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Froggatt HM, Burke KN, Chaparian RR, Miranda HA, Zhu X, Chambers BS, Heaton NS. Influenza A virus segments five and six can harbor artificial introns allowing expanded coding capacity. PLoS Pathog 2021; 17:e1009951. [PMID: 34570829 PMCID: PMC8496794 DOI: 10.1371/journal.ppat.1009951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 10/07/2021] [Accepted: 09/08/2021] [Indexed: 12/30/2022] Open
Abstract
Influenza A viruses encode their genomes across eight, negative sense RNA segments. The six largest segments produce mRNA transcripts that do not generally splice; however, the two smallest segments are actively spliced to produce the essential viral proteins NEP and M2. Thus, viral utilization of RNA splicing effectively expands the viral coding capacity without increasing the number of genomic segments. As a first step towards understanding why splicing is not more broadly utilized across genomic segments, we designed and inserted an artificial intron into the normally nonsplicing NA segment. This insertion was tolerated and, although viral mRNAs were incompletely spliced, we observed only minor effects on viral fitness. To take advantage of the unspliced viral RNAs, we encoded a reporter luciferase gene in frame with the viral ORF such that when the intron was not removed the reporter protein would be produced. This approach, which we also show can be applied to the NP encoding segment and in different viral genetic backgrounds, led to high levels of reporter protein expression with minimal effects on the kinetics of viral replication or the ability to cause disease in experimentally infected animals. These data together show that the influenza viral genome is more tolerant of splicing than previously appreciated and this knowledge can be leveraged to develop viral genetic platforms with utility for biotechnology applications. Unlike most host mRNAs, some viral mRNAs encode multiple discrete, functional proteins. One method influenza A viruses use to increase the protein products from two of their eight RNA genome segments is splicing. Splicing requires host machinery to remove part of the viral mRNA, the intron, to generate a different mRNA product. Although only certain influenza viral segments naturally splice, we were interested in whether additional segments could splice to produce multiple proteins. We inserted artificial introns harboring reporter genes into otherwise nonsplicing genomic segments of an H1N1 influenza A virus and found that this modification was well tolerated by the virus. We further demonstrated that an unrelated H3N2 influenza A virus could similarly support splicing and express a reporter protein from an artificial intron. These findings have implications for our understanding of how viruses expand their coding capacity with a limited genome. Additionally, encoding reporter proteins in spliced intronic sequences also represents a new method of generating reporter viruses requiring limited manipulation of the viral RNA.
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Affiliation(s)
- Heather M. Froggatt
- Department of Molecular Genetics and Microbiology Duke University School of Medicine Durham, North Carolina, United States of America
| | - Kaitlyn N. Burke
- Department of Molecular Genetics and Microbiology Duke University School of Medicine Durham, North Carolina, United States of America
| | - Ryan R. Chaparian
- Department of Molecular Genetics and Microbiology Duke University School of Medicine Durham, North Carolina, United States of America
| | - Hector A. Miranda
- Department of Molecular Genetics and Microbiology Duke University School of Medicine Durham, North Carolina, United States of America
| | - Xinyu Zhu
- Department of Molecular Genetics and Microbiology Duke University School of Medicine Durham, North Carolina, United States of America
| | - Benjamin S. Chambers
- Department of Molecular Genetics and Microbiology Duke University School of Medicine Durham, North Carolina, United States of America
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology Duke University School of Medicine Durham, North Carolina, United States of America
- Duke Human Vaccine Institute Duke University School of Medicine Durham, North Carolina, United States of America
- * E-mail:
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Cobey S, Gouma S, Parkhouse K, Chambers BS, Ertl HC, Schmader KE, Halpin RA, Lin X, Stockwell TB, Das SR, Landon E, Tesic V, Youngster I, Pinsky BA, Wentworth DE, Hensley SE, Grad YH. Poor Immunogenicity, Not Vaccine Strain Egg Adaptation, May Explain the Low H3N2 Influenza Vaccine Effectiveness in 2012-2013. Clin Infect Dis 2019; 67:327-333. [PMID: 29471464 PMCID: PMC6051447 DOI: 10.1093/cid/ciy097] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 02/03/2018] [Indexed: 12/28/2022] Open
Abstract
