1
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Wang S, Zhang TH, Hu M, Tang K, Sheng L, Hong M, Chen D, Chen L, Shi Y, Feng J, Qian J, Sun L, Ding K, Sun R, Du Y. Deep mutational scanning of influenza A virus neuraminidase facilitates the identification of drug resistance mutations in vivo. mSystems 2023; 8:e0067023. [PMID: 37772870 PMCID: PMC10654105 DOI: 10.1128/msystems.00670-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/09/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE NA is a crucial surface antigen and drug target of influenza A virus. A comprehensive understanding of NA's mutational effect and drug resistance profiles in vivo is essential for comprehending the evolutionary constraints and making informed choices regarding drug selection to combat resistance in clinical settings. In the current study, we established an efficient deep mutational screening system in mouse lung tissues and systematically evaluated the fitness effect and drug resistance to three neuraminidase inhibitors of NA single-nucleotide mutations. The fitness of NA mutants is generally correlated with a natural mutation in the database. The fitness of NA mutants is influenced by biophysical factors such as protein stability, complex formation, and the immune response triggered by viral infection. In addition to confirming previously reported drug-resistant mutations, novel mutations were identified. Interestingly, we identified an allosteric drug-resistance mutation that is not located within the drug-binding pocket but potentially affects drug binding by interfering with NA tetramerization. The dual assessments performed in this study provide a more accurate assessment of the evolutionary potential of drug-resistant mutations and offer guidance for the rational selection of antiviral drugs.
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Affiliation(s)
- Sihan Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tian-hao Zhang
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Menglong Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kejun Tang
- Department of Surgery, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Li Sheng
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California, USA
- School of Biomedical Sciences, LKS Faculty of Medicine, The Hong Kong University, Hong Kong, China
| | - Mengying Hong
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Dongdong Chen
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Liubo Chen
- Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Yuan Shi
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California, USA
| | - Jun Feng
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California, USA
| | - Jing Qian
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lifeng Sun
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kefeng Ding
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ren Sun
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California, USA
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Yushen Du
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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2
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Wittmund M, Cadet F, Davari MD. Learning Epistasis and Residue Coevolution Patterns: Current Trends and Future Perspectives for Advancing Enzyme Engineering. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marcel Wittmund
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Frederic Cadet
- Laboratory of Excellence LABEX GR, DSIMB, Inserm UMR S1134, University of Paris city & University of Reunion, Paris 75014, France
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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3
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Wang Y, Lei R, Nourmohammad A, Wu NC. Antigenic evolution of human influenza H3N2 neuraminidase is constrained by charge balancing. eLife 2021; 10:e72516. [PMID: 34878407 PMCID: PMC8683081 DOI: 10.7554/elife.72516] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
As one of the main influenza antigens, neuraminidase (NA) in H3N2 virus has evolved extensively for more than 50 years due to continuous immune pressure. While NA has recently emerged as an effective vaccine target, biophysical constraints on the antigenic evolution of NA remain largely elusive. Here, we apply combinatorial mutagenesis and next-generation sequencing to characterize the local fitness landscape in an antigenic region of NA in six different human H3N2 strains that were isolated around 10 years apart. The local fitness landscape correlates well among strains and the pairwise epistasis is highly conserved. Our analysis further demonstrates that local net charge governs the pairwise epistasis in this antigenic region. In addition, we show that residue coevolution in this antigenic region is correlated with the pairwise epistasis between charge states. Overall, this study demonstrates the importance of quantifying epistasis and the underlying biophysical constraint for building a model of influenza evolution.
