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Article: Structural basis for VLDLR recognition by eastern equine encephalitis virus.

Yang, Pan / Li, Wanyu / Fan, Xiaoyi / Pan, Junhua / Mann, Colin J / Varnum, Haley / Clark, Lars E / Clark, Sarah A / Coscia, Adrian / Smith, Katherine Nabel / Brusic, Vesna / Abraham, Jonathan

bioRxiv : the preprint server for biology

2023

Abstract: Alphaviruses are arthropod-borne enveloped RNA viruses that include several important human pathogens with outbreak potential. Among them, eastern equine encephalitis virus (EEEV) is the most virulent, and many survivors develop neurological sequelae, ... ...

Abstract	Alphaviruses are arthropod-borne enveloped RNA viruses that include several important human pathogens with outbreak potential. Among them, eastern equine encephalitis virus (EEEV) is the most virulent, and many survivors develop neurological sequelae, including paralysis and intellectual disability. The spike proteins of alphaviruses comprise trimers of heterodimers of their envelope glycoproteins E2 and E1 that mediate binding to cellular receptors and fusion of virus and host cell membranes during entry. We recently identified very-low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2), two closely related proteins that are expressed in the brain, as cellular receptors for EEEV and a distantly related alphavirus, Semliki forest virus (SFV)
Language	English
Publishing date	2023-11-14
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.14.567065
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Article ; Online: CD164 is a host factor for lymphocytic choriomeningitis virus entry.

Bakkers, Mark J G / Moon-Walker, Alex / Herlo, Rasmus / Brusic, Vesna / Stubbs, Sarah Hulsey / Hastie, Kathryn M / Saphire, Erica Ollmann / Kirchhausen, Tomas L / Whelan, Sean P J

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 119, Issue 10, Page(s) e2119676119

Abstract: Lymphocytic choriomeningitis virus (LCMV) is a rodent-borne zoonotic arenavirus that causes congenital abnormalities and can be fatal for transplant recipients. Using a genome-wide loss-of-function screen, we identify host factors required for LCMV entry ...

Abstract	Lymphocytic choriomeningitis virus (LCMV) is a rodent-borne zoonotic arenavirus that causes congenital abnormalities and can be fatal for transplant recipients. Using a genome-wide loss-of-function screen, we identify host factors required for LCMV entry into cells. We identify the lysosomal mucin CD164, glycosylation factors, the heparan sulfate biosynthesis machinery, and the known receptor alpha-dystroglycan (α-DG). Biochemical analysis revealed that the LCMV glycoprotein binds CD164 at acidic pH and requires a sialylated glycan at residue N104. We demonstrate that LCMV entry proceeds by the virus switching binding from heparan sulfate or α-DG at the plasma membrane to CD164 prior to membrane fusion, thus identifying additional potential targets for therapeutic intervention.
MeSH term(s)	A549 Cells ; CRISPR-Cas Systems ; Endolyn/physiology ; Gene Editing ; HEK293 Cells ; HeLa Cells ; Host-Pathogen Interactions ; Humans ; Hydrogen-Ion Concentration ; Lymphocytic choriomeningitis virus/pathogenicity ; Lymphocytic choriomeningitis virus/physiology ; Membrane Fusion ; Virulence Factors ; Virus Internalization
Chemical Substances	CD164 protein, human ; Endolyn ; Virulence Factors
Language	English
Publishing date	2022-03-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2119676119
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Article ; Online: Oligomerization of the Vesicular Stomatitis Virus Phosphoprotein Is Dispensable for mRNA Synthesis but Facilitates RNA Replication.

Bloyet, Louis-Marie / Morin, Benjamin / Brusic, Vesna / Gardner, Erica / Ross, Robin A / Vadakkan, Tegy / Kirchhausen, Tomas / Whelan, Sean P J

Journal of virology

2020 Volume 94, Issue 13

Abstract: Nonsegmented negative-strand (NNS) RNA viruses possess a ribonucleoprotein template in which the genomic RNA is sequestered within a homopolymer of nucleocapsid protein (N). The viral RNA-dependent RNA polymerase (RdRP) resides within an approximately ... ...

