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Article ; Online: Balancing Expediency and Scientific Rigor in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development.

Graepel, Kevin W / Kochhar, Sonali / Clayton, Ellen W / Edwards, Kathryn E

2020 Volume 222, Issue 2, Page(s) 180–182

MeSH term(s)	Animals ; Antibodies, Neutralizing/biosynthesis ; Antibodies, Neutralizing/immunology ; Antibodies, Viral/biosynthesis ; Antibodies, Viral/immunology ; Antibody-Dependent Enhancement ; Betacoronavirus/immunology ; COVID-19 ; COVID-19 Vaccines ; Clinical Trials as Topic ; Coronavirus Infections/immunology ; Coronavirus Infections/prevention & control ; Humans ; Immunogenicity, Vaccine ; Pandemics/prevention & control ; Pneumonia, Viral/immunology ; Pneumonia, Viral/prevention & control ; SARS-CoV-2 ; Viral Vaccines/adverse effects ; Viral Vaccines/immunology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 Vaccines ; Viral Vaccines
Keywords	covid19
Language	English
Publishing date	2020-05-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiaa234
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Article: Balancing Expediency and Scientific Rigor in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development

Graepel, Kevin W / Kochhar, Sonali / Clayton, Ellen W / Edwards, Kathryn E

J Infect Dis

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #165271
Database	COVID19

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Article ; Online: Fitness Barriers Limit Reversion of a Proofreading-Deficient Coronavirus.

Graepel, Kevin W / Agostini, Maria L / Lu, Xiaotao / Sexton, Nicole R / Denison, Mark R

Journal of virology

2019 Volume 93, Issue 20

Abstract: The 3'-to-5' exoribonuclease in coronavirus (CoV) nonstructural protein 14 (nsp14-ExoN) mediates RNA proofreading during genome replication. ExoN catalytic residues are arranged in three motifs: I (DE), II (E), and III (D). Alanine replacement of the ... ...

Abstract	The 3'-to-5' exoribonuclease in coronavirus (CoV) nonstructural protein 14 (nsp14-ExoN) mediates RNA proofreading during genome replication. ExoN catalytic residues are arranged in three motifs: I (DE), II (E), and III (D). Alanine replacement of the motif I residues (AA-E-D; four nucleotide substitutions) in murine hepatitis virus (MHV) and severe acute respiratory syndrome (SARS)-CoV yields viable mutants with impaired replication and fitness, increased mutation rates, and attenuated virulence
MeSH term(s)	Amino Acid Motifs ; Coronavirus/physiology ; Coronavirus Infections/virology ; Exoribonucleases/chemistry ; Exoribonucleases/metabolism ; Gene Expression Regulation, Viral ; Genetic Fitness ; Mutation ; Protein Binding ; Virus Replication
Chemical Substances	Exoribonucleases (EC 3.1.-)
Keywords	covid19
Language	English
Publishing date	2019-09-30
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.00711-19
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Article ; Online: Fitness barriers limit reversion of a proofreading-deficient coronavirus

Graepel, Kevin W. / Agostini, Maria L. / Lu, Xiaotao / Sexton, Nicole R. / Denison, Mark R.

bioRxiv

Abstract: The 3′-to-5′ exoribonuclease in coronavirus (CoV) nonstructural protein 14 (nsp14-ExoN) mediates RNA proofreading during genome replication. ExoN catalytic residues are arranged in three motifs: I (DE), II (E), III (D). Alanine substitution of the motif ... ...

