1
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Lei R, Liang W, Ouyang WO, Hernandez Garcia A, Kikuchi C, Wang S, McBride R, Tan TJC, Sun Y, Chen C, Graham CS, Rodriguez LA, Shen IR, Choi D, Bruzzone R, Paulson JC, Nair SK, Mok CKP, Wu NC. Epistasis mediates the evolution of the receptor binding mode in recent human H3N2 hemagglutinin. Nat Commun 2024; 15:5175. [PMID: 38890325 PMCID: PMC11189414 DOI: 10.1038/s41467-024-49487-4] [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: 11/12/2023] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
The receptor-binding site of influenza A virus hemagglutinin partially overlaps with major antigenic sites and constantly evolves. In this study, we observe that mutations G186D and D190N in the hemagglutinin receptor-binding site have coevolved in two recent human H3N2 clades. X-ray crystallography results show that these mutations coordinately drive the evolution of the hemagglutinin receptor binding mode. Epistasis between G186D and D190N is further demonstrated by glycan binding and thermostability analyses. Immunization and neutralization experiments using mouse and human samples indicate that the evolution of receptor binding mode is accompanied by a change in antigenicity. Besides, combinatorial mutagenesis reveals that G186D and D190N, along with other natural mutations in recent H3N2 strains, alter the compatibility with a common egg-adaptive mutation in seasonal influenza vaccines. Overall, our findings elucidate the role of epistasis in shaping the recent evolution of human H3N2 hemagglutinin and substantiate the high evolvability of its receptor-binding mode.
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MESH Headings
- Humans
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/metabolism
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Epistasis, Genetic
- Animals
- Evolution, Molecular
- Mice
- Binding Sites
- Influenza, Human/virology
- Mutation
- Crystallography, X-Ray
- Influenza Vaccines
- Protein Binding
- Receptors, Virus/metabolism
- Receptors, Virus/genetics
- Receptors, Virus/chemistry
- Female
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Weiwen Liang
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Wenhao O Ouyang
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Chika Kikuchi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Shengyang Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ryan McBride
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yuanxin Sun
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chunke Chen
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Claire S Graham
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Lucia A Rodriguez
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ivana R Shen
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Danbi Choi
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Cell Biology and Infection, Institut Pasteur, Paris, Cedex, 75015, France
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Chris K P Mok
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- S.H. Ho Research Centre for Infectious Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China.
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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2
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Kikuchi C, Antonopoulos A, Wang S, Maemura T, Karamanska R, Lee C, Thompson AJ, Dell A, Kawaoka Y, Haslam SM, Paulson JC. Glyco-engineered MDCK cells display preferred receptors of H3N2 influenza absent in eggs used for vaccines. Nat Commun 2023; 14:6178. [PMID: 37794004 PMCID: PMC10551000 DOI: 10.1038/s41467-023-41908-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
Evolution of human H3N2 influenza viruses driven by immune selection has narrowed the receptor specificity of the hemagglutinin (HA) to a restricted subset of human-type (Neu5Acα2-6 Gal) glycan receptors that have extended poly-LacNAc (Galβ1-4GlcNAc) repeats. This altered specificity has presented challenges for hemagglutination assays, growth in laboratory hosts, and vaccine production in eggs. To assess the impact of extended glycan receptors on virus binding, infection, and growth, we have engineered N-glycan extended (NExt) cell lines by overexpressing β3-Ν-acetylglucosaminyltransferase 2 in MDCK, SIAT, and hCK cell lines. Of these, SIAT-NExt cells exhibit markedly increased binding of H3 HAs and susceptibility to infection by recent H3N2 virus strains, but without impacting final virus titers. Glycome analysis of these cell lines and allantoic and amniotic egg membranes provide insights into the importance of extended glycan receptors for growth of recent H3N2 viruses and relevance to their production for cell- and egg-based vaccines.
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Affiliation(s)
- Chika Kikuchi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Shengyang Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tadashi Maemura
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Rositsa Karamanska
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Chiara Lee
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Andrew J Thompson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Anne Dell
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Pandemic Preparedness, Infection and Advanced Research Center, The University of Tokyo, Tokyo, Japan
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
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3
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Liang W, Tan TJC, Wang Y, Lv H, Sun Y, Bruzzone R, Mok CKP, Wu NC. Egg-adaptive mutations of human influenza H3N2 virus are contingent on natural evolution. PLoS Pathog 2022; 18:e1010875. [PMID: 36155668 PMCID: PMC9536752 DOI: 10.1371/journal.ppat.1010875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 10/06/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Egg-adaptive mutations in influenza hemagglutinin (HA) often emerge during the production of egg-based seasonal influenza vaccines, which contribute to the largest share in the global influenza vaccine market. While some egg-adaptive mutations have minimal impact on the HA antigenicity (e.g. G186V), others can alter it (e.g. L194P). Here, we show that the preference of egg-adaptive mutation in human H3N2 HA is strain-dependent. In particular, Thr160 and Asn190, which are found in many recent H3N2 strains, restrict the emergence of L194P but not G186V. Our results further suggest that natural amino acid variants at other HA residues also play a role in determining the preference of egg-adaptive mutation. Consistently, recent human H3N2 strains from different clades acquire different mutations during egg passaging. Overall, these results demonstrate that natural mutations in human H3N2 HA can influence the preference of egg-adaptation mutation, which has important implications in seed strain selection for egg-based influenza vaccine.
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Affiliation(s)
- Weiwen Liang
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Timothy J. C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yuanxin Sun
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Istituto Pasteur Italia, Rome, Italy
- Centre for Immunology & Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Chris K. P. Mok
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- * E-mail: (CKPM); (NCW)
| | - Nicholas C. Wu
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (CKPM); (NCW)
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4
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MADE: A Computational Tool for Predicting Vaccine Effectiveness for the Influenza A(H3N2) Virus Adapted to Embryonated Eggs. Vaccines (Basel) 2022; 10:vaccines10060907. [PMID: 35746515 PMCID: PMC9227319 DOI: 10.3390/vaccines10060907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/29/2022] [Accepted: 05/31/2022] [Indexed: 01/29/2023] Open
Abstract
Seasonal Influenza H3N2 virus poses a great threat to public health, but its vaccine efficacy remains suboptimal. One critical step in influenza vaccine production is the viral passage in embryonated eggs. Recently, the strength of egg passage adaptation was found to be rapidly increasing with time driven by convergent evolution at a set of functionally important codons in the hemagglutinin (HA1). In this study, we aim to take advantage of the negative correlation between egg passage adaptation and vaccine effectiveness (VE) and develop a computational tool for selecting the best candidate vaccine virus (CVV) for vaccine production. Using a probabilistic approach known as mutational mapping, we characterized the pattern of sequence evolution driven by egg passage adaptation and developed a new metric known as the adaptive distance (AD) which measures the overall strength of egg passage adaptation. We found that AD is negatively correlated with the influenza H3N2 vaccine effectiveness (VE) and ~75% of the variability in VE can be explained by AD. Based on these findings, we developed a computational package that can Measure the Adaptive Distance and predict vaccine Effectiveness (MADE). MADE provides a powerful tool for the community to calibrate the effect of egg passage adaptation and select more reliable strains with minimum egg-passaged changes as the seasonal A/H3N2 influenza vaccine.
