Risk assessment of a highly pathogenic H5N1 influenza virus from mink. Restori KH, Septer KM, Field CJ, Patel DR, VanInsberghe D, Raghunathan V, Lowen AC, Sutton TC.Nat Commun. 2024 May 15;15(1):4112. doi: 10.1038/s41467-024-48475-y.

Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections. VanInsberghe D, McBride DS, DaSilva J, Stark TJ, Lau MSY, Shepard SS, Barnes JR, Bowman AS, Lowen AC, Koelle K. PLOS Pathogens. 2024. doi: 10.1371/journal.ppat.1012131

Preprint: Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks. Holmes KE, VanInsberghe D, Ferreri LM, Elie B, Ganti K, Lee CY, Lowen AC. bioRxiv. 2023 Dec 26:2023.11.19.567585. doi: 10.1101/2023.11.19.567585.

Both Humoral and Cellular Immunity Limit the Ability of Live Attenuated Influenza Vaccines to Promote T Cell Responses. Lobby JL, Danzy S, Holmes KE, Lowen AC, Kohlmeier JE.J Immunol. 2024 Jan 1;212(1):107-116. doi: 10.4049/jimmunol.2300343.

Prevention of respiratory virus transmission by resident memory CD8+ T cells. Uddbäck I, Michalets SE, Saha A, Mattingly C, Kost KN, Williams ME, Lawrence LA, Hicks SL, Lowen AC, Ahmed H, Thomsen AR, Russell CJ, Scharer CD, Boss JM, Koelle K, Antia R, Christensen JP, Kohlmeier JE. Nature. 2023 Dec 12. doi: 10.1038/s41586-023-06937-1

Block the Spread: Barriers to Transmission of Influenza Viruses. Le Sage V, Lowen AC, Lakdawala SS. Annu Rev Virol. 2023 Sep 29;10(1):347-370. doi: 10.1146/annurev-virology-111821-115447.

Epistasis reduces fitness costs of influenza A virus escape from stem-binding antibodies. Lee CY, Raghunathan V, Caceres CJ, Geiger G, Seibert B, Cargnin Faccin F, Gay LC, Ferreri LM, Kaul D, Wrammert J, Tan GS, Perez DR, Lowen AC. Proc Natl Acad Sci U S A. 2023 Apr 25;120(17):e2208718120

Evolution of highly pathogenic H5N1 influenza A virus in the central nervous system of ferrets. Siegers JY, Ferreri L, Eggink D, Veldhuis Kroeze EJB, Te Velthuis AJW, van de Bildt M, Leijten L, van Run P, de Meulder D, Bestebroer T, Richard M, Kuiken T, Lowen AC, Herfst S, van Riel D. PLoS Pathog. 2023 Mar 10;19(3):e1011214.

Influenza A virus coinfection dynamics are shaped by distinct virus-virus interactions within and between cells. Delima GK, Ganti K, Holmes KE, Shartouny JR, Lowen AC. PLoS Pathog. 2023 Mar 2;19(3):e1010978. doi: 10.1371/journal.ppat.1010978.

Exclusion of latecomers yields a patchwork of viral subpopulations within hosts. Anice C. Lowen and Lucas M. Ferreri. PLOS Biology. 2023 doi:10.1371/journal.pbio.3001994

Beneficial effects of cellular coinfection resolve inefficiency in influenza A virus transcription. Jessica R. Shartouny, Chung-Young Lee, Gabrielle K. Delima, Anice C. Lowen. PLOS Pathog. 2022. doi:10.1371/journal.ppat.1010865

Influenza A virus reassortment in mammals gives rise to genetically distinct within-host sub-populations. Ketaki Ganti, Anish Bagga, Lucas M. Ferreri, Ginger Geiger, Silvia Carnaccini, C. Joaquin Caceres, Brittany Seibert, Yonghai Li, Liping Wang, Taeyong Kwon, Yuhao Li, Igor Morozov, Wenjun Ma, Juergen A. Richt, Daniel R. Perez, Katia Koelle, Anice C. Lowen. Nature Communications. 2022. doi:10.1038/s41467-022-34611-z

