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Wang Y, Tang CY, Wan XF. Antigenic characterization of influenza and SARS-CoV-2 viruses. Anal Bioanal Chem 2022; 414:2841-2881. [PMID: 34905077 PMCID: PMC8669429 DOI: 10.1007/s00216-021-03806-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022]
Abstract
Antigenic characterization of emerging and re-emerging viruses is necessary for the prevention of and response to outbreaks, evaluation of infection mechanisms, understanding of virus evolution, and selection of strains for vaccine development. Primary analytic methods, including enzyme-linked immunosorbent/lectin assays, hemagglutination inhibition, neuraminidase inhibition, micro-neutralization assays, and antigenic cartography, have been widely used in the field of influenza research. These techniques have been improved upon over time for increased analytical capacity, and some have been mobilized for the rapid characterization of the SARS-CoV-2 virus as well as its variants, facilitating the development of highly effective vaccines within 1 year of the initially reported outbreak. While great strides have been made for evaluating the antigenic properties of these viruses, multiple challenges prevent efficient vaccine strain selection and accurate assessment. For influenza, these barriers include the requirement for a large virus quantity to perform the assays, more than what can typically be provided by the clinical samples alone, cell- or egg-adapted mutations that can cause antigenic mismatch between the vaccine strain and circulating viruses, and up to a 6-month duration of vaccine development after vaccine strain selection, which allows viruses to continue evolving with potential for antigenic drift and, thus, antigenic mismatch between the vaccine strain and the emerging epidemic strain. SARS-CoV-2 characterization has faced similar challenges with the additional barrier of the need for facilities with high biosafety levels due to its infectious nature. In this study, we review the primary analytic methods used for antigenic characterization of influenza and SARS-CoV-2 and discuss the barriers of these methods and current developments for addressing these challenges.
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Affiliation(s)
- Yang Wang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Cynthia Y Tang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Xiu-Feng Wan
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
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2
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Van den Hoecke S, Ballegeer M, Vrancken B, Deng L, Job ER, Roose K, Schepens B, Van Hoecke L, Lemey P, Saelens X. In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. mBio 2021; 12:e0074521. [PMID: 34253060 PMCID: PMC8406285 DOI: 10.1128/mbio.00745-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022] Open
Abstract
The ectodomain of matrix protein 2 (M2e) of influenza A viruses is a universal influenza A vaccine candidate. Here, we report potential evasion strategies of influenza A viruses under in vivo passive anti-M2e IgG immune selection pressure in severe combined immune-deficient (SCID) mice. A/Puerto Rico/8/34-infected SCID mice were treated with the M2e-specific mouse IgG monoclonal antibodies (MAbs) MAb 65 (IgG2a) or MAb 37 (IgG1), which recognize amino acids 5 to 15 in M2e, or with MAb 148 (IgG1), which binds to the invariant N terminus of M2e. Treatment of challenged SCID mice with any of these MAbs significantly prolonged survival compared to isotype control IgG treatment. Furthermore, M2e-specific IgG2a protected significantly better than IgG1, and even resulted in virus clearance in some of the SCID mice. Deep sequencing analysis of viral RNA isolated at different time points after treatment revealed that the sequence variation in M2e was limited to P10H/L and/or I11T in anti-M2e MAb-treated mice. Remarkably, in half of the samples isolated from moribund MAb 37-treated mice and in all MAb 148-treated mice, virus was isolated with a wild-type M2 sequence but with nonsynonymous mutations in the polymerases and/or the hemagglutinin genes. Some of these mutations were associated with delayed M2 and other viral gene expression and with increased resistance to anti-M2e MAb treatment of SCID mice. Treatment with M2e-specific MAbs thus selects for viruses with limited variation in M2e. Importantly, influenza A viruses may also undergo an alternative escape route by acquiring mutations that result in delayed wild-type M2 expression. IMPORTANCE Broadly protective influenza vaccine candidates may have a higher barrier to immune evasion compared to conventional influenza vaccines. We used Illumina MiSeq deep sequence analysis to study the mutational patterns in A/Puerto Rico/8/34 viruses that evolve in chronically infected SCID mice that were treated with different M2e-specific MAbs. We show that under these circumstances, viruses emerged in vivo with mutations in M2e that were limited to positions 10 and 11. Moreover, we discovered an alternative route for anti-M2e antibody immune escape, in which a virus is selected with wild-type M2e but with mutations in other gene segments that result in delayed M2 and other viral protein expression. Delayed expression of the viral antigen that is targeted by a protective antibody thus represents an influenza virus immune escape mechanism that does not involve epitope alterations.
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Affiliation(s)
- Silvie Van den Hoecke
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Marlies Ballegeer
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Bram Vrancken
- KU Leuven—University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Lei Deng
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Emma R. Job
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Kenny Roose
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Bert Schepens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Lien Van Hoecke
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
| | - Philippe Lemey
- KU Leuven—University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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3
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Topham DJ, DeDiego ML, Nogales A, Sangster MY, Sant A. Immunity to Influenza Infection in Humans. Cold Spring Harb Perspect Med 2021; 11:a038729. [PMID: 31871226 PMCID: PMC7919402 DOI: 10.1101/cshperspect.a038729] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review discusses the human immune responses to influenza infection with some insights from studies using animal models, such as experimental infection of mice. Recent technological advances in the study of human immune responses have greatly added to our knowledge of the infection and immune responses, and therefore much of the focus is on recent studies that have moved the field forward. We consider the complexity of the adaptive response generated by many sequential encounters through infection and vaccination.
