• Babawale, P.I.,Guerrero-Plata, A., 2024. Respiratory Viral Coinfections: Insights into Epidemiology, Immune Response, Pathology, and Clinical Outcomes. Pathogens, 13.

  • Biswas, S.K., Boutz, P.L.,Nayak, D.P., 1998. Influenza virus nucleoprotein interacts with influenza virus polymerase proteins. J Virol, 72, 5493-5501.

  • Bouvier, N.M.,Palese, P., 2008. The biology of influenza viruses. Vaccine, 26 Suppl 4, D49-53.

  • Chen, J., Lin, S., Tang, J., Gao, M., Liu, Q., Du, J., Tan, C., Gong, Z., Liang, L., Zhu, T.,Liu, G., 2026. Cross-utilization of viral polymerase: parainfluenza virus hijacks the RdRp of porcine sapelovirus to facilitate its replication during co-infection. mBio, 17, e0381725.

  • Chen, Z., Tsui, J.L., Gutierrez, B., Busch Moreno, S., Du Plessis, L., Deng, X., Cai, J., Bajaj, S., Suchard, M.A., Pybus, O.G., Lemey, P., Kraemer, M.U.G.,Yu, H., 2024. COVID-19 pandemic interventions reshaped the global dispersal of seasonal influenza viruses. Science, 386, eadq3003.

  • Chin, T., Foxman, E.F., Watkins, T.A.,Lipsitch, M., 2024. Considerations for viral co-infection studies in human populations. mBio, 15, e0065824.

  • Colman, P.M., Varghese, J.N.,Laver, W.G., 1983. Structure of the catalytic and antigenic sites in influenza virus neuraminidase. Nature, 303, 41-44.

  • Dai, W., Zhang, B., Jiang, X.M., Su, H., Li, J., Zhao, Y., Xie, X., Jin, Z., Peng, J., Liu, F., Li, C., Li, Y., Bai, F., Wang, H., Cheng, X., Cen, X., Hu, S., Yang, X., Wang, J., Liu, X., Xiao, G., Jiang, H., Rao, Z., Zhang, L.K., Xu, Y., Yang, H., Liu, H., 2020. Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science, 368, 1331-1335.

  • Dowdle, W.R., Davenport, F.M., Fukumi, H., Schild, G.C., Tumova, B., Webster, R.G.,Zakstelskaja, L.Y., 1975. Orthomyxoviridae. Intervirology, 5, 245-251.

  • Du, L., Xie, Y., Zheng, K., Wang, N., Gao, M., Yu, T., Cao, L., Shao, Q., Zou, Y., Xia, W., Fang, Q., Zhao, B., Guo, D., Peng, X.,Pan, J.A., 2021. Oxidative stress transforms 3CLpro into an insoluble and more active form to promote SARS-CoV-2 replication. Redox Biol, 48, 102199.

  • Fodor, E., 2013. The RNA polymerase of influenza a virus: mechanisms of viral transcription and replication. Acta Virol, 57, 113-122.

  • Gabriel, G., Herwig, A.,Klenk, H.D., 2008. Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. PLoS Pathog, 4, e11.

  • Garnsey, M.R., Robinson, M.C., Nguyen, L.T., Cardin, R, Tillotson, J, Mashalidis, E., Yu, A., Aschenbrenner, L., Balesano, A., Behzadi, A., Boras B., Chang, J.S., Eng, H, Ephron, A., Foley, T., Ford, K.K., Frick, J.M., Gibson, S., Hao, L., Hurst, B., Kalgutkar, A.S., Korczynska, M., Lengyel-Zhand, Z., Gao, L, Meredith, H.R., Patel, N.C., Polivkova, J., Rai, D., Rose, C.R., Rothan, H., Sakata, S.K., Vargo, T.R., Qi, W., Wu, H., Liu, Y., Yurgelonis, I., Zhang, J., Zhu, Y., Zhang, L., Lee, A.A., 2024. Discovery of SARS-CoV-2 papain-like protease (PL(pro)) inhibitors with efficacy in a murine infection model. Sci Adv, 10, eado4288.