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Affiliation(s)
- Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Armita Nourmohammad
- Department of Physics, University of WashingtonSeattleUnited States
- Max Planck Institute for Dynamics and Self-OrganizationGöttingenGermany
- Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Carle Illinois College of Medicine, University of Illinois at Urbana-ChampaignUrbanaUnited States
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4
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Burton TD, Eyre NS. Applications of Deep Mutational Scanning in Virology. Viruses 2021; 13:1020. [PMID: 34071591 PMCID: PMC8227372 DOI: 10.3390/v13061020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Several recently developed high-throughput techniques have changed the field of molecular virology. For example, proteomics studies reveal complete interactomes of a viral protein, genome-wide CRISPR knockout and activation screens probe the importance of every single human gene in aiding or fighting a virus, and ChIP-seq experiments reveal genome-wide epigenetic changes in response to infection. Deep mutational scanning is a relatively novel form of protein science which allows the in-depth functional analysis of every nucleotide within a viral gene or genome, revealing regions of importance, flexibility, and mutational potential. In this review, we discuss the application of this technique to RNA viruses including members of the Flaviviridae family, Influenza A Virus and Severe Acute Respiratory Syndrome Coronavirus 2. We also briefly discuss the reverse genetics systems which allow for analysis of viral replication cycles, next-generation sequencing technologies and the bioinformatics tools that facilitate this research.
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Affiliation(s)
| | - Nicholas S. Eyre
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia;
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5
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Riaz N, Leung P, Barton K, Smith MA, Carswell S, Bull R, Lloyd AR, Rodrigo C. Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants. BMC Genomics 2021; 22:148. [PMID: 33653280 PMCID: PMC7923462 DOI: 10.1186/s12864-021-07460-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 02/19/2021] [Indexed: 01/23/2023] Open
Abstract
Background Hepatitis C (HCV) and many other RNA viruses exist as rapidly mutating quasi-species populations in a single infected host. High throughput characterization of full genome, within-host variants is still not possible despite advances in next generation sequencing. This limitation constrains viral genomic studies that depend on accurate identification of hemi-genome or whole genome, within-host variants, especially those occurring at low frequencies. With the advent of third generation long read sequencing technologies, including Oxford Nanopore Technology (ONT) and PacBio platforms, this problem is potentially surmountable. ONT is particularly attractive in this regard due to the portable nature of the MinION sequencer, which makes real-time sequencing in remote and resource-limited locations possible. However, this technology (termed here ‘nanopore sequencing’) has a comparatively high technical error rate. The present study aimed to assess the utility, accuracy and cost-effectiveness of nanopore sequencing for HCV genomes. We also introduce a new bioinformatics tool (Nano-Q) to differentiate within-host variants from nanopore sequencing. Results The Nanopore platform, when the coverage exceeded 300 reads, generated comparable consensus sequences to Illumina sequencing. Using HCV Envelope plasmids (~ 1800 nt) mixed in known proportions, the capacity of nanopore sequencing to reliably identify variants with an abundance as low as 0.1% was demonstrated, provided the autologous reference sequence was available to identify the matching reads. Successful pooling and nanopore sequencing of 52 samples from patients with HCV infection demonstrated its cost effectiveness (AUD$ 43 per sample with nanopore sequencing versus $100 with paired-end short read technology). The Nano-Q tool successfully separated between-host sequences, including those from the same subtype, by bulk sorting and phylogenetic clustering without an autologous reference sequence (using only a subtype-specific generic reference). The pipeline also identified within-host viral variants and their abundance when the parameters were appropriately adjusted. Conclusion Cost effective HCV whole genome sequencing and within-host variant identification without haplotype reconstruction are potential advantages of nanopore sequencing. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07460-1.
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Affiliation(s)
- Nasir Riaz
- Kirby Institute, UNSW Sydney, Sydney, NSW, 2052, Australia.,Department of Microbiology, Hazara University, KPK, Maneshra, 21120, Pakistan
| | - Preston Leung
- Kirby Institute, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Kirston Barton
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Martin A Smith
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Shaun Carswell
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Rowena Bull
- Kirby Institute, UNSW Sydney, Sydney, NSW, 2052, Australia.,Department of Pathology, School of Medical Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Andrew R Lloyd
- Kirby Institute, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Chaturaka Rodrigo
- Kirby Institute, UNSW Sydney, Sydney, NSW, 2052, Australia. .,Department of Pathology, School of Medical Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia.