Background Influenza vaccination aims to prevent infection by influenza virus and reduce associated morbidity and mortality; however, vaccine effectiveness (VE) can be modest, especially for subtype A(H3N2). Low VE has been attributed to mismatches between the vaccine and circulating influenza strains and to the vaccine’s elicitation of protective immunity in only a subset of the population. The low H3N2 VE in the 2012–2013 season was attributed to egg-adaptive mutations that created antigenic mismatch between the actual vaccine strain (IVR-165) and both the intended vaccine strain (A/Victoria/361/2011) and the predominant circulating strains (clades 3C.2 and 3C.3). Methods We investigated the basis of low VE in 2012–2013 by determining whether vaccinated and unvaccinated individuals were infected by different viral strains and by assessing the serologic responses to IVR-165, A/Victoria/361/2011, and 3C.2 and 3C.3 strains in an adult cohort before and after vaccination. Results We found no significant genetic differences between the strains that infected vaccinated and unvaccinated individuals. Vaccination increased titers to A/Victoria/361/2011 and 3C.2 and 3C.3 representative strains as much as to IVR-165. These results are consistent with the hypothesis that vaccination boosted cross-reactive immune responses instead of specific responses against unique vaccine epitopes. Only approximately one-third of the cohort achieved a ≥4-fold increase in titer. Conclusions In contrast to analyses based on ferret studies, low H3N2 VE in 2012–2013 in adults does not appear to be due to egg adaptation of the vaccine strain. Instead, low VE might have been caused by low vaccine immunogenicity in a subset of the population.
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Affiliation(s)
- Sarah Cobey
- Department of Ecology & Evolution, University of Chicago, Illinois
| | - Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Kaela Parkhouse
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Benjamin S Chambers
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Hildegund C Ertl
- Division of Geriatrics, Duke University Medical Center, North Carolina.,Geriatric Research, Education, and Clinical Center, Durham VA Medical Center, North Carolina
| | - Kenneth E Schmader
- Division of Geriatrics, Duke University Medical Center, North Carolina.,Geriatric Research, Education, and Clinical Center, Durham VA Medical Center, North Carolina
| | - Rebecca A Halpin
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, Maryland
| | - Xudong Lin
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, Maryland
| | - Timothy B Stockwell
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, Maryland
| | - Suman R Das
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, Maryland
| | - Emily Landon
- Department of Medicine, University of Chicago, Illinois
| | - Vera Tesic
- Department of Pathology, University of Chicago, Illinois
| | - Ilan Youngster
- Division of Pediatrics and the Center for Microbiome Research, Assaf Harofeh Medical Center, Tel Aviv University, Israel.,Division of Infectious Diseases, Boston Children's Hospital, Massachusetts
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, California.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, California
| | - David E Wentworth
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, Maryland
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts.,Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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Harding AT, Haas GD, Chambers BS, Heaton NS. Influenza viruses that require 10 genomic segments as antiviral therapeutics. PLoS Pathog 2019; 15:e1008098. [PMID: 31730644 PMCID: PMC6881065 DOI: 10.1371/journal.ppat.1008098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 11/27/2019] [Accepted: 09/20/2019] [Indexed: 11/19/2022] Open
Abstract
Influenza A viruses (IAVs) encode their genome across eight, negative sense RNA segments. During viral assembly, the failure to package all eight segments, or packaging a mutated segment, renders the resulting virion incompletely infectious. It is known that the accumulation of these defective particles can limit viral disease by interfering with the spread of fully infectious particles. In order to harness this phenomenon therapeutically, we defined which viral packaging signals were amenable to duplication and developed a viral genetic platform which produced replication competent IAVs that require up to two additional artificial genome segments for full infectivity. The modified and artificial genome segments propagated by this approach are capable of acting as "decoy" segments that, when packaged by coinfecting wild-type viruses, lead to the production of non-infectious viral particles. Although IAVs which require 10 genomic segments for full infectivity are able to replicate themselves and spread in vivo, their genomic modifications render them avirulent in mice. Administration of these viruses, both prophylactically and therapeutically, was able to rescue animals from a lethal influenza virus challenge. Together, our results show that replicating IAVs designed to propagate and spread defective genomic segments represent a potent anti-influenza biological therapy that can target the conserved process of particle assembly to limit viral disease.