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5
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Barnard KN, Wasik BR, Alford BK, Hayward JJ, Weichert WS, Voorhees IEH, Holmes EC, Parrish CR. Sequence dynamics of three influenza A virus strains grown in different MDCK cell lines, including those expressing different sialic acid receptors. J Evol Biol 2021; 34:1878-1900. [PMID: 34114711 DOI: 10.1111/jeb.13890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022]
Abstract
Viruses are often cultured in cell lines for research and vaccine development, and those often differ from the natural hosts or tissues. Cell lines can also differ in the presence of virus receptors, such as the sialic acid (Sia) receptors used by influenza A viruses (IAV), which can vary in linkage (α2,3- or α2,6-linkage) and form (N-glycolylneuraminic acid [Neu5Gc] or N-acetylneuraminic acid [Neu5Ac]). The selective pressures resulting from passaging viruses in cell types with host-specific variations in viral receptors are still only partially understood. IAV are commonly cultured in MDCK cells which are both derived from canine kidney tubule epithelium and inherently heterogeneous. MDCK cells naturally present Neu5Ac and α2,3-linked Sia forms. Here, we examine natural MDCK variant lineages, as well as engineered variants that synthesize Neu5Gc and/or α2,6-linkages. We determined how viral genetic variation occurred within human H3N2, H1N1 pandemic and canine H3N2 IAV populations when serially passaged in MDCK cell lines that vary in cell type (MDCK-Type I or MDCK-Type II clones) and in Sia display. Deep sequencing of viral genomes showed small numbers of consensus-level mutations, mostly within the hemagglutinin (HA) gene. Both human IAV showed variants in the HA stem and the HA receptor-binding site of populations passaged in cells displaying Neu5Gc. Canine H3N2 showed variants near the receptor-binding site when passaged in cells displaying Neu5Gc or α2,6-linkages. Viruses replicated to low titres in MDCK-Type II cells, suggesting that not all cell types in heterogeneous MDCK cell populations are equally permissive to infection.
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Affiliation(s)
- Karen N Barnard
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brian R Wasik
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Brynn K Alford
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Jessica J Hayward
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Wendy S Weichert
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Ian E H Voorhees
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Colin R Parrish
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
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6
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Chen H, Alvarez JJS, Ng SH, Nielsen R, Zhai W. Passage Adaptation Correlates With the Reduced Efficacy of the Influenza Vaccine. Clin Infect Dis 2020; 69:1198-1204. [PMID: 30561532 DOI: 10.1093/cid/ciy1065] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 12/13/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND As a dominant seasonal influenza virus, H3N2 virus rapidly evolves in humans and is a constant threat to public health. Despite sustained research efforts, the efficacy of H3N2 vaccine has decreased rapidly. Even though antigenic drift and passage adaptation (substitutions accumulated during vaccine production in embryonated eggs) have been implicated in reduced vaccine efficacy (VE), their respective contributions to the phenomenon remain controversial. METHODS We utilized mutational mapping, a powerful probabilistic method for studying sequence evolution, to analyze patterns of substitutions in different passage conditions for an unprecedented amount of H3N2 hemagglutinin sequences (n = 32 278). RESULTS We found that passage adaptation in embryonated eggs is driven by repeated convergent evolution over 12 codons. Based on substitution patterns at these sites, we developed a metric, adaptive distance (AD), to quantify the strength of passage adaptation and subsequently identified a strong negative correlation between AD and VE. CONCLUSIONS The high correlation between AD and VE implies that passage adaptation in embryonated eggs may be a strong contributor to the recent reduction in H3N2 VE. We developed a computational package called MADE (Measuring Adaptive Distance and vaccine Efficacy based on allelic barcodes) to measure the strength of passage adaptation and predict the efficacy of a candidate vaccine strain. Our findings shed light on strategies for reducing Darwinian evolution within the passaging medium in order to potentially restore an effective vaccine program in the future.
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Affiliation(s)
- Hui Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing.,Human Genetics, Genome Institute of Singapore, A*STAR, Singapore
| | - Jacob Josiah Santiago Alvarez
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing.,Department of Biological Science, National University of Singapore, Singapore
| | - Sock Hoon Ng
- Defence Medical and Environmental Research Institute, DSO National Labs, Singapore
| | - Rasmus Nielsen
- Department of Integrative Biology, Chinese Academy of Sciences, Kunming.,Department of Statistics, University of California-Berkeley, Chinese Academy of Sciences, Kunming
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing.,Human Genetics, Genome Institute of Singapore, A*STAR, Singapore.,School of Biological Sciences, Nanyang Technological University, Chinese Academy of Sciences, Kunming.,National Cancer Center, Singapore, Chinese Academy of Sciences, Kunming.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming
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7
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Wu NC, Thompson AJ, Lee JM, Su W, Arlian BM, Xie J, Lerner RA, Yen HL, Bloom JD, Wilson IA. Different genetic barriers for resistance to HA stem antibodies in influenza H3 and H1 viruses. Science 2020; 368:1335-1340. [PMID: 32554590 PMCID: PMC7412937 DOI: 10.1126/science.aaz5143] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
The discovery and characterization of broadly neutralizing human antibodies (bnAbs) to the highly conserved stem region of influenza hemagglutinin (HA) have contributed to considerations of a universal influenza vaccine. However, the potential for resistance to stem bnAbs also needs to be more thoroughly evaluated. Using deep mutational scanning, with a focus on epitope residues, we found that the genetic barrier to resistance to stem bnAbs is low for the H3 subtype but substantially higher for the H1 subtype owing to structural differences in the HA stem. Several strong resistance mutations in H3 can be observed in naturally circulating strains and do not reduce in vitro viral fitness and in vivo pathogenicity. This study highlights a potential challenge for development of a truly universal influenza vaccine.