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Affiliation(s)
- David J Topham
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Marta L DeDiego
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, 28049 Madrid, Spain
| | - Aitor Nogales
- Instituto Nacional de Investigación y Tecnologia Agraria y Ailmentaria, 28040 Madrid, Spain
| | - Mark Y Sangster
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Andrea Sant
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
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Liu Y, Wang Y, Liu B, Cong X, Ji Y, Guo X, Gao Y. Phylogenetic analysis and clinical characteristics of the co-occurring mutations in HA and NA genes of influenza A(H1N1)pdm09 viruses during 2015-2017 in Beijing, China. Virol J 2020; 17:182. [PMID: 33213486 PMCID: PMC7678287 DOI: 10.1186/s12985-020-01446-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 11/05/2020] [Indexed: 11/25/2022] Open
Abstract
Background Influenza A(H1N1)pdm09 viruses have undergone rapid evolution, and in recent years the complementary and antagonistic effects of HA and NA have gathered more attentions; however, the effects of co-occurring mutations in HA and NA on the patients’ clinical characteristics are still poorly understood. In this study, we analyzed molecular epidemiology and evolution of A(H1N1) pdm09, explored co-occurring mutations of HA and NA, and investigated effect of co-occurring mutations on patients’ clinical features. Methods A(H1N1)pdm09 was confirmed by reverse transcription-polymerase chain reaction. HA and NA genes were sequenced and phylogenetically analyzed. Clinical characteristics of the co-occurring mutations were analyzed statistically. Results By analyzing the HA and NA gene sequences of 33 A(H1N1)pdm09 viruses during the 2015–2017 influenza season, we found that all the viruses shared high similarities to each other and the HA genes of these viruses exclusively belonged to subclade 6B.1A. Several unreported substitutions in HA and NA proteins were observed, furthermore, co-occurring mutations of HA-V169T, A278S, E508G, D518E and NA-V67I were detected in 30.3% (10/33) A(H1N1)pdm09 virus strains when comparing with vaccine strains A/California/07/2009 and A/Michigan/45/2015 (H1N1). Sore throat was significantly associated with co-occurring mutations in HA and NA of A(H1N1)pdm09 (χ2, P < 0.05). Conclusions Co-occurring mutations in HA and NA were detected in A(H1N1)pdm09 isolated during 2015–2017 in Beijing. Symptomatically, sore throat was associated with co-occurring mutations in HA and NA of A(H1N1)pdm09. Therefore, studying the effect and mechanism of co-occurring mutations in HA and NA on patients’ clinical features is of note needed.
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Affiliation(s)
- Yafen Liu
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Yue Wang
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Baiyi Liu
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Xu Cong
- Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Ying Ji
- Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Xiaolin Guo
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Yan Gao
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China.
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5
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Chen F, Yang L, Zhai L, Huang Y, Chen F, Duan W, Yang J. Methyl brevifolincarboxylate, a novel influenza virus PB2 inhibitor from Canarium Album (Lour.) Raeusch. Chem Biol Drug Des 2020; 96:1280-1291. [PMID: 32519462 DOI: 10.1111/cbdd.13740] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 04/08/2020] [Accepted: 05/31/2020] [Indexed: 12/18/2022]
Abstract
Methyl brevifolincarboxylate (MBC) was isolated from ethyl acetate extract of Canarium album (Lour.) Raeusch. The structure was identified, and the effect on influenza A virus infection was evaluated. MBC exhibited inhibitory activity against influenza virus A/Puerto Rico/8/34 (H1N1) and A/Aichi/2/68 (H3N2) with IC50 values of 27.16 ± 1.39 μM and 33.41 ± 2.34 μM. Mechanism studies indicated that MBC inhibited the replication of influenza A virus by targeting PB2 cap-binding domain. Our results demonstrated MBC was a potent PB2 cap-binding inhibitor and represented as a new type of promising lead compound for the development of anti-influenza virus drugs from natural products.
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Affiliation(s)
- Fangzhao Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Luoping Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Lingyan Zhai
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yingna Huang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Feimin Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Wenjun Duan
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jie Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
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6
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Anderson CS, Sangster MY, Yang H, Mariani TJ, Chaudhury S, Topham DJ. Implementing sequence-based antigenic distance calculation into immunological shape space model. BMC Bioinformatics 2020; 21:256. [PMID: 32560624 PMCID: PMC7303933 DOI: 10.1186/s12859-020-03594-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 06/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In 2009, a novel influenza vaccine was distributed worldwide to combat the H1N1 influenza "swine flu" pandemic. However, antibodies induced by the vaccine display differences in their specificity and cross-reactivity dependent on pre-existing immunity. Here, we present a computational model that can capture the effect of pre-existing immunity on influenza vaccine responses. The model predicts the region of the virus hemagglutinin (HA) protein targeted by antibodies after vaccination as well as the level of cross-reactivity induced by the vaccine. We tested our model by simulating a scenario similar to the 2009 pandemic vaccine and compared the results to antibody binding data obtained from human subjects vaccinated with the monovalent 2009 H1N1 influenza vaccine. RESULTS We found that both specificity and cross-reactivity of the antibodies induced by the 2009 H1N1 influenza HA protein were affected by the viral strain the individual was originally exposed. Specifically, the level of antigenic relatedness between the original exposure HA antigen and the 2009 HA protein affected antigenic-site immunodominance. Moreover, antibody cross-reactivity was increased when the individual's pre-existing immunity was specific to an HA protein antigenically distinct from the 2009 pandemic strain. Comparison of simulation data with antibody binding data from human serum samples demonstrated qualitative and quantitative similarities between the model and real-life immune responses to the 2009 vaccine. CONCLUSION We provide a novel method to evaluate expected outcomes in antibody specificity and cross-reactivity after influenza vaccination in individuals with different influenza HA antigen exposure histories. The model produced similar outcomes as what has been previously reported in humans after receiving the 2009 influenza pandemic vaccine. Our results suggest that differences in cross-reactivity after influenza vaccination should be expected in individuals with different exposure histories.
