1
|
Pattinson D, Jester P, Gu C, Guan L, Armbrust T, Petrie JG, King JP, Nguyen HQ, Belongia EA, Halfmann P, Neumann G, Kawaoka Y. Ipsilateral and contralateral coadministration of influenza and COVID-19 vaccines produce similar antibody responses. EBioMedicine 2024; 103:105103. [PMID: 38574407 PMCID: PMC11004685 DOI: 10.1016/j.ebiom.2024.105103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND World Health Organisation (WHO) and USA Centers for Disease Control and Prevention (U.S. CDC) recommendations now allow simultaneous administration of COVID-19 and other vaccines. We compared antibody responses after coadministration of influenza and bivalent COVID-19 vaccines in the same (ipsilateral) arm vs. different (contralateral) arms. METHODS Pre- and post-vaccination serum samples from individuals in the Prospective Assessment of COVID-19 in a Community (PACC) cohort were used to conduct haemaglutination inhibition (HI) assays with the viruses in the 2022-2023 seasonal influenza vaccine and focus reduction neutralisation tests (FRNT) using a BA.5 SARS-CoV-2 virus. The effect of ipsilateral vs. contralateral vaccination on immune responses was inferred in a model that accounted for higher variance in vaccine responses at lower pre-vaccination titers. FINDINGS Ipsilateral vaccination did not cause higher influenza vaccine responses compared to contralateral vaccination. The response to SARS-CoV-2 was slightly increased in the ipsilateral group, but equivalence was not excluded. INTERPRETATION Coadministration of influenza and bivalent COVID-19 vaccines in the same arm or different arms did not strongly influence the antibody response to either vaccine. FUNDING This work was supported by the U.S. CDC (grant number: 75D30120C09259).
Collapse
Affiliation(s)
- David Pattinson
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peter Jester
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chunyang Gu
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lizheng Guan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tammy Armbrust
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua G Petrie
- Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Jennifer P King
- Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Huong Q Nguyen
- Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | | | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-0071, Japan; Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-0071, Japan.
| |
Collapse
|
2
|
Shafer MM, Bobholz MJ, Vuyk WC, Gregory DA, Roguet A, Haddock Soto LA, Rushford C, Janssen KH, Emmen IE, Ries HJ, Pilch HE, Mullen PA, Fahney RB, Wei W, Lambert M, Wenzel J, Halfmann P, Kawaoka Y, Wilson NA, Friedrich TC, Pray IW, Westergaard R, O'Connor DH, Johnson MC. Tracing the origin of SARS-CoV-2 omicron-like spike sequences detected in an urban sewershed: a targeted, longitudinal surveillance study of a cryptic wastewater lineage. Lancet Microbe 2024; 5:e335-e344. [PMID: 38484748 PMCID: PMC11049544 DOI: 10.1016/s2666-5247(23)00372-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/03/2023] [Accepted: 11/15/2023] [Indexed: 04/08/2024]
Abstract
BACKGROUND The origin of novel SARS-CoV-2 spike sequences found in wastewater, without corresponding detection in clinical specimens, remains unclear. We sought to determine the origin of one such cryptic wastewater lineage by tracking and characterising its persistence and genomic evolution over time. METHODS We first detected a cryptic lineage, WI-CL-001, in municipal wastewater in Wisconsin, USA, in January, 2022. To determine the source of WI-CL-001, we systematically sampled wastewater from targeted sub-sewershed lines and maintenance holes using compositing autosamplers. Viral concentrations in wastewater samples over time were measured by RT digital PCR. In addition to using metagenomic 12s rRNA sequencing to determine the virus's host species, we also sequenced SARS-CoV-2 spike receptor binding domains, and, where possible, whole viral genomes to identify and characterise the evolution of this lineage. FINDINGS We traced WI-CL-001 to its source at a single commercial building. There we detected the cryptic lineage at concentrations as high as 2·7 × 109 genome copies per L. The majority of 12s rRNA sequences detected in wastewater leaving the identified source building were human. Additionally, we generated over 100 viral receptor binding domain and whole-genome sequences from wastewater samples containing the cryptic lineage collected over the 13 consecutive months this virus was detectable (January, 2022, to January, 2023). These sequences contained a combination of fixed nucleotide substitutions characteristic of Pango lineage B.1.234, which circulated in humans in Wisconsin at low levels from October, 2020, to February, 2021. Despite this, mutations in the spike gene and elsewhere resembled those subsequently found in omicron variants. INTERPRETATION We propose that prolonged detection of WI-CL-001 in wastewater indicates persistent shedding of SARS-CoV-2 from a single human initially infected by an ancestral B.1.234 virus. The accumulation of convergent omicron-like mutations in WI-CL-001's ancestral B.1.234 genome probably reflects persistent infection and extensive within-host evolution. People who shed cryptic lineages could be an important source of highly divergent viruses that sporadically emerge and spread. FUNDING The Rockefeller Foundation, Wisconsin Department of Health Services, Centers for Disease Control and Prevention, National Institute on Drug Abuse, and the Center for Research on Influenza Pathogenesis and Transmission.
Collapse
Affiliation(s)
- Martin M Shafer
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Max J Bobholz
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - William C Vuyk
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Devon A Gregory
- School of Medicine, University of Missouri, Columbia, MO, USA
| | - Adelaide Roguet
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Luis A Haddock Soto
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Kayley H Janssen
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Isla E Emmen
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Hunter J Ries
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Hannah E Pilch
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Paige A Mullen
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Rebecca B Fahney
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Wanting Wei
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew Lambert
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; Wisconsin Department of Health Services, Madison, WI, USA
| | - Jeff Wenzel
- Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Peter Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Nancy A Wilson
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Ian W Pray
- Wisconsin Department of Health Services, Madison, WI, USA
| | - Ryan Westergaard
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; Wisconsin Department of Health Services, Madison, WI, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc C Johnson
- School of Medicine, University of Missouri, Columbia, MO, USA.
| |
Collapse
|
3
|
Whitworth I, Knoener RA, Puray-Chavez M, Halfmann P, Romero S, Baddouh M, Scalf M, Kawaoka Y, Kutluay SB, Smith LM, Sherer NM. Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs. J Proteome Res 2024; 23:149-160. [PMID: 38043095 PMCID: PMC10804885 DOI: 10.1021/acs.jproteome.3c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/31/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023]
Abstract
Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of viral replication. Here, for the first time, we demonstrate the successful isolation of SARS-CoV-2 genomic RNA and three distinct sgRNAs (N, S, and ORF8) from a single population of infected cells and characterize their protein interactomes. Over 500 protein interactors (including 260 previously unknown) were identified as associated with one or more target RNA. These included protein interactors unique to a single RNA pool and others present in multiple pools, highlighting our ability to discriminate between distinct viral RNA interactomes despite high sequence similarity. Individual interactomes indicated viral associations with cell response pathways, including regulation of cytoplasmic ribonucleoprotein granules and posttranscriptional gene silencing. We tested the significance of three protein interactors in these pathways (APOBEC3F, PPP1CC, and MSI2) using siRNA knockdowns, with several knockdowns affecting viral gene expression, most consistently PPP1CC. This study describes a new technology for high-resolution studies of SARS-CoV-2 RNA regulation and reveals a wealth of new viral RNA-associated host factors of potential functional significance to infection.
