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Article ; Online: Phenotypic and Genotypic Characterization of West Nile Virus Isolate 2004Hou3.

Ronca, Shannon E / Gorchakov, Rodion / Berry, Rebecca / Alvarado, R Elias / Gunter, Sarah M / Murray, Kristy O

International journal of molecular sciences

2019 Volume 20, Issue 8

Abstract: West Nile virus (WNV) is an arbovirus with important public health implications globally. This study characterizes a viral isolate, 2004Hou3, in comparison with the NY99 strain from the original WNV outbreak in New York, USA. NextGen sequencing was used ... ...

Abstract	West Nile virus (WNV) is an arbovirus with important public health implications globally. This study characterizes a viral isolate, 2004Hou3, in comparison with the NY99 strain from the original WNV outbreak in New York, USA. NextGen sequencing was used to compare the viral isolates genetically, while wild-type C57/BL6 mice were used to compare pathogenicity and viral persistence. Significant differences in survival and clinical presentations were noted, with minor genetic variations between the two strains potentially offering an explanation. One notable difference is that 5 of 35 mice infected with the 2004Hou3 strain developed hind limb flaccid paralysis, suggesting its possible use as a small animal pathogenesis model for this clinical characteristic often observed in human WN neuroinvasive disease patients but not reported in other animal models of infection. Overall, this study suggests that 2004Hou3 is a less pathogenic strain with potential for use in long-term outcome studies using small animal models.
MeSH term(s)	Animals ; Body Fluids/virology ; Cercopithecus aethiops ; Female ; Genotype ; Mice, Inbred C57BL ; Phenotype ; Sequence Analysis, DNA ; Survival Analysis ; Vero Cells ; West Nile Fever/virology ; West Nile virus/genetics ; West Nile virus/isolation & purification
Language	English
Publishing date	2019-04-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms20081936
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
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Article ; Online: The NSP3 protein of SARS-CoV-2 binds fragile X mental retardation proteins to disrupt UBAP2L interactions.

Garvanska, Dimitriya H / Alvarado, R Elias / Mundt, Filip Oskar / Lindqvist, Richard / Duel, Josephine Kerzel / Coscia, Fabian / Nilsson, Emma / Lokugamage, Kumari / Johnson, Bryan A / Plante, Jessica A / Morris, Dorothea R / Vu, Michelle N / Estes, Leah K / McLeland, Alyssa M / Walker, Jordyn / Crocquet-Valdes, Patricia A / Mendez, Blanca Lopez / Plante, Kenneth S / Walker, David H /

Weisser, Melanie Bianca / Överby, Anna K / Mann, Matthias / Menachery, Vineet D / Nilsson, Jakob

EMBO reports

2024 Volume 25, Issue 2, Page(s) 902–926

Abstract: Viruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these ... ...

Abstract	Viruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these interactions. Here, we uncover a novel interaction between the viral NSP3 protein and the fragile X mental retardation proteins (FMRPs: FMR1, FXR1-2). SARS-CoV-2 NSP3 mutant viruses preventing FMRP binding have attenuated replication in vitro and reduced levels of viral antigen in lungs during the early stages of infection. We show that a unique peptide motif in NSP3 binds directly to the two central KH domains of FMRPs and that this interaction is disrupted by the I304N mutation found in a patient with fragile X syndrome. NSP3 binding to FMRPs disrupts their interaction with the stress granule component UBAP2L through direct competition with a peptide motif in UBAP2L to prevent FMRP incorporation into stress granules. Collectively, our results provide novel insight into how SARS-CoV-2 hijacks host cell proteins and provides molecular insight into the possible underlying molecular defects in fragile X syndrome.
MeSH term(s)	Humans ; COVID-19 ; Fragile X Mental Retardation Protein/genetics ; Fragile X Mental Retardation Protein/metabolism ; Fragile X Syndrome/genetics ; Fragile X Syndrome/metabolism ; Peptides/metabolism ; RNA-Binding Proteins/genetics ; SARS-CoV-2
Chemical Substances	FMR1 protein, human ; Fragile X Mental Retardation Protein (139135-51-6) ; FXR1 protein, human ; Peptides ; RNA-Binding Proteins
Language	English
Publishing date	2024-01-02
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.1038/s44319-023-00043-z
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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: SARS-CoV-2 Uses Nonstructural Protein 16 to Evade Restriction by IFIT1 and IFIT3.