Abstract	Nonsegmented negative-strand (NNS) RNA viruses possess a ribonucleoprotein template in which the genomic RNA is sequestered within a homopolymer of nucleocapsid protein (N). The viral RNA-dependent RNA polymerase (RdRP) resides within an approximately 250-kDa large protein (L), along with unconventional mRNA capping enzymes: a GDP:polyribonucleotidyltransferase (PRNT) and a dual-specificity mRNA cap methylase (MT). To gain access to the N-RNA template and orchestrate the L
MeSH term(s)	Animals ; Cell Line ; Chlorocebus aethiops ; Humans ; Kinetics ; Nucleocapsid Proteins/genetics ; Nucleocapsid Proteins/metabolism ; Phosphoproteins/genetics ; Phosphoproteins/metabolism ; Protein Binding ; RNA, Messenger/metabolism ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; RNA-Dependent RNA Polymerase/metabolism ; Ribonucleoproteins/metabolism ; Transcription, Genetic/genetics ; Vero Cells ; Vesicular Stomatitis/virology ; Vesiculovirus/genetics ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Virus Replication/genetics
Chemical Substances	Nucleocapsid Proteins ; Phosphoproteins ; RNA, Messenger ; RNA, Viral ; Ribonucleoproteins ; Viral Proteins ; L protein, vesicular stomatitis virus (EC 2.7.7.48) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2020-06-16
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.00115-20
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Zs.A 609: Show issues

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Article ; Online: SARS-CoV-2 evolution in an immunocompromised host reveals shared neutralization escape mechanisms.

Clark, Sarah A / Clark, Lars E / Pan, Junhua / Coscia, Adrian / McKay, Lindsay G A / Shankar, Sundaresh / Johnson, Rebecca I / Brusic, Vesna / Choudhary, Manish C / Regan, James / Li, Jonathan Z / Griffiths, Anthony / Abraham, Jonathan

Cell

2021 Volume 184, Issue 10, Page(s) 2605–2617.e18

Abstract: Many individuals mount nearly identical antibody responses to SARS-CoV-2. To gain insight into how the viral spike (S) protein receptor-binding domain (RBD) might evolve in response to common antibody responses, we studied mutations occurring during ... ...

Abstract	Many individuals mount nearly identical antibody responses to SARS-CoV-2. To gain insight into how the viral spike (S) protein receptor-binding domain (RBD) might evolve in response to common antibody responses, we studied mutations occurring during virus evolution in a persistently infected immunocompromised individual. We use antibody Fab/RBD structures to predict, and pseudotypes to confirm, that mutations found in late-stage evolved S variants confer resistance to a common class of SARS-CoV-2 neutralizing antibodies we isolated from a healthy COVID-19 convalescent donor. Resistance extends to the polyclonal serum immunoglobulins of four out of four healthy convalescent donors we tested and to monoclonal antibodies in clinical use. We further show that affinity maturation is unimportant for wild-type virus neutralization but is critical to neutralization breadth. Because the mutations we studied foreshadowed emerging variants that are now circulating across the globe, our results have implications to the long-term efficacy of S-directed countermeasures.
MeSH term(s)	Antibodies, Neutralizing ; Antibodies, Viral/immunology ; COVID-19/genetics ; COVID-19/immunology ; Evolution, Molecular ; Female ; HEK293 Cells ; Humans ; Immune Evasion/immunology ; Immunocompromised Host ; Immunoglobulin Fab Fragments/immunology ; Male ; Protein Domains ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Immunoglobulin Fab Fragments ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.03.027
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Zs.A 1167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Structure of the Receptor Binding Domain of EnvP(b)1, an Endogenous Retroviral Envelope Protein Expressed in Human Tissues.