Timing of exposure is critical in a highly sensitive model of SARS-CoV-2 transmission. Ganti K, Ferreri LM, Lee CY, Bair CR, Delima GK, Holmes KE, Suthar MS, Lowen AC. PLoS Pathog. 2022 Mar 25. doi:10.1371/journal.ppat.1010181

Intra- and Inter-Host Evolution of H9N2 Influenza A Virus in Japanese Quail. Lucas M Ferreri, Ginger Geiger, Brittany Seibert, Adebimpe Obadan, Daniela Rajao, Anice C Lowen, Daniel R Perez. Virus Evolution. 2022. doi:10.1093/ve/veac001

Role of helical structure and dynamics in oligoadenylate synthetase 1 (OAS1) mismatch tolerance and activation by short dsRNAs. Schwartz SL, Dey D, Tanquary J, Bair CR, Lowen AC, Conn GL.Proc Natl Acad Sci U S A. 2022. doi:10.1073/pnas.2107111119

Mammalian orthoreovirus reassortment proceeds with little constraint on segment mixing. Hockman MR, Jacobs NT, Mainou BA, Koelle K, Lowen AC. J Virol. 2021. doi:10.1128/JVI.01832-21

Rab11a mediates cell-cell spread and reassortment of influenza A virus genomes via tunneling nanotubes. Ketaki Ganti, Julianna Han, Balaji Manicassamy, Anice C Lowen. PLOS Pathogens. 2021. doi:10.1371/journal.ppat.1009321

Recombinant SARS-CoV-2 Genomes Circulated at Low Levels Over The First Year of The Pandemic. David VanInsberghe, Andrew Neish, Anice C Lowen, Katia Koelle. Virus Evolution. 2021.  doi:10.1093/ve/veab059

Host factor Rab11a is critical for efficient assembly of influenza A virus genomic segments. Julianna Han, Ketaki Ganti, Veeresh Kumar Sali, Carly Twigg, Yifeng Zhang, Senthamizharasi Manivasagam, Chieh-Yu Liang, Olivia A Vogel, Iris Huang, Shanan N Emmanuel, Jesse Plung, Lillianna Radoshevich, Jasmine T Perez, Anice C Lowen, Balaji Manicassamy. PLOS Pathogens. 2021. doi:10.1371/journal.ppat.1009517

Filamentous viruses prevail under pressure. Anice C Lowen. Nature Microbiology. 2021. 6(5):536-537. doi:10.1038/s41564-021-00903-1

Animal models for SARS-CoV-2. Chung-Young Lee and Anice C Lowen. Current Opinion in Virology. 2021. 48:73-81. doi:10.1016/j.coviro.2021.03.009

A quantitative approach to assess influenza A virus fitness and transmission in guinea pigs. Shamika Danzy, Anice C Lowen and John Steel. Journal of Virology. 2021. doi: 10.1128/JVI.02320-20

Avian influenza A viruses reassort and diversify differently in mallards and mammals. Ketaki Ganti, Anish Bagga, Juliana DaSilva, Samuel S Shepard, John R Barnes, Susan Ann Shriner, Katia Koelle, Anice C Lowen. Viruses. 2021. doi:10.3390/v13030509

Type I and Type III IFN Restrict SARS-CoV-2 Infection of Human Airway Epithelial Cultures. Vanderheiden A, Ralfs P, Chirkova T, Upadhyay AA, Zimmerman MG, Bedoya S, Aoued H, Tharp GM, Pellegrini KL, Manfredi C, Sorscher E, Mainou B, Lobby JL, Kohlmeier JE, Lowen AC, Shi PY, Menachery VD, Anderson LJ, Grakoui A, Bosinger SE, Suthar MS. J Virol. 2020. doi:10.1128/JVI.00985-20

Human OAS1 activation is highly dependent on both RNA sequence and context of activating RNA motifs. Schwartz SL, Park EN, Vachon VK, Danzy S, Lowen AC, Conn GL. Nucleic Acids Res. 2020 Jul 27;48(13):7520-7531. doi:10.1093/nar/gkaa513