Schindewolf, Craig / Lokugamage, Kumari / Vu, Michelle N / Johnson, Bryan A / Scharton, Dionna / Plante, Jessica A / Kalveram, Birte / Crocquet-Valdes, Patricia A / Sotcheff, Stephanea / Jaworski, Elizabeth / Alvarado, R Elias / Debbink, Kari / Daugherty, Matthew D / Weaver, Scott C / Routh, Andrew L / Walker, David H / Plante, Kenneth S / Menachery, Vineet D

bioRxiv : the preprint server for biology

2022

Abstract: Understanding the molecular basis of innate immune evasion by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important consideration for designing the next wave of therapeutics. Here, we investigate the role of the nonstructural ... ...

Abstract	Understanding the molecular basis of innate immune evasion by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important consideration for designing the next wave of therapeutics. Here, we investigate the role of the nonstructural protein 16 (NSP16) of SARS-CoV-2 in infection and pathogenesis. NSP16, a ribonucleoside 2'- Importance: Similar to other coronaviruses, disruption of SARS-CoV-2 NSP16 function attenuates viral replication in a type I interferon-dependent manner.
Language	English
Publishing date	2022-09-26
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.09.26.509529
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Article ; Online: QTQTN motif upstream of the furin-cleavage site plays a key role in SARS-CoV-2 infection and pathogenesis.

Vu, Michelle N / Lokugamage, Kumari G / Plante, Jessica A / Scharton, Dionna / Bailey, Aaron O / Sotcheff, Stephanea / Swetnam, Daniele M / Johnson, Bryan A / Schindewolf, Craig / Alvarado, R Elias / Crocquet-Valdes, Patricia A / Debbink, Kari / Weaver, Scott C / Walker, David H / Russell, William K / Routh, Andrew L / Plante, Kenneth S / Menachery, Vineet D

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

2022 Volume 119, Issue 32, Page(s) e2205690119

Abstract: The furin cleavage site (FCS), an unusual feature in the SARS-CoV-2 spike protein, has been spotlighted as a factor key to facilitating infection and pathogenesis by increasing spike processing. Similarly, the QTQTN motif directly upstream of the FCS is ... ...

Abstract	The furin cleavage site (FCS), an unusual feature in the SARS-CoV-2 spike protein, has been spotlighted as a factor key to facilitating infection and pathogenesis by increasing spike processing. Similarly, the QTQTN motif directly upstream of the FCS is also an unusual feature for group 2B coronaviruses (CoVs). The QTQTN deletion has consistently been observed in in vitro cultured virus stocks and some clinical isolates. To determine whether the QTQTN motif is critical to SARS-CoV-2 replication and pathogenesis, we generated a mutant deleting the QTQTN motif (ΔQTQTN). Here, we report that the QTQTN deletion attenuates viral replication in respiratory cells in vitro and attenuates disease in vivo. The deletion results in a shortened, more rigid peptide loop that contains the FCS and is less accessible to host proteases, such as TMPRSS2. Thus, the deletion reduced the efficiency of spike processing and attenuates SARS-CoV-2 infection. Importantly, the QTQTN motif also contains residues that are glycosylated, and disruption of its glycosylation also attenuates virus replication in a TMPRSS2-dependent manner. Together, our results reveal that three aspects of the S1/S2 cleavage site-the FCS, loop length, and glycosylation-are required for efficient SARS-CoV-2 replication and pathogenesis.
MeSH term(s)	Amino Acid Motifs/genetics ; Animals ; COVID-19/virology ; Chlorocebus aethiops ; Furin/chemistry ; Humans ; Proteolysis ; SARS-CoV-2/genetics ; SARS-CoV-2/physiology ; Sequence Deletion ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Vero Cells ; Virus Replication/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Furin (EC 3.4.21.75)
Language	English
Publishing date	2022-07-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2205690119
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Article ; Online: Investigation of a SARS-CoV-2 outbreak in a Texas summer camp resulting from a single introduction