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Affiliation(s)
- Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew J Thompson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Juhye M Lee
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Wen Su
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Britni M Arlian
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jia Xie
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Richard A Lerner
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hui-Ling Yen
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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8
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Abstract
The evolutionary dynamics of a virus can differ within hosts and across populations. Studies of within-host evolution provide an important link between experimental studies of virus evolution and large-scale phylodynamic analyses. They can determine the extent to which global processes are recapitulated on local scales and how accurately experimental infections model natural ones. They may also inform epidemiologic models of disease spread and reveal how host-level dynamics contribute to a virus's evolution at a larger scale. Over the last decade, advances in viral sequencing have enabled detailed studies of viral genetic diversity within hosts. I review how within-host diversity is sampled, measured, and expressed, and how comparative studies of viral diversity can be leveraged to elucidate a virus's evolutionary dynamics. These concepts are illustrated with detailed reviews of recent research on the within-host evolution of influenza virus, dengue virus, and cytomegalovirus.
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Affiliation(s)
- Adam S Lauring
- Division of Infectious Diseases, Department of Internal Medicine, and Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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9
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Abstract
Influenza viruses rapidly diversify within individual human infections. Several recent studies have deep-sequenced clinical influenza infections to identify viral variation within hosts, but it remains unclear how within-host mutations fare at the between-host scale. Here, we compare the genetic variation of H3N2 influenza within and between hosts to link viral evolutionary dynamics across scales. Synonymous sites evolve at similar rates at both scales, indicating that global evolution at these putatively neutral sites results from the accumulation of within-host variation. However, nonsynonymous mutations are depleted between hosts compared to within hosts, suggesting that selection purges many of the protein-altering changes that arise within hosts. The exception is at antigenic sites, where selection detectably favors nonsynonymous mutations at the global scale, but not within hosts. These results suggest that selection against deleterious mutations and selection for antigenic change are the main forces that act on within-host variants of influenza virus as they transmit and circulate between hosts.
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Affiliation(s)
- Katherine S Xue
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 3550653720 15th Ave NE, Seattle WA 98195-5065, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109-1024, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Jesse D Bloom
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 3550653720 15th Ave NE, Seattle WA 98195-5065, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109-1024, USA.,Howard Hughes Medical Institute, 1100 Fairview Ave N, Seattle, WA 98109-1024, USA
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10
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Potter BI, Kondor R, Hadfield J, Huddleston J, Barnes J, Rowe T, Guo L, Xu X, Neher RA, Bedford T, Wentworth DE. Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season. Virus Evol 2019; 5:vez046. [PMID: 33282337 DOI: 10.1093/ve/vez046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The 2017-2018 North American influenza season caused more hospitalizations and deaths than any year since the 2009 H1N1 pandemic. The majority of recorded influenza infections were caused by A(H3N2) viruses, with most of the virus's North American diversity falling into the A2 clade. Within A2, we observe a subclade which we call A2/re that rose to comprise almost 70 per cent of A(H3N2) viruses circulating in North America by early 2018. Unlike most fast-growing clades, however, A2/re contains no amino acid substitutions in the hemagglutinin (HA) segment. Moreover, hemagglutination inhibition assays did not suggest substantial antigenic differences between A2/re viruses and viruses sampled during the 2016-2017 season. Rather, we observe that the A2/re clade was the result of a reassortment event that occurred in late 2016 or early 2017 and involved the combination of the HA and PB1 segments of an A2 virus with neuraminidase (NA) and other segments a virus from the clade A1b. The success of this clade shows the need for antigenic analysis that targets NA in addition to HA. Our results illustrate the potential for non-HA drivers of viral success and necessitate the need for more thorough tracking of full viral genomes to better understand the dynamics of influenza epidemics.
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Affiliation(s)
- Barney I Potter
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Rebecca Kondor
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA 30333, USA
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA.,Molecular and Cellular Biology Program, University of Washington, 4109 E Stevens Way NE, Seattle, WA 98105, USA
| | - John Barnes
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA 30333, USA
| | - Thomas Rowe
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA 30333, USA
| | - Lizheng Guo
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA 30333, USA
| | - Xiyan Xu
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA 30333, USA
| | - Richard A Neher
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - David E Wentworth
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA 30333, USA
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11
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Cell culture propagation of foot-and-mouth disease virus: adaptive amino acid substitutions in structural proteins and their functional implications. Virus Genes 2019; 56:1-15. [PMID: 31776851 PMCID: PMC6957568 DOI: 10.1007/s11262-019-01714-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/13/2019] [Indexed: 11/18/2022]
Abstract
Foot-and-mouth disease is endemic in livestock in large parts of Africa and Asia, where it is an important driver of food insecurity and a major obstacle to agricultural development and the international trade in animal products. Virtually all commercially available vaccines are inactivated whole-virus vaccines produced in cell culture, but the adaptation of a field isolate of the virus to growth in culture is laborious and time-consuming. This is of particular concern for the development of vaccines to newly emerging virus lineages, where long lead times from virus isolate to vaccine can delay the implementation of effective control programs. High antigen yields in production cells are also necessary to make vaccines affordable for less developed countries in endemic areas. Therefore, a rational approach to cell culture adaptation that combines prior knowledge of common adaptive mutations and reverse genetics techniques is urgently required. This review provides an overview of amino acid exchanges in the viral capsid proteins in the context of adaptation to cell culture.
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12
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Allele-specific nonstationarity in evolution of influenza A virus surface proteins. Proc Natl Acad Sci U S A 2019; 116:21104-21112. [PMID: 31578251 DOI: 10.1073/pnas.1904246116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Influenza A virus (IAV) is a major public health problem and a pandemic threat. Its evolution is largely driven by diversifying positive selection so that relative fitness of different amino acid variants changes with time due to changes in herd immunity or genomic context, and novel amino acid variants attain fitness advantage. Here, we hypothesize that diversifying selection also has another manifestation: the fitness associated with a particular amino acid variant should decline with time since its origin, as the herd immunity adapts to it. By tracing the evolution of antigenic sites at IAV surface proteins, we show that an amino acid variant becomes progressively more likely to become replaced by another variant with time since its origin-a phenomenon we call "senescence." Senescence is particularly pronounced at experimentally validated antigenic sites, implying that it is largely driven by host immunity. By contrast, at internal sites, existing variants become more favorable with time, probably due to arising contingent mutations at other epistatically interacting sites. Our findings reveal a previously undescribed facet of adaptive evolution and suggest approaches for prediction of evolutionary dynamics of pathogens.
