1
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Welsh FC, Eguia RT, Lee JM, Haddox HK, Galloway J, Van Vinh Chau N, Loes AN, Huddleston J, Yu TC, Quynh Le M, Nhat NTD, Thi Le Thanh N, Greninger AL, Chu HY, Englund JA, Bedford T, Matsen FA, Boni MF, Bloom JD. Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. Cell Host Microbe 2024; 32:1397-1411.e11. [PMID: 39032493 DOI: 10.1016/j.chom.2024.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/19/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
Human influenza virus evolves to escape neutralization by polyclonal antibodies. However, we have a limited understanding of how the antigenic effects of viral mutations vary across the human population and how this heterogeneity affects virus evolution. Here, we use deep mutational scanning to map how mutations to the hemagglutinin (HA) proteins of two H3N2 strains, A/Hong Kong/45/2019 and A/Perth/16/2009, affect neutralization by serum from individuals of a variety of ages. The effects of HA mutations on serum neutralization differ across age groups in ways that can be partially rationalized in terms of exposure histories. Mutations that were fixed in influenza variants after 2020 cause greater escape from sera from younger individuals compared with adults. Overall, these results demonstrate that influenza faces distinct antigenic selection regimes from different age groups and suggest approaches to understand how this heterogeneous selection shapes viral evolution.
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MESH Headings
- Humans
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Mutation
- Adult
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Influenza, Human/virology
- Influenza, Human/immunology
- Age Factors
- Middle Aged
- Young Adult
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Adolescent
- Evolution, Molecular
- Aged
- Child
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Affiliation(s)
- Frances C Welsh
- Molecular and Cellular Biology Graduate Program, University of Washington, and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA 98109, USA; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Rachel T Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Juhye M Lee
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Hugh K Haddox
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jared Galloway
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Nguyen Van Vinh Chau
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Andrea N Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Timothy C Yu
- Molecular and Cellular Biology Graduate Program, University of Washington, and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA 98109, USA; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mai Quynh Le
- National Institutes for Hygiene and Epidemiology, Hanoi, Vietnam
| | - Nguyen T D Nhat
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nguyen Thi Le Thanh
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, WA 98109, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frederick A Matsen
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Maciej F Boni
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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2
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Welsh FC, Eguia RT, Lee JM, Haddox HK, Galloway J, Chau NVV, Loes AN, Huddleston J, Yu TC, Le MQ, Nhat NTD, Thanh NTL, Greninger AL, Chu HY, Englund JA, Bedford T, Matsen FA, Boni MF, Bloom JD. Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571235. [PMID: 38168237 PMCID: PMC10760046 DOI: 10.1101/2023.12.12.571235] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Human influenza virus evolves to escape neutralization by polyclonal antibodies. However, we have a limited understanding of how the antigenic effects of viral mutations vary across the human population, and how this heterogeneity affects virus evolution. Here we use deep mutational scanning to map how mutations to the hemagglutinin (HA) proteins of the A/Hong Kong/45/2019 (H3N2) and A/Perth/16/2009 (H3N2) strains affect neutralization by serum from individuals of a variety of ages. The effects of HA mutations on serum neutralization differ across age groups in ways that can be partially rationalized in terms of exposure histories. Mutations that fixed in influenza variants after 2020 cause the greatest escape from sera from younger individuals. Overall, these results demonstrate that influenza faces distinct antigenic selection regimes from different age groups, and suggest approaches to understand how this heterogeneous selection shapes viral evolution.
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Affiliation(s)
- Frances C Welsh
- Molecular and Cellular Biology Graduate Program, University of Washington, and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA, 98109, USA
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Rachel T Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Juhye M Lee
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Hugh K Haddox
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Jared Galloway
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Nguyen Van Vinh Chau
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Andrea N Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Timothy C Yu
- Molecular and Cellular Biology Graduate Program, University of Washington, and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA, 98109, USA
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Mai Quynh Le
- National Institutes for Hygiene and Epidemiology, Hanoi, Vietnam
| | - Nguyen T D Nhat
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Nguyen Thi Le Thanh
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Seattle, WA, 98109, USA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Frederick A Matsen
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Maciej F Boni
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
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3
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Greaney AJ, Starr TN, Eguia RT, Loes AN, Khan K, Karim F, Cele S, Bowen JE, Logue JK, Corti D, Veesler D, Chu HY, Sigal A, Bloom JD. A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy. PLoS Pathog 2022; 18:e1010248. [PMID: 35134084 PMCID: PMC8856557 DOI: 10.1371/journal.ppat.1010248] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/18/2022] [Accepted: 01/06/2022] [Indexed: 12/22/2022] Open
Abstract
Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target the same or different regions of the viral spike as antibodies elicited by earlier viral isolates. Here we compare the specificities of polyclonal antibodies produced by humans infected with early 2020 isolates versus the B.1.351 variant of concern (also known as Beta or 20H/501Y.V2), which contains mutations in multiple key spike epitopes. The serum neutralizing activity of antibodies elicited by infection with both early 2020 viruses and B.1.351 is heavily focused on the spike receptor-binding domain (RBD). However, within the RBD, B.1.351-elicited antibodies are more focused on the "class 3" epitope spanning sites 443 to 452, and neutralization by these antibodies is notably less affected by mutations at residue 484. Our results show that SARS-CoV-2 variants can elicit polyclonal antibodies with different immunodominance hierarchies.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Rachel T. Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Andrea N. Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Sandile Cele
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Jennifer K. Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - David Veesler
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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4
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Oidtman RJ, Arevalo P, Bi Q, McGough L, Russo CJ, Vera Cruz D, Costa Vieira M, Gostic KM. Influenza immune escape under heterogeneous host immune histories. Trends Microbiol 2021; 29:1072-1082. [PMID: 34218981 PMCID: PMC8578193 DOI: 10.1016/j.tim.2021.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 11/30/2022]
Abstract
In a pattern called immune imprinting, individuals gain the strongest immune protection against the influenza strains encountered earliest in life. In many recent examples, differences in early infection history can explain birth year-associated differences in susceptibility (cohort effects). Susceptibility shapes strain fitness, but without a clear conceptual model linking host susceptibility to the identity and order of past infections general conclusions on the evolutionary and epidemic implications of cohort effects are not possible. Failure to differentiate between cohort effects caused by differences in the set, rather than the order (path), of past infections is a current source of confusion. We review and refine hypotheses for path-dependent cohort effects, which include imprinting. We highlight strategies to measure their underlying causes and emergent consequences.