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Affiliation(s)
- Alfred T. Harding
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States of America
| | - Griffin D. Haas
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States of America
| | - Benjamin S. Chambers
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States of America
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States of America
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Xue J, Chambers BS, Hensley SE, López CB. Propagation and Characterization of Influenza Virus Stocks That Lack High Levels of Defective Viral Genomes and Hemagglutinin Mutations. Front Microbiol 2016; 7:326. [PMID: 27047455 PMCID: PMC4803753 DOI: 10.3389/fmicb.2016.00326] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/01/2016] [Indexed: 12/01/2022] Open
Abstract
Influenza virus infections are responsible for more than 250,000 deaths annually. Influenza virus isolation, propagation, and characterization protocols are critical for completing reproducible basic research studies and for generating vaccine seed stocks. Detailed protocols for the isolation and identification of influenza virus have been recently reported (Eisfeld et al., 2014). However, there are few standardized protocols focused on the propagation and characterization of viral isolates, and as a result, viruses propagated in different conditions in different laboratories often have distinct in vitro and in vivo characteristics. Here, we focus on influenza A virus propagation and characterization in the laboratory taking into consideration the overall quality and composition of the virus stock to achieve consistency in virus yield, virulence, and immunostimulatory activity.
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Affiliation(s)
- Jia Xue
- Department of Pathobiology, School of Veterinary Medicine, University of PennsylvaniaPhiladelphia, PA, USA; Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Benjamin S Chambers
- Wistar Institute and Department of Microbiology, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Scott E Hensley
- Wistar Institute and Department of Microbiology, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Carolina B López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania Philadelphia, PA, USA
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Shaffer SM, Joshi RP, Chambers BS, Sterken D, Biaesch AG, Gabrieli DJ, Li Y, Feemster KA, Hensley SE, Issadore D, Raj A. Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip. Lab Chip 2015; 15:3170-82. [PMID: 26113495 PMCID: PMC4670042 DOI: 10.1039/c5lc00459d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Viral infections are a major cause of human disease, but many require molecular assays for conclusive diagnosis. Current assays typically rely on RT-PCR or ELISA; however, these tests often have limited speed, sensitivity or specificity. Here, we demonstrate that rapid RNA FISH is a viable alternative method that could improve upon these limitations. We describe a platform beginning with software to generate RNA FISH probes both for distinguishing related strains of virus (even those different by a single base) and for capturing large numbers of strains simultaneously. Next, we present a simple fluidic device for reliably performing RNA FISH assays in an automated fashion. Finally, we describe an automated image processing pipeline to robustly identify uninfected and infected samples. Together, our results establish RNA FISH as a methodology with potential for viral point-of-care diagnostics.
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Affiliation(s)
- Sydney M Shaffer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, USA.
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Chambers BS, Parkhouse K, Ross TM, Alby K, Hensley SE. Identification of Hemagglutinin Residues Responsible for H3N2 Antigenic Drift during the 2014-2015 Influenza Season. Cell Rep 2015; 12:1-6. [PMID: 26119736 DOI: 10.1016/j.celrep.2015.06.005] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/22/2015] [Accepted: 06/01/2015] [Indexed: 01/09/2023] Open
Abstract
Influenza vaccines must be updated regularly because influenza viruses continuously acquire mutations in antibody binding sites of hemagglutinin (HA). The majority of H3N2 strains circulating in the Northern Hemisphere during the 2014-2015 season are antigenically mismatched to the A/Texas/50/2012 H3N2 vaccine strain. Recent H3N2 strains possess several new HA mutations, and it is unknown which of these mutations contribute to the 2014-2015 vaccine mismatch. Here, we use reverse genetics to demonstrate that mutations in HA antigenic site B are primarily responsible for the current mismatch. Sera isolated from vaccinated humans and infected ferrets and sheep had reduced hemagglutination inhibition and in vitro neutralization titers against reverse-genetics-derived viruses possessing mutations in the HA antigenic site B. These data provide an antigenic explanation for the low influenza vaccine efficacy observed during the 2014-2015 influenza season. Furthermore, our data support the World Health Organization's decision to update the H3N2 component of future vaccine formulations.
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Affiliation(s)
- Benjamin S Chambers
- Wistar Institute, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Ted M Ross
- Department of Vaccine and Viral Immunity, Vaccine and Gene Therapy Institute of Florida, Port St. Lucie, FL 34987, USA
| | - Kevin Alby
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott E Hensley
- Wistar Institute, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Chambers BS, Pierrot AH. Recovery care centers. J Health Care Inter Des 1989; 2:141-8. [PMID: 10123934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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