McCarthy, Kevin R / Timpona, Joseph L / Jenni, Simon / Bloyet, Louis-Marie / Brusic, Vesna / Johnson, Welkin E / Whelan, Sean P J / Robinson-McCarthy, Lindsey R

mBio

2020 Volume 11, Issue 6

Abstract: EnvP(b)1 is an endogenous retroviral envelope gene found in human and other primate genomes. We report EnvP(b)1 sequences in primate genomes consistent with an integration event between 40 and 71 million years ago. Using a highly specific polyclonal ... ...

Abstract	EnvP(b)1 is an endogenous retroviral envelope gene found in human and other primate genomes. We report EnvP(b)1 sequences in primate genomes consistent with an integration event between 40 and 71 million years ago. Using a highly specific polyclonal antiserum raised against the putative receptor binding domain (RBD) of human EnvP(b)1, we detected expression in human placenta, ovaries, and thymus. We found that EnvP(b)1 is proteolytically processed, and using cell-cell fusion assays in multiple primate cell lines, we demonstrated that extant EnvP(b)1 proteins from a variety of primate genomes are fusogenic. This work supports the idea that EnvP(b)1 is under purifying selection and its fusogenic activity has been maintained for over 40 million years. We determined the structure of the RBD of human EnvP(b)1, which defines structural similarities with extant leukemia viruses, despite little sequence conservation. This structure highlights a common scaffold from which novel receptor binding specificities likely evolved. The evolutionary plasticity of this domain may underlie the diversity of related Envs in circulating viruses.
MeSH term(s)	Animals ; Biological Evolution ; Cell Fusion ; Cell Line ; Conserved Sequence/genetics ; Endogenous Retroviruses/genetics ; Endogenous Retroviruses/physiology ; Female ; Humans ; Models, Structural ; Phylogeny ; Placenta/virology ; Pregnancy ; Primates ; Protein Binding ; Protein Domains ; Viral Envelope Proteins/genetics ; Viral Envelope Proteins/metabolism
Chemical Substances	Viral Envelope Proteins
Language	English
Publishing date	2020-11-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.02772-20
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Article ; Online: Vesicular Stomatitis Virus Transcription Is Inhibited by TRIM69 in the Interferon-Induced Antiviral State.

Kueck, Tonya / Bloyet, Louis-Marie / Cassella, Elena / Zang, Trinity / Schmidt, Fabian / Brusic, Vesna / Tekes, Gergely / Pornillos, Owen / Whelan, Sean P J / Bieniasz, Paul D

Journal of virology

2019 Volume 93, Issue 24

Abstract: Interferons (IFNs) induce the expression of interferon-stimulated genes (ISGs), many of which are responsible for the cellular antiviral state in which the replication of numerous viruses is blocked. How the majority of individual ISGs inhibit the ... ...

Abstract	Interferons (IFNs) induce the expression of interferon-stimulated genes (ISGs), many of which are responsible for the cellular antiviral state in which the replication of numerous viruses is blocked. How the majority of individual ISGs inhibit the replication of particular viruses is unknown. We conducted a loss-of-function screen to identify genes required for the activity of alpha interferon (IFN-α) against vesicular stomatitis virus, Indiana serotype (VSV
MeSH term(s)	Antiviral Agents/pharmacology ; Cell Line ; Cytokines/pharmacology ; Humans ; Interferon-alpha/pharmacology ; Models, Molecular ; Phosphoproteins/genetics ; Protein Conformation ; Protein Domains ; RNA, Messenger/metabolism ; RNA, Viral/biosynthesis ; Tripartite Motif Proteins/antagonists & inhibitors ; Tripartite Motif Proteins/chemistry ; Ubiquitin-Protein Ligases/antagonists & inhibitors ; Ubiquitin-Protein Ligases/chemistry ; Vesicular Stomatitis/virology ; Vesicular stomatitis Indiana virus/drug effects ; Vesicular stomatitis Indiana virus/genetics ; Vesiculovirus/drug effects ; Vesiculovirus/genetics ; Viral Proteins ; Virus Replication/drug effects
Chemical Substances	Antiviral Agents ; Cytokines ; Interferon-alpha ; Phosphoproteins ; RNA, Messenger ; RNA, Viral ; Tripartite Motif Proteins ; Viral Proteins ; TRIM69 protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2019-11-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.01372-19
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Article: Repeatable Population Dynamics among Vesicular Stomatitis Virus Lineages Evolved under High Co-infection.

