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Article: Virus Binding and Internalization Assay for Adeno-associated Virus.

Berry, Garrett E / Tse, Longping V

2017 Volume 7, Issue 2

Abstract: The binding and internalization of adeno-associated virus (AAV) is an important determinant of viral infectivity and tropism. The ability to dissect these two tightly connected cellular processes would allow better understanding and provide insight on ... ...

Abstract	The binding and internalization of adeno-associated virus (AAV) is an important determinant of viral infectivity and tropism. The ability to dissect these two tightly connected cellular processes would allow better understanding and provide insight on virus entry and trafficking. In the following protocol, we describe a quantitative PCR (qPCR) based method to determine the amount of vector bound to the cell surface and the amount of subsequent virus internalization based on viral genome quantification. This protocol is optimized for studying AAV. Nevertheless, it can serve as a backbone for studying other viruses with careful modification.
Language	English
Publishing date	2017-12-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.2110
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The Current and Future State of Vaccines, Antivirals and Gene Therapies Against Emerging Coronaviruses.

Tse, Longping V / Meganck, Rita M / Graham, Rachel L / Baric, Ralph S

Frontiers in microbiology

2020 Volume 11, Page(s) 658

Abstract: Emerging coronaviruses (CoV) are constant global public health threats to society. Multiple ongoing clinical trials for vaccines and antivirals against CoVs showcase the availability of medical interventions to both prevent and treat the future emergence ...

Abstract	Emerging coronaviruses (CoV) are constant global public health threats to society. Multiple ongoing clinical trials for vaccines and antivirals against CoVs showcase the availability of medical interventions to both prevent and treat the future emergence of highly pathogenic CoVs in human. However, given the diverse nature of CoVs and our close interactions with wild, domestic and companion animals, the next epidemic zoonotic CoV could resist the existing vaccines and antivirals developed, which are primarily focused on Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS CoV). In late 2019, the novel CoV (SARS-CoV-2) emerged in Wuhan, China, causing global public health concern. In this review, we will summarize the key advancements of current vaccines and antivirals against SARS-CoV and MERS-CoV as well as discuss the challenge and opportunity in the current SARS-CoV-2 crisis. At the end, we advocate the development of a "plug-and-play" platform technologies that could allow quick manufacturing and administration of broad-spectrum countermeasures in an outbreak setting. We will discuss the potential of AAV-based gene therapy technology for
Keywords	covid19
Language	English
Publishing date	2020-04-24
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2020.00658
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Article ; Online: Evolution of a functionally intact but antigenically distinct DENV fusion loop.

Meganck, Rita M / Zhu, Deanna / Dong, Stephanie / Snoderly-Foster, Lisa J / Dalben, Yago R / Thiono, Devina / White, Laura J / DeSilva, Arivianda M / Baric, Ralph S / Tse, Longping V

eLife

2023 Volume 12

Abstract: A hallmark of dengue virus (DENV) pathogenesis is the potential for antibody-dependent enhancement, which is associated with deadly DENV secondary infection, complicates the identification of correlates of protection, and negatively impacts the safety ... ...

Abstract	A hallmark of dengue virus (DENV) pathogenesis is the potential for antibody-dependent enhancement, which is associated with deadly DENV secondary infection, complicates the identification of correlates of protection, and negatively impacts the safety and efficacy of DENV vaccines. Antibody-dependent enhancement is linked to antibodies targeting the fusion loop (FL) motif of the envelope protein, which is completely conserved in mosquito-borne flaviviruses and required for viral entry and fusion. In the current study, we utilized saturation mutagenesis and directed evolution to engineer a functional variant with a mutated FL (D2-FL), which is not neutralized by FL-targeting monoclonal antibodies. The FL mutations were combined with our previously evolved prM cleavage site to create a mature version of D2-FL (D2-FLM), which evades both prM- and FL-Abs but retains sensitivity to other type-specific and quaternary cross-reactive (CR) Abs. CR serum from heterotypic (DENV4)-infected non-human primates (NHP) showed lower neutralization titers against D2-FL and D2-FLM than isogenic wildtype DENV2 while similar neutralization titers were observed in serum from homotypic (DENV2)-infected NHP. We propose D2-FL and D2-FLM as valuable tools to delineate CR Ab subtypes in serum as well as an exciting platform for safer live-attenuated DENV vaccines suitable for naïve individuals and children.
MeSH term(s)	Animals ; Antibodies, Monoclonal ; Cross Reactions ; Culicidae ; Engineering ; Vaccines
Chemical Substances	Antibodies, Monoclonal ; Vaccines
Language	English
Publishing date	2023-09-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.87555
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Article: Evolution of a Functionally Intact but Antigenically Distinct DENV Fusion Loop.