Collective interactions augment influenza A virus replication in a host-dependent manner. Phipps KL, Ganti K, Jacobs NT, Lee CY, Carnaccini S, White MC, Manandhar M, Pickett BE, Tan GS, Ferreri LM, Perez DR, Lowen AC. Nature Microbiology. 2020 Jul 6. doi:10.1038/s41564-020-0749-2 

A method for the unbiased quantification of reassortment in segmented viruses. Hockman MR, Phipps KL, Holmes KE, Lowen AC. J Virol Methods. 2020 Apr 27;:113878. doi:10.1016/j.jviromet.2020.113878

Characterizing Emerging Canine H3 Influenza Viruses. Martinez-Sobrido L, Blanco-Lobo P, Rodriguez L, Fitzgerald T, Zhang H, Nguyen P, Anderson CS, Holden-Wiltse J, Bandyopadhyay S, Nogales A, DeDiego ML, Wasik BR, Miller BL, Henry C, Wilson PC, Sangster MY, Treanor JJ, Topham DJ, Byrd-Leotis L, Steinhauer DA, Cummings RD, Luczo JM, Tompkins SM, Sakamoto K, Jones CA, Steel J, Lowen AC, Danzy S, Tao H, Fink AL, Klein SL, Wohlgemuth N, Fenstermacher KJ, El Najjar F, Pekosz A, Sauer L, Lewis MK, Shaw-Saliba K, Rothman RE, Liu ZY, Chen KF, Parrish CR, Voorhees IEH, Kawaoka Y, Neumann G, Chiba S, Fan S, Hatta M, Kong H, Zhong G, Wang G, Uccellini MB, García-Sastre A, Perez DR, Ferreri LM, Herfst S, Richard M, Fouchier R, Burke D, Pattinson D, Smith DJ, Meliopoulos V, Freiden P, Livingston B, Sharp B, Cherry S, Dib JC, Yang G, Russell CJ, Barman S, Webby RJ, Krauss S, Danner A, Woodard K, Peiris M, Perera RAPM, Chan MCW, Govorkova EA, Marathe BM, Pascua PNQ, Smith G, Li YT, Thomas PG, Schultz-Cherry S.PLoS Pathog. 2020 Apr 14;16(4):e1008409. doi:10.1371/journal.ppat.1008409. eCollection 2020 Apr.

Influenza A viruses are transmitted via the air from the nasal respiratory epithelium of ferrets. Richard M, van den Brand JMA, Bestebroer TM, Lexmond P, de Meulder D, Fouchier RAM, Lowen AC, Herfst S. Nat Commun. 2020 Feb 7;11(1):766.

Incomplete influenza A virus genomes occur frequently but are readily complemented during localized viral spread. Jacobs NT, Onuoha NO, Antia A, Steel J, Antia R, Lowen AC. Nat Commun. 2019 Aug 6;10(1):3526.

Dysregulation of M segment gene expression contributes to influenza A virus host restriction. Calderon BM, Danzy S, Delima GK, Jacobs NT, Ganti K, Hockman MR, Conn GL, Lowen AC, Steel J. PLoS Pathog. 2019 Aug 15;15(8):e1007892.

H5N8 and H7N9 packaging signals constrain HA reassortment with a seasonal H3N2 influenza A virus. White MC, Tao H, Steel J, Lowen AC. Proc Natl Acad Sci U S A. 2019 

Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved? Li ZT, Zarnitsyna VI, Lowen AC, Weissman D, Koelle K, Kohlmeier JE, Antia R. J Virol. 2019. 5;93(6)

It's in the mix: Reassortment of segmented viral genomes. Lowen AC. PLoS Pathog. 2018 Sep 13;14(9):e1007200. Review.

Orally Efficacious Broad-Spectrum Ribonucleoside Analog Inhibitor of Influenza and Respiratory Syncytial Viruses. Yoon JJ, Toots M, Lee S, Lee ME, Ludeke B, Luczo JM, Ganti K, Cox RM, Sticher ZM, Edpuganti V, Mitchell DG, Lockwood MA, Kolykhalov AA, Greninger AL, Moore ML, Painter GR, Lowen AC, Tompkins SM, Fearns R, Natchus MG, Plemper RK. Antimicrob Agents Chemother. 2018. 62(8)

Implications of segment mismatch for influenza A virus evolution. White MC, Lowen AC. J Gen Virol. 2018 Jan;99(1):3-16. doi: 10.1099/jgv.0.000989. Epub 2017 Dec 15. Review.