  • Godinho, D.P., Rodrigues, L.R., Lefevre, S., Magalhaes, S.,Duncan, A.B., 2024. Coinfection accelerates transmission to new hosts despite no effects on virulence and parasite growth. Philos Trans R Soc Lond B Biol Sci, 379, 20230139.

  • Guo, J., Lai, Y., Yang, Z., Song, W., Zhou, J., Li, Z., Su, W., Xiao, S.,Fang, L., 2024. Coinfection and nonrandom recombination drive the evolution of swine enteric coronaviruses. Emerg Microbes Infect, 13, 2332653.

  • Hoffmann, M., Kleine-Weber, H., Schroeder, S., Kruger, N., Herrler, T., Erichsen, S., Schiergens, T.S., Herrler, G., Wu, N.H., Nitsche, A., Muller, M.A., Drosten, C.,Pohlmann, S., 2020. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell, 181, 271-280 e278.

  • Hou, Z., Wang, J., Tan, B.,Zhang, S., 2025. A Systematic Study of Bovine Viral Diarrhoea Virus Co-Infection with Other Pathogens. Viruses, 17.

  • Iuliano, A.D., Roguski, K.M., Chang, H.H., Muscatello, D.J., Palekar, R., Tempia, S., Cohen, C., Gran, J.M., Schanzer, D., Cowling, B.J., Wu, P., Kyncl, J., Ang, L.W., Park, M., Redlberger-Fritz, M., Yu, H., Espenhain, L., Krishnan, A., Emukule, G., van Asten, L., Pereira da Silva, S., Aungkulanon, S., Buchholz, U., Widdowson, M.A., Bresee, J.S., 2018. Estimates of global seasonal influenza-associated respiratory mortality: a modelling study. Lancet, 391, 1285-1300.

  • Jiang, Y., Tong, K., Yao, R., Zhou, Y., Lin, H., Du, L., Jin, Y., Cao, L., Tan, J., Zhang, X.D., Guo, D., Pan, J.A.,Peng, X., 2021. Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV-2 replication. Cell Biosci, 11, 140.

  • Jin, Y.Y., Lin, H., Cao, L., Wu, W.C., Ji, Y., Du, L., Jiang, Y., Xie, Y., Tong, K., Xing, F., Zheng, F., Shi, M., Pan, J.A., Peng, X.,Guo, D., 2021. A Convenient and Biosafe Replicon with Accessory Genes of SARS-CoV-2 and Its Potential Application in Antiviral Drug Discovery. Virol Sin, 36, 913-923.

  • Jin, Z., Zhao, Y., Sun, Y., Zhang, B., Wang, H., Wu, Y., Zhu, Y., Zhu, C., Hu, T., Du, X., et al., 2020. Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur. Nat Struct Mol Biol, 27, 529-532.

  • Kao, R.Y., Yang, D., Lau, L.S., Tsui, W.H., Hu, L., Dai, J., Chan, M.P., Chan, C.M., Wang, P., Zheng, B.J., Sun, J., Huang, J.D., Madar, J., Chen, G., Chen, H., Guan, Y.,Yuen, K.Y., 2010. Identification of influenza A nucleoprotein as an antiviral target. Nat Biotechnol, 28, 600-605.

  • Krammer, F., Smith, G.J.D., Fouchier, R.a.M., Peiris, M., Kedzierska, K., Doherty, P.C., Palese, P., Shaw, M.L., Treanor, J., Webster, R.G.,Garcia-Sastre, A., 2018. Influenza. Nat Rev Dis Primers, 4, 3.

  • Lansbury, L., Lim, B., Baskaran, V.,Lim, W.S., 2020. Co-infections in people with COVID-19: a systematic review and meta-analysis. J Infect, 81, 266-275.

  • Matrosovich, M.N., Matrosovich, T.Y., Gray, T., Roberts, N.A.,Klenk, H.D., 2004. Human and avian influenza viruses target different cell types in cultures of human airway epithelium. Proc Natl Acad Sci U S A, 101, 4620-4624.