Abstract	The 3′-to-5′ exoribonuclease in coronavirus (CoV) nonstructural protein 14 (nsp14-ExoN) mediates RNA proofreading during genome replication. ExoN catalytic residues are arranged in three motifs: I (DE), II (E), III (D). Alanine substitution of the motif I residues (AA-E-D, four nucleotide substitutions) in murine hepatitis virus (MHV) and SARS-CoV yields viable mutants with impaired replication and fitness, increased mutation rates, and attenuated virulence in vivo. Despite these impairments, MHV- and SARS-CoV ExoN motif I AA mutants (ExoN-AA) have not reverted at motif I in diverse in vitro and in vivo environments, suggesting that profound fitness barriers prevent motif I reversion. To test this hypothesis, we engineered MHV-ExoN-AA with 1, 2 or 3 nucleotide mutations along genetic pathways to AA-to-DE reversion. We show that engineered intermediate revertants were viable but had no increased replication or competitive fitness compared to MHV-ExoN-AA. In contrast, a low passage (P10) MHV-ExoN-AA showed increased replication and competitive fitness without reversion of ExoN-AA. Finally, engineered reversion of ExoN-AA to ExoN-DE in the presence of ExoN-AA passage-adaptive mutations resulted in significant fitness loss. These results demonstrate that while reversion is possible, at least one alternative adaptive pathway is more rapidly advantageous than intermediate revertants and may alter the genetic background to render reversion detrimental to fitness. Our results provide an evolutionary rationale for lack of ExoN-AA reversion, illuminate potential multi-protein replicase interactions and coevolution, and support future studies aimed at stabilizing attenuated CoV ExoN-AA mutants. Coronaviruses encode an exoribonuclease (ExoN) that is important for viral replication, fitness, and virulence, yet coronaviruses with a defective ExoN (ExoN-AA) have not reverted under diverse experimental conditions. In this study, we identify multiple impediments to MHV-ExoN-AA reversion. We show that ExoN-AA reversion is possible but evolutionarily unfavorable. Instead, compensatory mutations outside of ExoN-AA motif I are more accessible and beneficial than partial reversion. We also show that coevolution between replicase proteins over long-term passage partially compensates for ExoN-AA motif I but renders the virus inhospitable to a reverted ExoN. Our results reveal the evolutionary basis for the genetic stability of ExoN-inactivating mutations, illuminate complex functional and evolutionary relationships between coronavirus replicase proteins, and identify potential mechanisms for stabilization of ExoN-AA coronavirus mutants.
Keywords	covid19
Publisher	BioRxiv; MedRxiv
Document type	Article ; Online
DOI	10.1101/618249
Database	COVID19

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Article ; Online: Proofreading-Deficient Coronaviruses Adapt for Increased Fitness over Long-Term Passage without Reversion of Exoribonuclease-Inactivating Mutations.

Graepel, Kevin W / Lu, Xiaotao / Case, James Brett / Sexton, Nicole R / Smith, Everett Clinton / Denison, Mark R

mBio

2017 Volume 8, Issue 6

Abstract: The coronavirus (CoV) RNA genome is the largest among the single-stranded positive-sense RNA viruses. CoVs encode a proofreading 3'-to-5' exoribonuclease within nonstructural protein 14 (nsp14-ExoN) that is responsible for CoV high-fidelity replication. ... ...

Abstract	The coronavirus (CoV) RNA genome is the largest among the single-stranded positive-sense RNA viruses. CoVs encode a proofreading 3'-to-5' exoribonuclease within nonstructural protein 14 (nsp14-ExoN) that is responsible for CoV high-fidelity replication. Alanine substitution of ExoN catalytic residues [ExoN(-)] in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and murine hepatitis virus (MHV) disrupts ExoN activity, yielding viable mutant viruses with defective replication, up to 20-fold-decreased fidelity, and increased susceptibility to nucleoside analogues. To test the stability of the ExoN(-) genotype and phenotype, we passaged MHV-ExoN(-) 250 times in cultured cells (P250), in parallel with wild-type MHV (WT-MHV). Compared to MHV-ExoN(-) P3, MHV-ExoN(-) P250 demonstrated enhanced replication and increased competitive fitness without reversion at the ExoN(-) active site. Furthermore, MHV-ExoN(-) P250 was less susceptible than MHV-ExoN(-) P3 to multiple nucleoside analogues, suggesting that MHV-ExoN(-) was under selection for increased replication fidelity. We subsequently identified novel amino acid changes within the RNA-dependent RNA polymerase and nsp14 of MHV-ExoN(-) P250 that partially accounted for the reduced susceptibility to nucleoside analogues. Our results suggest that increased replication fidelity is selected in ExoN(-) CoVs and that there may be a significant barrier to ExoN(-) reversion. These results also support the hypothesis that high-fidelity replication is linked to CoV fitness and indicate that multiple replicase proteins could compensate for ExoN functions during replication.
MeSH term(s)	Animals ; Antiviral Agents/pharmacology ; Azacitidine/pharmacology ; Cell Line ; Coronavirus/drug effects ; Coronavirus/enzymology ; Coronavirus/genetics ; Coronavirus/pathogenicity ; Coronavirus Infections/virology ; Exoribonucleases/genetics ; Exoribonucleases/metabolism ; Genetic Fitness ; Genome, Viral ; Genotype ; Mice ; Mutation ; Phenotype ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; RNA-Dependent RNA Polymerase/metabolism ; Ribavirin/pharmacology ; Virus Replication/genetics
Chemical Substances	Antiviral Agents ; RNA, Viral ; Ribavirin (49717AWG6K) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; Exoribonucleases (EC 3.1.-) ; Azacitidine (M801H13NRU)
Keywords	covid19
Language	English
Publishing date	2017-11-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.01503-17
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Article ; Online: Selective Packaging in Murine Coronavirus Promotes Virulence by Limiting Type I Interferon Responses.