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Affiliation(s)
- Rachel J Oidtman
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Philip Arevalo
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Qifang Bi
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | | | - Diana Vera Cruz
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Marcos Costa Vieira
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Katelyn M Gostic
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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5
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A statistical analysis of antigenic similarity among influenza A (H3N2) viruses. Heliyon 2021; 7:e08384. [PMID: 34825090 PMCID: PMC8605065 DOI: 10.1016/j.heliyon.2021.e08384] [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: 03/29/2021] [Revised: 04/21/2021] [Accepted: 11/10/2021] [Indexed: 11/20/2022] Open
Abstract
An accurate assessment of antigenic similarity between influenza viruses is important for vaccine strain recommendations and influenza surveillance. Due to the mechanisms that result in frequent changes in the antigenicities of strains, it is desirable to obtain an antigenic similarity measure that accounts for specific changes in strains that are of epidemiological importance in influenza. Empirically grounded statistical models best achieve this. In this study, an interpretable machine-learning model was developed using distinguishing features of antigenic variants to analyze antigenic similarity. The features comprised of cluster information, amino acid sequences located in known antigenic and receptor-binding sites of influenza A (H3N2). In order to assess validity of parameters, accuracy and relevance of model to vaccine effectiveness, the model was applied to influenza A (H3N2) viruses due to their abundant genetic data and epidemiological relevance to influenza surveillance. An application of the model revealed that all model parameters were statistically significant to determining antigenic similarity between strains. Furthermore, upon evaluating the model for predicting antigenic similarity between strains, it achieved 95% area under Receiver Operating Characteristic curve (AUC), 94% accuracy, 76% precision, 97% specificity, 68% sensitivity and a diagnostic odds ratio (DOR) of 83.19. Above all, the model was found to be strongly related to influenza vaccine effectiveness to indicate the correlation between vaccine effectiveness and antigenic similarity between vaccine and circulating strains in an epidemic. The study predicts probabilities of antigenic similarity and estimates changes in strains that lead to antigenic variants. A successful application of the methods presented in this study would complement the global efforts in influenza surveillance.
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6
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Greaney AJ, Starr TN, Eguia RT, Loes AN, Khan K, Karim F, Cele S, Bowen JE, Logue JK, Corti D, Veesler D, Chu HY, Sigal A, Bloom JD. A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.10.12.464114. [PMID: 34671768 PMCID: PMC8528074 DOI: 10.1101/2021.10.12.464114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target the same or different regions of the viral spike as antibodies elicited by earlier viral isolates. Here we compare the specificities of polyclonal antibodies produced by humans infected with early 2020 isolates versus the B.1.351 variant of concern (also known as Beta or 20H/501Y.V2), which contains mutations in multiple key spike epitopes. The serum neutralizing activity of antibodies elicited by infection with both early 2020 viruses and B.1.351 is heavily focused on the spike receptor-binding domain (RBD). However, within the RBD, B.1.351-elicited antibodies are more focused on the "class 3" epitope spanning sites 443 to 452, and neutralization by these antibodies is notably less affected by mutations at residue 484. Our results show that SARS-CoV-2 variants can elicit polyclonal antibodies with different immunodominance hierarchies.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington; Seattle, WA 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Rachel T. Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
| | - Andrea N. Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Khadija Khan
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban 4001, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban 4001, South Africa
| | - Sandile Cele
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban 4001, South Africa
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jennifer K. Logue
- Division of Allergy and Infectious Diseases, University of Washington; Seattle, WA 98195, USA
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - David Veesler
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington; Seattle, WA 98195, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban 4001, South Africa
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
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7
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Adabor ES. Anticipating time-dependent antigenic variants of influenza A (H3N2) viruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 67:67-72. [PMID: 30391719 DOI: 10.1016/j.meegid.2018.10.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 10/16/2018] [Accepted: 10/31/2018] [Indexed: 11/19/2022]
Abstract
Frequent variations in influenza vaccines are necessary to match antigenic variants which appear in influenza epidemics. Antigenic variants of influenza viruses result from frequent mutations in amino acid residues located on their hemagglutinin (HA) proteins. Knowledge of specific changes in these amino acids helps to characterize distinct antigenic variants. In this paper, statistical models are developed and used to investigate changes in amino acids which accompany antigenic variants of epidemiological importance. Amino acid sequences of the HA proteins of influenza A (H3N2) strains isolated from 1968 to 2015 were obtained. The sequences were aligned using Clustal Omega and the number of differences in amino acid residues located on annotated positions of antigenic sites of the HA protein between pairs of strains were determined. These were linked in the statistical models and used to assess the relationship between any pair of influenza strains. The results revealed that both antigenic similarity between strains and the amino acid changes are affected by the time of isolation of the strains. Furthermore, the models predicted that rates of changes in amino acids located on the antigenic sites ranged between 5% and 6% per site per year. The findings of the study suggest that time-dependent antigenic variants of influenza A (H3N2) strains may occur as they evolve. The study has the potential to greatly improve influenza surveillance in as much as it supports vaccine designs.
