 39(1):i177-i184. https://doi.org/10.1093/bioinformatics/btad263.

The asymmetric cluster affinity cost - (Peer Reviewed Journal)
Wagle, S., Markin, A., Gorecki, P., Anderson, T.K., Eulenstein, O. 2023. The asymmetric cluster affinity cost. Research Computational Molecular Biology (RECOMB). 13883:131-145. https://doi.org/10.1007/978-3-031-36911-7_9.

Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine - (Peer Reviewed Journal)
Hufnagel, D.E., Young, K.M., Arendsee, Z., Gay, L.C., Caceres, C.J., Rajao, D., Perez, D.R., Baker, A.L., Anderson, T.K. 2023. Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine. Virus Evolution. 9(1). Article 10.1093. https://doi.org/10.1093/ve/vead015.

Introductions of human-origin seasonal H3N2, H1N2, and pre-2009 H1N1 influenza viruses to swine in Brazil - (Peer Reviewed Journal)
Tochetto, C., Junqueira, D.M., Anderson, T.K., Gava, D., Haach, V., Cantao, M.E., Baker, A.L., Schaefer, R. 2023. Introductions of human-origin seasonal H3N2, H1N2, and pre-2009 H1N1 influenza viruses to swine in Brazil. Viruses. 15(2). Article 576. https://doi.org/10.3390/v15020576.

Swine-to-ferret transmission of antigenically drifted contemporary swine H3N2 influenza A virus is an indicator of zoonotic risk to humans - (Peer Reviewed Journal)
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., Sharmi, T., Baker, A.L. 2023. Swine-to-ferret transmission of antigenically drifted contemporary swine H3N2 influenza A virus is an indicator of zoonotic risk to humans. Viruses. 15(2). Article 331. https://doi.org/10.3390/v15020331.

Live attenuated influenza A virus vaccine expressing an IgA-inducing protein protects pigs against replication and transmission. - (Peer Reviewed Journal)
Rajoa, D.S., Zanella, G.C., Brand, M.W., Khan, S., Miller, M.E., Ferreri, L.M., Caceres, C., Cadernas-Garcia, S., Souza, C.K., Anderson, T.K., Gauger, P.C., Baker, A.L., Perez, D.R. 2023. Live attenuated influenza A virus vaccine expressing an IgA-inducing protein protects pigs against replication and transmission.. Frontiers in Virology. 3. Article 1042724. https://doi.org/10.3389/fviro.2023.1042724.

Fine-Scale Analysis of Influenza A Virus in Swine Reveals Persistent Clade Circulation and Limited Clade Diversity within Owners - (Proceedings)
Arruda, B.L., Neveau, M., Baker, A.L., Anderson, T.K., De-Sousa-E-Silva, G., Gauger, P.C. 2023. Fine-Scale Analysis of Influenza A Virus in Swine Reveals Persistent Clade Circulation and Limited Clade Diversity within Owners. American Association of Swine Veterinarians Annual Meeting. American Association of Swine Veterinarians Annual Meeting, March 4-7, 2023, Aurora, Colorado.

Divergent pathology between highly pathogenic avian influenza A (H5N1) strains in swine - (Proceedings)
Arruda, B.L., Devries, A.C., Killian, M., Hines Bergeson, N., Torachetti, M., Baker, A.L. 2023. Divergent pathology between highly pathogenic avian influenza A (H5N1) strains in swine. American Association of Swine Veterinarians Annual Meeting. American Association of Swine Veterinarians Annual Meeting, March 4-7, 2023, Aurora, Colorado.

Veterinarian perceptions and practices in prevention and control of influenza virus in the midwest United States swine farms - (Peer Reviewed Journal)
Moraes, D.C., Baker, A.L., Wang, X., Zhu, Z., Berg, E., Trevisan, G., Zhang, J., Jayaraman, S., Linhares, D., Gauger, P.C., Silva, G.S. 2023. Veterinarian perceptions and practices in prevention and control of influenza virus in the midwest United States swine farms. Frontiers in Veterinary Infectious Diseases. 10. https://doi.org/10.3389/fvets.2023.1089132.

smot: a python package and CLI tool for contextual phylogenetic subsampling - (Peer Reviewed Journal)
Arendsee, Z.W., Baker, A.L., Anderson, T.K. 2022. smot: a python package and CLI tool for contextual phylogenetic subsampling. Journal of Open Source Software. 7(80). Article 4193. https://doi.org/10.21105/joss.04193.

Swine influenza A viruses and pandemic preparedness - (Peer Reviewed Journal)
Anderson, T.K., Baker, A.L. 2022. Swine influenza A viruses and pandemic preparedness. Council for Agricultural Science and Technology Issue Paper. SP33:26-28.

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 - (Peer Reviewed Journal)
Kimble, J., Souza, C.K., Anderson, T.K., Arendsee, Z.W., Hufnagel, D.E., Young, K.M., Lewis, N.S., Davis, C., Thor, S., Baker, A.L. 2022. 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. 14(11). Article 2398. https://doi.org/10.3390/v14112398.

Antigenic characterization and pandemic risk assessment of North American H1 influenza A viruses circulating in swine - (Peer Reviewed Journal)
Venkatesh, D., Anderson, T.K., Chang, J., Lopes, S., Kimble, B., Souza, C.K., Pekosz, A., Rothman, R.E., Chen, K., Baker, A.L., Lewis, N.S. 2022. Antigenic characterization and pandemic risk assessment of North American H1 influenza A viruses circulating in swine. Microbiology Spectrum. 10(6). Article e01781-22. https://doi.org/10.1128/spectrum.01781-22.