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13
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Wu NC, Lv H, Thompson AJ, Wu DC, Ng WWS, Kadam RU, Lin CW, Nycholat CM, McBride R, Liang W, Paulson JC, Mok CKP, Wilson IA. Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Cell Host Microbe 2019; 25:836-844.e5. [PMID: 31151913 PMCID: PMC6579542 DOI: 10.1016/j.chom.2019.04.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/01/2019] [Accepted: 04/26/2019] [Indexed: 12/23/2022]
Abstract
Egg-based seasonal influenza vaccines are the major preventive countermeasure against influenza virus. However, their effectiveness can be compromised when antigenic changes arise from egg-adaptive mutations on influenza hemagglutinin (HA). The L194P mutation is commonly observed in egg-based H3N2 vaccine seed strains and significantly alters HA antigenicity. An approach to prevent L194P would therefore be beneficial. We show that emergence of L194P during egg passaging can be impeded by preexistence of a G186V mutation, revealing strong incompatibility between these mutations. X-ray structures illustrate that individual G186V and L194P mutations have opposing effects on the HA receptor-binding site (RBS), and when both G186V and L194P are present, the RBS is severely disrupted. Importantly, wild-type HA antigenicity is maintained with G186V, but not L194P. Our results demonstrate that these epistatic interactions can be used to prevent the emergence of mutations that adversely alter antigenicity during egg adaptation. Most H3N2 egg isolates carry hemagglutinin mutation G186V or L194P, but not both Hemagglutinin double mutation G186V/L194P is highly deleterious to the virus Hemagglutinin double mutation G186V/L194P disrupts the receptor-binding site Wild-type hemagglutinin antigenicity is maintained in G186V, but not in L194P
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MESH Headings
- Adaptation, Biological
- Animals
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Binding Sites
- Chick Embryo
- Crystallography, X-Ray
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/growth & development
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza Vaccines/genetics
- Influenza Vaccines/immunology
- Mutation, Missense
- Protein Conformation
- Technology, Pharmaceutical/methods
- Virus Cultivation/methods
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Affiliation(s)
- Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Andrew J Thompson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Douglas C Wu
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Wilson W S Ng
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Rameshwar U Kadam
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chih-Wei Lin
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Corwin M Nycholat
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan McBride
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Weiwen Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - James C Paulson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chris K P Mok
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, China.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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14
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Structures and functions linked to genome-wide adaptation of human influenza A viruses. Sci Rep 2019; 9:6267. [PMID: 31000776 PMCID: PMC6472403 DOI: 10.1038/s41598-019-42614-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/27/2019] [Indexed: 11/12/2022] Open
Abstract
Human influenza A viruses elicit short-term respiratory infections with considerable mortality and morbidity. While H3N2 viruses circulate for more than 50 years, the recent introduction of pH1N1 viruses presents an excellent opportunity for a comparative analysis of the genome-wide evolutionary forces acting on both subtypes. Here, we inferred patches of sites relevant for adaptation, i.e. being under positive selection, on eleven viral protein structures, from all available data since 1968 and correlated these with known functional properties. Overall, pH1N1 have more patches than H3N2 viruses, especially in the viral polymerase complex, while antigenic evolution is more apparent for H3N2 viruses. In both subtypes, NS1 has the highest patch and patch site frequency, indicating that NS1-mediated viral attenuation of host inflammatory responses is a continuously intensifying process, elevated even in the longtime-circulating subtype H3N2. We confirmed the resistance-causing effects of two pH1N1 changes against oseltamivir in NA activity assays, demonstrating the value of the resource for discovering functionally relevant changes. Our results represent an atlas of protein regions and sites with links to host adaptation, antiviral drug resistance and immune evasion for both subtypes for further study.
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15
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Matsumoto S, Chong Y, Kang D, Ikematsu H. High genetic stability in MDCK-SIAT1 passaged human influenza viruses. J Infect Chemother 2019; 25:222-224. [DOI: 10.1016/j.jiac.2018.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/12/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
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16
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Jorquera PA, Mishin VP, Chesnokov A, Nguyen HT, Mann B, Garten R, Barnes J, Hodges E, De La Cruz J, Xu X, Katz J, Wentworth DE, Gubareva LV. Insights into the antigenic advancement of influenza A(H3N2) viruses, 2011-2018. Sci Rep 2019; 9:2676. [PMID: 30804469 PMCID: PMC6389938 DOI: 10.1038/s41598-019-39276-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/11/2019] [Indexed: 11/12/2022] Open
Abstract
Influenza A(H3N2) viruses evade human immunity primarily by acquiring antigenic changes in the haemagglutinin (HA). HA receptor-binding features of contemporary A(H3N2) viruses hinder traditional antigenic characterization using haemagglutination inhibition and promote selection of HA mutants. Thus, alternative approaches are needed to reliably assess antigenic relatedness between circulating viruses and vaccines. We developed a high content imaging-based neutralization test (HINT) to reduce antigenic mischaracterization resulting from virus adaptation to cell culture. Ferret reference antisera were raised using clinical specimens containing viruses representing recent vaccine strains. Analysis of viruses circulating during 2011–2018 showed that gain of an N158-linked glycosylation in HA was a molecular determinant of antigenic distancing between A/Hong Kong/4801/2014-like (clade 3C.2a) and A/Texas/50/2012-like viruses (clade 3C.1), while multiple evolutionary HA F193S substitution were linked to antigenic distancing from A/Switzerland/97152963/2013-like (clade 3C.3a) and further antigenic distancing from A/Texas/50/2012-like viruses. Additionally, a few viruses carrying HA T135K and/or I192T showed reduced neutralization by A/Hong Kong/4801/2014-like antiserum. Notably, this technique elucidated the antigenic characteristics of clinical specimens, enabling direct characterization of viruses produced in vivo, and eliminating in vitro culture, which rapidly alters the genotype/phenotype. HINT is a valuable new antigenic analysis tool for vaccine strain selection.