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MESH Headings
- Amino Acid Sequence
- Antigenic Variation/genetics
- Antigenic Variation/immunology
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza, Human/immunology
- Influenza, Human/virology
- Structure-Activity Relationship
- Time Factors
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Affiliation(s)
- Emmanuel S Adabor
- School of Technology, Ghana Institute for Management and Public Administration, P. O. Box AH50, Achimota, Accra, Ghana.
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8
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Beer K, Dai M, Howell S, Rijal P, Townsend AR, Lin Y, Wharton SA, Daniels RS, McCauley JW. Characterization of neutralizing epitopes in antigenic site B of recently circulating influenza A(H3N2) viruses. J Gen Virol 2018; 99:1001-1011. [PMID: 29944110 PMCID: PMC6171714 DOI: 10.1099/jgv.0.001101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Influenza A(H3N2) viruses are associated with outbreaks worldwide and can cause disease with severe complications. The impact can be reduced by vaccination, which induces neutralizing antibodies that mainly target the haemagglutinin glycoprotein (HA). In this study we generated neutralizing mouse monoclonal antibodies (mAbs) against A/Victoria/361/2011 and identified their epitopes by generating and sequencing escape viruses. The epitopes are located in antigenic site B, which is near the receptor-binding site and is immunodominant in humans. Amino acid (aa) substitutions at positions 156, 158, 159, 189, 190 and 193 in antigenic site B led to reduced ability of mAbs to block receptor-binding. The majority of A(H3N2) viruses that have been circulating since 2014 are antigenically distinct from previous A(H3N2) viruses. The neutralization-sensitive epitopes in antigenic site B of currently circulating viruses were examined with these mAbs. We found that clade 3C.2a viruses, possessing an additional potential glycosylation site at HA1 position N158, were poorly recognized by some of the mAbs, but other residues, notably at position 159, also affected antibody binding. Through a mass spectrometric (MS) analysis of HA, the glycosylated sites of HA1 were established and we determined that residue 158 of HA1 was glycosylated and so modified a neutralization-sensitive epitope. Understanding and monitoring individual epitopes is likely to improve vaccine strain selection.
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Affiliation(s)
- Kerstin Beer
- 1Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mian Dai
- 1Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Steven Howell
- 2Mass Spectrometry and Proteomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Pramila Rijal
- 3MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Alain R Townsend
- 3MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Yipu Lin
- 1Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen A Wharton
- 1Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rodney S Daniels
- 1Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - John W McCauley
- 1Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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9
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Liu F, Veguilla V, Gross FL, Gillis E, Rowe T, Xu X, Tumpey TM, Katz JM, Levine MZ, Lu X. Effect of Priming With Seasonal Influenza A(H3N2) Virus on the Prevalence of Cross-Reactive Hemagglutination-Inhibition Antibodies to Swine-Origin A(H3N2) Variants. J Infect Dis 2017; 216:S539-S547. [PMID: 28934461 DOI: 10.1093/infdis/jix093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Recent outbreaks of swine-origin influenza A(H3N2) variant (H3N2v) viruses have raised public health concerns. Previous studies indicated that older children and young adults had the highest levels of hemagglutination-inhibition (HI) antibodies to 2010-2011 H3N2v viruses. However, newly emerging 2013 H3N2v have acquired antigenic mutations in the hemagglutinin at amino acid position 145 (N145K/R). We estimated the levels of serologic cross-reactivity among humans primed with seasonal influenza A(H3N2) (sH3N2), using postinfection ferret antisera. We also explored age-related HI antibody responses to 2012-2013 H3N2v viruses. Methods Human and ferret antisera were tested in HI assays against 1 representative 2012 H3N2v (145N) and 2 2013 H3N2v (145K/R) viruses, together with 9 sH3N2 viruses circulating since 1968. Results Low levels of cross-reactivity between the H3N2v and sH3N2 viruses from the 1970s-1990s were observed using postinfection ferret antisera. The overall seroprevalence among the sH3N2-primed population against 2012-2013 H3N2v viruses was >50%, and age-related seroprevalence was observed. Seroprevalence was significantly higher to 2013 H3N2v than to 2012 H3N2v viruses among some children likely to have been primed with A/Sydney/5/97-like (145K) or A/Wuhan/359/95-like viruses (145K). Conclusions A single substitution (N145K/R) was sufficient to affect seropositivity to H3N2v viruses in some individuals. Insight into age-related antibody responses to newly emerging H3N2v viruses is critical for risk assessment and pandemic preparedness.
