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Article: Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation.

bioRxiv : the preprint server for biology

2024

Abstract: The evolution of SARS-CoV-2 variants and their respective phenotypes represents an important set of tools to understand basic coronavirus biology as well as the public health implications of individual mutations in variants of concern. While mutations ... ...

Abstract	The evolution of SARS-CoV-2 variants and their respective phenotypes represents an important set of tools to understand basic coronavirus biology as well as the public health implications of individual mutations in variants of concern. While mutations outside of Spike are not well studied, the entire viral genome is undergoing evolutionary selection, particularly the central disordered linker region of the nucleocapsid (N) protein. Here, we identify a mutation (G215C), characteristic of the Delta variant, that introduces a novel cysteine into this linker domain, which results in the formation of a disulfide bond and a stable N-N dimer. Using reverse genetics, we determined that this cysteine residue is necessary and sufficient for stable dimer formation in a WA1 SARS-CoV-2 background, where it results in significantly increased viral growth both
Language	English
Publishing date	2024-03-11
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.08.584120
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Engineering SARS-CoV-2 using a reverse genetic system.

Xie, Xuping / Lokugamage, Kumari G / Zhang, Xianwen / Vu, Michelle N / Muruato, Antonio E / Menachery, Vineet D / Shi, Pei-Yong

Nature protocols

2021 Volume 16, Issue 3, Page(s) 1761–1784

Abstract: Reverse genetic systems are a critical tool for studying viruses and identifying countermeasures. In response to the ongoing COVID-19 pandemic, we recently developed an infectious complementary DNA (cDNA) clone for severe acute respiratory syndrome ... ...

Abstract	Reverse genetic systems are a critical tool for studying viruses and identifying countermeasures. In response to the ongoing COVID-19 pandemic, we recently developed an infectious complementary DNA (cDNA) clone for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The reverse genetic system can be used to rapidly engineer viruses with desired mutations to study the virus in vitro and in vivo. Viruses can also be designed for live-attenuated vaccine development and engineered with reporter genes to facilitate serodiagnosis, vaccine evaluation and antiviral screening. Thus, the reverse genetic system of SARS-CoV-2 will be widely used for both basic and translational research. However, due to the large size of the coronavirus genome (~30,000 nucleotides long) and several toxic genomic elements, manipulation of the reverse genetic system of SARS-COV-2 is not a trivial task and requires sophisticated methods. Here, we describe the technical details of how to engineer recombinant SARS-CoV-2. Overall, the process includes six steps: (i) prepare seven plasmids containing SARS-CoV-2 cDNA fragment(s), (ii) prepare high-quality DNA fragments through restriction enzyme digestion of the seven plasmids, (iii) assemble the seven cDNA fragments into a genome-length cDNA, (iv) in vitro transcribe RNA from the genome-length cDNA, (iv) electroporate the genome-length RNA into cells to recover recombinant viruses and (vi) characterize the rescued viruses. This protocol will enable researchers from different research backgrounds to master the use of the reverse genetic system and, consequently, accelerate COVID-19 research.
MeSH term(s)	DNA, Viral/genetics ; Genetic Engineering/methods ; Genome, Viral/genetics ; Reverse Genetics/methods ; SARS-CoV-2/genetics
Chemical Substances	DNA, Viral
Language	English
Publishing date	2021-01-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-021-00491-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SARS-CoV-2 is sensitive to type I interferon pretreatment

Kumari G. Lokugamage / Adam Hage / Craig Schindewolf / Ricardo Rajsbaum / Vineet D. Menachery

Abstract: AbstractSARS-CoV-2, a novel coronavirus (CoV), has recently emerged causing an ongoing outbreak of viral pneumonia around the world. While genetically distinct from the original SARS-CoV, both group 2B CoVs share similar genome organization and origins ... ...