Transmission of human influenza A virus in pigs selects for adaptive mutations on the HA gene - (Peer Reviewed Journal)
Mo, J., Abente, E.J., Sutton, T.C., Ferreri, L.M., Geiger, G., Gauger, P.C., Perez, D.R., Baker, A.L., Rajao, D.S. 2022. Transmission of human influenza A virus in pigs selects for adaptive mutations on the HA gene. Journal of Virology. 96(22). Article e01480-22. https://doi.org/10.1128/jvi.01480-22.

Development and evaluation of antigen-specific dual matrix Pestivirus K ELISAs using longitudinal known infectious status samples - (Peer Reviewed Journal)
Arruda, B.L., Falkenberg, S.M., Mora-Diaz, J., Matias Ferreyra, F.S., Magtoto, R., Gimenez-Lirola, L. 2022. Development and evaluation of antigen-specific dual matrix Pestivirus K ELISAs using longitudinal known infectious status samples. Journal of Clinical Microbiology. 60(11). Article e00697-22. https://doi.org/10.1128/jcm.00697-22.

Changes in the hemagglutinin and internal gene segments were needed for human seasonal H3 influenza A virus to efficiently infect and replicate in swine - (Peer Reviewed Journal)
Rajao, D., Abente, E.J., Powell, J.D., Bolton, M.J., Gauger, P.C., Arruda, B.L., Anderson, T.K., Sutton, T., Perez, D.R., Baker, A.L. 2022. Changes in the hemagglutinin and internal gene segments were needed for human seasonal H3 influenza A virus to efficiently infect and replicate in swine. Pathogens. 11(9). Article 967. https://doi.org/10.3390/pathogens11090967.

Bivalent hemagglutinin and neuraminidase influenza replicon particle vaccines protect pigs against influenza a virus without causing vaccine associated enhanced respiratory disease - (Peer Reviewed Journal)
Wymore Brand, M., Anderson, T.K., Kitikoon, P., Kimble, B.J., Otis, N.J., Gauger, P.C., Souza, C.K., Kaplan, B.S., Mogler, M., Strait, E., Baker, A.L. 2022. Bivalent hemagglutinin and neuraminidase influenza replicon particle vaccines protect pigs against influenza a virus without causing vaccine associated enhanced respiratory disease. Vaccine. 40(38): 5569-5578. https://doi.org/10.1016/j.vaccine.2022.07.042.

Characterizing a century of genetic and antigenic diversity of N1 neuraminidase in influenza A virus from North American swine - (Abstract Only)
David, H.E., Young, K.M., Arendsee, Z.W., Gay, C.L., Caceres, J.C., Rajao, D.S., Perez, D.R., Baker, A.L., Anderson, T.K. 2022. Characterizing a century of genetic and antigenic diversity of N1 neuraminidase in influenza A virus from North American swine (abstract). Centers of Excellence for Influenza Research and Response (CEIRR) annual meeting. p. 144.

Machine learning for sequence classification and predicting antigenic phenotype - (Abstract Only)
Anderson, T.K., Baker, A.L. 2022. Machine learning for sequence classification and predicting antigenic phenotype (abstract). The 65th Annual Meeting of the American Association of Veterinary Laboratory Diagnosticians. p.6.

Use of the ISU FLUture multisequence identity tool for rapid interpretation of swine influenza A virus sequences in the United States - (Peer Reviewed Journal)
Zeller, M.A., Saxena, A., Anderson, T.K., Baker, A.L., Gauger, P.C. 2022. Use of the ISU FLUture multisequence identity tool for rapid interpretation of swine influenza A virus sequences in the United States. Journal of Veterinary Diagnostic Investigation. 34(5):874-878. https://doi.org/10.1177/10406387221111128.

OFFLU Swine Influenza Report: July 2021 to December 2021 - (Government Publication)
Markin, A., Hufnagel, D.E., Arendsee, Z., Snyder, C., Janas-Martindale, A., Inderski, B., Brown, I., Anderson, T.K., Lewis, N.S., Baker, A.L., Coggon, A., Sara, L., James, J., Mollet, B., Lewis, T. 2022. OFFLU Swine Influenza Report: July 2021 to December 2021. Technical report generated for the World Health Organization (WHO) Vaccine Consultation Meeting. p.62.

Overview of recent USDA surveillance data - (Proceedings)

Novel morbillivirus as a putative cause of fetal death and encephalitis among swine - (Proceedings)
Arruda, B.L., Li, G., Zheng, Y., Shen, H. 2021. Novel morbillivirus as a putative cause of fetal death and encephalitis among swine. Meeting Proceedings. (27)7-July 2021. https://doi.org/10.3201/eid2707.203971.

octoFLUshow: an interactive tool describing spatial and temporal trends in the genetic diversity of influenza A virus in U.S. swine - (Rapid Release Publication)
Arendsee, Z.W., Chang, J., Hufnagel, D.E., Markin, A., Baker, A.L., Anderson, T.K. 2021. octoFLUshow: an interactive tool describing spatial and temporal trends in the genetic diversity of influenza A virus in U.S. swine. Microbiology Resource Announcements. 10(50). Article e01081-21. https://doi.org/10.1128/MRA.01081-21.