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6
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Esposito D, Weile J, Shendure J, Starita LM, Papenfuss AT, Roth FP, Fowler DM, Rubin AF. MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. Genome Biol 2019; 20:223. [PMID: 31679514 PMCID: PMC6827219 DOI: 10.1186/s13059-019-1845-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/01/2019] [Indexed: 11/10/2022] Open
Abstract
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test thousands of sequence variants in a single experiment. Despite the importance of MAVE data for basic and clinical research, there is no standard resource for their discovery and distribution. Here, we present MaveDB ( https://www.mavedb.org ), a public repository for large-scale measurements of sequence variant impact, designed for interoperability with applications to interpret these datasets. We also describe the first such application, MaveVis, which retrieves, visualizes, and contextualizes variant effect maps. Together, the database and applications will empower the community to mine these powerful datasets.
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Affiliation(s)
- Daniel Esposito
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jochen Weile
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia
| | - Frederick P Roth
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
- Canadian Institute for Advanced Research, Toronto, ON, Canada.
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Canadian Institute for Advanced Research, Toronto, ON, Canada.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Alan F Rubin
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
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7
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Jacquot M, Rao PP, Yadav S, Nomikou K, Maan S, Jyothi YK, Reddy N, Putty K, Hemadri D, Singh KP, Maan NS, Hegde NR, Mertens P, Biek R. Contrasting selective patterns across the segmented genome of bluetongue virus in a global reassortment hotspot. Virus Evol 2019; 5:vez027. [PMID: 31392031 PMCID: PMC6680063 DOI: 10.1093/ve/vez027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
For segmented viruses, rapid genomic and phenotypic changes can occur through the process of reassortment, whereby co-infecting strains exchange entire segments creating novel progeny virus genotypes. However, for many viruses with segmented genomes, this process and its effect on transmission dynamics remain poorly understood. Here, we assessed the consequences of reassortment for selection on viral diversity through time using bluetongue virus (BTV), a segmented arbovirus that is the causative agent of a major disease of ruminants. We analysed ninety-two BTV genomes isolated across four decades from India, where BTV diversity, and thus opportunities for reassortment, are among the highest in the world. Our results point to frequent reassortment and segment turnover, some of which appear to be driven by selective sweeps and serial hitchhiking. Particularly, we found evidence for a recent selective sweep affecting segment 5 and its encoded NS1 protein that has allowed a single variant to essentially invade the full range of BTV genomic backgrounds and serotypes currently circulating in India. In contrast, diversifying selection was found to play an important role in maintaining genetic diversity in genes encoding outer surface proteins involved in virus interactions (VP2 and VP5, encoded by segments 2 and 6, respectively). Our results support the role of reassortment in driving rapid phenotypic change in segmented viruses and generate testable hypotheses for in vitro experiments aiming at understanding the specific mechanisms underlying differences in fitness and selection across viral genomes.
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Affiliation(s)
- Maude Jacquot
- Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Pavuluri P Rao
- Ella Foundation, Genome Valley Hyderabad, Hyderabad, Telangana, India
| | - Sarita Yadav
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Sushila Maan
- College of Veterinary Sciences, LLR University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Y Krishna Jyothi
- Veterinary Biological and Research Institute, Vijayawada, Andhra Pradesh, India
| | - Narasimha Reddy
- PVNR Telangana Veterinary University, Hyderabad, Telangana, India
| | - Kalyani Putty
- PVNR Telangana Veterinary University, Hyderabad, Telangana, India
| | - Divakar Hemadri
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Karam P Singh
- Centre for Animal Disease Research and Diagnosis, Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Narender Singh Maan
- College of Veterinary Sciences, LLR University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Nagendra R Hegde
- Ella Foundation, Genome Valley Hyderabad, Hyderabad, Telangana, India
| | - Peter Mertens
- The Pirbright Institute, Pirbright, Woking, Surrey, UK.,The School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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8
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Hom N, Gentles L, Bloom JD, Lee KK. Deep Mutational Scan of the Highly Conserved Influenza A Virus M1 Matrix Protein Reveals Substantial Intrinsic Mutational Tolerance. J Virol 2019; 93:e00161-19. [PMID: 31019050 PMCID: PMC6580950 DOI: 10.1128/jvi.00161-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/09/2019] [Indexed: 12/30/2022] Open