Collapse
Affiliation(s)
- Isabella
T. Whitworth
- Department
of Chemistry, University of Wisconsin-Madison
College of Letters and Sciences, Madison, Wisconsin 53706, United States
| | - Rachel A. Knoener
- Department
of Chemistry, University of Wisconsin-Madison
College of Letters and Sciences, Madison, Wisconsin 53706, United States
- McArdle
Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison School of Medicine
and Public Health, Madison, Wisconsin 53705, United States
- Institute
for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Maritza Puray-Chavez
- Department
of Molecular Microbiology, Washington University
School of Medicine, St. Louis, Missouri 63110, United States
| | - Peter Halfmann
- Influenza
Research Institute, Department of Pathobiological Sciences, School
of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Sofia Romero
- McArdle
Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison School of Medicine
and Public Health, Madison, Wisconsin 53705, United States
- Institute
for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - M’bark Baddouh
- McArdle
Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison School of Medicine
and Public Health, Madison, Wisconsin 53705, United States
- Institute
for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Mark Scalf
- Department
of Chemistry, University of Wisconsin-Madison
College of Letters and Sciences, Madison, Wisconsin 53706, United States
| | - Yoshihiro Kawaoka
- Influenza
Research Institute, Department of Pathobiological Sciences, School
of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin 53705, United States
- Division
of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The
Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Pandemic
Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan
| | - Sebla B. Kutluay
- Department
of Molecular Microbiology, Washington University
School of Medicine, St. Louis, Missouri 63110, United States
| | - Lloyd M. Smith
- Department
of Chemistry, University of Wisconsin-Madison
College of Letters and Sciences, Madison, Wisconsin 53706, United States
| | - Nathan M. Sherer
- McArdle
Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison School of Medicine
and Public Health, Madison, Wisconsin 53705, United States
- Institute
for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
4
|
Saphire E, Salie ZL, Ke Z, Halfmann P, DeWald LE, McArdle S, Grinyo A, Davidson E, Schendel S, Hariharan C, Norris M, Yu X, Chennareddy C, Xiong X, Heinrich M, Holbrook M, Doranz B, Crozier I, Hastie K, Kawaoka Y, Branco L, Kuhn J, Briggs J, Worwa G, Davis C, Ahmed R. Anti-Ebola virus mAb 3A6 with unprecedented potency protects highly viremic animals from fatal outcome and physically lifts its glycoprotein target from the virion membrane. Res Sq 2023:rs.3.rs-3722563. [PMID: 38196595 PMCID: PMC10775387 DOI: 10.21203/rs.3.rs-3722563/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Monoclonal antibodies (mAbs) against Ebola virus (EBOV) glycoprotein (GP1,2) are the standard of care for Ebola virus disease (EVD). Anti-GP1,2 mAbs targeting the stalk and membrane proximal external region (MPER) potently neutralize EBOV in vitro. However, their neutralization mechanism is poorly understood because they target a GP1,2 epitope that has evaded structural characterization. Moreover, their in vivo efficacy has only been evaluated in the mouse model of EVD. Using x-ray crystallography and cryo-electron tomography of 3A6 complexed with its stalk- GP1,2 MPER epitope we reveal a novel mechanism in which 3A6 elevates the stalk or stabilizes a conformation of GP1,2 that is lifted from the virion membrane. In domestic guinea pig and rhesus monkey EVD models, 3A6 provides therapeutic benefit at high viremia levels, advanced disease stages, and at the lowest dose yet demonstrated for any anti-EBOV mAb-based monotherapy. These findings can guide design of next-generation, highly potent anti-EBOV mAbs.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Xiaoli Xiong
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
| | | | - Michael Holbrook
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health (NIH)
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Maemura T, Guan L, Gu C, Eisfeld A, Biswas A, Halfmann P, Neumann G, Kawaoka Y. Characterization of highly pathogenic clade 2.3.4.4b H5N1 mink influenza viruses. EBioMedicine 2023; 97:104827. [PMID: 37812908 PMCID: PMC10579283 DOI: 10.1016/j.ebiom.2023.104827] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/11/2023] Open
Affiliation(s)
- Tadashi Maemura
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI 53711, USA
| | - Lizheng Guan
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI 53711, USA
| | - Chunyang Gu
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI 53711, USA
| | - Amie Eisfeld
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI 53711, USA
| | - Asim Biswas
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI 53711, USA
| | - Peter Halfmann
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI 53711, USA
| | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI 53711, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI 53711, USA; Division of Virology, Department of Microbiology and Immunology, International Research Center for Infectious Diseases, The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Research Center for Global Viral Diseases, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; The University of Tokyo, Pandemic Preparedness, Infection and Advanced Research (UTOPIA) Center, Tokyo 108-8639, Japan.
| |
Collapse
|
6
|
Hou YJ, Chiba S, Leist SR, Meganck RM, Martinez DR, Schäfer A, Catanzaro NJ, Sontake V, West A, Edwards CE, Yount B, Lee RE, Gallant SC, Zost SJ, Powers J, Adams L, Kong EF, Mattocks M, Tata A, Randell SH, Tata PR, Halfmann P, Crowe JE, Kawaoka Y, Baric RS. Host range, transmissibility and antigenicity of a pangolin coronavirus. Nat Microbiol 2023; 8:1820-1833. [PMID: 37749254 PMCID: PMC10522490 DOI: 10.1038/s41564-023-01476-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 08/14/2023] [Indexed: 09/27/2023]
Abstract
The pathogenic and cross-species transmission potential of SARS-CoV-2-related coronaviruses (CoVs) remain poorly characterized. Here we recovered a wild-type pangolin (Pg) CoV GD strain including derivatives encoding reporter genes using reverse genetics. In primary human cells, PgCoV replicated efficiently but with reduced fitness and showed less efficient transmission via airborne route compared with SARS-CoV-2 in hamsters. PgCoV was potently inhibited by US Food and Drug Administration approved drugs, and neutralized by COVID-19 patient sera and SARS-CoV-2 therapeutic antibodies in vitro. A pan-Sarbecovirus antibody and SARS-CoV-2 S2P recombinant protein vaccine protected BALB/c mice from PgCoV infection. In K18-hACE2 mice, PgCoV infection caused severe clinical disease, but mice were protected by a SARS-CoV-2 human antibody. Efficient PgCoV replication in primary human cells and hACE2 mice, coupled with a capacity for airborne spread, highlights an emergence potential. However, low competitive fitness, pre-immune humans and the benefit of COVID-19 countermeasures should impede its ability to spread globally in human populations.
Collapse
Affiliation(s)
- Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Moderna Inc., Cambridge, MA, USA
| | - Shiho Chiba
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rita M Meganck
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vishwaraj Sontake
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Catlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rhianna E Lee
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel C Gallant
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lily Adams
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Edgar F Kong
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa Mattocks
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aleksandra Tata
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Purushothama R Tata
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
7
|
Whitworth IT, Knoener RA, Puray-Chavez M, Halfmann P, Romero S, Baddouh M, Scalf M, Kawaoka Y, Kutluay SB, Smith LM, Sherer NM. Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs. bioRxiv 2023:2023.05.15.540806. [PMID: 37293069 PMCID: PMC10245570 DOI: 10.1101/2023.05.15.540806] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral defense mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of viral replication. Here, for the first time, we demonstrate the successful isolation of SARS-CoV-2 genomic RNA and three distinct sgRNAs (N, S, and ORF8) from a single population of infected cells and characterize their protein interactomes. Over 500 protein interactors (including 260 previously unknown) were identified as associated with one or more target RNA at either of two time points. These included protein interactors unique to a single RNA pool and others present in multiple pools, highlighting our ability to discriminate between distinct viral RNA interactomes despite high sequence similarity. The interactomes indicated viral associations with cell response pathways including regulation of cytoplasmic ribonucleoprotein granules and posttranscriptional gene silencing. We validated the significance of five protein interactors predicted to exhibit antiviral activity (APOBEC3F, TRIM71, PPP1CC, LIN28B, and MSI2) using siRNA knockdowns, with each knockdown yielding increases in viral production. This study describes new technology for studying SARS-CoV-2 and reveals a wealth of new viral RNA-associated host factors of potential functional significance to infection.
Collapse
Affiliation(s)
- Isabella T. Whitworth
- Department of Chemistry, University of Wisconsin-Madison College of Letters and Sciences, Madison, Wisconsin, 53706, United States
| | - Rachel A. Knoener
- Department of Chemistry, University of Wisconsin-Madison College of Letters and Sciences, Madison, Wisconsin, 53706, United States
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, 53705, United States
- Institute for Molecular Virology, University of Wisconsin-Madison Office of the Vice Chancellor for Research and Graduate Education, Madison, Wisconsin, 53706, United States
| | - Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, 63110, United States
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, 53705, United States
| | - Sofia Romero
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, 53705, United States
- Institute for Molecular Virology, University of Wisconsin-Madison Office of the Vice Chancellor for Research and Graduate Education, Madison, Wisconsin, 53706, United States
| | - M’bark Baddouh
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, 53705, United States
- Institute for Molecular Virology, University of Wisconsin-Madison Office of the Vice Chancellor for Research and Graduate Education, Madison, Wisconsin, 53706, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison College of Letters and Sciences, Madison, Wisconsin, 53706, United States
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, 53705, United States
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, 63110, United States
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin-Madison College of Letters and Sciences, Madison, Wisconsin, 53706, United States
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, 53705, United States
- Institute for Molecular Virology, University of Wisconsin-Madison Office of the Vice Chancellor for Research and Graduate Education, Madison, Wisconsin, 53706, United States
| |
Collapse
|
8
|
Chen S, Quan DH, Sam G, Ozberk V, Wang XT, Halfmann P, Pandey M, Good MF, Kawaoka Y, Britton WJ, Rehm BHA. Assembly of Immunogenic Protein Particles toward Advanced Synthetic Vaccines. Small 2023; 19:e2205819. [PMID: 36564365 DOI: 10.1002/smll.202205819] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Immunogenic carrier proteins such as the non-toxic diphtheria toxin variant, cross-reacting material 197 (CRM197), are widely used in subunit vaccine formulations to boost immunogenicity of chemically conjugated antigens. Conjugate vaccines are inherently expensive due to laborious manufacturing steps. Here, this work develops a particulate vaccine platform based on using engineered Escherichia coli to assemble CRM197-antigen fusion proteins into discrete submicron-sized particles. This approach enables precise loading of diverse antigens and epitopes enhancing their immunogenicity. A cost-effective, high-yield, and scalable biomanufacturing process is developed. Purified particulate CRM197-antigen vaccines are ambient-temperature stable. CRM197 particles incorporating pathogen-specific antigens or epitopes from SARS-CoV-2, Streptococcus pyogenes (group A), and Mycobacterium tuberculosis induced cell-mediated and humoral immune responses mediating protective immunity in respective animal models of infection. The CRM197 particle vaccine platform is versatile, enabling co-delivery of selected antigens/epitopes together with immunogenic CRM197 as discrete stable particles avoiding laborious manufacture of soluble CRM197 and antigen followed by chemical conjugation.