Swetnam, Daniele M. / Alvarado, R. Elias. / Sotcheff, Stephanea / Mitchell, Brooke M. / McConnell, Allan / Machado, Rafael R.G. / Saada, Nehad / Haseltine, Florence P. / Maknojia, Sara / Smith, Anajane / Ren, Ping / Keiser, Philip / Weaver, Scott C. / Routh, Andrew

medRxiv

Abstract: SARS-CoV-2 is the etiological agent responsible for the COVID-19 pandemic. It is estimated that only 10 aerosol-borne virus particles are sufficient to establish a secondary infection with SARS-CoV-2. However, the dispersal pattern of SARS-CoV-2 is ... ...

Abstract	SARS-CoV-2 is the etiological agent responsible for the COVID-19 pandemic. It is estimated that only 10 aerosol-borne virus particles are sufficient to establish a secondary infection with SARS-CoV-2. However, the dispersal pattern of SARS-CoV-2 is highly variable and only 10-20% of cases are responsible for up 80% of secondary infections. The heterogeneous nature of SARS-CoV-2 transmission suggests that super-spreader events play an important role in viral transmission. Super-spreader events occur when a single person is responsible for an unusually high number of secondary infections due to a combination of biological, environmental, and/or behavioral factors. While super-spreader events have been identified as a significant factor driving SARS-CoV-2 transmission, epidemiologic studies have consistently shown that education settings do not play a major role in community transmission. However, an outbreak of SARS-CoV-2 was recently reported among 186 children (aged 10-17) and adults (aged 18 +) after attending an overnight summer camp in Texas in June 2021. To understand the transmission dynamics of the outbreak, RNA was isolated from 36 nasopharyngeal swabs collected from patients that attended the camp and 19 control patients with no known connection to the outbreak. Genome sequencing on the Oxford Nanopore platform was performed using the ARTIC approaches for library preparation and bioinformatic analysis. SARS-CoV-2 amplicons were produced from all RNA samples and >70% of the viral genome was successfully reconstructed with >10X coverage for 46 samples. Phylogenetic methods were used to estimate the transmission history and suggested that the outbreak was the result of a single introduction. We also found evidence for secondary transmission from campers to the community. Together, these findings demonstrate that super-spreader events may occur during large gatherings of children.
Keywords	covid19
Language	English
Publishing date	2022-05-30
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2022.05.29.22275277
Database	COVID19

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

Vu, Michelle N / Morris, Dorothea R / Alvarado, R. Elias / Lokugamage, Kumari G / Zhou, Yiyang / Estes, Leak K / McLeland, Alyssa M / Schindewolf, Craig / Plante, Jessica A / Ahearn, Yani P / Morgan, Angelica L / Meyers, William M / Murray, Jordan T / Weaver, Scott / Walker, David H. / Russell, William K / Routh, Andrew Laurence / Plante, Kenneth S / Menachery, Vineet D

bioRxiv

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 the impact of receptor binding domain changes, mutations in the C-terminal of S1 (CTS1), adjacent to the furin ... ...

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 the impact of receptor binding domain changes, mutations in the C-terminal 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 in vitro and less disease in vivo. Mechanistically, the N679K mutant had reduced spike protein in purified virions compared to wild-type; spike protein decreases were further exacerbated in infected cell lysates. Importantly, exogenous spike expression also revealed that N679K reduced overall spike protein yield independent of infection. Together, the data show that N679K is a loss-of-function mutation reducing overall spike levels during omicron infection, which may have important implications for disease severity, immunity, and vaccine efficacy.
Keywords	covid19
Language	English
Publishing date	2023-04-18
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.04.17.536926
Database	COVID19

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Article ; Online: Optimizing PCR Detection of West Nile Virus from Body Fluid Specimens to Delineate Natural History in an Infected Human Cohort.