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Affiliation(s)
- Patricia A Jorquera
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA.,CNI Advantage, LLC. 17 Executive Park Dr NE, Atlanta, GA, 30329, USA
| | - Vasiliy P Mishin
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Anton Chesnokov
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Ha T Nguyen
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA.,Battelle Memorial Institute, 2987 Clairmont Rd, Suite 450, Atlanta, GA, 30329, USA
| | - Brian Mann
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA.,Battelle Memorial Institute, 2987 Clairmont Rd, Suite 450, Atlanta, GA, 30329, USA
| | - Rebecca Garten
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - John Barnes
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Erin Hodges
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA.,CNI Advantage, LLC. 17 Executive Park Dr NE, Atlanta, GA, 30329, USA
| | - Juan De La Cruz
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA.,Battelle Memorial Institute, 2987 Clairmont Rd, Suite 450, Atlanta, GA, 30329, USA
| | - Xiyan Xu
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Jackie Katz
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - David E Wentworth
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Larisa V Gubareva
- Influenza Division, Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA.
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17
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DuPai CD, McWhite CD, Smith CB, Garten R, Maurer-Stroh S, Wilke CO. Influenza passaging annotations: what they tell us and why we should listen. Virus Evol 2019; 5:vez016. [PMID: 31275610 PMCID: PMC6599686 DOI: 10.1093/ve/vez016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Influenza databases now contain over 100,000 worldwide sequence records for strains influenza A(H3N2) and A(H1N1). Although these data facilitate global research efforts and vaccine development practices, they also represent a stumbling block for researchers because of their confusing and heterogeneous annotation. Unclear passaging annotations are particularly concerning given the recent work highlighting the presence and risk of false adaptation signals introduced by cell passaging of viral isolates. With this in mind, we aim to provide a concise outline of why viruses are passaged, a clear overview of passaging annotation nomenclature currently in use, and suggestions for a standardized nomenclature going forward. Our hope is that this summary will empower researchers and clinicians alike to more easily understand a virus sample's passage history when analyzing influenza sequences.
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Affiliation(s)
- Cory D DuPai
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Claire D McWhite
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Catherine B Smith
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rebecca Garten
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore
| | - Claus O Wilke
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, USA
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18
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Han AX, Maurer-Stroh S, Russell CA. Individual immune selection pressure has limited impact on seasonal influenza virus evolution. Nat Ecol Evol 2018; 3:302-311. [DOI: 10.1038/s41559-018-0741-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/01/2018] [Indexed: 01/10/2023]
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19
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Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants. Proc Natl Acad Sci U S A 2018; 115:E8276-E8285. [PMID: 30104379 PMCID: PMC6126756 DOI: 10.1073/pnas.1806133115] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A key goal in the study of influenza virus evolution is to forecast which viral strains will persist and which ones will die out. Here we experimentally measure the effects of all amino acid mutations to the hemagglutinin protein from a human H3N2 influenza strain on viral growth in cell culture. We show that these measurements have utility for distinguishing among viral strains that do and do not succeed in nature. Overall, our work suggests that new high-throughput experimental approaches may be useful for understanding virus evolution in nature. Human influenza virus rapidly accumulates mutations in its major surface protein hemagglutinin (HA). The evolutionary success of influenza virus lineages depends on how these mutations affect HA’s functionality and antigenicity. Here we experimentally measure the effects on viral growth in cell culture of all single amino acid mutations to the HA from a recent human H3N2 influenza virus strain. We show that mutations that are measured to be more favorable for viral growth are enriched in evolutionarily successful H3N2 viral lineages relative to mutations that are measured to be less favorable for viral growth. Therefore, despite the well-known caveats about cell-culture measurements of viral fitness, such measurements can still be informative for understanding evolution in nature. We also compare our measurements for H3 HA to similar data previously generated for a distantly related H1 HA and find substantial differences in which amino acids are preferred at many sites. For instance, the H3 HA has less disparity in mutational tolerance between the head and stalk domains than the H1 HA. Overall, our work suggests that experimental measurements of mutational effects can be leveraged to help understand the evolutionary fates of viral lineages in nature—but only when the measurements are made on a viral strain similar to the ones being studied in nature.
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20
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Kirkpatrick E, Qiu X, Wilson PC, Bahl J, Krammer F. The influenza virus hemagglutinin head evolves faster than the stalk domain. Sci Rep 2018; 8:10432. [PMID: 29992986 PMCID: PMC6041311 DOI: 10.1038/s41598-018-28706-1] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/28/2018] [Indexed: 01/12/2023] Open
Abstract
The limited ability of current influenza virus vaccines to protect from antigenically drifted or shifted viruses creates a public health problem that has led to the need to develop effective, broadly protective vaccines. While current influenza virus vaccines mostly induce an immune response against the immunodominant and variable head domain of the hemagglutinin, the major surface glycoprotein of the virus, the hemagglutinin stalk domain has been identified to harbor neutralizing B-cell epitopes that are conserved among and even between influenza A virus subtypes. A complete understanding of the differences in evolution between the main target of current vaccines and this more conserved stalk region are missing. Here, we performed an evolutionary analysis of the stalk domains of the hemagglutinin of pre-pandemic seasonal H1N1, pandemic H1N1, seasonal H3N2, and influenza B viruses and show quantitatively for the first time that the stalk domain is evolving at a rate that is significantly slower than that of the head domain. Additionally, we found that the cross-reactive epitopes in the stalk domain targeted by broadly neutralizing monoclonal antibodies are evolving at an even slower rate compared to the full head and stalk regions of the protein. Finally, a fixed-effects likelihood selection analysis was performed for these virus groups in both the head and stalk domains. While several positive selection sites were found in the head domain, only a single site in the stalk domain of pre-pandemic seasonal H1 hemagglutinin was identified at amino acid position 468 (H1 numbering from methionine). This site is not located in or close to the epitopes of cross-reactive anti-stalk monoclonal antibodies. Furthermore, we found that changes in this site do not significantly impact virus binding or neutralization by human anti-stalk antibodies, suggesting that some positive selection in the stalk domain is independent of immune pressures. We conclude that, while the stalk domain does evolve over time, this evolution is slow and, historically, is not directed to aid in evading neutralizing antibody responses.
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MESH Headings
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Epitopes/immunology
- Evolution, Molecular
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinins/chemistry
- Hemagglutinins/genetics
- Hemagglutinins/immunology
- Humans
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza Vaccines/immunology
- Influenza, Human/immunology
- Influenza, Human/virology
- Kinetics
- Protein Domains/genetics
- Protein Domains/immunology
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Affiliation(s)
- Ericka Kirkpatrick
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xueting Qiu
- University of Texas School of Public Health, Houston, TX, USA
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Justin Bahl
- University of Texas School of Public Health, Houston, TX, USA.
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Graduate Medical School, Singapore, Singapore.
