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Article ; Online: Structure of the Inmazeb cocktail and resistance to Ebola virus escape.

Rayaprolu, Vamseedhar / Fulton, Benjamin O / Rafique, Ashique / Arturo, Emilia / Williams, Dewight / Hariharan, Chitra / Callaway, Heather / Parvate, Amar / Schendel, Sharon L / Parekh, Diptiben / Hui, Sean / Shaffer, Kelly / Pascal, Kristen E / Wloga, Elzbieta / Giordano, Stephanie / Negron, Nicole / Ni, Min / Copin, Richard / Atwal, Gurinder S /

Franklin, Matthew / Boytz, Ruth Mabel / Donahue, Callie / Davey, Robert / Baum, Alina / Kyratsous, Christos A / Saphire, Erica Ollmann

Cell host & microbe

2023 Volume 31, Issue 2, Page(s) 260–272.e7

Abstract: Monoclonal antibodies can provide important pre- or post-exposure protection against infectious disease for those not yet vaccinated or in individuals that fail to mount a protective immune response after vaccination. Inmazeb (REGN-EB3), a three-antibody ...

Abstract	Monoclonal antibodies can provide important pre- or post-exposure protection against infectious disease for those not yet vaccinated or in individuals that fail to mount a protective immune response after vaccination. Inmazeb (REGN-EB3), a three-antibody cocktail against Ebola virus, lessened disease and improved survival in a controlled trial. Here, we present the cryo-EM structure at 3.1 Å of the Ebola virus glycoprotein, determined without symmetry averaging, in a simultaneous complex with the antibodies in the Inmazeb cocktail. This structure allows the modeling of previously disordered portions of the glycoprotein glycan cap, maps the non-overlapping epitopes of Inmazeb, and illuminates the basis for complementary activities and residues critical for resistance to escape by these and other clinically relevant antibodies. We further provide direct evidence that Inmazeb protects against the rapid emergence of escape mutants, whereas monotherapies even against conserved epitopes do not, supporting the benefit of a cocktail versus a monotherapy approach.
MeSH term(s)	Humans ; Ebolavirus ; Hemorrhagic Fever, Ebola ; Antibodies, Viral ; Glycoproteins ; Epitopes ; Antibodies, Neutralizing
Chemical Substances	atoltivimab, maftivimab, and odesivimab-ebgn drug combination ; Antibodies, Viral ; Glycoproteins ; Epitopes ; Antibodies, Neutralizing
Language	English
Publishing date	2023-01-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2278004-X
ISSN	1934-6069 ; 1931-3128
ISSN (online)	1934-6069
ISSN	1931-3128
DOI	10.1016/j.chom.2023.01.002
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Article ; Online: Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies.

Baum, Alina / Fulton, Benjamin O / Wloga, Elzbieta / Copin, Richard / Pascal, Kristen E / Russo, Vincenzo / Giordano, Stephanie / Lanza, Kathryn / Negron, Nicole / Ni, Min / Wei, Yi / Atwal, Gurinder S / Murphy, Andrew J / Stahl, Neil / Yancopoulos, George D / Kyratsous, Christos A

Science (New York, N.Y.)

2020 Volume 369, Issue 6506, Page(s) 1014–1018

Abstract: Antibodies targeting the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) present a promising approach to combat the coronavirus disease 2019 (COVID-19) pandemic; however, concerns remain that mutations can yield antibody ... ...

Abstract	Antibodies targeting the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) present a promising approach to combat the coronavirus disease 2019 (COVID-19) pandemic; however, concerns remain that mutations can yield antibody resistance. We investigated the development of resistance against four antibodies to the spike protein that potently neutralize SARS-CoV-2, individually as well as when combined into cocktails. These antibodies remain effective against spike variants that have arisen in the human population. However, novel spike mutants rapidly appeared after in vitro passaging in the presence of individual antibodies, resulting in loss of neutralization; such escape also occurred with combinations of antibodies binding diverse but overlapping regions of the spike protein. Escape mutants were not generated after treatment with a noncompeting antibody cocktail.
MeSH term(s)	Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; Betacoronavirus/chemistry ; Betacoronavirus/genetics ; Betacoronavirus/immunology ; COVID-19 ; Coronavirus Infections/immunology ; Epitopes ; Genome, Viral ; Humans ; Mutant Proteins/chemistry ; Mutant Proteins/immunology ; Mutation ; Neutralization Tests ; Pandemics ; Pneumonia, Viral/immunology ; Protein Interaction Domains and Motifs ; SARS-CoV-2 ; Selection, Genetic ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Epitopes ; Mutant Proteins ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-06-15
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abd0831
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Article: Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant

Cell. 2020 Oct. 29, v. 183, no. 3

2020

Abstract: The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells ... ...