  • Medina, R.A.,Garcia-Sastre, A., 2011. Influenza A viruses: new research developments. Nat Rev Microbiol, 9, 590-603.

  • Nayak, D.P., Hui, E.K.,Barman, S., 2004. Assembly and budding of influenza virus. Virus Res, 106, 147-165.

  • Nicholson, K.G., Wood, J.M.,Zambon, M., 2003. Influenza. Lancet, 362, 1733-1745.

  • Olsen, S.J., Azziz-Baumgartner, E., Budd, A.P., Brammer, L., Sullivan, S., Pineda, R.F., Cohen, C.,Fry, A.M., 2020. Decreased Influenza Activity During the COVID-19 Pandemic - United States, Australia, Chile, and South Africa, 2020. MMWR Morb Mortal Wkly Rep, 69, 1305-1309.

  • Olsen, S.J., Winn, A.K., Budd, A.P., Prill, M.M., Steel, J., Midgley, C.M., Kniss, K., Burns, E., Rowe, T., Foust, A., et al., 2021. Changes in Influenza and Other Respiratory Virus Activity During the COVID-19 Pandemic - United States, 2020-2021. MMWR Morb Mortal Wkly Rep, 70, 1013-1019.

  • Omar, S.,Woodman, Z.L., 2024. The evolution of envelope function during coinfection with phylogenetically distinct human immunodeficiency virus. BMC Infect Dis, 24, 934.

  • Pan, J.A., Sun, Y., Jiang, Y.P., Bott, A.J., Jaber, N., Dou, Z., Yang, B., Chen, J.S., Catanzaro, J.M., Du, C., Ding, W.X., Diaz-Meco, M.T., Moscat, J., Ozato, K., Lin, R.Z.,Zong, W.X., 2016. TRIM21 Ubiquitylates SQSTM1/p62 and Suppresses Protein Sequestration to Regulate Redox Homeostasis. Mol Cell, 61, 720-733.

  • Pan, J.A., Ullman, E., Dou, Z.,Zong, W.X., 2011. Inhibition of protein degradation induces apoptosis through a microtubule-associated protein 1 light chain 3-mediated activation of caspase-8 at intracellular membranes. Mol Cell Biol, 31, 3158-3170.

  • Perez, D.R.,Donis, R.O., 2001. Functional analysis of PA binding by influenza a virus PB1: effects on polymerase activity and viral infectivity. J Virol, 75, 8127-8136.

  • Pflug, A., Guilligay, D., Reich, S.,Cusack, S., 2014. Structure of influenza A polymerase bound to the viral RNA promoter. Nature, 516, 355-360.

  • Pinto, L.H., Holsinger, L.J.,Lamb, R.A., 1992. Influenza virus M2 protein has ion channel activity. Cell, 69, 517-528.

  • Portela, A.,Digard, P., 2002. The influenza virus nucleoprotein: a multifunctional RNA-binding protein pivotal to virus replication. J Gen Virol, 83, 723-734.

  • Rosario-Ferreira, N., Preto, A.J., Melo, R., Moreira, I.S.,Brito, R.M.M., 2020. The Central Role of Non-Structural Protein 1 (NS1) in Influenza Biology and Infection. Int J Mol Sci, 21.

  • Rossman, J.S.,Lamb, R.A., 2011. Influenza virus assembly and budding. Virology, 411, 229-236.

  • Roy, D.,Chakraborty, N., 2024. Editorial: Impact of viral co-infection on cellular or human health and its clinical outcome. Front Cell Infect Microbiol, 14, 1399184.

  • Skehel, J.J.,Wiley, D.C., 2000. Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin. Annu Rev Biochem, 69, 531-569.

  • Stempel, H.E., Martin, E.T., Kuypers, J., Englund, J.A.,Zerr, D.M., 2009. Multiple viral respiratory pathogens in children with bronchiolitis. Acta Paediatr, 98, 123-126.