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Affiliation(s)
- Feng Liu
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Vic Veguilla
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - F Liaini Gross
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Eric Gillis
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Thomas Rowe
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Xiyan Xu
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Terrence M Tumpey
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jacqueline M Katz
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Min Z Levine
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Xiuhua Lu
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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10
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Peng B, Peng N, Zhang Y, Zhang F, Li X, Chang H, Fang F, Wang F, Lu F, Chen Z. Comparison of the Protective Efficacy of Neutralizing Epitopes of 2009 Pandemic H1N1 Influenza Hemagglutinin. Front Immunol 2017; 8:1070. [PMID: 28912784 PMCID: PMC5583165 DOI: 10.3389/fimmu.2017.01070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/16/2017] [Indexed: 12/03/2022] Open
Abstract
The 2009 H1N1 influenza (Pdm09) pandemic has been referred to as the first influenza pandemic of the twenty-first century. There is a marked difference in antigenicity between the pandemic H1N1 virus and past seasonal H1N1 viruses, which allowed the pandemic virus to spread rapidly in humans. Antibodies (Abs) against hemagglutinin (HA), especially neutralizing Abs against epitopes in the head of HA, play critical roles in defending the host against the virus. Some preexisting neutralizing Abs that recognize neutralizing epitopes of Pdm09 HA, thereby affording cross-protection, have been reported. To better understand the protective effects of epitopes in Pdm09 HA, we constructed a series of plasmid DNAs (DNA vaccines) by cloning various combinations of Pdm09 neutralizing epitopes into the HA backbone derived from A/PR/8/1934 (H1N1). We subsequently compared the protective immune responses induced by these various forms of HA in a mouse model. We found that the plasmid DNAs with epitope substitutions provided better protection against lethal virus challenge and induced higher strain-specific antibody titers, with epitope Sa being the most effective. Moreover, the combination of epitopes Sa and Sb provided almost complete protection in mice. These findings provide new insights into the protective efficacy of neutralizing epitopes of influenza HA.
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Affiliation(s)
- Bo Peng
- College of Life Science, Hunan Normal University, Changsha, China
| | - Na Peng
- College of Life Science, Hunan Normal University, Changsha, China
| | - Yanan Zhang
- College of Life Science, Hunan Normal University, Changsha, China
| | - Fenghua Zhang
- College of Life Science, Hunan Normal University, Changsha, China
| | - Xuguang Li
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
| | - Haiyan Chang
- College of Life Science, Hunan Normal University, Changsha, China
| | - Fang Fang
- College of Life Science, Hunan Normal University, Changsha, China
| | - Fuyan Wang
- Department of Immunology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Fangguo Lu
- School of Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Ze Chen
- College of Life Science, Hunan Normal University, Changsha, China.,Shanghai Institute of Biological Products, Shanghai, China
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11
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Cobey S, Hensley SE. Immune history and influenza virus susceptibility. Curr Opin Virol 2017; 22:105-111. [PMID: 28088686 DOI: 10.1016/j.coviro.2016.12.004] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/14/2016] [Accepted: 12/20/2016] [Indexed: 12/25/2022]
Abstract
Antibody responses to influenza viruses are critical for protection, but the ways in which repeated viral exposures shape antibody evolution and effectiveness over time remain controversial. Early observations demonstrated that viral exposure history has a profound effect on the specificity and magnitude of antibody responses to a new viral strain, a phenomenon called 'original antigenic sin.' Although 'sin' might suppress some aspects of the immune response, so far there is little indication that hosts with pre-existing immunity are more susceptible to viral infections compared to naïve hosts. However, the tendency of the immune response to focus on previously recognized conserved epitopes when encountering new viral strains can create an opportunity cost when mutations arise in these conserved epitopes. Hosts with different exposure histories may continue to experience distinct patterns of infection over time, which may influence influenza viruses' continued antigenic evolution. Understanding the dynamics of B cell competition that underlie the development of antibody responses might help explain the low effectiveness of current influenza vaccines and lead to better vaccination strategies.
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Affiliation(s)
- Sarah Cobey
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 19104, USA.
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA.
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12
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Abstract
The distinctive features of human influenza A phylogeny have inspired many mathematical and computational studies of viral infections spreading in a host population, but our understanding of the mechanisms that shape the coupled evolution of host immunity, disease incidence and viral antigenic properties is far from complete. In this paper we explore the epidemiology and the phylogeny of a rapidly mutating pathogen in a host population with a weak immune response, that allows re-infection by the same strain and provides little cross-immunity. We find that mutation generates explosive diversity and that, as diversity grows, the system is driven to a very high prevalence level. This is in stark contrast with the behavior of similar models where mutation gives rise to a large epidemic followed by disease extinction, under the assumption that infection with a strain provides lifelong immunity. For low mutation rates, the behavior of the system shows the main qualitative features of influenza evolution. Our results highlight the importance of heterogeneity in the human immune response for understanding influenza A phenomenology. They are meant as a first step toward computationally affordable, individual based models including more complex host-pathogen interactions.
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Affiliation(s)
- Tomás Aquino
- a Department of Civil & Environmental Engineering and Earth Sciences ; University of Notre Dame ; Notre Dame , IN USA
| | - Ana Nunes
- b BioISI Biosystems & Integrative Sciences Institute and Departamento de Física; Faculdade de Ciências da Universidade de Lisboa ; Lisboa , Portugal
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13
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Oda H, Ota M, Toh H. Profile comparison revealed deviation from structural constraint at the positively selected sites. Biosystems 2016; 147:67-77. [PMID: 27443483 DOI: 10.1016/j.biosystems.2016.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 07/13/2016] [Accepted: 07/16/2016] [Indexed: 11/18/2022]
Abstract
The amino acid substitutions at a site are affected by mixture of various constraints. It is also known that the amino acid substitutions are accelerated at sites under positive selection. However, the relationship between the substitutions at positively selected sites and the constraints has not been thoroughly examined. The advances in computational biology have enabled us to divide the mixture of the constraints into the structural constraint and the remainings by using the amino acid sequences and the tertiary structures, which is expressed as the deviation of the mixture of constraints from the structural constraint. Here, two types of profiles, or matrices with the size of 20 x (site length), are compared. One of the profiles represents the mixture of constraints, and is generated from a multiple amino acid sequence alignment, whereas the other is designed to represent the structural constraints. We applied the profile comparison method to proteins under positive selection to examine the relationship between the positive selection and constraints. The results suggested that the constraint at a site under positive selection tends to be deviated from the structural constraint at the site.