Athmer, Jeremiah / Fehr, Anthony R / Grunewald, Matthew E / Qu, Wen / Wheeler, D Lori / Graepel, Kevin W / Channappanavar, Rudragouda / Sekine, Aimee / Aldabeeb, Dana Saud / Gale, Michael / Denison, Mark R / Perlman, Stanley

mBio

2018 Volume 9, Issue 3

Abstract: Selective packaging is a mechanism used by multiple virus families to specifically incorporate genomic RNA (gRNA) into virions and exclude other types of RNA. Lineage A betacoronaviruses incorporate a 95-bp stem-loop structure, the packaging signal (PS), ...

Abstract	Selective packaging is a mechanism used by multiple virus families to specifically incorporate genomic RNA (gRNA) into virions and exclude other types of RNA. Lineage A betacoronaviruses incorporate a 95-bp stem-loop structure, the packaging signal (PS), into the nsp15 locus of ORF1b that is both necessary and sufficient for the packaging of RNAs. However, unlike other viral PSs, where mutations generally resulted in viral replication defects, mutation of the coronavirus (CoV) PS results in large increases in subgenomic RNA packaging with minimal effects on gRNA packaging
MeSH term(s)	Animals ; Coronavirus Infections/genetics ; Coronavirus Infections/immunology ; Coronavirus Infections/veterinary ; Coronavirus Infections/virology ; Host-Pathogen Interactions ; Interferon Type I/genetics ; Interferon Type I/immunology ; Inverted Repeat Sequences ; Male ; Mice ; Murine hepatitis virus/chemistry ; Murine hepatitis virus/genetics ; Murine hepatitis virus/pathogenicity ; Murine hepatitis virus/physiology ; Open Reading Frames ; RNA, Viral/chemistry ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Rodent Diseases/genetics ; Rodent Diseases/immunology ; Rodent Diseases/virology ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism ; Virulence ; Virus Assembly ; Virus Replication
Chemical Substances	Interferon Type I ; RNA, Viral ; Viral Nonstructural Proteins
Keywords	covid19
Language	English
Publishing date	2018-05-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.00272-18
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Article ; Online: Murine Hepatitis Virus nsp14 Exoribonuclease Activity Is Required for Resistance to Innate Immunity.

Case, James Brett / Li, Yize / Elliott, Ruth / Lu, Xiaotao / Graepel, Kevin W / Sexton, Nicole R / Smith, Everett Clinton / Weiss, Susan R / Denison, Mark R

Journal of virology

2017 Volume 92, Issue 1

Abstract: Coronaviruses (CoVs) are positive-sense RNA viruses that infect numerous mammalian and avian species and are capable of causing severe and lethal disease in humans. CoVs encode several innate immune antagonists that counteract the host innate immune ... ...