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Affiliation(s)
- Christopher S Anderson
- Department of Pediatrics, University of Rochester Medical Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
| | - Mark Y Sangster
- New York Influenza Center of Excellence at David Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Thomas J Mariani
- Department of Pediatrics, University of Rochester Medical Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Sidhartha Chaudhury
- Center for Enabling Capabilities, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - David J Topham
- New York Influenza Center of Excellence at David Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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7
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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. Characterizing Emerging Canine H3 Influenza Viruses. PLoS Pathog 2020; 16:e1008409. [PMID: 32287326 PMCID: PMC7182277 DOI: 10.1371/journal.ppat.1008409] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 04/24/2020] [Accepted: 02/19/2020] [Indexed: 01/06/2023] Open
Abstract
The continual emergence of novel influenza A strains from non-human hosts requires constant vigilance and the need for ongoing research to identify strains that may pose a human public health risk. Since 1999, canine H3 influenza A viruses (CIVs) have caused many thousands or millions of respiratory infections in dogs in the United States. While no human infections with CIVs have been reported to date, these viruses could pose a zoonotic risk. In these studies, the National Institutes of Allergy and Infectious Diseases (NIAID) Centers of Excellence for Influenza Research and Surveillance (CEIRS) network collaboratively demonstrated that CIVs replicated in some primary human cells and transmitted effectively in mammalian models. While people born after 1970 had little or no pre-existing humoral immunity against CIVs, the viruses were sensitive to existing antivirals and we identified a panel of H3 cross-reactive human monoclonal antibodies (hmAbs) that could have prophylactic and/or therapeutic value. Our data predict these CIVs posed a low risk to humans. Importantly, we showed that the CEIRS network could work together to provide basic research information important for characterizing emerging influenza viruses, although there were valuable lessons learned.
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MESH Headings
- Animals
- Communicable Diseases, Emerging/transmission
- Communicable Diseases, Emerging/veterinary
- Communicable Diseases, Emerging/virology
- Dog Diseases/transmission
- Dog Diseases/virology
- Dogs
- Ferrets
- Guinea Pigs
- Humans
- Influenza A Virus, H3N2 Subtype/classification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza A Virus, H3N8 Subtype/classification
- Influenza A Virus, H3N8 Subtype/genetics
- Influenza A Virus, H3N8 Subtype/isolation & purification
- Influenza A virus/classification
- Influenza A virus/genetics
- Influenza A virus/isolation & purification
- Influenza, Human/transmission
- Influenza, Human/virology
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Inbred DBA
- United States
- Zoonoses/transmission
- Zoonoses/virology
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Affiliation(s)
- Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Pilar Blanco-Lobo
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Laura Rodriguez
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Theresa Fitzgerald
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Hanyuan Zhang
- Department of Dermatology, University of Rochester, Rochester, New York, United States of America
- Materials Science Program, University of Rochester, Rochester, New York, United States of America
| | - Phuong Nguyen
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Christopher S. Anderson
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology and Clinical and Translational Science Institute, University of Rochester, Rochester, New York, United States of America
| | - Sanjukta Bandyopadhyay
- Department of Biostatistics and Computational Biology and Clinical and Translational Science Institute, University of Rochester, Rochester, New York, United States of America
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Marta L. DeDiego
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Brian R. Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Benjamin L. Miller
- Department of Dermatology, University of Rochester, Rochester, New York, United States of America
- Materials Science Program, University of Rochester, Rochester, New York, United States of America
| | - Carole Henry
- The Department of Medicine, Section of Rheumatology, The Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, Illinois, United States of America
| | - Patrick C. Wilson
- The Department of Medicine, Section of Rheumatology, The Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, Illinois, United States of America
| | - Mark Y. Sangster
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - John J. Treanor
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - David J. Topham
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Lauren Byrd-Leotis
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Beth Israel Deaconess Medical Center, Department of Surgery and Harvard Medical School Center for Glycoscience, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David A. Steinhauer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Richard D. Cummings
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Beth Israel Deaconess Medical Center, Department of Surgery and Harvard Medical School Center for Glycoscience, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jasmina M. Luczo
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
| | - Stephen M. Tompkins
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
| | - Kaori Sakamoto
- Department of Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Cheryl A. Jones
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
| | - John Steel
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Shamika Danzy
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Hui Tao
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Ashley L. Fink
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Sabra L. Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Nicholas Wohlgemuth
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Katherine J. Fenstermacher
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Farah el Najjar
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Lauren Sauer
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Mitra K. Lewis
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kathryn Shaw-Saliba
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Richard E. Rothman
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Zhen-Ying Liu
- Department of Emergency Medicine, Chang Gung Memorial Hospital, Taiwan
| | - Kuan-Fu Chen
- Department of Emergency Medicine, Chang Gung Memorial Hospital, Taiwan
| | - Colin R. Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Ian E. H. Voorhees
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison. Madison, Wisconsin, United States of America
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison. Madison, Wisconsin, United States of America
| | - Shiho Chiba
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison. Madison, Wisconsin, United States of America
| | - Shufang Fan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison. Madison, Wisconsin, United States of America
| | - Masato Hatta
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison. Madison, Wisconsin, United States of America
| | - Huihui Kong
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison. Madison, Wisconsin, United States of America
| | - Gongxun Zhong
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison. Madison, Wisconsin, United States of America
| | - Guojun Wang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Melissa B. Uccellini
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Daniel R. Perez
- Department of Population Health, University of Georgia, Athens, Georgia, United States of America
| | - Lucas M. Ferreri
- Department of Population Health, University of Georgia, Athens, Georgia, United States of America
| | - Sander Herfst
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Ron Fouchier
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - David Burke
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - David Pattinson
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Victoria Meliopoulos
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Pamela Freiden
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Brandi Livingston
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Bridgett Sharp
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Sean Cherry
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Juan Carlos Dib
- Tropical Health Foundation, Santa Marta, Magdalena, Colombia
| | - Guohua Yang
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Charles J. Russell
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Subrata Barman
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Scott Krauss
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Angela Danner
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Karlie Woodard
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Republic of China
| | - R. A. P. M. Perera
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Republic of China
| | - M. C. W. Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Republic of China
| | - Elena A. Govorkova
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Bindumadhav M. Marathe
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Philippe N. Q. Pascua
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Gavin Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yao-Tsun Li
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
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8
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Role of Memory B Cells in Hemagglutinin-Specific Antibody Production Following Human Influenza A Virus Infection. Pathogens 2019; 8:pathogens8040167. [PMID: 31569328 PMCID: PMC6963758 DOI: 10.3390/pathogens8040167] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 01/08/2023] Open
Abstract
When influenza A virus infects an immune individual, preexisting memory B cell (MBC) activation and rapid anamnestic antibody production plays a key role in viral clearance. The most effective neutralizing antibodies target the antigenically variable head of the viral hemagglutinin (HA); antibodies against the conserved HA stalk provide broader but less potent protection. In this review, we provide a comprehensive picture of an adult's HA-specific antibody response to influenza virus infection. The process is followed from preexisting HA-specific MBC activation and rapid production of anti-HA antibodies, through to germinal center seeding and adaptation of the response to novel features of the HA. A major focus of the review is the role of competition between preexisting MBCs in determining the character of the HA-reactive antibody response. HA novelty modifies this competition and can shift the response from the immunodominant head to the stalk. We suggest that antibodies resulting from preexisting MBC activation are important regulators of anti-HA antibody production and play a role in positive selection of germinal center B cells reactive to novel HA epitopes. Our review also considers the role of MBCs in the effects of early-life imprinting on HA head- and stalk-specific antibody responses to influenza infection. An understanding of the processes described in this review will guide development of vaccination strategies that provide broadly effective protection.