Collapse
Affiliation(s)
- Shuxiong Chen
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, 4111, Australia
| | - Diana H Quan
- Centenary Institute, The University of Sydney, Sydney, New South Wales, 2050, Australia
| | - Gayathri Sam
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, 4111, Australia
| | - Victoria Ozberk
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Xiaonan T Wang
- Centenary Institute, The University of Sydney, Sydney, New South Wales, 2050, Australia
| | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Manisha Pandey
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Michael F Good
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Warwick J Britton
- Centenary Institute, The University of Sydney, Sydney, New South Wales, 2050, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, 4111, Australia
- Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, 4215, Australia
| |
Collapse
|
9
|
Takashita E, Yamayoshi S, Halfmann P, Wilson N, Ries H, Richardson A, Bobholz M, Vuyk W, Maddox R, Baker DA, Friedrich TC, O'Connor DH, Uraki R, Ito M, Sakai-Tagawa Y, Adachi E, Saito M, Koga M, Tsutsumi T, Iwatsuki-Horimoto K, Kiso M, Yotsuyanagi H, Watanabe S, Hasegawa H, Imai M, Kawaoka Y. In Vitro Efficacy of Antiviral Agents against Omicron Subvariant BA.4.6. N Engl J Med 2022; 387:2094-2097. [PMID: 36383452 PMCID: PMC9730936 DOI: 10.1056/nejmc2211845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Emi Takashita
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | | | - Hunter Ries
- University of Wisconsin-Madison, Madison, WI
| | | | - Max Bobholz
- University of Wisconsin-Madison, Madison, WI
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Takashita E, Yamayoshi S, Fukushi S, Suzuki T, Maeda K, Sakai-Tagawa Y, Ito M, Uraki R, Halfmann P, Watanabe S, Takeda M, Hasegawa H, Imai M, Kawaoka Y. Efficacy of Antiviral Agents against the Omicron Subvariant BA.2.75. N Engl J Med 2022; 387:1236-1238. [PMID: 36121928 PMCID: PMC9511631 DOI: 10.1056/nejmc2209952] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Emi Takashita
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Tadaki Suzuki
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken Maeda
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | | | | | | | - Makoto Takeda
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | | |
Collapse
|
11
|
Takashita E, Yamayoshi S, Simon V, van Bakel H, Sordillo EM, Pekosz A, Fukushi S, Suzuki T, Maeda K, Halfmann P, Sakai-Tagawa Y, Ito M, Watanabe S, Imai M, Hasegawa H, Kawaoka Y. Efficacy of Antibodies and Antiviral Drugs against Omicron BA.2.12.1, BA.4, and BA.5 Subvariants. N Engl J Med 2022; 387:468-470. [PMID: 35857646 PMCID: PMC9342381 DOI: 10.1056/nejmc2207519] [Citation(s) in RCA: 178] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emi Takashita
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | | | | | - Tadaki Suzuki
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken Maeda
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Takashita E, Kinoshita N, Yamayoshi S, Sakai-Tagawa Y, Fujisaki S, Ito M, Iwatsuki-Horimoto K, Halfmann P, Watanabe S, Maeda K, Imai M, Mitsuya H, Ohmagari N, Takeda M, Hasegawa H, Kawaoka Y. Efficacy of Antiviral Agents against the SARS-CoV-2 Omicron Subvariant BA.2. N Engl J Med 2022; 386:1475-1477. [PMID: 35263535 PMCID: PMC8929374 DOI: 10.1056/nejmc2201933] [Citation(s) in RCA: 190] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Emi Takashita
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | | | | | | | | | | | | | - Kenji Maeda
- National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Hiroaki Mitsuya
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Norio Ohmagari
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Makoto Takeda
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | | |
Collapse
|
13
|
Takashita E, Kinoshita N, Yamayoshi S, Sakai-Tagawa Y, Fujisaki S, Ito M, Iwatsuki-Horimoto K, Chiba S, Halfmann P, Nagai H, Saito M, Adachi E, Sullivan D, Pekosz A, Watanabe S, Maeda K, Imai M, Yotsuyanagi H, Mitsuya H, Ohmagari N, Takeda M, Hasegawa H, Kawaoka Y. Efficacy of Antibodies and Antiviral Drugs against Covid-19 Omicron Variant. N Engl J Med 2022; 386:995-998. [PMID: 35081300 PMCID: PMC8809508 DOI: 10.1056/nejmc2119407] [Citation(s) in RCA: 246] [Impact Index Per Article: 123.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Emi Takashita
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | | | | | | | | | - Shiho Chiba
- University of Wisconsin-Madison, Madison, WI
| | | | | | | | | | - David Sullivan
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Andrew Pekosz
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | | | - Kenji Maeda
- National Center for Global Health and Medicine, Tokyo, Japan
| | | | | | - Hiroaki Mitsuya
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Norio Ohmagari
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Makoto Takeda
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | | |
Collapse
|
14
|
Pattinson D, Jester P, Guan L, Yamayoshi S, Chiba S, Presler R, Rao H, Iwatsuki-Horimoto K, Ikeda N, Hagihara M, Uchida T, Mitamura K, Halfmann P, Neumann G, Kawaoka Y. A Novel Method to Reduce ELISA Serial Dilution Assay Workload Applied to SARS-CoV-2 and Seasonal HCoVs. Viruses 2022; 14:v14030562. [PMID: 35336970 PMCID: PMC8955134 DOI: 10.3390/v14030562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Assays using ELISA measurements on serially diluted serum samples have been heavily used to measure serum reactivity to SARS-CoV-2 antigens and are widely used in virology and elsewhere in biology. We test a method using Bayesian hierarchical modelling to reduce the workload of these assays and measure reactivity of SARS-CoV-2 and HCoV antigens to human serum samples collected before and during the COVID-19 pandemic. Inflection titers for SARS-CoV-2 full-length spike protein (S1S2), spike protein receptor-binding domain (RBD), and nucleoprotein (N) inferred from 3 spread-out dilutions correlated with those inferred from 8 consecutive dilutions with an R2 value of 0.97 or higher. We confirm existing findings showing a small proportion of pre-pandemic human serum samples contain cross-reactive antibodies to SARS-CoV-2 S1S2 and N, and that SARS-CoV-2 infection increases serum reactivity to the beta-HCoVs OC43 and HKU1 S1S2. In serial dilution assays, large savings in resources and/or increases in throughput can be achieved by reducing the number of dilutions measured and using Bayesian hierarchical modelling to infer inflection or endpoint titers. We have released software for conducting these types of analysis.
Collapse
Affiliation(s)
- David Pattinson
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; (D.P.); (P.J.); (L.G.); (S.C.); (R.P.); (H.R.); (P.H.); (G.N.)
| | - Peter Jester
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; (D.P.); (P.J.); (L.G.); (S.C.); (R.P.); (H.R.); (P.H.); (G.N.)
| | - Lizheng Guan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; (D.P.); (P.J.); (L.G.); (S.C.); (R.P.); (H.R.); (P.H.); (G.N.)
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-0071, Japan; (S.Y.); (K.I.-H.)