Abstract	AbstractSARS-CoV-2, a novel coronavirus (CoV), has recently emerged causing an ongoing outbreak of viral pneumonia around the world. While genetically distinct from the original SARS-CoV, both group 2B CoVs share similar genome organization and origins to coronaviruses harbored in bats. Importantly, initial guidance has used insights from SARS-CoV infection to inform treatment and public health strategies. In this report, we evaluate type-I Interferon (IFN-I) sensitivity of SARS-CoV-2 relative to the original SARS-CoV. Our results indicate that while SARS-CoV-2 maintains similar viral replication kinetics to SARS-CoV in Vero cell, the novel CoV is much more sensitive to IFN-I pretreatment. Examining transcriptional factor activation and interferon stimulated gene (ISG) induction, SARS-CoV-2 in the context of type I IFN induces phosphorylation of STAT1 and increased ISG proteins. In contrast, the original SARS-CoV has no evidence for STAT1 phosphorylation or ISG protein increases even in the presence of type I IFN pretreatment. Finally, we examined homology between SARS-CoV and SARS-CoV-2 in viral proteins shown to be interferon antagonist. The absence of open reading frame (ORF) 3b and significant changes to ORF6 suggest the two key IFN antagonists may not maintain equivalent function in SARS-CoV-2. Together, the results identify key differences in susceptibility to the IFN-I response between SARS-CoV and SARS-CoV-2. that could help inform disease progression, treatment options, and animal model development.ImportanceWith the ongoing outbreak of COVID-19 disease, differences between the SARS-CoV-2 and the original SARS-CoV could be leveraged to inform disease progression and eventual treatment options. In addition, these findings could have key implications for animal model development as well as further research into how SARS-CoV-2 modulates the type I IFN response early during infection.Article SummarySARS-CoV-2 has similar replication kinetics to SARS-CoV, but demonstrates significant sensitivity to type I interferon treatment.
Keywords	covid19
Publisher	biorxiv
Document type	Article ; Online
DOI	10.1101/2020.03.07.982264
Database	COVID19

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Article: Loss-of-function mutation in Omicron variants reduces spike protein expression and attenuates SARS-CoV-2 infection.

bioRxiv : the preprint server for biology

2023

Abstract: SARS-CoV-2 Omicron variants emerged in 2022 with >30 novel amino acid mutations in the spike protein alone. While most studies focus on receptor binding domain changes, mutations in the C-terminus of S1 (CTS1), adjacent to the furin cleavage site, have ... ...

Abstract	SARS-CoV-2 Omicron variants emerged in 2022 with >30 novel amino acid mutations in the spike protein alone. While most studies focus on receptor binding domain changes, mutations in the C-terminus of S1 (CTS1), adjacent to the furin cleavage site, have largely been ignored. In this study, we examined three Omicron mutations in CTS1: H655Y, N679K, and P681H. Generating a SARS-CoV-2 triple mutant (YKH), we found that the mutant increased spike processing, consistent with prior reports for H655Y and P681H individually. Next, we generated a single N679K mutant, finding reduced viral replication
Language	English
Publishing date	2023-07-10
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.04.17.536926
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Article: Type I interferon susceptibility distinguishes SARS-CoV-2 from SARS-CoV.

Lokugamage, Kumari G / Hage, Adam / de Vries, Maren / Valero-Jimenez, Ana M / Schindewolf, Craig / Dittmann, Meike / Rajsbaum, Ricardo / Menachery, Vineet D

bioRxiv : the preprint server for biology

2020

Abstract: SARS-CoV-2, a novel coronavirus (CoV) that causes COVID-19, has recently emerged causing an ongoing outbreak of viral pneumonia around the world. While distinct from SARS-CoV, both group 2B CoVs share similar genome organization, origins to bat CoVs, and ...