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9
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Lee JM, Eguia R, Zost SJ, Choudhary S, Wilson PC, Bedford T, Stevens-Ayers T, Boeckh M, Hurt AC, Lakdawala SS, Hensley SE, Bloom JD. Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin. eLife 2019; 8:e49324. [PMID: 31452511 PMCID: PMC6711711 DOI: 10.7554/elife.49324] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 07/27/2019] [Indexed: 12/11/2022] Open
Abstract
A longstanding question is how influenza virus evolves to escape human immunity, which is polyclonal and can target many distinct epitopes. Here, we map how all amino-acid mutations to influenza's major surface protein affect viral neutralization by polyclonal human sera. The serum of some individuals is so focused that it selects single mutations that reduce viral neutralization by over an order of magnitude. However, different viral mutations escape the sera of different individuals. This individual-to-individual variation in viral escape mutations is not present among ferrets that have been infected just once with a defined viral strain. Our results show how different single mutations help influenza virus escape the immunity of different members of the human population, a phenomenon that could shape viral evolution and disease susceptibility.
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Affiliation(s)
- Juhye M Lee
- Basic Sciences DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | - Rachel Eguia
- Basic Sciences DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Seth J Zost
- Department of MicrobiologyPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Saket Choudhary
- Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesUnited States
| | - Patrick C Wilson
- Department of MedicineSection of Rheumatology, University of ChicagoChicagoUnited States
| | - Trevor Bedford
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Terry Stevens-Ayers
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Michael Boeckh
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Seema S Lakdawala
- Department of Microbiology and Molecular GeneticsSchool of Medicine, University of PittsburghPittsburghUnited States
| | - Scott E Hensley
- Department of MicrobiologyPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Jesse D Bloom
- Basic Sciences DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
- Howard Hughes Medical InstituteSeattleUnited States
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10
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Fox A, Quinn KM, Subbarao K. Extending the Breadth of Influenza Vaccines: Status and Prospects for a Universal Vaccine. Drugs 2019; 78:1297-1308. [PMID: 30088204 DOI: 10.1007/s40265-018-0958-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite the widespread use of seasonal influenza vaccines, there is urgent need for a universal influenza vaccine to provide broad, long-term protection. A number of factors underpin this urgency, including threats posed by zoonotic and pandemic influenza A viruses, suboptimal effectiveness of seasonal influenza vaccines, and concerns surrounding the effects of annual vaccination. In this article, we discuss approaches that are being investigated to increase influenza vaccine breadth, which are near-term, readily achievable approaches to increase the range of strains recognized within a subtype, or longer-term more challenging approaches to produce a truly universal influenza vaccine. Adjuvanted and neuraminidase-optimized vaccines are emerging as the most feasible and promising approaches to extend protection to cover a broader range of strains within a subtype. The goal of developing a universal vaccine has also been advanced with the design of immunogenic influenza HA-stem constructs that induce broadly neutralizing antibodies. However, these constructs are not yet sufficiently immunogenic to induce lasting universal immunity in humans. Advances in understanding how T cells mediate protection, and how viruses are packaged, have facilitated the rationale design and delivery of replication-incompetent virus vaccines that induce broad protection mediated by lung-resident memory T cells. While the lack of clear mechanistic correlates of protection, other than haemagglutination-inhibiting antibodies, remains an impediment to further advancing novel influenza vaccines, the pressing need for such a vaccine is supporting development of highly innovative and effective strategies.
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Affiliation(s)
- Annette Fox
- WHO Collaborating Centre for Reference and Research on Influenza, and the Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC, Australia
| | - Kylie M Quinn
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, and the Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC, Australia.