- The Research Center for Global Viral Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8665, Japan
| | - Shiho Chiba
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; (D.P.); (P.J.); (L.G.); (S.C.); (R.P.); (H.R.); (P.H.); (G.N.)
| | - Robert Presler
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; (D.P.); (P.J.); (L.G.); (S.C.); (R.P.); (H.R.); (P.H.); (G.N.)
| | - Hongyu Rao
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; (D.P.); (P.J.); (L.G.); (S.C.); (R.P.); (H.R.); (P.H.); (G.N.)
| | - Kiyoko Iwatsuki-Horimoto
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-0071, Japan; (S.Y.); (K.I.-H.)
| | - Nobuhiro Ikeda
- Department of General Internal Medicine, Eiju General Hospital, Tokyo 104-0045, Japan;
| | - Masao Hagihara
- Department of Hematology, Eiju General Hospital, Tokyo 104-0045, Japan; (M.H.); (T.U.)
| | - Tomoyuki Uchida
- Department of Hematology, Eiju General Hospital, Tokyo 104-0045, Japan; (M.H.); (T.U.)
| | - Keiko Mitamura
- Division of Infection Control, Eiju General Hospital, Tokyo 104-0045, Japan;
| | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; (D.P.); (P.J.); (L.G.); (S.C.); (R.P.); (H.R.); (P.H.); (G.N.)
| | - Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; (D.P.); (P.J.); (L.G.); (S.C.); (R.P.); (H.R.); (P.H.); (G.N.)
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; (D.P.); (P.J.); (L.G.); (S.C.); (R.P.); (H.R.); (P.H.); (G.N.)
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-0071, Japan; (S.Y.); (K.I.-H.)
- Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-0071, Japan
- Correspondence: ; Tel.: +1-608-265-4925
| |
Collapse
|
15
|
McMahan K, Giffin V, Tostanoski LH, Chung B, Siamatu M, Suthar MS, Halfmann P, Kawaoka Y, Piedra-Mora C, Jain N, Ducat S, Kar S, Andersen H, Lewis MG, Martinot AJ, Barouch DH. Reduced Pathogenicity of the SARS-CoV-2 Omicron Variant in Hamsters. Med 2022; 3:262-268.e4. [PMID: 35313451 PMCID: PMC8926874 DOI: 10.1016/j.medj.2022.03.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/26/2022]
Abstract
Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron (B.1.1.529) variant has proven to be highly transmissible and has outcompeted the Delta variant in many regions of the world. Early reports have also suggested that Omicron may result in less severe clinical disease in humans. Here, we show that Omicron is less pathogenic than prior SARS-CoV-2 variants in Syrian golden hamsters. Methods Hamsters were inoculated with either SARS-CoV-2 Omicron or other SARS-CoV-2 variants. Animals were followed for weight loss, and upper and lower respiratory tract tissues were assessed for viral loads and histopathology. Findings Infection of hamsters with the SARS-CoV-2 WA1/2020, Alpha, Beta, or Delta strains led to 4%–10% weight loss by day 4 and 10%–17% weight loss by day 6. In contrast, infection of hamsters with two different Omicron challenge stocks did not result in any detectable weight loss, even at high challenge doses. Omicron infection led to substantial viral replication in both the upper and lower respiratory tracts but demonstrated lower viral loads in lung parenchyma and reduced pulmonary pathology compared with WA1/2020 infection. Conclusions These data suggest that the SARS-CoV-2 Omicron variant may result in robust upper respiratory tract infection, but less severe lower respiratory tract clinical disease, compared with prior SARS-CoV-2 variants. Funding Funding for this study was provided by NIH grant CA260476, the Massachusetts Consortium for Pathogen Readiness, the Ragon Institute, and the Musk Foundation. The SARS-CoV-2 Omicron variant has proven highly transmissible and has outcompeted the Delta variant in many regions of the world. In this study, investigators studied Omicron infection in Syrian golden hamsters. Although infection with prior SARS-CoV-2 variants led to substantial weight loss following infection in hamsters, infection with the Omicron variant did not result in any detectable weight loss, even at high challenge doses. Moreover, Omicron infection led to lower viral loads and reduced pathology in the lung compared with prior SARS-CoV-2 variants. These findings show that the SARS-CoV-2 Omicron variant led to less severe lower respiratory tract disease compared with prior SARS-CoV-2 variants in hamsters.
Collapse
|
16
|
Kawaoka Y, Uraki R, Kiso M, Iida S, Imai M, Takashita E, Kuroda M, Halfmann P, Loeber S, Maemura T, Yamayoshi S, Fujisaki S, Wang Z, Ito M, Ujie M, Iwatsuki-Horimoto K, Furusawa Y, Wright R, Chong Z, Ozono S, Yasuhara A, Ueki H, Sakai Y, Li R, Liu Y, Larson D, Koga M, Tsutsumi T, Adachi E, Saito M, Yamamoto S, Matsubara S, Hagihara M, Mitamura K, Sato T, Hojo M, Hattori SI, Maeda K, Okuda M, Murakami J, Duong C, Godbole S, Douek D, Watanabe S, Ohmagari N, Yotsuyanagi H, Diamond M, Hasegawa H, Mitsuya H, Suzuki T. Characterization and antiviral susceptibility of SARS-CoV-2 Omicron/BA.2. Res Sq 2022:rs.3.rs-1375091. [PMID: 35233565 PMCID: PMC8887076 DOI: 10.21203/rs.3.rs-1375091/v1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The recent emergence of SARS-CoV-2 Omicron variants possessing large numbers of mutations has raised concerns of decreased effectiveness of current vaccines, therapeutic monoclonal antibodies, and antiviral drugs for COVID-19 against these variants1,2. While the original Omicron lineage, BA.1, has become dominant in many countries, BA.2 has been detected in at least 67 countries and has become dominant in the Philippines, India, and Denmark. Here, we evaluated the replicative ability and pathogenicity of an authentic infectious BA.2 isolate in immunocompetent and human ACE2 (hACE2)-expressing mice and hamsters. In contrast to recent data with chimeric, recombinant SARS-CoV-2 strains expressing the spike proteins of BA.1 and BA.2 on an ancestral WK-521 backbone3, we observed similar infectivity and pathogenicity in mice and hamsters between BA.2 and BA.1, and less pathogenicity compared to early SARS-CoV-2 strains. We also observed a marked and significant reduction in the neutralizing activity of plasma from COVID-19 convalescent individuals and vaccine recipients against BA.2 compared to ancestral and Delta variant strains. In addition, we found that some therapeutic monoclonal antibodies (REGN10987/REGN10933, COV2-2196/COV2-2130, and S309) and antiviral drugs (molnupiravir, nirmatrelvir, and S-217622) can restrict viral infection in the respiratory organs of hamsters infected with BA.2. These findings suggest that the replication and pathogenicity of BA.2 is comparable to that of BA.1 in rodents and that several therapeutic monoclonal antibodies and antiviral compounds are effective against Omicron/BA.2 variants.