Abstract
Influenza A virus matrix protein M1 is involved in multiple stages of the viral infectious cycle. Despite its functional importance, our present understanding of this essential viral protein is limited. The roles of a small subset of specific amino acids have been reported, but a more comprehensive understanding of the relationship between M1 sequence, structure, and virus fitness remains elusive. In this study, we used deep mutational scanning to measure the effect of every amino acid substitution in M1 on viral replication in cell culture. The map of amino acid mutational tolerance we have generated allows us to identify sites that are functionally constrained in cell culture as well as sites that are less constrained. Several sites that exhibit low tolerance to mutation have been found to be critical for M1 function and production of viable virions. Surprisingly, significant portions of the M1 sequence, especially in the C-terminal domain, whose structure is undetermined, were found to be highly tolerant of amino acid variation, despite having extremely low levels of sequence diversity among natural influenza virus strains. This unexpected discrepancy indicates that not all sites in M1 that exhibit high sequence conservation in nature are under strong constraint during selection for viral replication in cell culture.IMPORTANCE The M1 matrix protein is critical for many stages of the influenza virus infection cycle. Currently, we have an incomplete understanding of this highly conserved protein's function and structure. Key regions of M1, particularly in the C terminus of the protein, remain poorly characterized. In this study, we used deep mutational scanning to determine the extent of M1's tolerance to mutation. Surprisingly, nearly two-thirds of the M1 sequence exhibits a high tolerance for substitutions, contrary to the extremely low sequence diversity observed across naturally occurring M1 isolates. Sites with low mutational tolerance were also identified, suggesting that they likely play critical functional roles and are under selective pressure. These results reveal the intrinsic mutational tolerance throughout M1 and shape future inquiries probing the functions of this essential influenza A virus protein.
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Affiliation(s)
- Nancy Hom
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Lauren Gentles
- Department of Microbiology, University of Washington, Seattle, Washington, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jesse D Bloom
- Department of Microbiology, University of Washington, Seattle, Washington, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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9
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Wang RR, Liu WS, Zhou L, Ma Y, Wang RL. Probing the acting mode and advantages of RMC-4550 as an Src-homology 2 domain-containing protein tyrosine phosphatase (SHP2) inhibitor at molecular level through molecular docking and molecular dynamics. J Biomol Struct Dyn 2019; 38:1525-1538. [DOI: 10.1080/07391102.2019.1613266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wen-Shan Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Liang Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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10
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Rodrigo C, Luciani F. Dynamic interactions between RNA viruses and human hosts unravelled by a decade of next generation sequencing. Biochim Biophys Acta Gen Subj 2018; 1863:511-519. [PMID: 30528489 DOI: 10.1016/j.bbagen.2018.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 01/15/2023]
Abstract
BACKGROUND Next generation sequencing (NGS) methods have significantly contributed to a paradigm shift in genomic research for nearly a decade now. These methods have been useful in studying the dynamic interactions between RNA viruses and human hosts. SCOPE OF THE REVIEW In this review, we summarise and discuss key applications of NGS in studying the host - pathogen interactions in RNA viral infections of humans with examples. MAJOR CONCLUSIONS Use of NGS to study globally relevant RNA viral infections have revolutionized our understanding of the within host and between host evolution of these viruses. These methods have also been useful in clinical decision-making and in guiding biomedical research on vaccine design. GENERAL SIGNIFICANCE NGS has been instrumental in viral genomic studies in resolving within-host viral genomic variants and the distribution of nucleotide polymorphisms along the full-length of viral genomes in a high throughput, cost effective manner. In the future, novel advances such as long read, single molecule sequencing of viral genomes and simultaneous sequencing of host and pathogens may become the standard of practice in research and clinical settings. This will also bring on new challenges in big data analysis.
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Affiliation(s)
- Chaturaka Rodrigo
- School of Medical Sciences and Kirby Institute for Infection and Immunity, UNSW Australia, 2052, NSW, Australia
| | - Fabio Luciani
- School of Medical Sciences and Kirby Institute for Infection and Immunity, UNSW Australia, 2052, NSW, Australia.