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Affiliation(s)
- Hiroyuki Oda
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan.
| | - Motonori Ota
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya City, Aichi 464-8601, Japan
| | - Hiroyuki Toh
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
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14
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Pessia A, Grad Y, Cobey S, Puranen JS, Corander J. K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets. Microb Genom 2015; 1:e000025. [PMID: 28348810 PMCID: PMC5320600 DOI: 10.1099/mgen.0.000025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022] Open
Abstract
The recent growth in publicly available sequence data has introduced new opportunities for studying microbial evolution and spread. Because the pace of sequence accumulation tends to exceed the pace of experimental studies of protein function and the roles of individual amino acids, statistical tools to identify meaningful patterns in protein diversity are essential. Large sequence alignments from fast-evolving micro-organisms are particularly challenging to dissect using standard tools from phylogenetics and multivariate statistics because biologically relevant functional signals are easily masked by neutral variation and noise. To meet this need, a novel computational method is introduced that is easily executed in parallel using a cluster environment and can handle thousands of sequences with minimal subjective input from the user. The usefulness of this kind of machine learning is demonstrated by applying it to nearly 5000 haemagglutinin sequences of influenza A/H3N2.Antigenic and 3D structural mapping of the results show that the method can recover the major jumps in antigenic phenotype that occurred between 1968 and 2013 and identify specific amino acids associated with these changes. The method is expected to provide a useful tool to uncover patterns of protein evolution.
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Affiliation(s)
- Alberto Pessia
- Department of Mathematics and Statistics, University of Helsinki, Finland
| | - Yonatan Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | | | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Finland
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15
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Characterization of the endemic equilibrium and response to mutant injection in a multi-strain disease model. J Theor Biol 2015; 368:27-36. [PMID: 25496729 DOI: 10.1016/j.jtbi.2014.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 11/17/2014] [Accepted: 12/03/2014] [Indexed: 11/23/2022]
Abstract
We explore a model of an antigenically diverse infection whose otherwise identical strains compete through cross-immunity. We assume that individuals may produce upon infection different numbers of antibody types, each of which matches the antigenic configuration of a particular epitope, and that one matching antibody type grants total immunity against a challenging strain. In order to reduce the number of equations involved in the analytic description of the dynamics, we follow the strategy proposed by Kryazhimskiy et al. (2007) and apply a low-order closure reminiscent of a pair approximation. Using this approximation, we go beyond the numerical studies of Kryazhimskiy et al. (2007) and explore the analytic properties of the ensuing model in the absence of mutation. We characterize its endemic equilibrium, comparing with the results of agent based simulations of the full model to assess the performance of the closure assumption. We show that a particular choice of immune response leads to a degenerate endemic equilibrium, where different strain prevalences may exist, breaking the symmetry of the model. Finally we study the behavior of the system under the injection of mutant strains. We find that the build up of diversity from a single founding strain is extremely unlikely for different choices of the population׳s immune response.
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16
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Gulati S, Smith DF, Cummings RD, Couch RB, Griesemer SB, St. George K, Webster RG, Air GM. Human H3N2 Influenza Viruses Isolated from 1968 To 2012 Show Varying Preference for Receptor Substructures with No Apparent Consequences for Disease or Spread. PLoS One 2013; 8:e66325. [PMID: 23805213 PMCID: PMC3689742 DOI: 10.1371/journal.pone.0066325] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 05/03/2013] [Indexed: 12/20/2022] Open
Abstract
It is generally accepted that human influenza viruses bind glycans containing sialic acid linked α2–6 to the next sugar, that avian influenza viruses bind glycans containing the α2–3 linkage, and that mutations that change the binding specificity might change the host tropism. We noted that human H3N2 viruses showed dramatic differences in their binding specificity, and so we embarked on a study of representative human H3N2 influenza viruses, isolated from 1968 to 2012, that had been isolated and minimally passaged only in mammalian cells, never in eggs. The 45 viruses were grown in MDCK cells, purified, fluorescently labeled and screened on the Consortium for Functional Glycomics Glycan Array. Viruses isolated in the same season have similar binding specificity profiles but the profiles show marked year-to-year variation. None of the 610 glycans on the array (166 sialylated glycans) bound to all viruses; the closest was Neu5Acα2–6(Galβ1–4GlcNAc)3 in either a linear or biantennary form, that bound 42 of the 45 viruses. The earliest human H3N2 viruses preferentially bound short, branched sialylated glycans while recent viruses bind better to long polylactosamine chains terminating in sialic acid. Viruses isolated in 1996, 2006, 2010 and 2012 bind glycans with α2–3 linked sialic acid; for 2006, 2010 and 2012 viruses this binding was inhibited by oseltamivir, indicating binding of α2–3 sialylated glycans by neuraminidase. More significantly, oseltamivir inhibited virus entry of 2010 and 2012 viruses into MDCK cells. All of these viruses were representative of epidemic strains that spread around the world, so all could infect and transmit between humans with high efficiency. We conclude that the year-to-year variation in receptor binding specificity is a consequence of amino acid sequence changes driven by antigenic drift, and that viruses with quite different binding specificity and avidity are equally fit to infect and transmit in the human population.