Collapse
Affiliation(s)
| | - Ryuta Uraki
- National Center for Global Health and Medicine Research Institute
| | - Maki Kiso
- Institute of Medical Sciences, University of Tokyo
| | - Shun Iida
- National Institute of Infectious Diseases
| | | | | | | | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | | | | | | | | | | | - Mutsumi Ito
- University of Tokyo, Institute of Medical Science
| | - Michiko Ujie
- Division of Virology, Institute of Medical Science, University of Tokyo
| | | | - Yuri Furusawa
- Division of Virology, Institute of Medical Science, University of Tokyo
| | - Ryan Wright
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison
| | | | | | - Atsuhiro Yasuhara
- Division of Virology, Institute of Medical Science, University of Tokyo
| | | | - Yuko Sakai
- Institute of Medical Sciences, University of Tokyo
| | - Rong Li
- Department of Animal Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University
| | - Yanan Liu
- Department of Animal Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University
| | - Deanna Larson
- Utah State University, College of Agriculture and Applied Sciences
| | - Michiko Koga
- The Institute of Medical Science, the University of Tokyo
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo
| | - Eisuke Adachi
- The Institute of Medical Science, the University of Tokyo
| | - Makoto Saito
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo
| | - Shinya Yamamoto
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo
| | - Shohei Matsubara
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo
| | | | | | - Tetsuro Sato
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital
| | - Masayuki Hojo
- Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital
| | | | - Kenji Maeda
- National Center For Global Health and Medicine
| | - Moe Okuda
- Department of Virology, Institute of Medical Science, University of Tokyo
| | - Jurika Murakami
- Department of Virology, Institute of Medical Science, University of Tokyo
| | - Calvin Duong
- Department of Virology, Institute of Medical Science, University of Tokyo
| | - Sucheta Godbole
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | | | | | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine
| | | | | | | | - Hiroaki Mitsuya
- National Center for Global Health and Medicine Research Institute
| | | |
Collapse
|
17
|
Chen S, Evert B, Adeniyi A, Salla‐Martret M, Lua LH, Ozberk V, Pandey M, Good MF, Suhrbier A, Halfmann P, Kawaoka Y, Rehm BHA. Ambient Temperature Stable, Scalable COVID‐19 Polymer Particle Vaccines Induce Protective Immunity (Adv. Healthcare Mater. 3/2022). Adv Healthc Mater 2022. [DOI: 10.1002/adhm.202270017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
18
|
Chen S, Evert B, Adeniyi A, Salla‐Martret M, Lua LH, Ozberk V, Pandey M, Good MF, Suhrbier A, Halfmann P, Kawaoka Y, Rehm BHA. Ambient Temperature Stable, Scalable COVID-19 Polymer Particle Vaccines Induce Protective Immunity. Adv Healthc Mater 2022; 11:e2102089. [PMID: 34716678 PMCID: PMC8652985 DOI: 10.1002/adhm.202102089] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Indexed: 12/15/2022]
Abstract
There is an unmet need for safe and effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines that are stable and can be cost-effectively produced at large scale. Here, a biopolymer particle (BP) vaccine technology that can be quickly adapted to new and emerging variants of SARS-CoV-2 is used. Coronavirus antigen-coated BPs are described as vaccines against SARS-CoV-2. The spike protein subunit S1 or epitopes from S and M proteins (SM) plus/minus the nucleocapsid protein (N) are selected as antigens to either coat BPs during assembly inside engineered Escherichia coli or BPs are engineered to specifically ligate glycosylated spike protein (S1-ICC) produced by using baculovirus expression in insect cell culture (ICC). BP vaccines are safe and immunogenic in mice. BP vaccines, SM-BP-N and S1-ICC-BP induced protective immunity in the hamster SARS-CoV-2 infection model as shown by reduction of virus titers up to viral clearance in lungs post infection. The BP platform offers the possibility for rapid design and cost-effective large-scale manufacture of ambient temperature stable and globally available vaccines to combat the coronavirus disease 2019 (COVID-19) pandemic.
Collapse
Affiliation(s)
- Shuxiong Chen
- Centre for Cell Factories and Biopolymers Griffith Institute for Drug Discovery Griffith University Nathan QLD 4111 Australia
| | - Benjamin Evert
- Centre for Cell Factories and Biopolymers Griffith Institute for Drug Discovery Griffith University Nathan QLD 4111 Australia
| | - Adetayo Adeniyi
- Protein Expression Facility University of Queensland Brisbane QLD 4072 Australia
| | - Mercè Salla‐Martret
- Protein Expression Facility University of Queensland Brisbane QLD 4072 Australia
| | - Linda H.‐L. Lua
- Protein Expression Facility University of Queensland Brisbane QLD 4072 Australia
| | - Victoria Ozberk
- Institute for Glycomics Griffith University Gold Coast QLD 4215 Australia
| | - Manisha Pandey
- Institute for Glycomics Griffith University Gold Coast QLD 4215 Australia
| | - Michael F. Good
- Institute for Glycomics Griffith University Gold Coast QLD 4215 Australia
| | - Andreas Suhrbier
- QIMR Berghofer Medical Research Institute Brisbane QLD 4006 Australia
| | - Peter Halfmann
- Department of Pathobiological Sciences School of Veterinary Medicine University of Wisconsin‐Madison Madison WI 53706 USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences School of Veterinary Medicine University of Wisconsin‐Madison Madison WI 53706 USA
| | - Bernd H. A. Rehm
- Centre for Cell Factories and Biopolymers Griffith Institute for Drug Discovery Griffith University Nathan QLD 4111 Australia
- Menzies Health Institute Queensland Griffith University Gold Coast 4222 Australia
| |
Collapse
|
19
|
Suthar MS, Arunachalam PS, Hu M, Reis N, Trisal M, Raeber O, Chinthrajah S, Davis-Gardner ME, Manning K, Mudvari P, Boritz E, Godbole S, Henry AR, Douek DC, Halfmann P, Kawaoka Y, Boyd SD, Davis MM, Zarnitsyna VI, Nadeau K, Pulendran B. Durability of immune responses to the BNT162b2 mRNA vaccine. Med 2022; 3:25-27. [PMID: 35590141 PMCID: PMC9304003 DOI: 10.1016/j.medj.2021.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 01/16/2023]
Abstract
Antibody responses to the Pfizer-BioNTech mRNA vaccine waned substantially 6 months after the second vaccination.
Collapse
Affiliation(s)
- Mehul S Suthar
- Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA.
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Noah Reis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Meera Trisal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Olivia Raeber
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford, CA, USA
| | - Sharon Chinthrajah
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford, CA, USA
| | - Meredith E Davis-Gardner
- Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Kelly Manning
- Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Eli Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sucheta Godbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Yoshihiro Kawaoka
- University of Wisconsin, Madison, WI, USA; National Center for Global Health and Medicine, Tokyo, Japan; University of Tokyo, Tokyo, Japan
| | - Scott D Boyd
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Kari Nadeau
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford, CA, USA; Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
| |
Collapse
|
20
|
Diamond M, Halfmann P, Maemura T, Iwatsuki-Horimoto K, Iida S, Kiso M, Scheaffer S, Darling T, Joshi A, Loeber S, Foster S, Ying B, Whitener B, Floyd K, Ujie M, Nakajima N, Ito M, Wright R, Uraki R, Li R, Sakai Y, Liu Y, Larson D, Osorio J, Hernandez-Ortiz J, Čiuoderis K, Florek K, Patel M, Bateman A, Odle A, Wong LY, Wang Z, Edara VV, Chong Z, Thackray L, Ueki H, Yamayoshi S, Imai M, Perlman S, Webby R, Seder R, Suthar M, Garcia-Sastre A, Schotsaert M, Suzuki T, Boon A, Kawaoka Y, Douek D, Moliva J, Sullivan N, Gagne M, Ransier A, Case J, Jeevan T, Franks J, Fabrizio T, DeBeauchamp J, Kercher L, Seiler P, Singh G, Warang P, Gonzalez-Reiche AS, Sordillo E, van Bakel H, Simon V. The SARS-CoV-2 B.1.1.529 Omicron virus causes attenuated infection and disease in mice and hamsters. Res Sq 2021:rs.3.rs-1211792. [PMID: 34981044 PMCID: PMC8722607 DOI: 10.21203/rs.3.rs-1211792/v1] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Despite the development and deployment of antibody and vaccine countermeasures, rapidly-spreading SARS-CoV-2 variants with mutations at key antigenic sites in the spike protein jeopardize their efficacy. The recent emergence of B.1.1.529, the Omicron variant1,2, which has more than 30 mutations in the spike protein, has raised concerns for escape from protection by vaccines and therapeutic antibodies. A key test for potential countermeasures against B.1.1.529 is their activity in pre-clinical rodent models of respiratory tract disease. Here, using the collaborative network of the SARS-CoV-2 Assessment of Viral Evolution (SAVE) program of the National Institute of Allergy and Infectious Diseases (NIAID), we evaluated the ability of multiple B.1.1.529 Omicron isolates to cause infection and disease in immunocompetent and human ACE2 (hACE2) expressing mice and hamsters. Despite modeling and binding data suggesting that B.1.1.529 spike can bind more avidly to murine ACE2, we observed attenuation of infection in 129, C57BL/6, and BALB/c mice as compared with previous SARS-CoV-2 variants, with limited weight loss and lower viral burden in the upper and lower respiratory tracts. Although K18-hACE2 transgenic mice sustained infection in the lungs, these animals did not lose weight. In wild-type and hACE2 transgenic hamsters, lung infection, clinical disease, and pathology with B.1.1.529 also were milder compared to historical isolates or other SARS-CoV-2 variants of concern. Overall, experiments from multiple independent laboratories of the SAVE/NIAID network with several different B.1.1.529 isolates demonstrate attenuated lung disease in rodents, which parallels preliminary human clinical data.