Abstract	The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells rendered permissive by ectopic expression of human ACE2 or of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin. D614G did not alter S protein synthesis, processing, or incorporation into SARS-CoV-2 particles, but D614G affinity for ACE2 was reduced due to a faster dissociation rate. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts an interprotomer contact and that the conformation is shifted toward an ACE2 binding-competent state, which is modeled to be on pathway for virion membrane fusion with target cells. Consistent with this more open conformation, neutralization potency of antibodies targeting the S protein receptor-binding domain was not attenuated.
Keywords	Manis javanica ; Rhinolophus ; Severe acute respiratory syndrome coronavirus 2 ; colon ; cryo-electron microscopy ; dissociation ; humans ; lungs ; membrane fusion ; neutralization ; protein synthesis ; virion ; viruses
Language	English
Dates of publication	2020-1029
Size	p. 739-751.e8.
Publishing place	Elsevier Inc.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2020.09.032
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Article: Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.

bioRxiv : the preprint server for biology

2020

Abstract: The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and cells rendered permissive by ectopic ... ...

Abstract	The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and cells rendered permissive by ectopic expression of various mammalian ACE2 orthologs. Nonetheless, D614G affinity for ACE2 was reduced due to a faster dissociation rate. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts a critical interprotomer contact and that this dramatically shifts the S protein trimer conformation toward an ACE2-binding and fusion-competent state. Consistent with the more open conformation, neutralization potency of antibodies targeting the S protein receptor-binding domain was not attenuated. These results indicate that D614G adopts conformations that make virion membrane fusion with the target cell membrane more probable but that D614G retains susceptibility to therapies that disrupt interaction of the SARS-CoV-2 S protein with the ACE2 receptor.
Keywords	covid19
Language	English
Publishing date	2020-07-15
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.07.04.187757
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.

Cell

2020 Volume 183, Issue 3, Page(s) 739–751.e8

Abstract	The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells rendered permissive by ectopic expression of human ACE2 or of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin. D614G did not alter S protein synthesis, processing, or incorporation into SARS-CoV-2 particles, but D614G affinity for ACE2 was reduced due to a faster dissociation rate. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts an interprotomer contact and that the conformation is shifted toward an ACE2 binding-competent state, which is modeled to be on pathway for virion membrane fusion with target cells. Consistent with this more open conformation, neutralization potency of antibodies targeting the S protein receptor-binding domain was not attenuated.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Animals ; Antibodies, Monoclonal/immunology ; Antibodies, Viral/immunology ; Betacoronavirus/pathogenicity ; Betacoronavirus/physiology ; Betacoronavirus/ultrastructure ; COVID-19 ; Cells, Cultured ; Coronavirus Infections/virology ; Female ; Genetic Variation ; HEK293 Cells ; Humans ; Male ; Models, Molecular ; Pandemics ; Peptidyl-Dipeptidase A/metabolism ; Pneumonia, Viral/virology ; Protein Conformation ; Protein Processing, Post-Translational ; Receptors, Coronavirus ; Receptors, Virus/metabolism ; SARS-CoV-2 ; Species Specificity ; Spike Glycoprotein, Coronavirus/physiology ; Spike Glycoprotein, Coronavirus/ultrastructure
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Viral ; Receptors, Coronavirus ; Receptors, Virus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-09-15
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.2020.09.032
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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: Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies

Science

Abstract	Antibodies targeting the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) present a promising approach to combat the coronavirus disease 2019 (COVID-19) pandemic; however, concerns remain that mutations can yield antibody resistance. We investigated the development of resistance against four antibodies to the spike protein that potently neutralize SARS-CoV-2, individually as well as when combined into cocktails. These antibodies remain effective against spike variants that have arisen in the human population. However, novel spike mutants rapidly appeared after in vitro passaging in the presence of individual antibodies, resulting in loss of neutralization; such escape also occurred with combinations of antibodies binding diverse but overlapping regions of the spike protein. Escape mutants were not generated after treatment with a noncompeting antibody cocktail.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #599039
Database	COVID19

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Article: SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain

Yurkovetskiy, Leonid / Pascal, Kristen E. / Tompkins-Tinch, Christopher / Nyalile, Thomas / Wang, Yetao / Baum, Alina / Diehl, William E. / Dauphin, Ann / Carbone, Claudia / Veinotte, Kristen / Egri, Shawn B. / Schaffner, Stephen F. / Lemieux, Jacob E. / Munro, James / Sabeti, Pardis C. / Kyratsous, Christos / Shen, Kuang / Luban, Jeremy

Abstract: Virus genome sequence variants that appear over the course of an outbreak can be exploited to map the trajectory of the virus from one susceptible host to another While such variants are usually of no functional significance, in some cases they may allow ...