Abstract	Coronaviruses (CoVs) are positive-sense RNA viruses that infect numerous mammalian and avian species and are capable of causing severe and lethal disease in humans. CoVs encode several innate immune antagonists that counteract the host innate immune response to facilitate efficient viral replication. CoV nonstructural protein 14 (nsp14) encodes 3'-to-5' exoribonuclease activity (ExoN), which performs a proofreading function and is required for high-fidelity replication. Outside of the order
MeSH term(s)	Animals ; Antiviral Agents/pharmacology ; Exoribonucleases/genetics ; Exoribonucleases/metabolism ; Genome, Viral ; Immunity, Innate ; Interferon-beta/pharmacology ; Mice ; Murine hepatitis virus/drug effects ; Murine hepatitis virus/enzymology ; Murine hepatitis virus/genetics ; Murine hepatitis virus/immunology ; Mutagenesis ; Mutation ; RNA, Viral/metabolism ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/immunology ; Viral Nonstructural Proteins/metabolism ; Virus Replication/drug effects
Chemical Substances	Antiviral Agents ; RNA, Viral ; Viral Nonstructural Proteins ; Interferon-beta (77238-31-4) ; Exoribonucleases (EC 3.1.-)
Keywords	covid19
Language	English
Publishing date	2017-12-14
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.01531-17
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Article ; Online: Proofreading-deficient coronaviruses adapt over long-term passage for increased fidelity and fitness without reversion of exoribonuclease-inactivating mutations

Graepel, Kevin W. / Lu, Xiaotao / Case, James Brett / Sexton, Nicole R. / Smith, Everett Clinton / Denison, Mark R.

bioRxiv

Abstract: The coronavirus (CoV) RNA genome is the largest among single-stranded positive sense RNA viruses. CoVs encode a proofreading 3′→5′exoribonuclease within nonstructural protein 14 (nsp14-ExoN) that is responsible for CoV high-fidelity replication. Alanine ... ...

Abstract	The coronavirus (CoV) RNA genome is the largest among single-stranded positive sense RNA viruses. CoVs encode a proofreading 3′→5′exoribonuclease within nonstructural protein 14 (nsp14-ExoN) that is responsible for CoV high-fidelity replication. Alanine substitution of ExoN catalytic residues [ExoN(-)] in SARS-CoV and murine hepatitis virus (MHV) disrupts ExoN activity, yielding viable mutant viruses with defective replication, up to 20-fold decreased fidelity, and increased susceptibility to nucleoside analogs. To test the stability of the ExoN(-) genotype and phenotype, we passaged MHV-ExoN(-) 250 times in cultured cells (P250), in parallel with WT-MHV. Compared to MHV-ExoN(-) P3, MHV-ExoN(-) P250 demonstrated enhanced replication, reduced susceptibility to nucleoside analogs, and increased competitive fitness. However, passage did not select for complete or partial reversion at the ExoN-inactivating mutations. We identified novel amino acid changes within the RNA-dependent RNA polymerase (nsp12-RdRp) and nsp14 of MHV-ExoN(-) P250 that partially account for the observed changes in replication, susceptibility to nucleoside analogs, and competitive fitness observed in the passaged virus population, indicating that additional determinants can compensate for the activities of nsp14-ExoN. Our results suggest that while selection favors restoration of replication fidelity in ExoN(-) CoVs, there may be a significant barrier to ExoN(-) reversion. These results also support the hypothesis that high-fidelity replication is linked to CoV fitness and identify additional candidate proteins that may regulate CoV replication fidelity. Unique among RNA viruses, CoVs encode a proofreading exoribonuclease (ExoN) in nsp14 that mediates high-fidelity RNA genome replication. Proofreading-deficient CoVs with disrupted ExoN activity [ExoN(-)] are either non-viable or have significant defects in replication, RNA synthesis, fidelity, fitness, and virulence. In this study, we show that ExoN(-) murine hepatitis virus can adapt over long-term passage for increased replication and fitness without reverting the ExoN-inactivating mutations. Passage-adapted ExoN(-) mutants also demonstrate increasing resistance to nucleoside analogs that is only partially explained by secondary mutations in nsp12 and nsp14. These data suggest that enhanced resistance to nucleoside analogs is mediated by the interplay of multiple replicase proteins and support the proposed link between CoV fidelity and fitness.
Keywords	covid19
Publisher	BioRxiv; MedRxiv
Document type	Article ; Online
DOI	10.1101/175562
Database	COVID19

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Article ; Online: Donor-derived Ehrlichiosis: 2 Clusters Following Solid Organ Transplantation.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2021 Volume 74, Issue 5, Page(s) 918–923

Abstract: Ehrlichiosis has been infrequently described as transmissible through organ transplantation. Two donor-derived clusters of ehrlichiosis are described here. During the summer of 2020, 2 cases of ehrlichiosis were reported to the Organ Procurement and ... ...