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11
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Tesini BL, Kanagaiah P, Wang J, Hahn M, Halliley JL, Chaves FA, Nguyen PQT, Nogales A, DeDiego ML, Anderson CS, Ellebedy AH, Strohmeier S, Krammer F, Yang H, Bandyopadhyay S, Ahmed R, Treanor JJ, Martinez-Sobrido L, Golding H, Khurana S, Zand MS, Topham DJ, Sangster MY. Broad Hemagglutinin-Specific Memory B Cell Expansion by Seasonal Influenza Virus Infection Reflects Early-Life Imprinting and Adaptation to the Infecting Virus. J Virol 2019; 93:e00169-19. [PMID: 30728266 PMCID: PMC6450111 DOI: 10.1128/jvi.00169-19] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
Memory B cells (MBCs) are key determinants of the B cell response to influenza virus infection and vaccination, but the effect of different forms of influenza antigen exposure on MBC populations has received little attention. We analyzed peripheral blood mononuclear cells and plasma collected following human H3N2 influenza infection to investigate the relationship between hemagglutinin-specific antibody production and changes in the size and character of hemagglutinin-reactive MBC populations. Infection produced increased concentrations of plasma IgG reactive to the H3 head of the infecting virus, to the conserved stalk, and to a broad chronological range of H3s consistent with original antigenic sin responses. H3-reactive IgG MBC expansion after infection included reactivity to head and stalk domains. Notably, expansion of H3 head-reactive MBC populations was particularly broad and reflected original antigenic sin patterns of IgG production. Findings also suggest that early-life H3N2 infection "imprints" for strong H3 stalk-specific MBC expansion. Despite the breadth of MBC expansion, the MBC response included an increase in affinity for the H3 head of the infecting virus. Overall, our findings indicate that H3-reactive MBC expansion following H3N2 infection is consistent with maintenance of response patterns established early in life, but nevertheless includes MBC adaptation to the infecting virus.IMPORTANCE Rapid and vigorous virus-specific antibody responses to influenza virus infection and vaccination result from activation of preexisting virus-specific memory B cells (MBCs). Understanding the effects of different forms of influenza virus exposure on MBC populations is therefore an important guide to the development of effective immunization strategies. We demonstrate that exposure to the influenza hemagglutinin via natural infection enhances broad protection through expansion of hemagglutinin-reactive MBC populations that recognize head and stalk regions of the molecule. Notably, we show that hemagglutinin-reactive MBC expansion reflects imprinting by early-life infection and that this might apply to stalk-reactive, as well as to head-reactive, MBCs. Our findings provide experimental support for the role of MBCs in maintaining imprinting effects and suggest a mechanism by which imprinting might confer heterosubtypic protection against avian influenza viruses. It will be important to compare our findings to the situation after influenza vaccination.
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Affiliation(s)
- Brenda L Tesini
- Division of Infectious Diseases, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA
| | - Preshetha Kanagaiah
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Jiong Wang
- Division of Nephrology Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Megan Hahn
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Jessica L Halliley
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Francisco A Chaves
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Phuong Q T Nguyen
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Marta L DeDiego
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Christopher S Anderson
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Ali H Ellebedy
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, New York, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, New York, USA
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Sanjukta Bandyopadhyay
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - John J Treanor
- Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Hana Golding
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Surender Khurana
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Martin S Zand
- Division of Nephrology Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - David J Topham
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Mark Y Sangster
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
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12
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Nogales A, Martinez-Sobrido L, Topham DJ, DeDiego ML. Modulation of Innate Immune Responses by the Influenza A NS1 and PA-X Proteins. Viruses 2018; 10:v10120708. [PMID: 30545063 PMCID: PMC6315843 DOI: 10.3390/v10120708] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/06/2018] [Accepted: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
Influenza A viruses (IAV) can infect a broad range of animal hosts, including humans. In humans, IAV causes seasonal annual epidemics and occasional pandemics, representing a serious public health and economic problem, which is most effectively prevented through vaccination. The defense mechanisms that the host innate immune system provides restrict IAV replication and infection. Consequently, to successfully replicate in interferon (IFN)-competent systems, IAV has to counteract host antiviral activities, mainly the production of IFN and the activities of IFN-induced host proteins that inhibit virus replication. The IAV multifunctional proteins PA-X and NS1 are virulence factors that modulate the innate immune response and virus pathogenicity. Notably, these two viral proteins have synergistic effects in the inhibition of host protein synthesis in infected cells, although using different mechanisms of action. Moreover, the control of innate immune responses by the IAV NS1 and PA-X proteins is subject to a balance that can determine virus pathogenesis and fitness, and recent evidence shows co-evolution of these proteins in seasonal viruses, indicating that they should be monitored for enhanced virulence. Importantly, inhibition of host gene expression by the influenza NS1 and/or PA-X proteins could be explored to develop improved live-attenuated influenza vaccines (LAIV) by modulating the ability of the virus to counteract antiviral host responses. Likewise, both viral proteins represent a reasonable target for the development of new antivirals for the control of IAV infections. In this review, we summarize the role of IAV NS1 and PA-X in controlling the antiviral response during viral infection.
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Affiliation(s)
- Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
- Centro de Investigación en Sanidad Animal (CISA)-INIA, Valdeolmos, 28130 Madrid, Spain.
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
| | - David J Topham
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
| | - Marta L DeDiego
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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13
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Directed selection of amino acid changes in the influenza hemagglutinin and neuraminidase affecting protein antigenicity. Vaccine 2018; 36:6383-6392. [PMID: 30224200 DOI: 10.1016/j.vaccine.2018.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/22/2018] [Accepted: 09/02/2018] [Indexed: 11/23/2022]
Abstract
Influenza virus hemagglutinin (HA) and neuraminidase (NA) proteins elicit protective antibody responses and therefore, are used as targets for vaccination, especially the HA protein. However, these proteins are subject to antigenic drift, decreasing vaccine efficacy, and few to no studies have analyzed antigenic variability of these proteins by growing the viruses under immune pressure provided by human sera. In this work, we show that after growing different influenza virus strains under immune pressure, the selection of amino acid changes in the NA protein is much more limited than the selection in the HA protein, suggesting that the NA protein could remain more conserved under immune pressure. Interestingly, all the mutations in the HA and NA proteins affected protein antigenicity, and many of the selected amino acid changes were located at the same positions found in viruses circulating. These studies could help to inform HA and NA protein residues targeted by antibody responses after virus infection in humans and are very relevant to update the strains used for influenza virus vaccination each year and to improve the currently available vaccines.