Williams, Elizabeth S C P / Morales, Nadya M / Wasik, Brian R / Brusic, Vesna / Whelan, Sean P J / Turner, Paul E

Frontiers in microbiology

2016 Volume 7, Page(s) 370

Abstract: Parasites and hosts can experience oscillatory cycles, where the densities of these interacting species dynamically fluctuate through time. Viruses with different replication strategies can also interact to produce cyclical dynamics. Frequent cellular co- ...

Abstract	Parasites and hosts can experience oscillatory cycles, where the densities of these interacting species dynamically fluctuate through time. Viruses with different replication strategies can also interact to produce cyclical dynamics. Frequent cellular co-infection can select for defective-interfering particles (DIPs): "cheater" viruses with shortened genomes that interfere with intracellular replication of full-length (ordinary) viruses. DIPs are positively selected when rare because they out-replicate ordinary viruses during co-infection, but DIPs are negatively selected when common because ordinary viruses become unavailable for intracellular exploitation via cheating. Here, we tested whether oscillatory dynamics of ordinary viruses were similar across independently evolved populations of vesicular stomatitis virus (VSV). Results showed identical cyclical dynamics across populations in the first 10 experimental passages, which transitioned to repeatable dampened oscillations by passage 20. Genomic analyses revealed parallel molecular substitutions across populations, particularly novel mutations that became dominant by passage 10. Our study showed that oscillatory dynamics and molecular evolution of interacting viruses were highly repeatable in VSV populations passaged under frequent co-infection. Furthermore, our data suggested that frequent co-infection with DIPs caused lowered performance of full-length viruses, by reducing their population densities by orders of magnitude compared to reproduction of ordinary viruses during strictly clonal infections.
Language	English
Publishing date	2016-03-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2016.00370
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Article ; Online: Phenotypic lentivirus screens to identify functional single domain antibodies.

Schmidt, Florian I / Hanke, Leo / Morin, Benjamin / Brewer, Rebeccah / Brusic, Vesna / Whelan, Sean P J / Ploegh, Hidde L

Nature microbiology

2016 Volume 1, Issue 8, Page(s) 16080

Abstract: Manipulation of proteins is key in assessing their in vivo function. Although genetic ablation is straightforward, reversible and specific perturbation of protein function remains a challenge. Single domain antibody fragments, such as camelid-derived ... ...

Abstract	Manipulation of proteins is key in assessing their in vivo function. Although genetic ablation is straightforward, reversible and specific perturbation of protein function remains a challenge. Single domain antibody fragments, such as camelid-derived VHHs, can serve as inhibitors or activators of intracellular protein function, but functional testing of identified VHHs is laborious. To address this challenge, we have developed a lentiviral screening approach to identify VHHs that elicit a phenotype when expressed intracellularly. We identified 19 antiviral VHHs that protect human A549 cells from lethal infection with influenza A virus (IAV) or vesicular stomatitis virus (VSV), respectively. Both negative-sense RNA viruses are vulnerable to VHHs uniquely specific for their respective nucleoproteins. Antiviral VHHs prevented nuclear import of viral ribonucleoproteins or mRNA transcription, respectively, and may provide clues for novel antiviral reagents. In principle, the screening approach described here should be applicable to identify inhibitors of any pathogen or biological pathway.
MeSH term(s)	A549 Cells ; Antiviral Agents/isolation & purification ; Drug Evaluation, Preclinical/methods ; Humans ; Influenza A virus/pathogenicity ; Single-Domain Antibodies/isolation & purification ; Vesiculovirus/pathogenicity
Chemical Substances	Antiviral Agents ; Single-Domain Antibodies
Language	English
Publishing date	2016-06-20
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/nmicrobiol.2016.80
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Article ; Online: VLDLR and ApoER2 are receptors for multiple alphaviruses.

