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Guan L, Babujee L, Browning VL, Presler R, Pattinson D, Nguyen HLK, Hoang VMP, Le MQ, van Bakel H, Neumann G, Kawaoka Y. Continued Circulation of Highly Pathogenic H5 Influenza Viruses in Vietnamese Live Bird Markets in 2018-2021. Viruses 2023; 15:1596. [PMID: 37515281 PMCID: PMC10384249 DOI: 10.3390/v15071596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
We isolated 77 highly pathogenic avian influenza viruses during routine surveillance in live poultry markets in northern provinces of Vietnam from 2018 to 2021. These viruses are of the H5N6 subtype and belong to HA clades 2.3.4.4g and 2.3.4.4h. Interestingly, we did not detect viruses of clade 2.3.4.4b, which in recent years have dominated in different parts of the world. The viruses isolated in this current study do not encode major determinants of mammalian adaptation (e.g., PB2-E627K or PB1-D701N) but possess amino acid substitutions that may affect viral receptor-binding, replication, or the responses to human antiviral factors. Several of the highly pathogenic H5N6 virus samples contained other influenza viruses, providing an opportunity for reassortment. Collectively, our study demonstrates that the highly pathogenic H5 viruses circulating in Vietnam in 2018-2021 were different from those in other parts of the world, and that the Vietnamese H5 viruses continue to evolve through mutations and reassortment.
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Affiliation(s)
- Lizheng Guan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
| | - Lavanya Babujee
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
| | - Victoria L. Browning
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
| | - Robert Presler
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
| | - David Pattinson
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
| | - Hang Le Khanh Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (H.L.K.N.); (V.M.P.H.); (M.Q.L.)
| | - Vu Mai Phuong Hoang
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (H.L.K.N.); (V.M.P.H.); (M.Q.L.)
| | - Mai Quynh Le
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (H.L.K.N.); (V.M.P.H.); (M.Q.L.)
| | - Harm van Bakel
- Department of Genetics and Genomic Services, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
- Division of Virology, Department of Microbiology and Immunology, International Research Center for Infectious Diseases, The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Research Center for Global Viral Diseases, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
- The University of Tokyo Pandemic Preparedness, Infection and Advanced Research (UTOPIA) Center, Tokyo 108-8639, Japan
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DeDiego ML, Nogales A, Lambert-Emo K, Martinez-Sobrido L, Topham DJ. NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. J Virol 2016; 90:9693-9711. [PMID: 27535054 PMCID: PMC5068522 DOI: 10.1128/jvi.01039-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/07/2016] [Indexed: 01/03/2023] Open
Abstract
Influenza NS1 protein is the main viral protein counteracting host innate immune responses, allowing the virus to efficiently replicate in interferon (IFN)-competent systems. In this study, we analyzed NS1 protein variability within influenza A (IAV) H3N2 viruses infecting humans during the 2012-2013 season. We also evaluated the impact of the mutations on the ability of NS1 proteins to inhibit host innate immune responses and general gene expression. Surprisingly, a previously unidentified mutation in the double-stranded RNA (dsRNA)-binding domain (I64T) decreased NS1-mediated general inhibition of host protein synthesis by decreasing its interaction with cleavage and polyadenylation specificity factor 30 (CPSF30), leading to increased innate immune responses after viral infection. Notably, a recombinant A/Puerto Rico/8/34 H1N1 virus encoding the H3N2 NS1-T64 protein was highly attenuated in mice, most likely because of its ability to induce higher antiviral IFN responses at early times after infection and because this virus is highly sensitive to the IFN-induced antiviral state. Interestingly, using peripheral blood mononuclear cells (PBMCs) collected at the acute visit (2 to 3 days after infection), we show that the subject infected with the NS1-T64 attenuated virus has diminished responses to interferon and to interferon induction, suggesting why this subject could be infected with this highly IFN-sensitive virus. These data demonstrate the importance of influenza virus surveillance in identifying new mutations in the NS1 protein, affecting its ability to inhibit innate immune responses and, as a consequence, the pathogenicity of the virus. IMPORTANCE Influenza A and B viruses are one of the most common causes of respiratory infections in humans, causing 1 billion infections and between 300,000 and 500,000 deaths annually. Influenza virus surveillance to identify new mutations in the NS1 protein affecting innate immune responses and, as a consequence, the pathogenicity of the circulating viruses is highly relevant. Here, we analyzed amino acid variability in the NS1 proteins from human seasonal viruses and the effect of the mutations in innate immune responses and virus pathogenesis. A previously unidentified mutation in the dsRNA-binding domain decreased NS1-mediated general inhibition of host protein synthesis and the interaction of the protein with CPSF30. This mutation led to increased innate immune responses after viral infection, augmented IFN sensitivity, and virus attenuation in mice. Interestingly, using PBMCs, the subject infected with the virus encoding the attenuating mutation induced decreased antiviral responses, suggesting why this subject could be infected with this virus.