  • Szymanski, K., Cieslak, K., Kowalczyk, D.,Brydak, L.B., 2017. Co-infection with Influenza Viruses and Influenza-Like Virus During the 2015/2016 Epidemic Season. Adv Exp Med Biol, 968, 7-12.

  • Taubenberger, J.K.,Morens, D.M., 2008. The pathology of influenza virus infections. Annu Rev Pathol, 3, 499-522.

  • Vogels, C.B.F., Ruckert, C., Cavany, S.M., Perkins, T.A., Ebel, G.D.,Grubaugh, N.D., 2019. Arbovirus coinfection and co-transmission: A neglected public health concern? PLoS Biol, 17, e3000130.

  • Wagner, R., Matrosovich, M.,Klenk, H.D., 2002. Functional balance between haemagglutinin and neuraminidase in influenza virus infections. Rev Med Virol, 12, 159-166.

  • Wang, W., Peng, X., Jin, Y., Pan, J.A.,Guo, D., 2022. Reverse genetics systems for SARS-CoV-2. J Med Virol, 94, 3017-3031.

  • Webster, R.G., Bean, W.J., Gorman, O.T., Chambers, T.M.,Kawaoka, Y., 1992. Evolution and ecology of influenza A viruses. Microbiol Rev, 56, 152-179.

  • Wolfel, R., Corman, V.M., Guggemos, W., Seilmaier, M., Zange, S., Muller, M.A., Niemeyer, D., Jones, T.C., Vollmar, P., Rothe, C., Hoelscher, M., Bleicker, T., Brunink, S., Schneider, J., Ehmann, R., Zwirglmaier, K., Drosten, C.,Wendtner, C., 2020. Virological assessment of hospitalized patients with COVID-2019. Nature, 581, 465-469.

  • Yan, L., Ge, J., Zheng, L., Zhang, Y., Gao, Y., Wang, T., Huang, Y., Yang, Y., Gao, S., Li, M., Liu, Z., Wang, H., Li, Y., Chen, Y., Guddat, L.W., Wang, Q., Rao, Z.,Lou, Z., 2021. Cryo-EM Structure of an Extended SARS-CoV-2 Replication and Transcription Complex Reveals an Intermediate State in Cap Synthesis. Cell, 184, 184-193 e110.

  • Yan, L., Huang, Y., Liu, Y., Ge, J., Gao, S., Tan, L., Liu, L., Liu, Z., Ye, S., Wang, J., Xiong, J., Zhou, Y., Zhao, H., Zhao, X., Guddat, L.W., Gao, Y., Zhu, L., Rao, Z.,Lou, Z., 2025. Structural basis for the concurrence of template recycling and RNA capping in SARS-CoV-2. Cell, 188, 7194-7205 e7110.

  • Yan, T., Zhu, S., Wang, H., Li, C., Diao, Y.,Tang, Y., 2020. Synergistic pathogenicity in sequential coinfection with fowl adenovirus type 4 and avian orthoreovirus. Vet Microbiol, 251, 108880.

  • Zhang, L., Yang, Q., Shao, Y., Ding, S., Guo, J., Gao, G.F.,Deng, T., 2025. Influenza A virus NS2 protein acts on vRNA-resident polymerase to drive the transcription to replication switch. Nucleic Acids Res, 53.

  • Zhao, Y., Du, X., Duan, Y., Pan, X., Sun, Y., You, T., Han, L., Jin, Z., Shang, W., Yu, J., et al., 2021. High-throughput screening identifies established drugs as SARS-CoV-2 PLpro inhibitors. Protein Cell, 12, 877-888.

  • Zhou, J., Zhou, D., Du, X., Xue, J., Yang, J., Wang, G.,Cheng, Z., 2022. Interaction between Avian Leukosis Virus Subgroup J Surface Protein and Doublecortin-Like Kinase 1 Accelerates Cell Proliferation and Epithelial-Mesenchymal Transition. J Virol, 96, e0165721.