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Affiliation(s)
- Shelly Gulati
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - David F. Smith
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Richard D. Cummings
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Robert B. Couch
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara B. Griesemer
- New York State Department of Health, Wadsworth Center, Albany, New York, United States of America
| | - Kirsten St. George
- New York State Department of Health, Wadsworth Center, Albany, New York, United States of America
| | - Robert G. Webster
- St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Gillian M. Air
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- * E-mail:
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17
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Parisi A, Lopes JS, Nunes A, Gomes MGM. Heterogeneity in antibody range and the antigenic drift of influenza A viruses. ECOLOGICAL COMPLEXITY 2013. [DOI: 10.1016/j.ecocom.2012.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Wikramaratna PS, Sandeman M, Recker M, Gupta S. The antigenic evolution of influenza: drift or thrift? Philos Trans R Soc Lond B Biol Sci 2013; 368:20120200. [PMID: 23382423 PMCID: PMC3678325 DOI: 10.1098/rstb.2012.0200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
It is commonly assumed that antibody responses against the influenza virus are polarized in the following manner: strong antibody responses are directed at highly variable antigenic epitopes, which consequently undergo 'antigenic drift', while weak antibody responses develop against conserved epitopes. As the highly variable epitopes are in a constant state of flux, current antibody-based vaccine strategies are focused on the conserved epitopes in the expectation that they will provide some level of clinical protection after appropriate boosting. Here, we use a theoretical model to suggest the existence of epitopes of low variability, which elicit a high degree of both clinical and transmission-blocking immunity. We show that several epidemiological features of influenza and its serological and molecular profiles are consistent with this model of 'antigenic thrift', and that identifying the protective epitopes of low variability predicted by this model could offer a more viable alternative to regularly update the influenza vaccine than exploiting responses to weakly immunogenic conserved regions.
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19
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Popova L, Smith K, West AH, Wilson PC, James JA, Thompson LF, Air GM. Immunodominance of antigenic site B over site A of hemagglutinin of recent H3N2 influenza viruses. PLoS One 2012; 7:e41895. [PMID: 22848649 PMCID: PMC3405050 DOI: 10.1371/journal.pone.0041895] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 06/29/2012] [Indexed: 11/17/2022] Open
Abstract
H3N2 influenza viruses have now circulated in the human population for 43 years since the pandemic of 1968, accumulating sequence changes in the hemagglutinin (HA) and neuraminidase (NA) that are believed to be predominantly due to selection for escape from antibodies. Examination of mutations that persist and accumulate led to identification of antigenically significant mutations that are contained in five antigenic sites (A–E) mapped on to the H3 HA. In early H3N2 isolates, antigenic site A appeared to be dominant while in the 1990s site B seemed more important. To obtain experimental evidence for dominance of antigenic sites on modern H3 HAs, we have measured antibodies in plasma of human subjects who received the 2006–07 trivalent subunit influenza vaccine (H3 component A/Wisconsin/67/05) or the 2008–09 formulation (H3 component A/Uruguay/716/07). Plasmas were tested against expressed HA of Wisconsin-like influenza A/Oklahoma/309/06 and site-directed mutants in antigenic site A (NNES121-124ITEG, N126T, N133D, TSSS135-138GSNA, K140I, RSNNS142-146PGSG), and antigenic site B (HL156-157KS, KFK158-160GST, NDQI189-192QEQT, A196V). “Native ELISA” analysis and escape mutant selection with two human monoclonal antibodies demonstrated that antibody E05 binds to antigenic site A and 1_C02 binds to site B. We find that most individuals, after vaccination in seasons 2006–07 and/or 2008–09, showed dominance of antigenic site B recognition over antigenic site A. A minority showed dominance of site A in 2006 but these were reduced in 2008 when the vaccine virus had a site A mutation. A better understanding of immunodominance may allow prediction of future antigenic drift and assist in vaccine strain selection.
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Affiliation(s)
- Lyubov Popova
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
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20
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Nobusawa E, Omagari K, Nakajima S, Nakajima K. Reactivity of human convalescent sera with influenza virus hemagglutinin protein mutants at antigenic site A. Microbiol Immunol 2012; 56:99-106. [PMID: 22309642 DOI: 10.1111/j.1348-0421.2012.00412.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
How the antibodies of individual convalescent human sera bind to each amino acid residue at the antigenic sites of hemagglutinin (HA) of influenza viruses, and how the antigenic drift strains of influenza viruses are selected by human sera, is not well understood. In our previous study, it was found by a binding assay with a chimeric HA between A/Kamata/14/91 (Ka/91) and A/Aichi/2/68 that convalescent human sera, following Ka/91 like (H3N2) virus infection, bind to antigenic site A of Ka/91 HA. Here using chimeric HAs possessing single amino acid substitutions at site A, it was determined how those human sera recognize each amino acid residue at antigenic site A. It was found that the capacity of human sera to recognize amino acid substitutions at site A differs from one person to another and that some amino acid substitutions result in all convalescent human sera losing their binding capacity. Among these amino acid substitutions, certain ones might be selected by chance, thus creating successive antigenic drift. Phylogenetic analysis of the drift strains of Ka/91 showed amino acid substitutions at positions 133, 135 and 145 were on the main stream of the phylogenetic tree. Indeed, all of the investigated convalescent sera failed to recognize one of them.