Collapse
Affiliation(s)
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | | | | | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo
| | - Maki Kiso
- Institute of Medical Sciences, University of Tokyo
| | | | | | | | | | - Stephanie Foster
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine
| | | | - Bradley Whitener
- Departments of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Michiko Ujie
- Division of Virology, Institute of Medical Science, University of Tokyo
| | | | - Mutsumi Ito
- University of Tokyo, Institute of Medical Science
| | - Ryan Wright
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison
| | - Ryuta Uraki
- National Center for Global Health and Medicine Research Institute
| | - Rong Li
- Department of Animal Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University
| | - Yuko Sakai
- Institute of Medical Sciences, University of Tokyo
| | - Yanan Liu
- Department of Animal Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University
| | - Deanna Larson
- Department of Animal Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University
| | | | - Juan Hernandez-Ortiz
- Department of Pathobiological Sciences, School of Veterinary Medicine. University of Wisconsin, Madison
| | | | | | - Mit Patel
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine
| | | | - Abby Odle
- Department of Microbiology and Immunology, University of Iowa
| | - Lok-Yin Wong
- Department of Microbiology and Immunology, University of Iowa
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - James Case
- Washington University School of Medicine
| | | | - John Franks
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | | | - Lisa Kercher
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Patrick Seiler
- Department of Infectious Diseases, St. Jude Children's Research Hospital
| | | | | | | | | | | | | |
Collapse
|
21
|
VanBlargan L, Errico J, Halfmann P, Zost S, Crowe J, Purcell L, Kawaoka Y, Corti D, Fremont D, Diamond M. An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies. Res Sq 2021:rs.3.rs-1175516. [PMID: 34981042 PMCID: PMC8722605 DOI: 10.21203/rs.3.rs-1175516/v1] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The emergence of the highly-transmissible B.1.1.529 Omicron variant of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is concerning for antibody countermeasure efficacy because of the number of mutations in the spike protein. Here, we tested a panel of anti-receptor binding domain monoclonal antibodies (mAbs) corresponding to those in clinical use by Vir Biotechnology (S309, the parent mAb of VIR-7831 [Sotrovimab]), AstraZeneca (COV2-2196 and COV2-2130, the parent mAbs of AZD8895 and AZD1061), Regeneron (REGN10933 and REGN10987), Lilly (LY-CoV555 and LY-CoV016), and Celltrion (CT-P59) for their ability to neutralize an infectious B.1.1.529 Omicron isolate. Several mAbs (LY-CoV555, LY-CoV016, REGN10933, REGN10987, and CT-P59) completely lost neutralizing activity against B.1.1.529 virus in both Vero-TMPRSS2 and Vero-hACE2-TMPRSS2 cells, whereas others were reduced (COV2-2196 and COV2-2130 combination, ~12-fold decrease) or minimally affected (S309). Our results suggest that several, but not all, of the antibodies in clinical use may lose efficacy against the B.1.1.529 Omicron variant.
Collapse
Affiliation(s)
- Laura VanBlargan
- Department of Medicine, Washington University School of Medicine
| | - John Errico
- Department of Pathology & Immunology, Washington University School of Medicine
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison
| | - Seth Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Department of Pediatrics Vanderbilt University Medical Center
| | - James Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Department of Pediatrics Vanderbilt University Medical Center; Department of Pathology, and Microbiology and Immunology, Vanderbilt University Medical Center
| | | | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology
| | - Daved Fremont
- Department of Pathology & Immunology, Washington University School of Medicine; Department of Molecular Microbiology, Washington University School of Medicine; Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine
| | - Michael Diamond
- Department of Medicine and Department of Pathology & Immunology and Department of Molecular Microbiology, Washington University School of Medicine; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine
| |
Collapse
|
22
|
Halfmann P, Nakajima N, Sato Y, Takahashi K, Accola M, Chibo S, Fan S, Neumann G, Rehrauer W, Suzuki T, Kawaoka Y. SARS-CoV-2 Interference of Influenza Virus Replication in Syrian Hamsters. J Infect Dis 2021; 225:282-286. [PMID: 34875072 PMCID: PMC8689717 DOI: 10.1093/infdis/jiab587] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/30/2021] [Indexed: 11/25/2022] Open
Abstract
In hamsters, SARS-CoV-2 infection at the same time as or before H3N2 influenza virus infection resulted in significantly reduced influenza virus titers in the lungs and nasal turbinates. This interference may be correlated with SARS-CoV-2–induced expression of MX1.
Collapse
Affiliation(s)
- Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Noriko Nakajima
- Department of Pathology, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan
| | - Yuko Sato
- Department of Pathology, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan
| | - Kenta Takahashi
- Department of Pathology, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan
| | - Molly Accola
- UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - Shiho Chibo
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Shufang Fan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - William Rehrauer
- UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI, USA.,Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
| |
Collapse
|
23
|
Zhang S, Liu F, Halfmann P, Behrens RT, Liu P, Mcilwain SJ, Ong IM, Donahue K, Wang Y, Kawaoka Y, Sherer N, Xu W. Mediator complex subunit 12 is a gatekeeper of SARS-CoV-2 infection in breast cancer cells. Genes Dis 2021; 9:5-8. [PMID: 34423104 PMCID: PMC8372481 DOI: 10.1016/j.gendis.2021.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 01/27/2023] Open
Affiliation(s)
- Shengjie Zhang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA,Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Fabao Liu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Ryan T. Behrens
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peng Liu
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA,Department of Biostatistics and Medical Informatics, Carbone Cancer Center, University of Wisconsin, Madison, WI 53706, USA
| | - Sean J. Mcilwain
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Irene M. Ong
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA,Department of Obstetrics and Gynecology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Kristine Donahue
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yidan Wang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Nathan Sherer
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA,Corresponding author. 7459 WIMR II, 1111 Highland Avenue, University of Wisconsin-Madison, Madison, WI 53705-2275, USA.
| |
Collapse
|
24
|
Wilson P, Changrob S, Fu Y, Guthmiller J, Halfmann P, Li L, Stamper C, Dugan H, Accola M, Rehrauer W, Zheng NY, Huang M, Wang J, Erickson S, Utset H, Graves H, Amanat F, Sather DN, Krammer F, Kawaoka Y. Cross neutralization of emerging SARS-CoV-2 variants of concern by antibodies targeting distinct epitopes on spike. Res Sq 2021:rs.3.rs-678247. [PMID: 34312615 PMCID: PMC8312900 DOI: 10.21203/rs.3.rs-678247/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have arisen that exhibit increased viral transmissibility and partial evasion of immunity induced by natural infection and vaccination. To address the specific antibody targets that were affected by recent viral variants, we generated 43 monoclonal antibodies (mAbs) from 10 convalescent donors that bound three distinct domains of the SARS-CoV-2 spike. Viral variants harboring mutations at K417, E484 and N501 could escape most of the highly potent antibodies against the receptor binding domain (RBD). Despite this, we identified 12 neutralizing mAbs against three distinct regions of the spike protein that neutralize SARS-CoV-2 and the variants of concern, including B.1.1.7 (alpha), P.1 (gamma) and B.1.617.2 (delta). Notably, antibodies targeting distinct epitopes could neutralize discrete variants, suggesting different variants may have evolved to disrupt the binding of particular neutralizing antibody classes. These results underscore that humans exposed to wildtype (WT) SARS-CoV-2 do possess neutralizing antibodies against current variants and that it is critical to induce antibodies targeting multiple distinct epitopes of the spike that can neutralize emerging variants of concern.
Collapse
|
25
|
Guthmiller JJ, Stovicek O, Wang J, Changrob S, Li L, Halfmann P, Zheng NY, Utset H, Stamper CT, Dugan HL, Miller WD, Huang M, Dai YN, Nelson CA, Hall PD, Jansen M, Shanmugarajah K, Donington JS, Krammer F, Fremont DH, Joachimiak A, Kawaoka Y, Tesic V, Madariaga ML, Wilson PC. SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike. mBio 2021; 12:e02940-20. [PMID: 33468695 PMCID: PMC7845638 DOI: 10.1128/mbio.02940-20] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/16/2020] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently causing a global pandemic. The antigen specificity of the antibody response mounted against this novel virus is not understood in detail. Here, we report that subjects with a more severe SARS-CoV-2 infection exhibit a larger antibody response against the spike and nucleocapsid protein and epitope spreading to subdominant viral antigens, such as open reading frame 8 and nonstructural proteins. Subjects with a greater antibody response mounted a larger memory B cell response against the spike, but not the nucleocapsid protein. Additionally, we revealed that antibodies against the spike are still capable of binding the D614G spike mutant and cross-react with the SARS-CoV-1 receptor binding domain. Together, this study reveals that subjects with a more severe SARS-CoV-2 infection exhibit a greater overall antibody response to the spike and nucleocapsid protein and a larger memory B cell response against the spike.IMPORTANCE With the ongoing pandemic, it is critical to understand how natural immunity against SARS-CoV-2 and COVID-19 develops. We have identified that subjects with more severe COVID-19 disease mount a more robust and neutralizing antibody response against SARS-CoV-2 spike protein. Subjects who mounted a larger response against the spike also mounted antibody responses against other viral antigens, including the nucleocapsid protein and ORF8. Additionally, this study reveals that subjects with more severe disease mount a larger memory B cell response against the spike. These data suggest that subjects with more severe COVID-19 disease are likely better protected from reinfection with SARS-CoV-2.