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14
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Sera from Individuals with Narrowly Focused Influenza Virus Antibodies Rapidly Select Viral Escape Mutations In Ovo. J Virol 2018; 92:JVI.00859-18. [PMID: 30045982 DOI: 10.1128/jvi.00859-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/19/2018] [Indexed: 02/05/2023] Open
Abstract
Influenza viruses use distinct antibody escape mechanisms depending on the overall complexity of the antibody response that is encountered. When grown in the presence of a hemagglutinin (HA) monoclonal antibody, influenza viruses typically acquire a single HA mutation that reduces the binding of that specific monoclonal antibody. In contrast, when confronted with mixtures of HA monoclonal antibodies or polyclonal sera that have antibodies that bind several HA epitopes, influenza viruses acquire mutations that increase HA binding to host cells. Recent data from our laboratory and others suggest that some humans possess antibodies that are narrowly focused on HA epitopes that were present in influenza virus strains that they were likely exposed to in childhood. Here, we completed a series of experiments to determine if humans with narrowly focused HA antibody responses are able to select for influenza virus antigenic escape variants in ovo We identified three human donors that possessed HA antibody responses that were heavily focused on a single HA antigenic site. Sera from all three of these donors selected single HA escape mutations during in ovo passage experiments, similar to what has been previously reported for single monoclonal antibodies. These single HA mutations directly reduced binding of serum antibodies used for selection. We propose that new antigenic variants of influenza viruses might originate in individuals who produce antibodies that are narrowly focused on HA epitopes that were present in viral strains that they encountered in childhood.IMPORTANCE Influenza vaccine strains must be updated frequently since circulating viral strains continuously change in antigenically important epitopes. Our previous studies have demonstrated that some individuals possess antibody responses that are narrowly focused on epitopes that were present in viral strains that they encountered during childhood. Here, we show that influenza viruses rapidly escape this type of polyclonal antibody response when grown in ovo by acquiring single mutations that directly prevent antibody binding. These studies improve our understanding of how influenza viruses evolve when confronted with narrowly focused polyclonal human antibodies.
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15
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Zhang H, Henry C, Anderson CS, Nogales A, DeDiego ML, Bucukovski J, Martinez-Sobrido L, Wilson PC, Topham DJ, Miller BL. Crowd on a Chip: Label-Free Human Monoclonal Antibody Arrays for Serotyping Influenza. Anal Chem 2018; 90:9583-9590. [PMID: 29985597 PMCID: PMC6082710 DOI: 10.1021/acs.analchem.8b02479] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Rapid changes in influenza A virus (IAV) antigenicity create challenges in surveillance, disease diagnosis, and vaccine development. Further, serological methods for studying antigenic properties of influenza viruses often rely on animal models and therefore may not fully reflect the dynamics of human immunity. We hypothesized that arrays of human monoclonal antibodies (hmAbs) to influenza could be employed in a pattern-recognition approach to expedite IAV serology and to study the antigenic evolution of newly emerging viruses. Using the multiplex, label-free Arrayed Imaging Reflectometry (AIR) platform, we have demonstrated that such arrays readily discriminated among various subtypes of IAVs, including H1, H3 seasonal strains, and avian-sourced human H7 viruses. Array responses also allowed the first determination of antigenic relationships among IAV strains directly from hmAb responses. Finally, correlation analysis of antibody binding to all tested IAV subtypes allowed efficient identification of broadly reactive clones. In addition to specific applications in the context of understanding influenza biology with potential utility in "universal" flu vaccine development, these studies validate AIR as a platform technology for studying antigenic properties of viruses and also antibody properties in a high-throughput manner. We further anticipate that this approach will facilitate advances in the study of other viral pathogens.
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Affiliation(s)
- Hanyuan Zhang
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York 14642
- Materials Science Program, University of Rochester, Rochester, New York 14627
| | - Carole Henry
- Department of Medicine, University of Chicago, Chicago, Illinois 60637
| | - Christopher S. Anderson
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Marta L. DeDiego
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Joseph Bucukovski
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York 14642
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Patrick C. Wilson
- Department of Medicine, University of Chicago, Chicago, Illinois 60637
| | - David J. Topham
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Benjamin L. Miller
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York 14642
- Materials Science Program, University of Rochester, Rochester, New York 14627
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16
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Topham DJ, Nguyen P, Sangster MY. Pandemic influenza vaccines: what they have taught us about B cell immunology. Curr Opin Immunol 2018; 53:203-208. [PMID: 29957457 DOI: 10.1016/j.coi.2018.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 10/28/2022]
Abstract
The emergence of avian influenza viruses stimulated pandemic concerns and efforts to develop protective vaccines. Studies of the immune responses to experimental vaccines for pandemic influenza have taught us lessons about human immunity to influenza in general that can be applied to seasonal, pandemic, and even universal vaccine responses. For example, the concepts of targeting the hemagglutinin stalk and elicitation of stalk reactive antibodies grew out of studies of the 2009 pandemic H1N1 vaccines. More recently, the phenomenon of imprinting, the influence of early life exposure to influenza modifying responses to the viruses or vaccines later in life, has been reinforced through the study of potential pandemic influenza virus vaccines such as H7N9. These studies have also revealed potential strategies to improve responses to novel influenza strains and produce more broadly cross-reactive B cell and antibody responses. These concepts are discussed in detail in this review.
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Affiliation(s)
- David J Topham
- New York Influenza Center of Excellence, David H. Smith Center for Vaccine Biology & Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 609, Rochester, NY 14642, USA.
| | - Phuong Nguyen
- New York Influenza Center of Excellence, David H. Smith Center for Vaccine Biology & Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 609, Rochester, NY 14642, USA
| | - Mark Y Sangster
- New York Influenza Center of Excellence, David H. Smith Center for Vaccine Biology & Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 609, Rochester, NY 14642, USA
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The Potential Role of Fc-Receptor Functions in the Development of a Universal Influenza Vaccine. Vaccines (Basel) 2018; 6:vaccines6020027. [PMID: 29772781 PMCID: PMC6027188 DOI: 10.3390/vaccines6020027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/08/2018] [Accepted: 05/10/2018] [Indexed: 01/02/2023] Open
Abstract
Despite global vaccination efforts, influenza virus continues to cause yearly epidemics and periodic pandemics throughout most of the world. Many of us consider the generation of broader, potent and long-lasting immunity against influenza viruses as critical in curtailing the global health and economic impact that influenza currently plays. To date, classical vaccinology has relied on the generation of neutralizing antibodies as the benchmark to measure vaccine effectiveness. However, recent developments in numerous related fields of biomedical research including, HIV, HSV and DENV have emphasized the importance of Fc-mediate effector functions in pathogenesis and immunity. The concept of Fc effector functions in contributing to protection from illness is not a new concept and has been investigated in the field for over four decades. However, in recent years the application and study of Fc effector functions has become revitalized with new knowledge and technologies to characterize their potential importance in immunity. In this perspective, we describe the current state of the field of Influenza Fc effector functions and discuss its potential utility in universal vaccine design in the future.