Influenza A virus reassortment is limited by anatomical compartmentalization following co-infection via distinct routes. Richard M, Herfst S, Tao H, Jacobs NT, Lowen AC. J Virol. 2017 Dec 6. pii: JVI.02063-17. doi: 10.1128/JVI.02063-17. 

Seasonal H3N2 and 2009 pandemic H1N1 influenza A viruses reassort efficiently but produce attenuated progeny. Phipps KL, Marshall N, Tao H, Danzy S, Onuoha N, Steel J, Lowen AC. Journal of Virology. 2017 Jun 21.  pii: JVI.00830-17.

Constraints, Drivers, and Implications of Influenza A Virus Reassortment. Lowen AC. Annu Rev Virol. 2017 May 26. doi: 10.1146/annurev-virology-101416-041726. Review.

Heterologous packaging signals on HA, but not NA or NS, limit influenza A virus reassortment. White MC, Steel J, Lowen AC. Journal of Virology. 2017 Mar 22. pii: JVI.00195-17

Droplet digital PCR: A novel method for detection of influenza virus defective interfering particles. Schwartz SL and Lowen AC. Journal of Virological Methods. 2016; 237:159-165.

Identification and Characterization of Influenza Virus Entry Inhibitors through Dual Myxovirus High-Throughput Screening. Weisshaar M, Cox R, Morehouse Z, Kumar Kyasa S, Yan D, Oberacker P, Mao S, Golden JE, Lowen AC, Natchus MG, Plemper RK. Journal of Virology. 2016; 90:7368-87.

Virology: Host protein clips bird flu's wings in mammals. Lowen AC. Nature. 2016; 529(7584):30-1. Commentary.

Influenza Virus Reassortment Is Enhanced by Semi-infectious Particles but Can Be Suppressed by Defective Interfering Particles. Fonville JM, Marshall N, Tao H, Steel J, Lowen AC. PLOS pathogens. 2015; 11(10):e1005204.

Influenza A Virus Coinfection through Transmission Can Support High Levels of Reassortment. Tao H, Li L, White MC, Steel J, Lowen AC. Journal of Virology. 2015; 89(16):8453-61.

Competitive fitness of influenza B viruses with neuraminidase inhibitor-resistant substitutions in a coinfection model of the human airway epithelium. Burnham AJ, Armstrong J, Lowen AC, Webster RG, Govorkova EA. Journal of Virology. 2015; 89(8):4575-87.

Mutations to PB2 and NP proteins of an avian influenza virus combine to confer efficient growth in primary human respiratory cells. Danzy S, Studdard LR, Manicassamy B, Solorzano A, Marshall N, García-Sastre A, Steel J, Lowen AC. Journal of Virology. 2014; 88(22):13436-46.

Intrahost dynamics of influenza virus reassortment. Tao H, Steel J, Lowen AC. Journal of virology. 2014; 88(13):7485-92.

Residue 41 of the Eurasian avian-like swine influenza a virus matrix protein modulates virion filament length and efficiency of contact transmission. Campbell PJ, Kyriakis CS, Marshall N, Suppiah S, Seladi-Schulman J, Danzy S, Lowen AC, Steel J. Journal of Virology. 2014; 88(13):7569-77.

Roles of humidity and temperature in shaping influenza seasonality. Lowen AC, Steel J. Journal of virology. 2014; 88(14):7692-5. Review.

The M segment of the 2009 pandemic influenza virus confers increased neuraminidase activity, filamentous morphology, and efficient contact transmissibility to A/Puerto Rico/8/1934-based reassortant viruses. Campbell PJ, Danzy S, Kyriakis CS, Deymier MJ, Lowen AC, Steel J. Journal of Virology. 2014; 88(7):3802-14.

Novel avian-origin influenza A (H7N9) virus attachment to the respiratory tract of five animal models. Siegers JY, Short KR, Leijten LM, de Graaf M, Spronken MI, Schrauwen EJ, Marshall N, Lowen AC, Gabriel G, Osterhaus AD, Kuiken T, van Riel D. Journal of Virology. 2014; 88(8):4595-9.