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11
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Hartman EC, Lobba MJ, Favor AH, Robinson SA, Francis MB, Tullman-Ercek D. Experimental Evaluation of Coevolution in a Self-Assembling Particle. Biochemistry 2018; 58:1527-1538. [DOI: 10.1021/acs.biochem.8b00948] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Emily C. Hartman
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Marco J. Lobba
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Andrew H. Favor
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Stephanie A. Robinson
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Matthew B. Francis
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720-1460, United States
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208-3120, United States
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12
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Lyons DM, Lauring AS. Mutation and Epistasis in Influenza Virus Evolution. Viruses 2018; 10:E407. [PMID: 30081492 PMCID: PMC6115771 DOI: 10.3390/v10080407] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 07/30/2018] [Accepted: 07/30/2018] [Indexed: 12/25/2022] Open
Abstract
Influenza remains a persistent public health challenge, because the rapid evolution of influenza viruses has led to marginal vaccine efficacy, antiviral resistance, and the annual emergence of novel strains. This evolvability is driven, in part, by the virus's capacity to generate diversity through mutation and reassortment. Because many new traits require multiple mutations and mutations are frequently combined by reassortment, epistatic interactions between mutations play an important role in influenza virus evolution. While mutation and epistasis are fundamental to the adaptability of influenza viruses, they also constrain the evolutionary process in important ways. Here, we review recent work on mutational effects and epistasis in influenza viruses.
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Affiliation(s)
- Daniel M Lyons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Adam S Lauring
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
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13
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Du Y, Xin L, Shi Y, Zhang TH, Wu NC, Dai L, Gong D, Brar G, Shu S, Luo J, Reiley W, Tseng YW, Bai H, Wu TT, Wang J, Shu Y, Sun R. Genome-wide identification of interferon-sensitive mutations enables influenza vaccine design. Science 2018; 359:290-296. [PMID: 29348231 DOI: 10.1126/science.aan8806] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 11/15/2017] [Indexed: 12/11/2022]
Abstract
In conventional attenuated viral vaccines, immunogenicity is often suboptimal. Here we present a systematic approach for vaccine development that eliminates interferon (IFN)-modulating functions genome-wide while maintaining virus replication fitness. We applied a quantitative high-throughput genomics system to influenza A virus that simultaneously measured the replication fitness and IFN sensitivity of mutations across the entire genome. By incorporating eight IFN-sensitive mutations, we generated a hyper-interferon-sensitive (HIS) virus as a vaccine candidate. HIS virus is highly attenuated in IFN-competent hosts but able to induce transient IFN responses, elicits robust humoral and cellular immune responses, and provides protection against homologous and heterologous viral challenges. Our approach, which attenuates the virus and promotes immune responses concurrently, is broadly applicable for vaccine development against other pathogens.
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Affiliation(s)
- Yushen Du
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA. .,Cancer Institute, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Li Xin
- National Institute for Viral Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, Beijing 102206, China
| | - Yuan Shi
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Tian-Hao Zhang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Nicholas C Wu
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Lei Dai
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Danyang Gong
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Gurpreet Brar
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Sara Shu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Jiadi Luo
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA.,Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.,Department of Pathology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410005, China
| | | | - Yen-Wen Tseng
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Hongyan Bai
- National Institute for Viral Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, Beijing 102206, China
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Jieru Wang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA.,Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, Beijing 102206, China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong 510275, China
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA. .,Cancer Institute, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Zhejiang University, Hangzhou 310058, China.,Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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14
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Abstract
The deterministic force of natural selection and stochastic influence of drift shape RNA virus evolution. New deep-sequencing and microfluidics technologies allow us to quantify the effect of mutations and trace the evolution of viral populations with single-genome and single-nucleotide resolution. Such experiments can reveal the topography of the genotype-fitness landscapes that shape the path of viral evolution. By combining historical analyses, like phylogenetic approaches, with high-throughput and high-resolution evolutionary experiments, we can observe parallel patterns of evolution that drive important phenotypic transitions. These developments provide a framework for quantifying and anticipating potential evolutionary events. Here, we examine emerging technologies that can map the selective landscapes of viruses, focusing on their application to pathogenic viruses. We identify areas where these technologies can bolster our ability to study the evolution of viruses and to anticipate and possibly intervene in evolutionary events and prevent viral disease.