Meganck, Rita M / Zhu, Deanna / Dong, Stephanie / Snoderly-Foster, Lisa J / Dalben, Yago R / Thiono, Devina / White, Laura J / DeSilva, Aravinda M / Baric, Ralph S / Tse, Longping V

bioRxiv : the preprint server for biology

2023

Abstract: A hallmark of Dengue virus (DENV) pathogenesis is the potential for antibody-dependent enhancement, which is associated with deadly DENV secondary infection, complicates the identification of correlates of protection, and negatively impacts the safety ... ...

Abstract	A hallmark of Dengue virus (DENV) pathogenesis is the potential for antibody-dependent enhancement, which is associated with deadly DENV secondary infection, complicates the identification of correlates of protection, and negatively impacts the safety and efficacy of DENV vaccines. ADE is linked to antibodies targeting the fusion loop (FL) motif of the envelope protein, which is completely conserved in mosquito-borne flaviviruses and required for viral entry and fusion. In the current study, we utilized saturation mutagenesis and directed evolution to engineer a functional variant with a mutated FL (D2-FL) which is not neutralized by FL-targeting monoclonal antibodies. The FL mutations were combined with our previously evolved prM cleavage site to create a mature version of D2-FL (D2-FLM), which evades both prM- and FL-Abs but retains sensitivity to other type-specific and quaternary cross-reactive (CR) Abs. CR serum from heterotypic (DENV4) infected non-human primates (NHP) showed lower neutralization titers against D2-FL and D2-FLM than isogenic wildtype DENV2 while similar neutralization titers were observed in serum from homotypic (DENV2) infected NHP. We propose D2-FL and D2-FLM as valuable tools to delineate CR Ab subtypes in serum as well as an exciting platform for safer live attenuated DENV vaccines suitable for naïve individuals and children.
Language	English
Publishing date	2023-08-04
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.22.533803
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Article ; Online: Generation of Mature DENVs via Genetic Modification and Directed Evolution.

Tse, Longping V / Meganck, Rita M / Dong, Stephanie / Adams, Lily E / White, Laura J / Mallory, Michael L / Jadi, Ramesh / de Silva, Aravinda M / Baric, Ralph S

mBio

2022 Volume 13, Issue 3, Page(s) e0038622

Abstract: Maturation of dengue viruses (DENVs) alters the structure, immunity, and infectivity of the virion and highly mature particles represent the dominant ... ...

Abstract	Maturation of dengue viruses (DENVs) alters the structure, immunity, and infectivity of the virion and highly mature particles represent the dominant form
MeSH term(s)	Animals ; Antibodies, Viral ; Dengue ; Dengue Virus/physiology ; Furin/genetics ; Mammals ; Serogroup ; Viral Envelope Proteins/genetics ; Virion
Chemical Substances	Antibodies, Viral ; Viral Envelope Proteins ; Furin (EC 3.4.21.75)
Language	English
Publishing date	2022-04-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.00386-22
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Article ; Online: Modification of the hemagglutinin cleavage site allows indirect activation of avian influenza virus H9N2 by bacterial staphylokinase.

Tse, Longping V / Whittaker, Gary R

Virology

2015 Volume 482, Page(s) 1–8

Abstract: Influenza H9N2 is considered to be a low pathogenicity avian influenza (LPAI) virus that commonly infects avian species and can also infect humans. In 1996, the influenza virus, A/chicken/Korea/MS96-CE6/1996/H9N2 (MS96) was isolated from an outbreak in ... ...

Abstract	Influenza H9N2 is considered to be a low pathogenicity avian influenza (LPAI) virus that commonly infects avian species and can also infect humans. In 1996, the influenza virus, A/chicken/Korea/MS96-CE6/1996/H9N2 (MS96) was isolated from an outbreak in multiple farms in South Korea that resulted in upwards of 30% mortality in infected chickens, with the virus infecting a number of extrapulmonary tissues, indicating internal spread. However, in experimental infections, complete recovery of specific pathogen free (SPF) chickens occurred. Such a discrepancy indicated an alternative pathway for MS96 virus to gain virulence in farmed chickens. A key determinant of influenza pathogenesis is the susceptibility of the viral hemagglutinin (HA) to proteolytic cleavage/activation. Here, we identified that an amino acid substitution, Ser to Tyr found at the P2 position of the MS96 HA cleavage site optimizes cleavage by the protease plasmin (Pm). Importantly, we identified that certain Staphylococcus sp. are able to cleave and activate MS96 HA by activating plasminogen (Plg) to plasmin by use of a virulence factor, staphylokinase. Overall, these studies provide an in-vitro mechanism for bacterially mediated enhancement of influenza activation, and allow insight into the microbiological mechanisms underlying the avian influenza H9N2 outbreak in Korea in1996.
MeSH term(s)	Animals ; Chickens ; Disease Outbreaks ; Fibrinolysin/metabolism ; Hemagglutinin Glycoproteins, Influenza Virus/genetics ; Hemagglutinin Glycoproteins, Influenza Virus/metabolism ; Influenza A Virus, H9N2 Subtype/drug effects ; Influenza A Virus, H9N2 Subtype/genetics ; Influenza A Virus, H9N2 Subtype/isolation & purification ; Influenza in Birds/epidemiology ; Influenza in Birds/virology ; Korea ; Metalloendopeptidases/metabolism ; Microbial Interactions ; Mutation, Missense ; Virulence
Chemical Substances	Hemagglutinin Glycoproteins, Influenza Virus ; Fibrinolysin (EC 3.4.21.7) ; Metalloendopeptidases (EC 3.4.24.-) ; auR protein, Staphylococcus aureus (EC 3.4.24.29)
Keywords	covid19
Language	English
Publishing date	2015-08
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2015.03.023
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Article ; Online: The Current and Future State of Vaccines, Antivirals and Gene Therapies Against Emerging Coronaviruses