Gorchakov, Rodion / Gulas-Wroblewski, Bonnie E / Ronca, Shannon E / Ruff, Jeanne C / Nolan, Melissa S / Berry, Rebecca / Alvarado, R Elias / Gunter, Sarah M / Murray, Kristy O

International journal of molecular sciences

2019 Volume 20, Issue 8

Abstract: West Nile virus (WNV), a mosquito-borne arbovirus, remains a major global health concern. In this study, we optimized PCR methods then assessed serially-collected whole blood (WB), urine (UR), saliva, and semen specimens from a large cohort of WNV- ... ...

Abstract	West Nile virus (WNV), a mosquito-borne arbovirus, remains a major global health concern. In this study, we optimized PCR methods then assessed serially-collected whole blood (WB), urine (UR), saliva, and semen specimens from a large cohort of WNV-positive participants to evaluate the natural history of infection and persistent shedding of WNV RNA. Viral RNA extraction protocols for frozen WB and UR specimens were optimized and validated through spiking experiments to maximize recovery of viral RNA from archived specimens and to assess the degradation of WNV RNA in stored UR specimens. The resultant procedures were used in conjunction with PCR detection to identify WNV-positive specimens and to quantify their viral loads. A total of 59 of 352 WB, 10 of 38 UR, and 2 of 34 saliva specimens tested positive for WNV RNA. Although a single semen specimen was positive 22 days post onset, we could not definitively confirm the presence of WNV RNA in the remaining specimens. WNV RNA-positive UR specimens exhibited profound loss of viral RNA during storage, highlighting the need for optimal preservation pre-storage. This study provides optimized methods for WNV RNA detection among different fluid types and offers alternative options for diagnostic testing during the acute stages of WNV.
MeSH term(s)	Body Fluids/virology ; Cohort Studies ; Humans ; Male ; Polymerase Chain Reaction/methods ; RNA, Viral/isolation & purification ; Saliva/virology ; Semen/virology ; West Nile Fever/blood ; West Nile Fever/urine ; West Nile Fever/virology ; West Nile virus/isolation & purification
Chemical Substances	RNA, Viral
Language	English
Publishing date	2019-04-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms20081934
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Article ; Online: QTQTN motif upstream of the furin-cleavage site plays key role in SARS-CoV-2 infection and pathogenesis.

Vu, Michelle N / Lokugamage, Kumari / Plante, Jessica A / Scharton, Dionna / Johnson, Bryan A / Sotcheff, Stephanea / Swetnam, Daniele / Schindewolf, Craig / Alvarado, R Elias / Crocquet-Valdes, Patricia A / Debbink, Kari / Weaver, Scott / Walker, David H / Routh, Andrew Laurence / Plante, Kenneth S / Menachery, Vineet D

bioRxiv

Abstract: The furin cleavage site (FCS), an unusual feature in the SARS-CoV-2 spike protein, has been spotlighted as a factor key to facilitating infection and pathogenesis by increasing spike processing 1,2. Similarly, the QTQTN motif directly upstream of the FCS ...

Abstract	The furin cleavage site (FCS), an unusual feature in the SARS-CoV-2 spike protein, has been spotlighted as a factor key to facilitating infection and pathogenesis by increasing spike processing 1,2. Similarly, the QTQTN motif directly upstream of the FCS is also an unusual feature for group 2B coronaviruses (CoVs). The QTQTN deletion has consistently been observed in in vitro cultured virus stocks and some clinical isolates 3. To determine whether the QTQTN motif is critical to SARS-CoV-2 replication and pathogenesis, we generated a mutant deleting the QTQTN motif (ΔQTQTN). Here we report that the QTQTN deletion attenuates viral replication in respiratory cells in vitro and attenuates disease in vivo. The deletion results in a shortened, more rigid peptide loop that contains the FCS, and is less accessible to host proteases, such as TMPRSS2. Thus, the deletion reduced the efficiency of spike processing and attenuates SARS-CoV-2 infection. Importantly, the QTQTN motif also contains residues that are glycosylated4, and disruption its glycosylation also attenuates virus replication in a TMPRSS2-dependent manner. Together, our results reveal that three aspects of the S1/S2 cleavage site (the FCS, loop length, and glycosylation) are required for efficient SARS-CoV-2 replication and pathogenesis.
Keywords	covid19
Language	English
Publishing date	2021-12-17
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.12.15.472450
Database	COVID19

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