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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21
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Hsp90 shapes protein and RNA evolution to balance trade-offs between protein stability and aggregation. Nat Commun 2018; 9:1781. [PMID: 29725062 PMCID: PMC5934419 DOI: 10.1038/s41467-018-04203-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/10/2018] [Indexed: 01/16/2023] Open
Abstract
Acquisition of mutations is central to evolution; however, the detrimental effects of most mutations on protein folding and stability limit protein evolvability. Molecular chaperones, which suppress aggregation and facilitate polypeptide folding, may alleviate the effects of destabilizing mutations thus promoting sequence diversification. To illuminate how chaperones can influence protein evolution, we examined the effect of reduced activity of the chaperone Hsp90 on poliovirus evolution. We find that Hsp90 offsets evolutionary trade-offs between protein stability and aggregation. Lower chaperone levels favor variants of reduced hydrophobicity and protein aggregation propensity but at a cost to protein stability. Notably, reducing Hsp90 activity also promotes clusters of codon-deoptimized synonymous mutations at inter-domain boundaries, likely to facilitate cotranslational domain folding. Our results reveal how a chaperone can shape the sequence landscape at both the protein and RNA levels to harmonize competing constraints posed by protein stability, aggregation propensity, and translation rate on successful protein biogenesis.
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22
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Morris DH, Gostic KM, Pompei S, Bedford T, Łuksza M, Neher RA, Grenfell BT, Lässig M, McCauley JW. Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology. Trends Microbiol 2018; 26:102-118. [PMID: 29097090 PMCID: PMC5830126 DOI: 10.1016/j.tim.2017.09.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/06/2017] [Accepted: 09/19/2017] [Indexed: 01/16/2023]
Abstract
Seasonal influenza is controlled through vaccination campaigns. Evolution of influenza virus antigens means that vaccines must be updated to match novel strains, and vaccine effectiveness depends on the ability of scientists to predict nearly a year in advance which influenza variants will dominate in upcoming seasons. In this review, we highlight a promising new surveillance tool: predictive models. Based on data-sharing and close collaboration between the World Health Organization and academic scientists, these models use surveillance data to make quantitative predictions regarding influenza evolution. Predictive models demonstrate the potential of applied evolutionary biology to improve public health and disease control. We review the state of influenza predictive modeling and discuss next steps and recommendations to ensure that these models deliver upon their considerable biomedical promise.
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Affiliation(s)
- Dylan H Morris
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Katelyn M Gostic
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Simone Pompei
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marta Łuksza
- Institute for Advanced Study, Princeton, NJ, USA
| | - Richard A Neher
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Michael Lässig
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
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23
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Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. mSphere 2018; 3:mSphere00552-17. [PMID: 29299533 PMCID: PMC5750391 DOI: 10.1128/mspheredirect.00552-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 11/30/2017] [Indexed: 12/20/2022] Open
Abstract
Viruses mutate rapidly, and recent studies of RNA viruses have shown that related viral variants can sometimes cooperate to improve each other’s growth. We previously described two variants of H3N2 influenza virus that cooperate in cell culture. The mutation responsible for cooperation is often observed when human samples of influenza virus are grown in the lab before sequencing, but it is unclear whether the mutation also exists in human infections or is exclusively the result of lab passage. We identified nine human isolates of influenza virus that had developed the cooperating mutation after being grown in the lab and performed highly sensitive deep sequencing of the unpassaged clinical samples to determine whether the mutation existed in the original human infections. We found no evidence of the cooperating mutation in the unpassaged samples, suggesting that the cooperation arises primarily under laboratory conditions. The high mutation rates of RNA viruses lead to rapid genetic diversification, which can enable cooperative interactions between variants in a viral population. We previously described two distinct variants of H3N2 influenza virus that cooperate in cell culture. These variants differ by a single mutation, D151G, in the neuraminidase protein. The D151G mutation reaches a stable frequency of about 50% when virus is passaged in cell culture. However, it is unclear whether selection for the cooperative benefits of D151G is a cell culture phenomenon or whether the mutation is also sometimes present at appreciable frequency in virus populations sampled directly from infected humans. Prior work has not detected D151G in unpassaged clinical samples, but those studies have used methods like Sanger sequencing and pyrosequencing, which are relatively insensitive to low-frequency variation. We identified nine samples of human H3N2 influenza virus collected between 2013 and 2015 in which Sanger sequencing had detected a high frequency of the D151G mutation following one to three passages in cell culture. We deep sequenced the unpassaged clinical samples to identify low-frequency viral variants. The frequency of D151G did not exceed the frequency of library preparation and sequencing errors in any of the sequenced samples. We conclude that passage in cell culture is primarily responsible for the frequent observations of D151G in recent H3N2 influenza virus strains. IMPORTANCE Viruses mutate rapidly, and recent studies of RNA viruses have shown that related viral variants can sometimes cooperate to improve each other’s growth. We previously described two variants of H3N2 influenza virus that cooperate in cell culture. The mutation responsible for cooperation is often observed when human samples of influenza virus are grown in the lab before sequencing, but it is unclear whether the mutation also exists in human infections or is exclusively the result of lab passage. We identified nine human isolates of influenza virus that had developed the cooperating mutation after being grown in the lab and performed highly sensitive deep sequencing of the unpassaged clinical samples to determine whether the mutation existed in the original human infections. We found no evidence of the cooperating mutation in the unpassaged samples, suggesting that the cooperation arises primarily under laboratory conditions.
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Goldstein EJ, Harvey WT, Wilkie GS, Shepherd SJ, MacLean AR, Murcia PR, Gunson RN. Integrating patient and whole-genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses. Microb Genom 2017; 4. [PMID: 29310750 PMCID: PMC5857367 DOI: 10.1099/mgen.0.000137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Genetic surveillance of seasonal influenza is largely focused on sequencing of the haemagglutinin gene. Consequently, our understanding of the contribution of the remaining seven gene segments to the evolution and epidemiological dynamics of seasonal influenza is relatively limited. The increased availability of next-generation sequencing technologies allows rapid and economic whole-genome sequencing (WGS) of influenza virus. Here, 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland, were sequenced directly using both Sanger sequencing of the HA1 region and WGS using the Illumina MiSeq platform. Sequences generated by the two methods were highly correlated, and WGS provided on average >90 % whole genome coverage. As reported in other European countries during 2014/15, all strains belonged to genetic group 3C, with subgroup 3C.2a predominating. Multiple inter-subgroup reassortants were identified, including three 3C.3 viruses descended from a single reassortment event, which had persisted in the population. Cases of severe acute respiratory illness were significantly clustered on phylogenies of multiple gene segments indicating potential genetic factors warranting further investigation. Severe cases were also more likely to be associated with reassortant viruses and to occur later in the season. These results suggest that WGS provides an opportunity to develop our understanding of the relationship between the influenza genome and disease severity and the epidemiological consequences of within-subtype reassortment. Therefore, increased levels of WGS, linked to clinical and epidemiological data, could improve influenza surveillance.