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Affiliation(s)
- Patrick T Dolan
- Department of Biology, Stanford University, E200 Clark Center, 318 Campus Drive, Stanford, CA 94305, USA; Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA
| | - Zachary J Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA.
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15
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Gong D, Zhang TH, Zhao D, Du Y, Chapa TJ, Shi Y, Wang L, Contreras D, Zeng G, Shi PY, Wu TT, Arumugaswami V, Sun R. High-Throughput Fitness Profiling of Zika Virus E Protein Reveals Different Roles for Glycosylation during Infection of Mammalian and Mosquito Cells. iScience 2018; 1:97-111. [PMID: 30227960 PMCID: PMC6135943 DOI: 10.1016/j.isci.2018.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 01/26/2018] [Accepted: 02/12/2018] [Indexed: 12/29/2022] Open
Abstract
Zika virus (ZIKV) infection causes Guillain-Barré syndrome and severe birth defects. ZIKV envelope (E) protein is the major viral protein involved in cell receptor binding and entry and is therefore considered one of the major determinants in ZIKV pathogenesis. Here we report a gene-wide mapping of functional residues of ZIKV E protein using a mutant library, with changes covering every nucleotide position. By comparing the replication fitness of every viral mutant between mosquito and human cells, we identified that mutations affecting glycosylation display the most divergence. By characterizing individual mutants, we show that ablation of glycosylation selectively benefits ZIKV infection of mosquito cells by enhancing cell entry, whereas it either has little impact on ZIKV infection on certain human cells or leads to decreased infection through the entry factor DC-SIGN. In conclusion, we define the roles of individual residues of ZIKV envelope protein, which contribute to ZIKV replication fitness in human and mosquito cells.
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Affiliation(s)
- Danyang Gong
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Tian-Hao Zhang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Dawei Zhao
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Yushen Du
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Travis J Chapa
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Yuan Shi
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Laurie Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Deisy Contreras
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Gang Zeng
- Department of Urology, University of California, Los Angeles, CA 90095, USA
| | - Pei-Yong Shi
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | | | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA.
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16
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Dingens AS, Haddox HK, Overbaugh J, Bloom JD. Comprehensive Mapping of HIV-1 Escape from a Broadly Neutralizing Antibody. Cell Host Microbe 2017; 21:777-787.e4. [PMID: 28579254 DOI: 10.1016/j.chom.2017.05.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/27/2017] [Accepted: 05/09/2017] [Indexed: 11/24/2022]
Abstract
Precisely defining how viral mutations affect HIV's sensitivity to antibodies is vital to develop and evaluate vaccines and antibody immunotherapeutics. Despite great effort, a full map of escape mutants has not been delineated for an anti-HIV antibody. We describe a massively parallel experimental approach to quantify how all single amino acid mutations to HIV Envelope (Env) affect neutralizing antibody sensitivity in the context of replication-competent virus. We apply this approach to PGT151, a broadly neutralizing antibody recognizing a combination of Env residues and glycans. We confirm sites previously defined by structural and functional studies and reveal additional sites of escape, such as positively charged mutations in the antibody-Env interface. Evaluating the effect of each amino acid at each site lends insight into biochemical mechanisms of escape throughout the epitope, highlighting roles for charge-charge repulsions. Thus, comprehensively mapping HIV antibody escape gives a quantitative, mutation-level view of Env evasion of neutralization.