Longping V. Tse / Rita M. Meganck / Rachel L. Graham / Ralph S. Baric

Frontiers in Microbiology, Vol

2020 Volume 11

Abstract	Emerging coronaviruses (CoV) are constant global public health threats to society. Multiple ongoing clinical trials for vaccines and antivirals against CoVs showcase the availability of medical interventions to both prevent and treat the future emergence of highly pathogenic CoVs in human. However, given the diverse nature of CoVs and our close interactions with wild, domestic and companion animals, the next epidemic zoonotic CoV could resist the existing vaccines and antivirals developed, which are primarily focused on Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS CoV). In late 2019, the novel CoV (SARS-CoV-2) emerged in Wuhan, China, causing global public health concern. In this review, we will summarize the key advancements of current vaccines and antivirals against SARS-CoV and MERS-CoV as well as discuss the challenge and opportunity in the current SARS-CoV-2 crisis. At the end, we advocate the development of a “plug-and-play” platform technologies that could allow quick manufacturing and administration of broad-spectrum countermeasures in an outbreak setting. We will discuss the potential of AAV-based gene therapy technology for in vivo therapeutic antibody delivery to combat SARS-CoV-2 outbreak and the future emergence of severe CoVs.
Keywords	coronavirus (CoV) ; vaccine ; antivirals ; adeno-associate virus ; passive immunization strategy ; MERS- and SARS-CoV ; Microbiology ; QR1-502 ; covid19
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Mapping and Engineering Functional Domains of the Assembly-Activating Protein of Adeno-associated Viruses.

Tse, Longping V / Moller-Tank, Sven / Meganck, Rita M / Asokan, Aravind

Journal of virology

2018 Volume 92, Issue 14

Abstract: Adeno-associated viruses (AAVs) encode a unique assembly-activating protein (AAP) within their genomes that is essential for capsid assembly. Studies to date have focused on establishing the role of AAP as a chaperone that mediates the stability, ... ...

Abstract	Adeno-associated viruses (AAVs) encode a unique assembly-activating protein (AAP) within their genomes that is essential for capsid assembly. Studies to date have focused on establishing the role of AAP as a chaperone that mediates the stability, nucleolar transport, and assembly of AAV capsid proteins. Here, we map structure-function correlates of AAP using secondary structure analysis, followed by deletion and substitutional mutagenesis of specific domains, namely, the N-terminal hydrophobic region (HR), conserved core (CC), proline-rich region (PRR), threonine/serine-rich region (T/S), and basic region (BR). First, we establish that the centrally located PRR and T/S are flexible linker domains that can either be deleted completely or replaced by heterologous functional domains that enable ancillary functions such as fluorescent imaging or increased AAP stability. We also demonstrate that the C-terminal BR domains can be substituted with heterologous nuclear or nucleolar localization sequences that display various abilities to support AAV capsid assembly. Further, by replacing the BR domain with immunoglobulin (IgG) Fc domains, we assessed AAP complexation with AAV capsid subunits and demonstrate that the hydrophobic region (HR) and the conserved core (CC) in the AAP N terminus are the sole determinants for viral protein (VP) recognition. However, VP recognition alone is not sufficient for capsid assembly. Our study sheds light on the modular structure-function correlates of AAP and provides multiple approaches to engineer AAP that might prove useful toward understanding and controlling AAV capsid assembly.
MeSH term(s)	Capsid Proteins/chemistry ; Capsid Proteins/metabolism ; Cell Nucleus/metabolism ; Dependovirus/physiology ; HeLa Cells ; Humans ; Nuclear Localization Signals ; Parvoviridae Infections/virology ; Protein Conformation ; Protein Domains ; Protein Stability ; Protein Transport ; Virion ; Virus Assembly
Chemical Substances	Capsid Proteins ; Nuclear Localization Signals
Language	English
Publishing date	2018-06-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00393-18
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Article ; Online: SARS-CoV-2 variant of concern fitness and adaptation in primary human airway epithelia.