Novel H7N9 influenza virus shows low infectious dose, high growth rate, and efficient contact transmission in the guinea pig model. Gabbard JD, Dlugolenski D, Van Riel D, Marshall N, Galloway SE, Howerth EW, Campbell PJ, Jones C, Johnson S, Byrd-Leotis L, Steinhauer DA, Kuiken T, Tompkins SM, Tripp R, Lowen AC, Steel J. Journal of Virology. 2014; 88(3):1502-12.

Transmission in the guinea pig model. Lowen AC, Bouvier NM, Steel J. Current topics in microbiology and immunology. 2014; 385:157-83. Review.

Influenza A virus reassortment. Steel J, Lowen AC. Current topics in microbiology and immunology. 2014; 385:377-401. Review.

Filament-producing mutants of influenza A/Puerto Rico/8/1934 (H1N1) virus have higher neuraminidase activities than the spherical wild-type. Seladi-Schulman J, Campbell PJ, Suppiah S, Steel J, Lowen AC. PLOS one. 2014; 9(11):e112462.

Spherical influenza viruses have a fitness advantage in embryonated eggs, while filament-producing strains are selected in vivo. Seladi-Schulman J, Steel J, Lowen AC. Journal of Virology. 2013; 87(24):13343-53.

Influenza virus reassortment occurs with high frequency in the absence of segment mismatch. Marshall N, Priyamvada L, Ende Z, Steel J, Lowen AC. PLOS Pathogens. 2013; 9(6):e1003421.

The small genome segment of Bunyamwera orthobunyavirus harbours a single transcription-termination signal. Blakqori G, Lowen AC, Elliott RM. The Journal of General Virology. 2012; 93(Pt 7):1449-55.

The DBA.2 mouse is susceptible to disease following infection with a broad, but limited, range of influenza A and B viruses. Pica N, Iyer A, Ramos I, Bouvier NM, Fernandez-Sesma A, García-Sastre A, Lowen AC, Palese P, Steel J. Journal of Virology. 2011; 85(23):12825-9.

The M segment of the 2009 new pandemic H1N1 influenza virus is critical for its high transmission efficiency in the guinea pig model. Chou YY, Albrecht RA, Pica N, Lowen AC, Richt JA, García-Sastre A, Palese P, Hai R. Journal of Virology. 2011; 85(21):11235-41.

Effects of receptor binding specificity of avian influenza virus on the human innate immune response. Ramos I, Bernal-Rubio D, Durham N, Belicha-Villanueva A, Lowen AC, Steel J, Fernandez-Sesma A. Journal of Virology. 2011; 85(9):4421-31.

Transmission of a 2009 pandemic influenza virus shows a sensitivity to temperature and humidity similar to that of an H3N2 seasonal strain. Steel J, Palese P, Lowen AC. Journal of Virology. 2011; 85(3):1400-2.

Virulence-associated substitution D222G in the hemagglutinin of 2009 pandemic influenza A(H1N1) virus affects receptor binding. Chutinimitkul S, Herfst S, Steel J, Lowen AC, Ye J, van Riel D, Schrauwen EJ, Bestebroer TM, Koel B, Burke DF, Sutherland-Cash KH, Whittleston CS, Russell CA, Wales DJ, Smith DJ, Jonges M, Meijer A, Koopmans M, Rimmelzwaan GF, Kuiken T, Osterhaus AD, García-Sastre A, Perez DR, Fouchier RA. Journal of Virology. 2010; 84(22):11802-13.

A nine-segment influenza a virus carrying subtype H1 and H3 hemagglutinins. Gao Q, Lowen AC, Wang TT, Palese P. Journal of Virology. 2010; 84(16):8062-71.

Inefficient control of host gene expression by the 2009 pandemic H1N1 influenza A virus NS1 protein. Hale BG, Steel J, Medina RA, Manicassamy B, Ye J, Hickman D, Hai R, Schmolke M, Lowen AC, Perez DR, García-Sastre A. Journal of Virology. 2010; 84(14):6909-22.

Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. Hale BG, Steel J, Manicassamy B, Medina RA, Ye J, Hickman D, Lowen AC, Perez DR, García-Sastre A. The Journal of General Virology. 2010; 91(Pt 7):1737-42.

Influenza virus vaccine based on the conserved hemagglutinin stalk domain. Steel J, Lowen AC, Wang TT, Yondola M, Gao Q, Haye K, García-Sastre A, Palese P. mBio. 2010; 1(1).

Animal Models for Influenza Virus Pathogenesis and Transmission. Bouvier NM, Lowen AC. Viruses. 2010; 2(8):1530-1563.

Transmission of pandemic H1N1 influenza virus and impact of prior exposure to seasonal strains or interferon treatment. Steel J, Staeheli P, Mubareka S, García-Sastre A, Palese P, Lowen AC. Journal of Virology. 2010; 84(1):21-6.

Blocking interhost transmission of influenza virus by vaccination in the guinea pig model. Lowen AC, Steel J, Mubareka S, Carnero E, García-Sastre A, Palese P. Journal of Virology. 2009; 83(7):2803-18.

Transmission of influenza virus via aerosols and fomites in the guinea pig model. Mubareka S, Lowen AC, Steel J, Coates AL, García-Sastre A, Palese P. The Journal of infectious diseases. 2009; 199(6):858-65

Live attenuated influenza viruses containing NS1 truncations as vaccine candidates against H5N1 highly pathogenic avian influenza. Steel J, Lowen AC, Pena L, Angel M, Solórzano A, Albrecht R, Perez DR, García-Sastre A, Palese P. Journal of Virology. 2009; 83(4):1742-53.

Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. Steel J, Lowen AC, Mubareka S, Palese P. PLoS pathogens. 2009; 5(1):e1000252.

Oseltamivir-resistant influenza A viruses are transmitted efficiently among guinea pigs by direct contact but not by aerosol. Bouvier NM, Lowen AC, Palese P. Journal of virology. 2008; 82(20):10052-8.

High temperature (30 degrees C) blocks aerosol but not contact transmission of influenza virus. Lowen AC, Steel J, Mubareka S, Palese P. Journal of virology. 2008; 82(11):5650-2.

Influenza virus transmission: basic science and implications for the use of antiviral drugs during a pandemic. Lowen AC, Palese P. Infectious disorders drug targets. 2007; 7(4):318-28.

Influenza virus transmission is dependent on relative humidity and temperature. Lowen AC, Mubareka S, Steel J, Palese P. PLoS pathogens. 2007; 3(10):1470-6.

The guinea pig as a transmission model for human influenza viruses. Lowen AC, Mubareka S, Tumpey TM, García-Sastre A, Palese P. Proceedings of the National Academy of Sciences of the United States of America. 2006; 103(26):9988-92.

Genetic elements regulating packaging of the Bunyamwera orthobunyavirus genome. Kohl A, Lowen AC, Léonard VH, Elliott RM. The Journal of general virology. 2006; 87(Pt 1):177-87.

Mutational analyses of the nonconserved sequences in the Bunyamwera Orthobunyavirus S segment untranslated regions. Lowen AC, Elliott RM. Journal of virology. 2005; 79(20):12861-70.

Attenuation of bunyavirus replication by rearrangement of viral coding and noncoding sequences. Lowen AC, Boyd A, Fazakerley JK, Elliott RM. Journal of virology. 2005; 79(11):6940-6.

Efficient bunyavirus rescue from cloned cDNA. Lowen AC, Noonan C, McLees A, Elliott RM. Virology. 2004; 330(2):493-500.

Complementarity, sequence and structural elements within the 3' and 5' non-coding regions of the Bunyamwera orthobunyavirus S segment determine promoter strength. Kohl A, Dunn EF, Lowen AC, Elliott RM. The Journal of general virology. 2004; 85(Pt 11):3269-78.

Thyroid hormone receptor alpha 1 regulates expression of the Na+/H+ exchanger (NHE1). Li X, Misik AJ, Rieder CV, Solaro RJ, Lowen A, Fliegel L. The Journal of biological chemistry. 2002; 277(32):28656-62.