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Affiliation(s)
- Emily J Goldstein
- 1West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - William T Harvey
- 2Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Gavin S Wilkie
- 3Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Samantha J Shepherd
- 1West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Alasdair R MacLean
- 1West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Pablo R Murcia
- 3Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Rory N Gunson
- 1West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
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25
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Fitness cost of reassortment in human influenza. PLoS Pathog 2017; 13:e1006685. [PMID: 29112968 PMCID: PMC5675378 DOI: 10.1371/journal.ppat.1006685] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/09/2017] [Indexed: 12/15/2022] Open
Abstract
Reassortment, which is the exchange of genome sequence between viruses co-infecting a host cell, plays an important role in the evolution of segmented viruses. In the human influenza virus, reassortment happens most frequently between co-existing variants within the same lineage. This process breaks genetic linkage and fitness correlations between viral genome segments, but the resulting net effect on viral fitness has remained unclear. In this paper, we determine rate and average selective effect of reassortment processes in the human influenza lineage A/H3N2. For the surface proteins hemagglutinin and neuraminidase, reassortant variants with a mean distance of at least 3 nucleotides to their parent strains get established at a rate of about 10−2 in units of the neutral point mutation rate. Our inference is based on a new method to map reassortment events from joint genealogies of multiple genome segments, which is tested by extensive simulations. We show that intra-lineage reassortment processes are, on average, under substantial negative selection that increases in strength with increasing sequence distance between the parent strains. The deleterious effects of reassortment manifest themselves in two ways: there are fewer reassortment events than expected from a null model of neutral reassortment, and reassortant strains have fewer descendants than their non-reassortant counterparts. Our results suggest that influenza evolves under ubiquitous epistasis across proteins, which produces fitness barriers against reassortment even between co-circulating strains within one lineage. The genome of the human influenza virus consists of 8 disjoint RNA polymer segments. These segments can undergo reassortment: when two viruses co-infect a host cell, they can produce viral offspring with a new combination of segments. In this paper, we show that reassortment within a given influenza lineage induces a fitness cost that increases in strength with increasing genetic distance of the parent viruses. Our finding suggests that evolution continuously produces viral proteins whose fitness depends on each other; reassortment reduces fitness by breaking up successful combinations of proteins. Thus, selection across proteins constrains viral evolution within a given lineage, and it may be an important factor in defining a viral species.
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26
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Lequime S, Richard V, Cao-Lormeau VM, Lambrechts L. Full-genome dengue virus sequencing in mosquito saliva shows lack of convergent positive selection during transmission by Aedes aegypti. Virus Evol 2017; 3:vex031. [PMID: 29497564 PMCID: PMC5782851 DOI: 10.1093/ve/vex031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Like other pathogens with high mutation and replication rates, within-host dengue virus
(DENV) populations evolve during infection of their main mosquito vector, Aedes
aegypti. Within-host DENV evolution during transmission provides opportunities
for adaptation and emergence of novel virus variants. Recent studies of DENV genetic
diversity failed to detect convergent evolution of adaptive mutations in mosquito tissues
such as midgut and salivary glands, suggesting that convergent positive selection is not a
major driver of within-host DENV evolution in the vector. However, it is unknown whether
this conclusion extends to the transmitted viral subpopulation because it is technically
difficult to sequence DENV genomes in mosquito saliva. Here, we achieved DENV full-genome
sequencing by pooling saliva samples collected non-sacrificially from 49 to 163 individual
Ae. aegypti mosquitoes previously infected with one of two DENV-1
genotypes. We compared the transmitted viral subpopulations found in the pooled saliva
samples collected in time series with the input viral population present in the infectious
blood meal. In all pooled saliva samples examined, the full-genome consensus sequence of
the input viral population was unchanged. Although the pooling strategy prevents analysis
of individual saliva samples, our results demonstrate the lack of strong convergent
positive selection during a single round of DENV transmission by Ae.
aegypti. This finding reinforces the idea that genetic drift and purifying
selection are the dominant evolutionary forces shaping within-host DENV genetic diversity
during transmission by mosquitoes.
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Affiliation(s)
- Sebastian Lequime
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France.,Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, 25-28 rue du Docteur Roux, 75015 Paris, France.,Université Pierre et Marie Curie, Cellule Pasteur UPMC, 4 place Jussieu, 75005 Paris, France
| | - Vaea Richard
- Unit of Emerging Infectious Diseases, Institut Louis Malardé, BP 30, 98713 Papeete, Tahiti, French Polynesia
| | - Van-Mai Cao-Lormeau
- Unit of Emerging Infectious Diseases, Institut Louis Malardé, BP 30, 98713 Papeete, Tahiti, French Polynesia
| | - Louis Lambrechts
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France.,Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, 25-28 rue du Docteur Roux, 75015 Paris, France
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27
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28
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Wu NC, Zost SJ, Thompson AJ, Oyen D, Nycholat CM, McBride R, Paulson JC, Hensley SE, Wilson IA. A structural explanation for the low effectiveness of the seasonal influenza H3N2 vaccine. PLoS Pathog 2017; 13:e1006682. [PMID: 29059230 PMCID: PMC5667890 DOI: 10.1371/journal.ppat.1006682] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/02/2017] [Accepted: 10/05/2017] [Indexed: 11/24/2022] Open
Abstract
The effectiveness of the annual influenza vaccine has declined in recent years, especially for the H3N2 component, and is a concern for global public health. A major cause for this lack in effectiveness has been attributed to the egg-based vaccine production process. Substitutions on the hemagglutinin glycoprotein (HA) often arise during virus passaging that change its antigenicity and hence vaccine effectiveness. Here, we characterize the effect of a prevalent substitution, L194P, in egg-passaged H3N2 viruses. X-ray structural analysis reveals that this substitution surprisingly increases the mobility of the 190-helix and neighboring regions in antigenic site B, which forms one side of the receptor binding site (RBS) and is immunodominant in recent human H3N2 viruses. Importantly, the L194P substitution decreases binding and neutralization by an RBS-targeted broadly neutralizing antibody by three orders of magnitude and significantly changes the HA antigenicity as measured by binding of human serum antibodies. The receptor binding mode and specificity are also altered to adapt to avian receptors during egg passaging. Overall, these findings help explain the low effectiveness of the seasonal vaccine against H3N2 viruses, and suggest that alternative approaches should be accelerated for producing influenza vaccines as well as isolating clinical isolates. Seasonal influenza vaccine does not always confer protection in vaccinated individuals. Vaccine candidates are selected from clinical isolates based on their antigenic properties. It is common to use chicken eggs for culturing clinical isolates and for large-scale production of vaccines. However, influenza virus often mutates to adapt to being grown in chicken eggs, which can influence antigenicity and hence vaccine effectiveness. Here, we structurally characterize an egg-adaptive substitution, namely L194P, in H3N2 virus hemagglutinin. Our results reveal that the L194P substitution substantially increases the flexibility of an epitope region that is commonly targeted by antibodies. Based on the binding affinity of a broadly neutralizing antibody and a panel of human serum antibodies, we further show that the L194P substitution dramatically changes the HA antigenicity. The change of the receptor-binding mode associated with the L194P substitution provides an explanation for its ability to successfully grow in eggs. Our study describes a mechanism for the low influenza vaccine effectiveness and reaffirms the urgency for replacing the egg-based production of influenza vaccines.