Abstract	SARS-CoV-2, a novel coronavirus (CoV) that causes COVID-19, has recently emerged causing an ongoing outbreak of viral pneumonia around the world. While distinct from SARS-CoV, both group 2B CoVs share similar genome organization, origins to bat CoVs, and an arsenal of immune antagonists. In this report, we evaluate type-I interferon (IFN-I) sensitivity of SARS-CoV-2 relative to the original SARS-CoV. Our results indicate that while SARS-CoV-2 maintains similar viral replication to SARS-CoV, the novel CoV is much more sensitive to IFN-I. In Vero and in Calu3 cells, SARS-CoV-2 is substantially attenuated in the context of IFN-I pretreatment, while SARS-CoV is not. In line with these findings, SARS-CoV-2 fails to counteract phosphorylation of STAT1 and expression of ISG proteins, while SARS-CoV is able to suppress both. Comparing SARS-CoV-2 and influenza A virus in human airway epithelial cultures (HAEC), we observe the absence of IFN-I stimulation by SARS-CoV-2 alone, but detect failure to counteract STAT1 phosphorylation upon IFN-I pretreatment resulting in near ablation of SARS-CoV-2 infection. Next, we evaluated IFN-I treatment post infection and found SARS-CoV-2 was sensitive even after establishing infection. Finally, we examined homology between SARS-CoV and SARS-CoV-2 in viral proteins shown to be interferon antagonists. The absence of an equivalent open reading frame (ORF) 3b and changes to ORF6 suggest the two key IFN-I antagonists may not maintain equivalent function in SARS-CoV-2. Together, the results identify key differences in susceptibility to IFN-I responses between SARS-CoV and SARS-CoV-2 that may help inform disease progression, treatment options, and animal model development.
Keywords	covid19
Language	English
Publishing date	2020-07-13
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.03.07.982264
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication and pathogenicity.

Yang, Zemin / Johnson, Bryan A / Meliopoulos, Victoria A / Ju, Xiaohui / Zhang, Peipei / Hughes, Michael P / Wu, Jinjun / Koreski, Kaitlin P / Clary, Jemma E / Chang, Ti-Cheng / Wu, Gang / Hixon, Jeff / Duffner, Jay / Wong, Kathy / Lemieux, Rene / Lokugamage, Kumari G / Alvarado, R Elias / Crocquet-Valdes, Patricia A / Walker, David H /

Plante, Kenneth S / Plante, Jessica A / Weaver, Scott C / Kim, Hong Joo / Meyers, Rachel / Schultz-Cherry, Stacey / Ding, Qiang / Menachery, Vineet D / Taylor, J Paul

Cell reports

2024 Volume 43, Issue 3, Page(s) 113965

Abstract: G3BP1/2 are paralogous proteins that promote stress granule formation in response to cellular stresses, including viral infection. The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inhibits stress granule ... ...

Abstract	G3BP1/2 are paralogous proteins that promote stress granule formation in response to cellular stresses, including viral infection. The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inhibits stress granule assembly and interacts with G3BP1/2 via an ITFG motif, including residue F17, in the N protein. Prior studies examining the impact of the G3PB1-N interaction on SARS-CoV-2 replication have produced inconsistent findings, and the role of this interaction in pathogenesis is unknown. Here, we use structural and biochemical analyses to define the residues required for G3BP1-N interaction and structure-guided mutagenesis to selectively disrupt this interaction. We find that N-F17A mutation causes highly specific loss of interaction with G3BP1/2. SARS-CoV-2 N-F17A fails to inhibit stress granule assembly in cells, has decreased viral replication, and causes decreased pathology in vivo. Further mechanistic studies indicate that the N-F17-mediated G3BP1-N interaction promotes infection by limiting sequestration of viral genomic RNA (gRNA) into stress granules.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; DNA Helicases/metabolism ; RNA Helicases/metabolism ; RNA Recognition Motif Proteins/metabolism ; Poly-ADP-Ribose Binding Proteins/metabolism ; Virulence ; COVID-19 ; RNA, Guide, CRISPR-Cas Systems ; Nucleocapsid Proteins ; Virus Replication ; RNA, Viral/genetics
Chemical Substances	DNA Helicases (EC 3.6.4.-) ; RNA Helicases (EC 3.6.4.13) ; RNA Recognition Motif Proteins ; Poly-ADP-Ribose Binding Proteins ; RNA, Guide, CRISPR-Cas Systems ; Nucleocapsid Proteins ; RNA, Viral ; G3BP1 protein, human (EC 3.6.4.12)
Language	English
Publishing date	2024-03-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2024.113965
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Type I Interferon Susceptibility Distinguishes SARS-CoV-2 from SARS-CoV.