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MESH Headings
- A549 Cells
- Animals
- Antiviral Agents/pharmacology
- Cell Line
- Cell Line, Tumor
- Chlorocebus aethiops
- Cleavage And Polyadenylation Specificity Factor/genetics
- HEK293 Cells
- Humans
- Immune Evasion/drug effects
- Immune Evasion/genetics
- Immunity, Innate/genetics
- Influenza A Virus, H1N1 Subtype/drug effects
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza A Virus, H3N2 Subtype/drug effects
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/pathogenicity
- Influenza, Human/virology
- Interferons/pharmacology
- Leukocytes, Mononuclear/virology
- Mutation/genetics
- RNA, Double-Stranded/genetics
- Vero Cells
- Viral Nonstructural Proteins/genetics
- Virulence/drug effects
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Affiliation(s)
- Marta L DeDiego
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, USA Department of Microbiology and Immunology, University of Rochester, Rochester, New York, USA
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, USA
| | - Kris Lambert-Emo
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, USA Department of Microbiology and Immunology, University of Rochester, Rochester, New York, USA
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, USA
| | - David J Topham
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, USA Department of Microbiology and Immunology, University of Rochester, Rochester, New York, USA
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Fluorescence-Activated Cell Sorting-Based Analysis Reveals an Asymmetric Induction of Interferon-Stimulated Genes in Response to Seasonal Influenza A Virus. J Virol 2015; 89:6982-93. [PMID: 25903337 DOI: 10.1128/jvi.00857-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/18/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Influenza A virus (IAV) infection provokes an antiviral response involving the expression of type I and III interferons (IFN) and IFN-stimulated genes (ISGs) in infected cell cultures. However, the spatiotemporal dynamics of the IFN reaction are incompletely understood, as previous studies investigated mainly the population responses of virus-infected cultures, although substantial cell-to-cell variability has been documented. We devised a fluorescence-activated cell sorting-based assay to simultaneously quantify expression of viral antigens and ISGs, such as ISG15, MxA, and IFIT1, in IAV-infected cell cultures at the single-cell level. This approach revealed that seasonal IAV triggers an unexpected asymmetric response, as the major cell populations expressed either viral antigen or ISG, but rarely both. Further investigations identified a role of the viral NS1 protein in blocking ISG expression in infected cells, which surprisingly did not reduce paracrine IFN signaling to noninfected cells. Interestingly, viral ISG control was impaired in cultures infected with avian-origin IAV, including the H7N9 virus from eastern China. This phenotype was traced back to polymorphic NS1 amino acids known to be important for stable binding of the polyadenylation factor CPSF30 and concomitant suppression of host cell gene expression. Most significantly, mutation of two amino acids within the CPSF30 attachment site of NS1 from seasonal IAV diminished the strict control of ISG expression in infected cells and substantially attenuated virus replication. In conclusion, our approach revealed an asymmetric, NS1-dependent ISG induction in cultures infected with seasonal IAV, which appears to be essential for efficient virus propagation. IMPORTANCE Interferons are expressed by infected cells in response to IAV infection and play important roles in the antiviral immune response by inducing hundreds of interferon-stimulated genes (ISGs). Unlike many previous studies, we investigated the ISG response at the single-cell level, enabling novel insights into this virus-host interaction. Hence, cell cultures infected with seasonal IAV displayed an asymmetric ISG induction that was confined almost exclusively to noninfected cells. In comparison, ISG expression was observed in larger cell populations infected with avian-origin IAV, suggesting a more resolute antiviral response to these strains. Strict control of ISG expression by seasonal IAV was explained by the binding of the viral NS1 protein to the polyadenylation factor CPSF30, which reduces host cell gene expression. Mutational disruption of CPSF30 binding within NS1 concomitantly attenuated ISG control and replication of seasonal IAV, illustrating the importance of maintaining an asymmetric ISG response for efficient virus propagation.
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