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Affiliation(s)
- Nicholas C. Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Seth J. Zost
- Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, United States of America
| | - Andrew J. Thompson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - David Oyen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Corwin M. Nycholat
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Ryan McBride
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - James C. Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Scott E. Hensley
- Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, United States of America
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States of America
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, United States of America
- * E-mail:
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29
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Klingen TR, Reimering S, Guzmán CA, McHardy AC. In Silico Vaccine Strain Prediction for Human Influenza Viruses. Trends Microbiol 2017; 26:119-131. [PMID: 29032900 DOI: 10.1016/j.tim.2017.09.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/21/2017] [Accepted: 09/06/2017] [Indexed: 02/02/2023]
Abstract
Vaccines preventing seasonal influenza infections save many lives every year; however, due to rapid viral evolution, they have to be updated frequently to remain effective. To identify appropriate vaccine strains, the World Health Organization (WHO) operates a global program that continually generates and interprets surveillance data. Over the past decade, sophisticated computational techniques, drawing from multiple theoretical disciplines, have been developed that predict viral lineages rising to predominance, assess their suitability as vaccine strains, link genetic to antigenic alterations, as well as integrate and visualize genetic, epidemiological, structural, and antigenic data. These could form the basis of an objective and reproducible vaccine strain-selection procedure utilizing the complex, large-scale data types from surveillance. To this end, computational techniques should already be incorporated into the vaccine-selection process in an independent, parallel track, and their performance continuously evaluated.
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Affiliation(s)
- Thorsten R Klingen
- Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany; Co-first authors
| | - Susanne Reimering
- Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany; Co-first authors
| | - Carlos A Guzmán
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany; German Centre for Infection Research (DZIF)
| | - Alice C McHardy
- Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany; German Centre for Infection Research (DZIF).
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30
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Bloom JD. Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models. Biol Direct 2017; 12:1. [PMID: 28095902 PMCID: PMC5240389 DOI: 10.1186/s13062-016-0172-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/14/2016] [Indexed: 12/23/2022] Open
Abstract
Background Sites of positive selection are identified by comparing observed evolutionary patterns to those expected under a null model for evolution in the absence of such selection. For protein-coding genes, the most common null model is that nonsynonymous and synonymous mutations fix at equal rates; this unrealistic model has limited power to detect many interesting forms of selection. Results I describe a new approach that uses a null model based on experimental measurements of a gene’s site-specific amino-acid preferences generated by deep mutational scanning in the lab. This null model makes it possible to identify both diversifying selection for repeated amino-acid change and differential selection for mutations to amino acids that are unexpected given the measurements made in the lab. I show that this approach identifies sites of adaptive substitutions in four genes (lactamase, Gal4, influenza nucleoprotein, and influenza hemagglutinin) far better than a comparable method that simply compares the rates of nonsynonymous and synonymous substitutions. Conclusions As rapid increases in biological data enable increasingly nuanced descriptions of the constraints on individual protein sites, approaches like the one here can improve our ability to identify many interesting forms of selection in natural sequences. Reviewers This article was reviewed by Sebastian Maurer-Stroh, Olivier Tenaillon, and Tal Pupko. All three reviewers are members of the Biology Direct editorial board. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0172-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jesse D Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, 98109, WA, USA.
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31
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Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA. Viral factors in influenza pandemic risk assessment. eLife 2016; 5. [PMID: 27834632 PMCID: PMC5156527 DOI: 10.7554/elife.18491] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/03/2016] [Indexed: 12/13/2022] Open
Abstract
The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of which spark sustained transmission in humans. To date, no pandemic emergence of a new influenza strain has been preceded by detection of a closely related precursor in an animal or human. Nonetheless, influenza surveillance efforts are expanding, prompting a need for tools to assess the pandemic risk posed by a detected virus. The goal would be to use genetic sequence and/or biological assays of viral traits to identify those non-human influenza viruses with the greatest risk of evolving into pandemic threats, and/or to understand drivers of such evolution, to prioritize pandemic prevention or response measures. We describe such efforts, identify progress and ongoing challenges, and discuss three specific traits of influenza viruses (hemagglutinin receptor binding specificity, hemagglutinin pH of activation, and polymerase complex efficiency) that contribute to pandemic risk.
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Affiliation(s)
- Marc Lipsitch
- Center for Communicable Disease Dynamics, Harvard T. H Chan School of Public Health, Boston, United States.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | - Wendy Barclay
- Division of Infectious Disease, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Rahul Raman
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Charles J Russell
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, United States
| | - Jessica A Belser
- Centers for Disease Control and Prevention, Atlanta, United States
| | - Sarah Cobey
- Department of Ecology and Evolutionary Biology, University of Chicago, Chicago, United States
| | - Peter M Kasson
- Department of Biomedical Engineering, University of Virginia, Charlottesville, United States.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, United States.,Fogarty International Center, National Institutes of Health, Bethesda, United States
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, Singapore.,National Public Health Laboratory, Communicable Diseases Division, Ministry of Health, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Steven Riley
- MRC Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College London, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | | | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, United States
| | - Andreas Handel
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, United States
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Pablo R Murcia
- MRC-University of Glasgow Centre For Virus Research, Glasgow, United Kingdom
| | | | - Claus O Wilke
- Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, United States.,Department of Integrative Biology, The University of Texas at Austin, Austin, United States
| | - Colin A Russell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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