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Affiliation(s)
- Eri Nobusawa
- Department of Virology, Nagoya City University Graduate School of Medical Science, Nagoya City, Aichi, Japan.
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21
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Cobey S, Pascual M. Consequences of host heterogeneity, epitope immunodominance, and immune breadth for strain competition. J Theor Biol 2010; 270:80-7. [PMID: 21093455 PMCID: PMC3042250 DOI: 10.1016/j.jtbi.2010.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 11/04/2010] [Accepted: 11/04/2010] [Indexed: 11/28/2022]
Abstract
Consumer-resource dynamics of hosts with their pathogens are modulated by complex interactions between various branches of hosts' immune systems and the imperfectly perceived pathogen. Multistrain SIR models tend to sweep competitive interaction terms between different pathogen strains into a single parameter representing cross-immunity. After reviewing several hypotheses about the generation of immune responses, we look into the consequences of assuming that hosts with identical immune repertoires respond to new pathogens identically. In particular, we vary the breadth of the typical immune response, or the average number of pathogen epitopes a host perceives, and the probability of perceiving a particular epitope. The latter quantity in our model is equivalent both to the degree of diversity in host responses at the population level and the relative immunodominance of different epitopes. We find that a sharp transition to strain coexistence occurs as host responses become narrow or skewed toward one epitope. Increasing the breadth of the immune response and the immunogenicity of different epitopes typically increases the range of cross-immunity values in which chaotic strain dynamics and competitive exclusion occur. Models attempting to predict the outcomes of strain competition should thus consider the potential diversity and specificity of hosts' responses to infection.
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Affiliation(s)
- Sarah Cobey
- Department of Ecology and Evolutionary Biology, 830 North University Avenue, University of Michigan, Ann Arbor, MI 48109, USA.
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22
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The impact of key amino acid substitutions in the hemagglutinin of influenza A (H3N2) viruses on vaccine production and antibody response. Vaccine 2010; 28:4079-85. [DOI: 10.1016/j.vaccine.2010.03.078] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 03/24/2010] [Accepted: 03/26/2010] [Indexed: 11/20/2022]
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23
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Ito M, Nagai M, Hayakawa Y, Komae H, Murakami N, Yotsuya S, Asakura S, Sakoda Y, Kida H. Genetic Analyses of an H3N8 Influenza Virus Isolate, Causative Strain of the Outbreak of Equine Influenza at the Kanazawa Racecourse in Japan in 2007. J Vet Med Sci 2008; 70:899-906. [PMID: 18840963 DOI: 10.1292/jvms.70.899] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In August 2007, an outbreak of equine influenza occurred among vaccinated racehorses with Japanese commercial equine influenza vaccine at Kanazawa Racecourse in Ishikawa prefecture in Japan. Apparent symptoms were pyrexia (38.2-41.0 degrees C) and nasal discharge with or without coughing, although approximately half of the infected horses were subclinical. All horses had been shot with a vaccine that contained two inactivated H3N8 influenza virus strains [A/equine/La Plata/93 (La Plata/93) of American lineage and A/equine/Avesta/93 (Avesta/93) of European lineage] and an H7N7 strain (A/equine/Newmarket/1/77). Influenza virus, A/equine/Kanazawa/1/2007 (H3N8) (Kanazawa/07), was isolated from one of the nasal swab samples of diseased horses. Phylogenetic analysis indicated that Kanazawa/07 was classified into the American sublineage Florida. In addition, four amino acid substitutions were found in the antigenic sites B and E in the HA1 subunit protein of Kanazawa/07 in comparison with that of La Plata/93. Hemagglutination-inhibition (HI) test using 16 serum samples from recovering horses revealed that 1.4- to 8-fold difference in titers between Kanazawa/07 and either of the vaccine strains. The present findings suggest that Japanese commercial inactivated vaccine contributed to reducing the morbidity rate and manifestation of the clinical signs of horses infected with Kanazawa/07 that may be antigenically different from the vaccine strains.
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Affiliation(s)
- Mika Ito
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa, Japan
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24
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Fairlie-Clarke KJ, Shuker DM, Graham AL. Why do adaptive immune responses cross-react? Evol Appl 2008; 2:122-31. [PMID: 25567852 PMCID: PMC3352416 DOI: 10.1111/j.1752-4571.2008.00052.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Accepted: 11/06/2008] [Indexed: 11/29/2022] Open
Abstract
Antigen specificity of adaptive immune responses is often in the host's best interests, but with important and as yet unpredictable exceptions. For example, antibodies that bind to multiple flaviviral or malarial species can provide hosts with simultaneous protection against many parasite genotypes. Vaccinology often aims to harness such imprecision, because cross-reactive antibodies might provide broad-spectrum protection in the face of antigenic variation by parasites. However, the causes of cross-reactivity among immune responses are not always known, and here, we explore potential proximate and evolutionary explanations for cross-reactivity. We particularly consider whether cross-reactivity is the result of constraints on the ability of the immune system to process information about the world of antigens, or whether an intermediate level of cross-reactivity may instead represent an evolutionary optimum. We conclude with a series of open questions for future interdisciplinary research, including the suggestion that the evolutionary ecology of information processing might benefit from close examination of immunological data.