Abstract	Virus genome sequence variants that appear over the course of an outbreak can be exploited to map the trajectory of the virus from one susceptible host to another While such variants are usually of no functional significance, in some cases they may allow the virus to transmit faster, change disease severity, or confer resistance to antiviral therapies Since the discovery of SARS-CoV-2 as the cause of COVID-19, the virus has spread around the globe, and thousands of SARS-CoV-2 genomes have been sequenced The rate of sequence variation among SARS-CoV-2 isolates is modest for an RNA virus but the enormous number of human-to-human transmission events has provided abundant opportunity for selection of sequence variants Among these, the SARS-CoV-2 Spike protein variant, D614G, was not present in the presumptive common ancestor of this zoonotic virus, but was first detected in late January in Germany and China The D614G variant steadily increased in frequency and now constitutes >97% of isolates world-wide, raising the question whether D614G confers a replication advantage to SARS-CoV-2 Structural models predict that D614G would disrupt contacts between the S1 and S2 domains of the Spike protein and cause significant shifts in conformation Using single-cycle vectors we showed that D614G is three to nine-fold more infectious than the ancestral form on human lung and colon cell lines, as well as on other human cell lines rendered permissive by ectopic expression of human ACE2 and TMPRSS2, or by ACE2 orthologues from pangolin, pig, dog, or cat Nonetheless, monoclonal antibodies targeting the receptor binding domain of the SARS-CoV-2 Spike protein retain full neutralization potency These results suggest that D614G was selected for increased human-to-human transmission, that it contributed to the rapidity of SARS-CoV-2 spread around the world, and that it does not confer resistance to antiviral therapies targeting the receptor binding domain
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #637849
Database	COVID19

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Article ; Online: Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies

Baum, Alina / Fulton, Benjamin O. / Wloga, Elzbieta / Copin, Richard / Pascal, Kristen E. / Russo, Vincenzo / Giordano, Stephanie / Lanza, Kathryn / Negron, Nicole / Ni, Min / Wei, Yi / Atwal, Gurinder S. / Murphy, Andrew J. / Stahl, Neil / Yancopoulos, George D. / Kyratsous, Christos A.

Science

2020 , Page(s) eabd0831

Abstract: Antibodies targeting the spike protein of SARS-CoV-2 present a promising approach to combat the COVID19 pandemic; however, concerns remain that mutations can yield antibody resistance. We investigate the development of resistance against four antibodies ... ...

Abstract	Antibodies targeting the spike protein of SARS-CoV-2 present a promising approach to combat the COVID19 pandemic; however, concerns remain that mutations can yield antibody resistance. We investigate the development of resistance against four antibodies to the spike protein that potently neutralize SARS-CoV-2, individually as well as when combined into cocktails. These antibodies remain effective against spike variants that have arisen in the human population. However, novel spike mutants rapidly appeared following in vitro passaging in the presence of individual antibodies, resulting in loss of neutralization; such escape also occurred with combinations of antibodies binding diverse but overlapping regions of the spike protein. Importantly, escape mutants were not generated following treatment with a non-competing antibody cocktail.
Keywords	Multidisciplinary ; covid19
Language	English
Publisher	American Association for the Advancement of Science (AAAS)
Publishing country	us
Document type	Article ; Online
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abd0831
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The monoclonal antibody combination REGEN-COV protects against SARS-CoV-2 mutational escape in preclinical and human studies

Copin, Richard / Baum, Alina / Wloga, Elzbieta / Pascal, Kristen E / Giordano, Stephanie / Fulton, Benjamin O / Zhou, Anbo / Negron, Nicole / Lanza, Kathryn / Chan, Newton / Coppola, Angel / Chiu, Joyce / Ni, Min / Wei, Yi / Atwal, Gurinder S / Hernandez, Annabel Romero / Saotome, Kei / Zhou, Yi / Franklin, Matthew C /