Lokugamage, Kumari G / Hage, Adam / de Vries, Maren / Valero-Jimenez, Ana M / Schindewolf, Craig / Dittmann, Meike / Rajsbaum, Ricardo / Menachery, Vineet D

Journal of virology

2020 Volume 94, Issue 23

Abstract	SARS-CoV-2, a novel coronavirus (CoV) that causes COVID-19, has recently emerged causing an ongoing outbreak of viral pneumonia around the world. While distinct from SARS-CoV, both group 2B CoVs share similar genome organization, origins to bat CoVs, and an arsenal of immune antagonists. In this report, we evaluate type I interferon (IFN-I) sensitivity of SARS-CoV-2 relative to the original SARS-CoV. Our results indicate that while SARS-CoV-2 maintains similar viral replication to SARS-CoV, the novel CoV is much more sensitive to IFN-I. In Vero E6 and in Calu3 cells, SARS-CoV-2 is substantially attenuated in the context of IFN-I pretreatment, whereas SARS-CoV is not. In line with these findings, SARS-CoV-2 fails to counteract phosphorylation of STAT1 and expression of ISG proteins, while SARS-CoV is able to suppress both. Comparing SARS-CoV-2 and influenza A virus in human airway epithelial cultures, we observe the absence of IFN-I stimulation by SARS-CoV-2 alone but detect the failure to counteract STAT1 phosphorylation upon IFN-I pretreatment, resulting in near ablation of SARS-CoV-2 infection. Next, we evaluated IFN-I treatment postinfection and found that SARS-CoV-2 was sensitive even after establishing infection. Finally, we examined homology between SARS-CoV and SARS-CoV-2 in viral proteins shown to be interferon antagonists. The absence of an equivalent open reading frame 3b (ORF3b) and genetic differences versus ORF6 suggest that the two key IFN-I antagonists may not maintain equivalent function in SARS-CoV-2. Together, the results identify key differences in susceptibility to IFN-I responses between SARS-CoV and SARS-CoV-2 that may help inform disease progression, treatment options, and animal model development.
MeSH term(s)	Animals ; Antiviral Agents/antagonists & inhibitors ; Antiviral Agents/metabolism ; Antiviral Agents/pharmacology ; Betacoronavirus/drug effects ; Betacoronavirus/immunology ; Betacoronavirus/physiology ; Cell Line ; Cell Line, Tumor ; Chlorocebus aethiops ; Humans ; Interferon Type I/antagonists & inhibitors ; Interferon Type I/immunology ; Interferon Type I/metabolism ; Interferon Type I/pharmacology ; Interferon-alpha/antagonists & inhibitors ; Interferon-alpha/immunology ; Interferon-alpha/metabolism ; Interferon-alpha/pharmacology ; Phosphorylation ; Recombinant Proteins/pharmacology ; Severe acute respiratory syndrome-related coronavirus/drug effects ; Severe acute respiratory syndrome-related coronavirus/immunology ; Severe acute respiratory syndrome-related coronavirus/physiology ; SARS-CoV-2 ; STAT1 Transcription Factor/metabolism ; Signal Transduction ; Vero Cells ; Viral Proteins/chemistry ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Virus Replication/drug effects
Chemical Substances	Antiviral Agents ; Interferon Type I ; Interferon-alpha ; Recombinant Proteins ; STAT1 Transcription Factor ; Viral Proteins
Keywords	covid19
Language	English
Publishing date	2020-11-09
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.01410-20
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Article ; Online: Interplay between coronavirus, a cytoplasmic RNA virus, and nonsense-mediated mRNA decay pathway.

Wada, Masami / Lokugamage, Kumari G / Nakagawa, Keisuke / Narayanan, Krishna / Makino, Shinji

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

2018 Volume 115, Issue 43, Page(s) E10157–E10166

Abstract: Coronaviruses (CoVs), including severe acute respiratory syndrome CoV and Middle East respiratory syndrome CoV, are enveloped RNA viruses that carry a large positive-sense single-stranded RNA genome and cause a variety of diseases in humans and domestic ... ...