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Affiliation(s)
- Karen J Fairlie-Clarke
- Institutes of Evolution, Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories King's Buildings, Edinburgh, UK
| | - David M Shuker
- Institutes of Evolution, Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories King's Buildings, Edinburgh, UK
| | - Andrea L Graham
- Institutes of Evolution, Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories King's Buildings, Edinburgh, UK
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Xiu W, Wen Y, Shen X, Xie J, Yang S, Wu B, Wang M. Molecular evolution of influenza A (H3N2) viruses circulated in Fujian Province, China during the 1996–2004 period. ACTA ACUST UNITED AC 2008; 51:373-80. [DOI: 10.1007/s11427-008-0050-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Accepted: 01/07/2008] [Indexed: 01/19/2023]
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26
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McDonald NJ, Smith CB, Cox NJ. Antigenic drift in the evolution of H1N1 influenza A viruses resulting from deletion of a single amino acid in the haemagglutinin gene. J Gen Virol 2008; 88:3209-3213. [PMID: 18024888 DOI: 10.1099/vir.0.83184-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two genetically distinct lineages of H1N1 influenza A viruses, circulated worldwide before 1994, were antigenically indistinguishable. In 1994, viruses emerged in China, including A/Beijing/262/95, with profound antigenic differences from the contemporary circulating H1N1 strains. Haemagglutinin sequence comparisons of either a predecessor virus, A/Hebei/52/94, or one representative of the cocirculating A/Bayern/7/95-like clade, A/Shenzhen/227/95, revealed a deletion of K at position 134 (H3 numbering) in the antigenic variants. The K134 deletion conferred a selective advantage to the Chinese deletion lineage, such that it eventually gave rise to currently circulating H1 viruses. Using reverse genetics to generate viruses with either an insertion or deletion of aa 134, we have confirmed that the K134 deletion, rather than a constellation of sublineage specific amino acid changes, was sufficient for the antigenic difference observed in the Chinese deletion lineage, and reinsertion of K134 revealed the requirement of a compatible neuraminidase surface glycoprotein for viral growth.
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Affiliation(s)
- Natalie J McDonald
- Influenza Division, Coordinating Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Catherine B Smith
- Influenza Division, Coordinating Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nancy J Cox
- Influenza Division, Coordinating Centers for Disease Control and Prevention, Atlanta, GA, USA
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27
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Koelle K, Cobey S, Grenfell B, Pascual M. Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science 2007; 314:1898-903. [PMID: 17185596 DOI: 10.1126/science.1132745] [Citation(s) in RCA: 334] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human influenza A (subtype H3N2) is characterized genetically by the limited standing diversity of its hemagglutinin and antigenically by clusters that emerge and replace each other within 2 to 8 years. By introducing an epidemiological model that allows for differences between the genetic and antigenic properties of the virus's hemagglutinin, we show that these patterns can arise from cluster-specific immunity alone. Central to the formulation is a genotype-to-phenotype mapping, based on neutral networks, with antigenic phenotypes, not genotypes, determining the degree of strain cross-immunity. The model parsimoniously explains well-known, as well as previously unremarked, features of interpandemic influenza dynamics and evolution. It captures the observed boom-and-bust pattern of viral evolution, with periods of antigenic stasis during which genetic diversity grows, and with episodic contraction of this diversity during cluster transitions.
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MESH Headings
- Amino Acid Substitution
- Antigenic Variation
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Computer Simulation
- Cross Reactions
- Disease Outbreaks
- Disease Susceptibility
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- Evolution, Molecular
- Genotype
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Immunity, Herd
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza, Human/epidemiology
- Influenza, Human/immunology
- Influenza, Human/transmission
- Influenza, Human/virology
- Models, Biological
- Models, Statistical
- Phenotype
- Phylogeny
- Point Mutation
- Polymorphism, Genetic
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Affiliation(s)
- Katia Koelle
- Department of Ecology and Evolutionary Biology, 2019 Kraus Natural Science Building, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA.
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28
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Nakajima K, Nobusawa E, Nagy A, Nakajima S. Accumulation of amino acid substitutions promotes irreversible structural changes in the hemagglutinin of human influenza AH3 virus during evolution. J Virol 2005; 79:6472-7. [PMID: 15858030 PMCID: PMC1091720 DOI: 10.1128/jvi.79.10.6472-6477.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to clarify the effect of an accumulation of amino acid substitutions on the hemadsorption character of the influenza AH3 virus hemagglutinin (HA) protein, we introduced single-point amino acid changes into the HA1 domain of the HA proteins of influenza viruses isolated in 1968 (A/Aichi/2/68) and 1997 (A/Sydney/5/97) by using PCR-based random mutation or site-directed mutagenesis. These substitutions were classified as positive or negative according to their effects on the hemadsorption activity. The rate of positive substitutions was about 50% for both strains. Of 44 amino acid changes that were identical in the two strains with regard to both the substituted amino acids and their positions in the HA1 domain, 22% of the changes that were positive in A/Aichi/2/68 were negative in A/Sydney/5/97 and 27% of the changes that were negative in A/Aichi/2/68 were positive in A/Sydney/5/97. A similar discordance rate was also seen for the antigenic sites. These results suggest that the accumulation of amino acid substitutions in the HA protein during evolution promoted irreversible structural changes and therefore that antigenic changes in the H3HA protein may not be limited.
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Affiliation(s)
- Katsuhisa Nakajima
- Department of Virology, Medical School, Nagoya City University, 1 Kawasumi, Mizuho-chou, Mizuho-ku, Nagoya 467-8601, Japan.
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