Hooper, Andrea T / McCarthy, Shane / Hamon, Sara / Hamilton, Jennifer D / Staples, Hilary M / Alfson, Kendra / Carrion, Ricardo / Ali, Shazia / Norton, Thomas / Somersan-Karakaya, Selin / Sivapalasingam, Sumathi / Herman, Gary A / Weinreich, David M / Lipsich, Leah / Stahl, Neil / Murphy, Andrew J / Yancopoulos, George D / Kyratsous, Christos A

Cell. 2021 May 28,

2021

Abstract: Monoclonal antibodies against SARS-CoV-2 are a clinically validated therapeutic option against COVID-19. Because rapidly emerging virus mutants are becoming the next major concern in the fight against the global pandemic, it is imperative that these ... ...

Abstract	Monoclonal antibodies against SARS-CoV-2 are a clinically validated therapeutic option against COVID-19. Because rapidly emerging virus mutants are becoming the next major concern in the fight against the global pandemic, it is imperative that these therapeutic treatments provide coverage against circulating variants and do not contribute to development of treatment-induced emergent resistance. To this end, we investigated the sequence diversity of the spike protein and monitored emergence of virus variants in SARS-COV-2 isolates found in COVID-19 patients treated with the two-antibody combination REGEN-COV, as well as in preclinical in vitro studies using single, dual, or triple antibody combinations, and in hamster in vivo studies using REGEN-COV or single monoclonal antibody treatments. Our study demonstrates that the combination of non-competing antibodies in REGEN-COV provides protection against all current SARS-CoV-2 variants of concern/interest and also protects against emergence of new variants and their potential seeding into the population in a clinical setting.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; hamsters ; humans ; monoclonal antibodies ; pandemic ; sequence diversity ; sowing ; therapeutics ; viruses
Language	English
Dates of publication	2021-0528
Publishing place	Elsevier Inc.
Document type	Article
Note	Pre-press version
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.06.002
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Article: Rapid detection of Atopobium vaginae and association with organisms implicated in bacterial vaginosis.

Trama, Jason P / Pascal, Kristen E / Zimmerman, Jessica / Self, Matthew J / Mordechai, Eli / Adelson, Martin E

Molecular and cellular probes

2008 Volume 22, Issue 2, Page(s) 96–102

Abstract: Atopobium vaginae, a fastidious, anaerobic, Gram-positive cocci-shaped bacterium that generates large quantities of lactic acid, is associated with bacterial vaginosis (BV). Published nucleic acid amplification tests for identifying A. vaginae are ... ...

Abstract	Atopobium vaginae, a fastidious, anaerobic, Gram-positive cocci-shaped bacterium that generates large quantities of lactic acid, is associated with bacterial vaginosis (BV). Published nucleic acid amplification tests for identifying A. vaginae are directed toward the 16S ribosomal DNA with suboptimal specificity and require isolation of the organism. Here, sequencing of an A. vaginae genomic library has led to the development of a highly specific and sensitive real-time PCR test for detection of A. vaginae directly from gynecological cervicovaginal swab samples. The real-time PCR did not cross-react with DNA extracted from other members of the Atopobium genus, species with closely related 16S ribosomal DNA, and a panel of 51 other human pathogens. The DNA extraction and PCR assembly were amenable to automation using Corbett Robotics X-tractor Gene and CAS-4200N liquid handling systems. The real-time PCR was used to analyze 96 cervicovaginal swab samples submitted to our clinical laboratory for detection of organisms associated with BV. Of those samples, 28 were positive for A. vaginae. Of the 28 positive samples, 23 were concomitant with Gardnerella vaginalis detection. These results suggest that further clinical study of the relationship of A. vaginae with G. vaginalis and the development of BV should be performed.
MeSH term(s)	Actinobacteria/classification ; Actinobacteria/genetics ; DNA, Bacterial/analysis ; DNA, Bacterial/genetics ; Female ; Gardnerella vaginalis/classification ; Gardnerella vaginalis/genetics ; Humans ; Polymerase Chain Reaction ; Vaginosis, Bacterial/microbiology
Chemical Substances	DNA, Bacterial
Language	English
Publishing date	2008-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639082-1
ISSN	1096-1194 ; 0890-8508
ISSN (online)	1096-1194
ISSN	0890-8508
DOI	10.1016/j.mcp.2007.08.002
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