Abstract	Coronaviruses (CoVs), including severe acute respiratory syndrome CoV and Middle East respiratory syndrome CoV, are enveloped RNA viruses that carry a large positive-sense single-stranded RNA genome and cause a variety of diseases in humans and domestic animals. Very little is known about the host pathways that regulate the stability of CoV mRNAs, which carry some unusual features. Nonsense-mediated decay (NMD) is a eukaryotic RNA surveillance pathway that detects mRNAs harboring aberrant features and targets them for degradation. Although CoV mRNAs are of cytoplasmic origin, the presence of several NMD-inducing features (including multiple ORFs with internal termination codons that create a long 3' untranslated region) in CoV mRNAs led us to explore the interplay between the NMD pathway and CoVs. Our study using murine hepatitis virus as a model CoV showed that CoV mRNAs are recognized by the NMD pathway as a substrate, resulting in their degradation. Furthermore, CoV replication induced the inhibition of the NMD pathway, and N protein (a viral structural protein) had an NMD inhibitory function that protected viral mRNAs from rapid decay. Our data further suggest that the NMD pathway interferes with optimal viral replication by degrading viral mRNAs early in infection, before sufficient accumulation of N protein. Our study presents clear evidence for the biological importance of the NMD pathway in controlling the stability of mRNAs and the efficiency of replication of a cytoplasmic RNA virus.
MeSH term(s)	3' Untranslated Regions/genetics ; Animals ; Coronavirus/genetics ; Cytoplasm/genetics ; Mice ; Nonsense Mediated mRNA Decay/genetics ; Open Reading Frames/genetics ; RNA Stability/genetics ; RNA Viruses/genetics ; RNA, Messenger/genetics ; Virus Replication/genetics
Chemical Substances	3' Untranslated Regions ; RNA, Messenger
Keywords	covid19
Language	English
Publishing date	2018-10-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1811675115
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Article ; Online: Author Correction: A nanoluciferase SARS-CoV-2 for rapid neutralization testing and screening of anti-infective drugs for COVID-19.

Xie, Xuping / Muruato, Antonio E / Zhang, Xianwen / Lokugamage, Kumari G / Fontes-Garfias, Camila R / Zou, Jing / Liu, Jianying / Ren, Ping / Balakrishnan, Mini / Cihlar, Tomas / Tseng, Chien-Te K / Makino, Shinji / Menachery, Vineet D / Bilello, John P / Shi, Pei-Yong

Nature communications

2021 Volume 12, Issue 1, Page(s) 3984

Language	English
Publishing date	2021-06-21
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-24300-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SARS-CoV-2 is sensitive to type I interferon pretreatment

Lokugamage, Kumari G. / Hage, Adam / Schindewolf, Craig / Rajsbaum, Ricardo / Menachery, Vineet D.

bioRxiv

Abstract: SARS-CoV-2, a novel coronavirus (CoV), has recently emerged causing an ongoing outbreak of viral pneumonia around the world. While genetically distinct from the original SARS-CoV, both group 2B coronaviruses share similar genome organization and origins ... ...

Abstract	SARS-CoV-2, a novel coronavirus (CoV), has recently emerged causing an ongoing outbreak of viral pneumonia around the world. While genetically distinct from the original SARS-CoV, both group 2B coronaviruses share similar genome organization and origins to coronaviruses harbored in bats. Importantly, initial guidance has used insights from SARS-CoV infection to inform treatment and public health strategies. In this report, we evaluate SARS-CoV-2 relative to the original SARS-CoV. Our results indicate that while SARS-CoV-2 maintains similar viral replication kinetics to SARS-CoV in Vero cell, the novel coronavirus is much more sensitive to type I interferon pretreatment. We subsequently examined homology between SARS-CoV and SARS-CoV-2 in viral proteins shown to be interferon antagonist. The absence of open reading frame (ORF) 3b and significant changes to ORF6 suggest the two key IFN antagonists may not maintain equivalent function in SARS-CoV-2. Together, the results identify key differences in susceptibility to the IFN response between SARS-CoV and SARS-CoV-2 that could help inform disease progression, treatment options, and animal model development.
Keywords	covid19
Language	English
Publishing date	2020-03-18
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.03.07.982264
Database	COVID19

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