Abstract	Ehrlichiosis has been infrequently described as transmissible through organ transplantation. Two donor-derived clusters of ehrlichiosis are described here. During the summer of 2020, 2 cases of ehrlichiosis were reported to the Organ Procurement and Transplantation Network (OPTN) and the Centers for Disease Control and Prevention (CDC) for investigation. Additional transplant centers were contacted to investigate similar illness in other recipients and samples were sent to the CDC. Two kidney recipients from a common donor developed fatal ehrlichiosis-induced hemophagocytic lymphocytic histiocytosis. Two kidney recipients and a liver recipient from another common donor developed ehrlichiosis. All 3 were successfully treated. Clinicians should consider donor-derived ehrlichiosis when evaluating recipients with fever early after transplantation after more common causes are ruled out, especially if the donor has epidemiological risk factors for infection. Suspected cases should be reported to the organ procurement organization and the OPTN for further investigation by public health authorities.
MeSH term(s)	Ehrlichiosis/diagnosis ; Ehrlichiosis/etiology ; Humans ; Kidney Transplantation/adverse effects ; Organ Transplantation/adverse effects ; Tissue Donors ; Tissue and Organ Procurement
Language	English
Publishing date	2021-07-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciab667
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Article ; Online: Structural basis of respiratory syncytial virus subtype-dependent neutralization by an antibody targeting the fusion glycoprotein.

Tian, Daiyin / Battles, Michael B / Moin, Syed M / Chen, Man / Modjarrad, Kayvon / Kumar, Azad / Kanekiyo, Masaru / Graepel, Kevin W / Taher, Noor M / Hotard, Anne L / Moore, Martin L / Zhao, Min / Zheng, Zi-Zheng / Xia, Ning-Shao / McLellan, Jason S / Graham, Barney S

Nature communications

2017 Volume 8, Issue 1, Page(s) 1877

Abstract: A licensed vaccine for respiratory syncytial virus (RSV) is unavailable, and passive prophylaxis with the antibody palivizumab is restricted to high-risk infants. Recently isolated antibodies 5C4 and D25 are substantially more potent than palivizumab, ... ...

Abstract	A licensed vaccine for respiratory syncytial virus (RSV) is unavailable, and passive prophylaxis with the antibody palivizumab is restricted to high-risk infants. Recently isolated antibodies 5C4 and D25 are substantially more potent than palivizumab, and a derivative of D25 is in clinical trials. Here we show that unlike D25, 5C4 preferentially neutralizes subtype A viruses. The crystal structure of 5C4 bound to the RSV fusion (F) protein reveals that the overall binding mode of 5C4 is similar to that of D25, but their angles of approach are substantially different. Mutagenesis and virological studies demonstrate that RSV F residue 201 is largely responsible for the subtype specificity of 5C4. These results improve our understanding of subtype-specific immunity and the neutralization breadth requirements of next-generation antibodies, and thereby contribute to the design of broadly protective RSV vaccines.
MeSH term(s)	Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; Antibody Specificity ; Antiviral Agents/therapeutic use ; Crystallography, X-Ray ; HEK293 Cells ; Humans ; Palivizumab/therapeutic use ; Protein Binding ; Respiratory Syncytial Virus Infections/drug therapy ; Respiratory Syncytial Virus Infections/prevention & control ; Respiratory Syncytial Virus Vaccines/therapeutic use ; Respiratory Syncytial Virus, Human/immunology ; Surface Plasmon Resonance ; Viral Fusion Proteins/immunology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Antiviral Agents ; Respiratory Syncytial Virus Vaccines ; Viral Fusion Proteins ; Palivizumab (DQ448MW7KS)
Language	English
Publishing date	2017-11-30
Publishing country	England
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.
ISSN	2041-1723
ISSN (online)	2041-1723
DOI	10.1038/s41467-017-01858-w
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