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18
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Wang J, Hilchey SP, DeDiego M, Perry S, Hyrien O, Nogales A, Garigen J, Amanat F, Huertas N, Krammer F, Martinez-Sobrido L, Topham DJ, Treanor JJ, Sangster MY, Zand MS. Broad cross-reactive IgG responses elicited by adjuvanted vaccination with recombinant influenza hemagglutinin (rHA) in ferrets and mice. PLoS One 2018; 13:e0193680. [PMID: 29641537 PMCID: PMC5894995 DOI: 10.1371/journal.pone.0193680] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/15/2018] [Indexed: 12/17/2022] Open
Abstract
Annual immunization against influenza virus is a large international public health effort. Accumulating evidence suggests that antibody mediated cross-reactive immunity against influenza hemagglutinin (HA) strongly correlates with long-lasting cross-protection against influenza virus strains that differ from the primary infection or vaccination strain. However, the optimal strategies for achieving highly cross-reactive antibodies to the influenza virus HA have not yet to be defined. In the current study, using Luminex-based mPlex-Flu assay, developed by our laboratory, to quantitatively measure influenza specific IgG antibody mediated cross-reactivity, we found that prime-boost-boost vaccination of ferrets with rHA proteins admixed with adjuvant elicited higher magnitude and broader cross-reactive antibody responses than that induced by actual influenza viral infection, and this cross-reactive response likely correlated with increased anti-stalk reactive antibodies. We observed a similar phenomenon in mice receiving three sequential vaccinations with rHA proteins from either A/California/07/2009 (H1N1) or A/Hong Kong/1/1968 (H3N2) viruses admixed with Addavax, an MF59-like adjuvant. Using this same mouse vaccination model, we determined that Addavax plays a more significant role in the initial priming event than in subsequent boosts. We also characterized the generation of cross-reactive antibody secreting cells (ASCs) and memory B cells (MBCs) when comparing vaccination to viral infection. We have also found that adjuvant plays a critical role in the generation of long-lived ASCs and MBCs cross-reactive to influenza viruses as a result of vaccination with rHA of influenza virus, and the observed increase in stalk-reactive antibodies likely contributes to this IgG mediated broad cross-reactivity.
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Affiliation(s)
- Jiong Wang
- Division of Nephrology, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Shannon P. Hilchey
- Division of Nephrology, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Marta DeDiego
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Sheldon Perry
- Division of Nephrology, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Ollivier Hyrien
- Biostatistics, Bioinformatics, and Epidemiology Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Aitor Nogales
- Biostatistics, Bioinformatics, and Epidemiology Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jessica Garigen
- Division of Nephrology, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Fatima Amanat
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Nelson Huertas
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Luis Martinez-Sobrido
- Biostatistics, Bioinformatics, and Epidemiology Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David J. Topham
- Biostatistics, Bioinformatics, and Epidemiology Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - John J. Treanor
- Division of Infectious Disease, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Mark Y. Sangster
- Biostatistics, Bioinformatics, and Epidemiology Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Martin S. Zand
- Division of Nephrology, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
- Rochester Center for Health Informatics, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail:
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19
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Anderson CS, McCall PR, Stern HA, Yang H, Topham DJ. Antigenic cartography of H1N1 influenza viruses using sequence-based antigenic distance calculation. BMC Bioinformatics 2018; 19:51. [PMID: 29433425 PMCID: PMC5809904 DOI: 10.1186/s12859-018-2042-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/24/2018] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The ease at which influenza virus sequence data can be used to estimate antigenic relationships between strains and the existence of databases containing sequence data for hundreds of thousands influenza strains make sequence-based antigenic distance estimates an attractive approach to researchers. Antigenic mismatch between circulating strains and vaccine strains results in significantly decreased vaccine effectiveness. Furthermore, antigenic relatedness between the vaccine strain and the strains an individual was originally primed with can affect the cross-reactivity of the antibody response. Thus, understanding the antigenic relationships between influenza viruses that have circulated is important to both vaccinologists and immunologists. RESULTS Here we develop a method of mapping antigenic relationships between influenza virus stains using a sequence-based antigenic distance approach (SBM). We used a modified version of the p-all-epitope sequence-based antigenic distance calculation, which determines the antigenic relatedness between strains using influenza hemagglutinin (HA) genetic coding sequence data and provide experimental validation of the p-all-epitope calculation. We calculated the antigenic distance between 4838 H1N1 viruses isolated from infected humans between 1918 and 2016. We demonstrate, for the first time, that sequence-based antigenic distances of H1N1 Influenza viruses can be accurately represented in 2-dimenstional antigenic cartography using classic multidimensional scaling. Additionally, the model correctly predicted decreases in cross-reactive antibody levels with 87% accuracy and was highly reproducible with even when small numbers of sequences were used. CONCLUSION This work provides a highly accurate and precise bioinformatics tool that can be used to assess immune risk as well as design optimized vaccination strategies. SBM accurately estimated the antigenic relationship between strains using HA sequence data. Antigenic maps of H1N1 virus strains reveal that strains cluster antigenically similar to what has been reported for H3N2 viruses. Furthermore, we demonstrated that genetic variation differs across antigenic sites and discuss the implications.