Collapse
Affiliation(s)
- Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Olivia Stovicek
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Jiaolong Wang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Siriruk Changrob
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Lei Li
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Henry Utset
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | | | - Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
| | - William D Miller
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
| | - Ya-Nan Dai
- Department of Pathology and Immunology and Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christopher A Nelson
- Department of Pathology and Immunology and Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Paige D Hall
- Department of Pathology and Immunology and Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Maud Jansen
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | | | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Daved H Fremont
- Department of Pathology and Immunology and Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Vera Tesic
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | | | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
| |
Collapse
|
26
|
Alzhanova D, Corcoran K, Bailey AG, Long K, Taft-Benz S, Graham RL, Broussard GS, Heise M, Neumann G, Halfmann P, Kawaoka Y, Baric RS, Damania B, Dittmer DP. Novel modulators of p53-signaling encoded by unknown genes of emerging viruses. PLoS Pathog 2021; 17:e1009033. [PMID: 33411764 PMCID: PMC7790267 DOI: 10.1371/journal.ppat.1009033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023] Open
Abstract
The p53 transcription factor plays a key role both in cancer and in the cell-intrinsic response to infections. The ORFEOME project hypothesized that novel p53-virus interactions reside in hitherto uncharacterized, unknown, or hypothetical open reading frames (orfs) of human viruses. Hence, 172 orfs of unknown function from the emerging viruses SARS-Coronavirus, MERS-Coronavirus, influenza, Ebola, Zika (ZIKV), Chikungunya and Kaposi Sarcoma-associated herpesvirus (KSHV) were de novo synthesized, validated and tested in a functional screen of p53 signaling. This screen revealed novel mechanisms of p53 virus interactions and two viral proteins KSHV orf10 and ZIKV NS2A binding to p53. Originally identified as the target of small DNA tumor viruses, these experiments reinforce the notion that all viruses, including RNA viruses, interfere with p53 functions. These results validate this resource for analogous systems biology approaches to identify functional properties of uncharacterized viral proteins, long non-coding RNAs and micro RNAs. New viruses are constantly emerging. The ORFEOME project was based on the hypothesis that every virus, regardless of its molecular makeup and biology should encode functions that intersect the p53 signaling network, since p53 guards the cell from genomic insults, of which depositing a foreign, viral nucleic acid is one. The result of the ORFEOME screen of proteins without any known function, of predicted open reading frames and of suspected non-coding RNAs is the identification of two viral proteins that interact with p53. The first one, orf10, is encoded by Kaposi Sarcoma-associated herpesvirus and the second one, NS2A, is encoded by the Zika virus.
Collapse
Affiliation(s)
- Dina Alzhanova
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kathleen Corcoran
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Aubrey G. Bailey
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kristin Long
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina, United States of America
| | - Sharon Taft-Benz
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina, United States of America
| | - Rachel L. Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, United States of America
| | - Grant S. Broussard
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Mark Heise
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina, United States of America
| | - Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ralph S. Baric
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, United States of America
| | - Blossom Damania
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Dirk P. Dittmer
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
27
|
Hou YJ, Chiba S, Halfmann P, Ehre C, Kuroda M, Dinnon KH, Leist SR, Schäfer A, Nakajima N, Takahashi K, Lee RE, Mascenik TM, Graham R, Edwards CE, Tse LV, Okuda K, Markmann AJ, Bartelt L, de Silva A, Margolis DM, Boucher RC, Randell SH, Suzuki T, Gralinski LE, Kawaoka Y, Baric RS. SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Science 2020; 370:1464-1468. [PMID: 33184236 PMCID: PMC7775736 DOI: 10.1126/science.abe8499] [Citation(s) in RCA: 630] [Impact Index Per Article: 157.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022]
Abstract
The spike aspartic acid-614 to glycine (D614G) substitution is prevalent in global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains, but its effects on viral pathogenesis and transmissibility remain unclear. We engineered a SARS-CoV-2 variant containing this substitution. The variant exhibits more efficient infection, replication, and competitive fitness in primary human airway epithelial cells but maintains similar morphology and in vitro neutralization properties, compared with the ancestral wild-type virus. Infection of human angiotensin-converting enzyme 2 (ACE2) transgenic mice and Syrian hamsters with both viruses resulted in similar viral titers in respiratory tissues and pulmonary disease. However, the D614G variant transmits significantly faster and displayed increased competitive fitness than the wild-type virus in hamsters. These data show that the D614G substitution enhances SARS-CoV-2 infectivity, competitive fitness, and transmission in primary human cells and animal models.
Collapse
Affiliation(s)
- Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shiho Chiba
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Camille Ehre
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Noriko Nakajima
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenta Takahashi
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Rhianna E Lee
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Teresa M Mascenik
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rachel Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Longping V Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenichi Okuda
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alena J Markmann
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Luther Bartelt
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aravinda de Silva
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David M Margolis
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA.
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
28
|
Abstract
Multiple cell surface molecules including TAM receptors (TYRO3, AXL, and MERTK), a family of tyrosine kinase receptors, can serve as attachment receptors for Ebola virus (EBOV) entry into cells. The interaction of these receptors with EBOV particles is believed to trigger the initial internalization events that lead to macropinocytosis. However, the details of how these interactions lead to EBOV internalization have yet to be elucidated. Here, we screened receptor tyrosine kinase (RTK) inhibitors for anti-EBOV activity by using our previously established biologically contained Ebola virus that lacks the VP30 gene (EBOVΔVP30) and identified several RTKs, including human epidermal growth factor receptor 2 (HER2), as potential targets of anti-EBOV inhibitors and as novel host factors that have a role in EBOV infection. Of these identified RTKs, it was only HER2 whose knockdown by siRNAs impaired EBOVΔVP30-induced AKT1 phosphorylation, an event that is required for AKT1 activation and subsequent macropinocytosis. Stable expression of HER2 resulted in constitutive activation of AKT1, resulting in the enhancement of EBOVΔVP30 growth, EBOV GP-mediated entry, and macropinocytosis. Moreover, we found that HER2 interacts with the TAM receptors, and in particular forms a complex with TYRO3 and EBOVΔVP30 particles on the cell surface. Interestingly, HER2 was required for EBOVΔVP30-induced TYRO3 and AKT1 activation, but the other TAM receptors (TYRO3 and MERTK) were not essential for EBOVΔVP30-induced HER2 and AKT1 activation. Our findings demonstrate that HER2 plays an important role in EBOV entry and provide novel insights for the development of therapeutics against the virus.
Collapse
Affiliation(s)
- Makoto Kuroda
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Microbiology and Immunology, Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| |
Collapse
|
29
|
Hou YJ, Chiba S, Halfmann P, Ehre C, Kuroda M, Dinnon KH, Leist SR, Schäfer A, Nakajima N, Takahashi K, Lee RE, Mascenik TM, Edwards CE, Tse LV, Boucher RC, Randell SH, Suzuki T, Gralinski LE, Kawaoka Y, Baric RS. SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. bioRxiv 2020:2020.09.28.317685. [PMID: 33024969 PMCID: PMC7536872 DOI: 10.1101/2020.09.28.317685] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The D614G substitution in the S protein is most prevalent SARS-CoV-2 strain circulating globally, but its effects in viral pathogenesis and transmission remain unclear. We engineered SARS-CoV-2 variants harboring the D614G substitution with or without nanoluciferase. The D614G variant replicates more efficiency in primary human proximal airway epithelial cells and is more fit than wildtype (WT) virus in competition studies. With similar morphology to the WT virion, the D614G virus is also more sensitive to SARS-CoV-2 neutralizing antibodies. Infection of human ACE2 transgenic mice and Syrian hamsters with the WT or D614G viruses produced similar titers in respiratory tissue and pulmonary disease. However, the D614G variant exhibited significantly faster droplet transmission between hamsters than the WT virus, early after infection. Our study demonstrated the SARS-CoV2 D614G substitution enhances infectivity, replication fitness, and early transmission.