Clark, Lars E / Clark, Sarah A / Lin, ChieYu / Liu, Jianying / Coscia, Adrian / Nabel, Katherine G / Yang, Pan / Neel, Dylan V / Lee, Hyo / Brusic, Vesna / Stryapunina, Iryna / Plante, Kenneth S / Ahmed, Asim A / Catteruccia, Flaminia / Young-Pearse, Tracy L / Chiu, Isaac M / Llopis, Paula Montero / Weaver, Scott C / Abraham, Jonathan

Nature

2021 Volume 602, Issue 7897, Page(s) 475–480

Abstract: Alphaviruses, like many other arthropod-borne viruses, infect vertebrate species and insect vectors separated by hundreds of millions of years of evolutionary history. Entry into evolutionarily divergent host cells can be accomplished by recognition of ... ...

Abstract	Alphaviruses, like many other arthropod-borne viruses, infect vertebrate species and insect vectors separated by hundreds of millions of years of evolutionary history. Entry into evolutionarily divergent host cells can be accomplished by recognition of different cellular receptors in different species, or by binding to receptors that are highly conserved across species. Although multiple alphavirus receptors have been described
MeSH term(s)	Animals ; LDL-Receptor Related Proteins ; Ligands ; Mice ; Mosquito Vectors ; Receptors, LDL ; Semliki forest virus/metabolism ; Sindbis Virus/physiology
Chemical Substances	LDL-Receptor Related Proteins ; Ligands ; Receptors, LDL ; VLDL receptor ; low density lipoprotein receptor-related protein 8
Language	English
Publishing date	2021-12-20
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-021-04326-0
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Article ; Online: Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain.

Nabel, Katherine G / Clark, Sarah A / Shankar, Sundaresh / Pan, Junhua / Clark, Lars E / Yang, Pan / Coscia, Adrian / McKay, Lindsay G A / Varnum, Haley H / Brusic, Vesna / Tolan, Nicole V / Zhou, Guohai / Desjardins, Michaël / Turbett, Sarah E / Kanjilal, Sanjat / Sherman, Amy C / Dighe, Anand / LaRocque, Regina C / Ryan, Edward T /

Tylek, Casey / Cohen-Solal, Joel F / Darcy, Anhdao T / Tavella, Davide / Clabbers, Anca / Fan, Yao / Griffiths, Anthony / Correia, Ivan R / Seagal, Jane / Baden, Lindsey R / Charles, Richelle C / Abraham, Jonathan

Science (New York, N.Y.)

2022 Volume 375, Issue 6578, Page(s) eabl6251

Abstract: Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we evaluate the consequences of further viral evolution. We ... ...

Abstract	Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we evaluate the consequences of further viral evolution. We demonstrate mechanisms through which the SARS-CoV-2 receptor binding domain (RBD) can tolerate large numbers of simultaneous antibody escape mutations and show that pseudotypes containing up to seven mutations, as opposed to the one to three found in previously studied variants of concern, are more resistant to neutralization by therapeutic antibodies and serum from vaccine recipients. We identify an antibody that binds the RBD core to neutralize pseudotypes for all tested variants but show that the RBD can acquire an N-linked glycan to escape neutralization. Our findings portend continued emergence of escape variants as SARS-CoV-2 adapts to humans.
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/metabolism ; Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; BNT162 Vaccine/immunology ; Betacoronavirus/immunology ; COVID-19/immunology ; COVID-19/virology ; Cross Reactions ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Epitopes ; Evolution, Molecular ; Humans ; Immune Evasion ; Models, Molecular ; Mutation ; Polysaccharides/analysis ; Protein Binding ; Protein Domains ; Receptors, Coronavirus/chemistry ; Receptors, Coronavirus/metabolism ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology ; Viral Pseudotyping
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Epitopes ; Polysaccharides ; Receptors, Coronavirus ; Spike Glycoprotein, Coronavirus ; spike glycoprotein, SARS-CoV ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; BNT162 Vaccine (N38TVC63NU)
Language	English
Publishing date	2022-01-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abl6251
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