Meganck, Rita M / Edwards, Caitlin E / Mallory, Michael L / Lee, Rhianna E / Dang, Hong / Bailey, Alexis B / Wykoff, Jason A / Gallant, Samuel C / Zhu, Deanna R / Yount, Boyd L / Kato, Takafumi / Shaffer, Kendall M / Nakano, Satoko / Cawley, Anne Marie / Sontake, Vishwaraj / Wang, Jeremy R / Hagan, Robert S / Miller, Melissa B / Tata, Purushothama Rao /

Randell, Scott H / Tse, Longping V / Ehre, Camille / Okuda, Kenichi / Boucher, Richard C / Baric, Ralph S

Cell reports

2024 Volume 43, Issue 4, Page(s) 114076

Abstract: The severe acute respiratory syndrome coronavirus 2 pandemic is characterized by the emergence of novel variants of concern (VOCs) that replace ancestral strains. Here, we dissect the complex selective pressures by evaluating variant fitness and ... ...

Abstract	The severe acute respiratory syndrome coronavirus 2 pandemic is characterized by the emergence of novel variants of concern (VOCs) that replace ancestral strains. Here, we dissect the complex selective pressures by evaluating variant fitness and adaptation in human respiratory tissues. We evaluate viral properties and host responses to reconstruct forces behind D614G through Omicron (BA.1) emergence. We observe differential replication in airway epithelia, differences in cellular tropism, and virus-induced cytotoxicity. D614G accumulates the most mutations after infection, supporting zoonosis and adaptation to the human airway. We perform head-to-head competitions and observe the highest fitness for Gamma and Delta. Under these conditions, RNA recombination favors variants encoding the B.1.617.1 lineage 3' end. Based on viral growth kinetics, Alpha, Gamma, and Delta exhibit increased fitness compared to D614G. In contrast, the global success of Omicron likely derives from increased transmission and antigenic variation. Our data provide molecular evidence to support epidemiological observations of VOC emergence.
MeSH term(s)	Humans ; SARS-CoV-2/physiology ; SARS-CoV-2/genetics ; COVID-19/virology ; COVID-19/transmission ; Virus Replication ; Mutation/genetics ; Respiratory Mucosa/virology ; Genetic Fitness ; Animals ; Epithelial Cells/virology ; Chlorocebus aethiops ; Adaptation, Physiological/genetics ; Vero Cells
Language	English
Publishing date	2024-04-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2024.114076
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Article ; Online: A MERS-CoV antibody neutralizes a pre-emerging group 2c bat coronavirus.

Tse, Longping V / Hou, Yixuan J / McFadden, Elizabeth / Lee, Rhianna E / Scobey, Trevor D / Leist, Sarah R / Martinez, David R / Meganck, Rita M / Schäfer, Alexandra / Yount, Boyd L / Mascenik, Teresa / Powers, John M / Randell, Scott H / Zhang, Yi / Wang, Lingshu / Mascola, John / McLellan, Jason S / Baric, Ralph S

Science translational medicine

2023 Volume 15, Issue 715, Page(s) eadg5567

Abstract: The repeated emergence of zoonotic human betacoronaviruses (β-CoVs) dictates the need for broad therapeutics and conserved epitope targets for countermeasure design. Middle East respiratory syndrome (MERS)-related coronaviruses (CoVs) remain a pressing ... ...

Abstract	The repeated emergence of zoonotic human betacoronaviruses (β-CoVs) dictates the need for broad therapeutics and conserved epitope targets for countermeasure design. Middle East respiratory syndrome (MERS)-related coronaviruses (CoVs) remain a pressing concern for global health preparedness. Using metagenomic sequence data and CoV reverse genetics, we recovered a full-length wild-type MERS-like BtCoV/
MeSH term(s)	Humans ; Animals ; Mice ; Middle East Respiratory Syndrome Coronavirus ; Dipeptidyl Peptidase 4/genetics ; Dipeptidyl Peptidase 4/metabolism ; Chiroptera ; Cryoelectron Microscopy ; Coronavirus Infections ; Antibodies, Monoclonal/metabolism
Chemical Substances	Dipeptidyl Peptidase 4 (EC 3.4.14.5) ; Antibodies, Monoclonal
Language	English
Publishing date	2023-09-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2518854-9
ISSN	1946-6242 ; 1946-6234
ISSN (online)	1946-6242
ISSN	1946-6234
DOI	10.1126/scitranslmed.adg5567
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