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Affiliation(s)
- Adam S Dingens
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Human Biology and Epidemiology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA 98195, USA
| | - Hugh K Haddox
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA 98195, USA
| | - Julie Overbaugh
- Division of Human Biology and Epidemiology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Jesse D Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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17
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Ashenberg O, Padmakumar J, Doud MB, Bloom JD. Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA. PLoS Pathog 2017; 13:e1006288. [PMID: 28346537 PMCID: PMC5383324 DOI: 10.1371/journal.ppat.1006288] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 04/06/2017] [Accepted: 03/10/2017] [Indexed: 01/24/2023] Open
Abstract
The innate-immune restriction factor MxA inhibits influenza replication by targeting the viral nucleoprotein (NP). Human influenza virus is more resistant than avian influenza virus to inhibition by human MxA, and prior work has compared human and avian viral strains to identify amino-acid differences in NP that affect sensitivity to MxA. However, this strategy is limited to identifying sites in NP where mutations that affect MxA sensitivity have fixed during the small number of documented zoonotic transmissions of influenza to humans. Here we use an unbiased deep mutational scanning approach to quantify how all single amino-acid mutations to NP affect MxA sensitivity in the context of replication-competent virus. We both identify new sites in NP where mutations affect MxA resistance and re-identify mutations known to have increased MxA resistance during historical adaptations of influenza to humans. Most of the sites where mutations have the greatest effect are almost completely conserved across all influenza A viruses, and the amino acids at these sites confer relatively high resistance to MxA. These sites cluster in regions of NP that appear to be important for its recognition by MxA. Overall, our work systematically identifies the sites in influenza nucleoprotein where mutations affect sensitivity to MxA. We also demonstrate a powerful new strategy for identifying regions of viral proteins that affect inhibition by host factors. During viral infection, human cells express proteins that can restrict virus replication. However, in many cases it remains unclear what determines the sensitivity of a given viral strain to a particular restriction factor. Here we use a high-throughput approach to measure how all amino-acid mutations to the nucleoprotein of influenza virus affect restriction by the human protein MxA. We find several dozen sites where mutations substantially affect the sensitivity of influenza virus to MxA. While a few of these sites are known to have fixed mutations during past adaptations of influenza virus to humans, most of the sites are broadly conserved across all influenza strains and have never previously been described as affecting MxA resistance. Our results therefore show that the known historical evolution of influenza has only involved substitutions at a small fraction of the sites where mutations can in principle affect MxA resistance. We suggest that this is because many sites are already broadly fixed at amino acids that confer high resistance.
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Affiliation(s)
- Orr Ashenberg
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jai Padmakumar
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael B. Doud
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA, USA
| | - Jesse D. Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- * E-mail:
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18
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Doud MB, Hensley SE, Bloom JD. Complete mapping of viral escape from neutralizing antibodies. PLoS Pathog 2017; 13:e1006271. [PMID: 28288189 PMCID: PMC5363992 DOI: 10.1371/journal.ppat.1006271] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/23/2017] [Accepted: 03/06/2017] [Indexed: 11/18/2022] Open
Abstract
Identifying viral mutations that confer escape from antibodies is crucial for understanding the interplay between immunity and viral evolution. We describe a high-throughput approach to quantify the selection that monoclonal antibodies exert on all single amino-acid mutations to a viral protein. This approach, mutational antigenic profiling, involves creating all replication-competent protein variants of a virus, selecting with antibody, and using deep sequencing to identify enriched mutations. We use mutational antigenic profiling to comprehensively identify mutations that enable influenza virus to escape four monoclonal antibodies targeting hemagglutinin, and validate key findings with neutralization assays. We find remarkable mutation-level idiosyncrasy in antibody escape: for instance, at a single residue targeted by two antibodies, some mutations escape both antibodies while other mutations escape only one or the other. Because mutational antigenic profiling rapidly maps all mutations selected by an antibody, it is useful for elucidating immune specificities and interpreting the antigenic consequences of viral genetic variation.