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Affiliation(s)
- Christopher S. Anderson
- New York Influenza Center of Excellence at David Smith Center for Immunology and Vaccine Biology, Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY USA
| | - Patrick R. McCall
- New York Influenza Center of Excellence at David Smith Center for Immunology and Vaccine Biology, Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY USA
| | - Harry A. Stern
- Center for Integrated Research Computing, University of Rochester, Rochester, NY USA
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY USA
| | - David J. Topham
- New York Influenza Center of Excellence at David Smith Center for Immunology and Vaccine Biology, Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY USA
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20
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Clark AM, DeDiego ML, Anderson CS, Wang J, Yang H, Nogales A, Martinez-Sobrido L, Zand MS, Sangster MY, Topham DJ. Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. PLoS One 2017; 12:e0188267. [PMID: 29145498 PMCID: PMC5690631 DOI: 10.1371/journal.pone.0188267] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/05/2017] [Indexed: 11/18/2022] Open
Abstract
Antigenic drift of the hemagglutinin (HA) and neuraminidase (NA) influenza virus proteins contributes to reduced vaccine efficacy. To analyze antigenic drift in human seasonal H1N1 viruses derived from the 2009 pandemic H1N1 virus (pH1N1-like viruses) accounts for the limited effectiveness (around 40%) of vaccination against pH1N1-like viruses during the 2015-2016 season, nasal washes/swabs collected from adult subjects in the Rochester, NY area, were used to sequence and isolate the circulating viruses. The HA and NA proteins from viruses circulating during the 2015-2016 season encoded eighteen and fourteen amino acid differences, respectively, when compared to A/California/04/2009, a strain circulating at the origin of the 2009 pandemic. The circulating strains belonged to subclade 6B.1, defined by HA amino acid substitutions S101N, S179N, and I233T. Hemagglutination-inhibiting (HAI) and HA-specific neutralizing serum antibody (Ab) titers from around 50% of pH1N1-like virus-infected subjects and immune ferrets were 2-4 fold lower for the 2015-2016 circulating strains compared to the vaccine strain. In addition, using a luminex-based mPlex HA assay, the binding of human sera from subjects infected with pH1N1-like viruses to the HA proteins from circulating and vaccine strains was not identical, strongly suggesting antigenic differences in the HA protein. Additionally, NA inhibition (NAI) Ab titers in human sera from pH1N1-like virus-infected subjects increased after the infection and there were measurable antigenic differences between the NA protein of circulating strains and the vaccine strain using both ferret and human antisera. Despite having been vaccinated, infected subjects exhibited low HAI Ab titers against the vaccine and circulating strains. This suggests that poor responses to the H1N1 component of the vaccine as well as antigenic differences in the HA and NA proteins of currently circulating pH1N1-like viruses could be contributing to risk of infection even after vaccination.
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Affiliation(s)
- Amelia M. Clark
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Marta L. DeDiego
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail: (DT); (MD)
| | - Christopher S. Anderson
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Jiong Wang
- Division of Nephrology, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Martin S. Zand
- Division of Nephrology, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Mark Y. Sangster
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - David J. Topham
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail: (DT); (MD)
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21
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Abstract
Safe and efficacious vaccines are arguably the most successful medical interventions of all time. Yet the ongoing discovery of new pathogens, along with emergence of antibiotic-resistant pathogens and a burgeoning population at risk of such infections, imposes unprecedented public health challenges. To meet these challenges, innovative strategies to discover and develop new or improved anti-infective vaccines are necessary. These approaches must intersect the most meaningful insights into protective immunity and advanced technologies with capabilities to deliver immunogens for optimal immune protection. This goal is considered through several recent advances in host-pathogen relationships, conceptual strides in vaccinology, and emerging technologies. Given a clear and growing risk of pandemic disease should the threat of infection go unmet, developing vaccines that optimize protective immunity against high-priority and antibiotic-resistant pathogens represents an urgent and unifying imperative.
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Affiliation(s)
- Michael R Yeaman
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California 90024.,Division of Molecular Medicine, Department of Medicine, Harbor-UCLA Medical Center, Torrance, California 90509; .,Division of Infectious Diseases, Department of Medicine, Harbor-UCLA Medical Center, Torrance, California 90509.,Los Angeles Biomedical Research Institute, Torrance, California 90502
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22
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Anderson CS, Ortega S, Chaves FA, Clark AM, Yang H, Topham DJ, DeDiego ML. Natural and directed antigenic drift of the H1 influenza virus hemagglutinin stalk domain. Sci Rep 2017; 7:14614. [PMID: 29097696 PMCID: PMC5668287 DOI: 10.1038/s41598-017-14931-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/18/2017] [Indexed: 12/02/2022] Open
Abstract
The induction of antibodies specific for the influenza HA protein stalk domain is being pursued as a universal strategy against influenza virus infections. However, little work has been done looking at natural or induced antigenic variability in this domain and the effects on viral fitness. We analyzed human H1 HA head and stalk domain sequences and found substantial variability in both, although variability was highest in the head region. Furthermore, using human immune sera from pandemic A/California/04/2009 immune subjects and mAbs specific for the stalk domain, viruses were selected in vitro containing mutations in both domains that partially contributed to immune evasion. Recombinant viruses encoding amino acid changes in the HA stalk domain replicated well in vitro, and viruses incorporating two of the stalk mutations retained pathogenicity in vivo. These findings demonstrate that the HA protein stalk domain can undergo limited drift under immune pressure and the viruses can retain fitness and virulence in vivo, findings which are important to consider in the context of vaccination targeting this domain.
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Affiliation(s)
- Christopher S Anderson
- David H. Smith Center for Vaccine Biology and Immunology, and Department of Microbiology and Immunology, Rochester, NY, United States
| | - Sandra Ortega
- David H. Smith Center for Vaccine Biology and Immunology, and Department of Microbiology and Immunology, Rochester, NY, United States
| | - Francisco A Chaves
- David H. Smith Center for Vaccine Biology and Immunology, and Department of Microbiology and Immunology, Rochester, NY, United States
| | - Amelia M Clark
- David H. Smith Center for Vaccine Biology and Immunology, and Department of Microbiology and Immunology, Rochester, NY, United States
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, 14642, United States
| | - David J Topham
- David H. Smith Center for Vaccine Biology and Immunology, and Department of Microbiology and Immunology, Rochester, NY, United States.
| | - Marta L DeDiego
- David H. Smith Center for Vaccine Biology and Immunology, and Department of Microbiology and Immunology, Rochester, NY, United States.
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23
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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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