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Affiliation(s)
- Michael B. Doud
- Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - Scott E. Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jesse D. Bloom
- Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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19
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Rodrigo C, Walker MR, Leung P, Eltahla AA, Grebely J, Dore GJ, Applegate T, Page K, Dwivedi S, Bruneau J, Morris MD, Cox AL, Osburn W, Kim AY, Schinkel J, Shoukry NH, Lauer GM, Maher L, Hellard M, Prins M, Luciani F, Lloyd AR, Bull RA. Limited naturally occurring escape in broadly neutralizing antibody epitopes in hepatitis C glycoprotein E2 and constrained sequence usage in acute infection. INFECTION GENETICS AND EVOLUTION 2017; 49:88-96. [PMID: 28065804 DOI: 10.1016/j.meegid.2017.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/07/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022]
Abstract
Broadly neutralizing antibodies have been associated with spontaneous clearance of the hepatitis C infection as well as viral persistence by immune escape. Further study of neutralizing antibody epitopes is needed to unravel pathways of resistance to virus neutralization, and to identify conserved regions for vaccine design. All reported broadly neutralizing antibody (BNAb) epitopes in the HCV Envelope (E2) glycoprotein were identified. The critical contact residues of these epitopes were mapped onto the linear E2 sequence. All publicly available E2 sequences were then downloaded and the contact residues within the BNAb epitopes were assessed for the level of conservation, as well as the frequency of occurrence of experimentally-proven resistance mutations. Epitopes were also compared between two sequence datasets obtained from samples collected at well-defined time points from acute (<180days) and chronic (>180days) infections, to identify any significant differences in residue usage. The contact residues for all BNAbs were contained within 3 linear regions of the E2 protein sequence. An analysis of 1749 full length E2 sequences from public databases showed that only 10 out of 29 experimentally-proven resistance mutations were present at a frequency >5%. Comparison of subtype 1a viral sequences obtained from samples collected during acute or chronic infection revealed significant differences at positions 610 and 655 with changes in residue (p<0.05), and at position 422 (p<0.001) with a significant difference in variability (entropy). The majority of experimentally-described escape variants do not occur frequently in nature. The observed differences between acute and chronically isolated sequences suggest constraints on residue usage early in infection.
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Affiliation(s)
- Chaturaka Rodrigo
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
| | - Melanie R Walker
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Preston Leung
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Auda A Eltahla
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Jason Grebely
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Gregory J Dore
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Tanya Applegate
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Kimberly Page
- Department of Epidemiology and Biostatistics, University of New Mexico, Albuquerque, NM, USA
| | - Sunita Dwivedi
- Department of Epidemiology and Biostatistics, University of New Mexico, Albuquerque, NM, USA
| | - Julie Bruneau
- CRCHUM, Université de Montréal, Montreal, QC, Canada
| | - Meghan D Morris
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Andrea L Cox
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - William Osburn
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | | | - Janke Schinkel
- Department of Internal Medicine, Division of Infectious Diseases, Tropical Medicine and AIDS, Center for Infection and Immunity Amsterdam, Academic Medical Center, Meibergdreef, Amsterdam, The Netherlands
| | | | | | - Lisa Maher
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Margaret Hellard
- Burnet Institute, Melbourne, VIC, Australia; Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia
| | - Maria Prins
- Department of Internal Medicine, Division of Infectious Diseases, Tropical Medicine and AIDS, Center for Infection and Immunity Amsterdam, Academic Medical Center, Meibergdreef, Amsterdam, The Netherlands; GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Fabio Luciani
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Andrew R Lloyd
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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20
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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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21
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Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin. Viruses 2016; 8:v8060155. [PMID: 27271655 PMCID: PMC4926175 DOI: 10.3390/v8060155] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 05/21/2016] [Accepted: 05/25/2016] [Indexed: 12/17/2022] Open
Abstract
Influenza genes evolve mostly via point mutations, and so knowing the effect of every amino-acid mutation provides information about evolutionary paths available to the virus. We and others have combined high-throughput mutagenesis with deep sequencing to estimate the effects of large numbers of mutations to influenza genes. However, these measurements have suffered from substantial experimental noise due to a variety of technical problems, the most prominent of which is bottlenecking during the generation of mutant viruses from plasmids. Here we describe advances that ameliorate these problems, enabling us to measure with greatly improved accuracy and reproducibility the effects of all amino-acid mutations to an H1 influenza hemagglutinin on viral replication in cell culture. The largest improvements come from using a helper virus to reduce bottlenecks when generating viruses from plasmids. Our measurements confirm at much higher resolution the results of previous studies suggesting that antigenic sites on the globular head of hemagglutinin are highly tolerant of mutations. We also show that other regions of hemagglutinin—including the stalk epitopes targeted by broadly neutralizing antibodies—have a much lower inherent capacity to tolerate point mutations. The ability to accurately measure the effects of all influenza mutations should enhance efforts to understand and predict viral evolution.
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