Collapse
Affiliation(s)
- Yixuan J. Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shiho Chiba
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Camille Ehre
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Noriko Nakajima
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenta Takahashi
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Rhianna E. Lee
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Teresa M. Mascenik
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caitlin E. Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Longping V. Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard C. Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott H. Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Lisa E. Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
30
|
Guthmiller JJ, Stovicek O, Wang J, Changrob S, Li L, Halfmann P, Zheng NY, Utset H, Stamper CT, Dugan HL, Miller WD, Huang M, Dai YN, Nelson CA, Hall PD, Jansen M, Shanmugarajah K, Donington JS, Krammer F, Fremont DH, Joachimiak A, Kawaoka Y, Tesic V, Madariaga ML, Wilson PC. SARS-CoV-2 infection severity is linked to superior humoral immunity against the spike. bioRxiv 2020:2020.09.12.294066. [PMID: 32935099 PMCID: PMC7491512 DOI: 10.1101/2020.09.12.294066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently causing a global pandemic. The antigen specificity and kinetics of the antibody response mounted against this novel virus are not understood in detail. Here, we report that subjects with a more severe SARS-CoV-2 infection exhibit a larger antibody response against the spike and nucleocapsid protein and epitope spreading to subdominant viral antigens, such as open reading frame 8 and non-structural proteins. Subjects with a greater antibody response mounted a larger memory B cell response against the spike, but not the nucleocapsid protein. Additionally, we revealed that antibodies against the spike are still capable of binding the D614G spike mutant and cross-react with the SARS-CoV-1 receptor binding domain. Together, this study reveals that subjects with a more severe SARS-CoV-2 infection exhibit a greater overall antibody response to the spike and nucleocapsid protein and a larger memory B cell response against the spike.
Collapse
Affiliation(s)
- Jenna J. Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
- These authors contributed equally
| | - Olivia Stovicek
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
- These authors contributed equally
| | - Jiaolong Wang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
- These authors contributed equally
| | - Siriruk Changrob
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Lei Li
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53711
| | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Henry Utset
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | | | - Haley L. Dugan
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - William D. Miller
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Ya-Nan Dai
- Department of Pathology and Immunology and Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christopher A. Nelson
- Department of Pathology and Immunology and Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Paige D. Hall
- Department of Pathology and Immunology and Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Maud Jansen
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | | | | | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daved H. Fremont
- Department of Pathology and Immunology and Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53711
| | - Vera Tesic
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | | | - Patrick C. Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
31
|
Westmark CJ, Kiso M, Halfmann P, Westmark PR, Kawaoka Y. Repurposing Fragile X Drugs to Inhibit SARS-CoV-2 Viral Reproduction. Front Cell Dev Biol 2020; 8:856. [PMID: 32984339 PMCID: PMC7479061 DOI: 10.3389/fcell.2020.00856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic is a global health crisis that requires the application of interdisciplinary research to address numerous knowledge gaps including molecular strategies to prevent viral reproduction in affected individuals. In response to the Frontiers Research Topic, "Coronavirus disease (COVID-19): Pathophysiology, Epidemiology, Clinical Management, and Public Health Response," this Hypothesis article proposes a novel therapeutic strategy to repurpose metabotropic glutamate 5 receptor (mGluR5) inhibitors to interfere with viral hijacking of the host protein synthesis machinery. We review pertinent background on SARS-CoV-2, fragile X syndrome (FXS) and metabotropic glutamate receptor 5 (mGluR5) and provide a mechanistic-based hypothesis and preliminary data to support testing mGluR5 inhibitors in COVID-19 research.
Collapse
Affiliation(s)
- Cara J Westmark
- Department of Neurology, University of Wisconsin-Madison, Madison, WI, United States
| | - Maki Kiso
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Pamela R Westmark
- Department of Neurology, University of Wisconsin-Madison, Madison, WI, United States
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI, United States.,Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
32
|
Alfano R, Pennybaker A, Halfmann P, Huang CYH. Formulation and production of a blood-free and chemically defined virus production media for VERO cells. Biotechnol Bioeng 2020; 117:3277-3285. [PMID: 32648943 PMCID: PMC7689730 DOI: 10.1002/bit.27486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/05/2020] [Accepted: 07/07/2020] [Indexed: 11/09/2022]
Abstract
Vaccines provide effective protection against many infectious diseases as well as therapeutics for select pathologies, such as cancer. Many viral vaccines require amplification of virus in cell cultures during manufacture. Traditionally, cell cultures, such as VERO, have been used for virus production in bovine serum-containing culture media. However, due to concerns of potential adventitious agents present in fetal bovine serum (FBS), regulatory agencies suggest avoiding the use of bovine serum in vaccine production. Current serum-free media suitable for VERO-based virus production contains high concentrations of undefined plant hydrolysates. Although these media have been extensively used, the lack of chemical definition has the potential to adversely affect cell growth kinetics and subsequent virus production. As plant hydrolysates are made from plant raw materials, performance variations could be significant among different lots of production. We developed a chemically defined, serum-free medium, OptiVERO, which was optimized specifically for VERO cells. VERO cell growth kinetics were demonstrated to be equivalent to EMEM-10% FBS in this chemically defined medium while the plant hydrolysate-containing medium demonstrated a slower doubling time in both two-dimensional (2D) and 3D cultures. Virus production comparisons demonstrated that the chemically defined OptiVERO medium performed at least as good as the EMEM-10%FBS and better than the plant hydrolysate-containing media. We report the success in using recombinant proteins to replace undefined plant hydrolysates to formulate a chemically defined medium that can efficiently support VERO cell expansion and virus production.
Collapse
Affiliation(s)
- Randall Alfano
- InVitria, Junction City, Kansas.,Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado
| | | | - Peter Halfmann
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin
| | - Claire Y-H Huang
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado
| |
Collapse
|
33
|
Halfmann P, Hill-Batorski L, Kawaoka Y. The Induction of IL-1β Secretion Through the NLRP3 Inflammasome During Ebola Virus Infection. J Infect Dis 2019; 218:S504-S507. [PMID: 30060221 DOI: 10.1093/infdis/jiy433] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The inflammasome is part of the innate immune system that regulates the secretion of proinflammatory cytokines such as interleukin-1β (IL-1β). Ebola virus (EBOV) infection of monocytes and macrophages (primary target cells early during infection) leads to the production of proinflammatory cytokines; however, the mechanism behind the activation and release of these cytokines is not fully understood. Here, we demonstrate that EBOV infection leads to the activation of the NLRP3 inflammasome and the subsequent secretion of IL-1β and IL-18. This process is dependent on protease caspase-1, a component of the NLRP3 inflammasome complex, but is independent of virus replication. These findings may lead to the development of novel drugs that impede the pathogenesis of EBOV infection.
Collapse
Affiliation(s)
- Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison
| | - Lindsay Hill-Batorski
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison.,Department of Microbiology and Immunology, Division of Virology, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Japan
| |
Collapse
|
34
|
Zhong G, Fan S, Lopes TJS, Le MQ, van Bakel H, Dutta J, Smith GJD, Jayakumar J, Nguyen HLK, Hoang PVM, Halfmann P, Hatta M, Su YCF, Neumann G, Kawaoka Y. Isolation of Highly Pathogenic H5N1 Influenza Viruses in 2009-2013 in Vietnam. Front Microbiol 2019; 10:1411. [PMID: 31293548 PMCID: PMC6603144 DOI: 10.3389/fmicb.2019.01411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 06/05/2019] [Indexed: 11/13/2022] Open
Abstract
Routine surveillance and surveillance in response to influenza outbreaks in avian species in Vietnam in 2009-2013 resulted in the isolation of numerous H5N1 influenza viruses of clades 1.1.2, 2.3.2.1a, 2.3.2.1b, 2.3.2.1c, and 2.3.4.1. Consistent with other studies, we found that viruses of clade 2.3.2.1c were dominant in Vietnam in 2013 and circulated in the northern, central, and southern parts of the country. Phylogenetic analysis revealed reassortment among viruses of clades 2.3.2.1a, 2.3.2.1b, and 2.3.2.1c; in contrast, no reassortment was detected between clade 2.3.2.1 viruses and viruses of clades 1.1.2 or 2.3.4.1, respectively. Deep-sequencing of 42 of the 53 isolated H5N1 viruses revealed viral subpopulations encoding variants that may affect virulence, host range, or sensitivity to antiviral compounds; virus isolates containing these subpopulations may have a higher potential to transmit and adapt to mammals. Among the viruses sequenced, a relatively high number of non-synonymous nucleotide polymorphisms was detected in a virus isolated from a barn swallow, possibly suggesting influenza virus adaption to this host.
Collapse
Affiliation(s)
- Gongxun Zhong
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Shufang Fan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Tiago J S Lopes
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Mai Quynh Le
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jayeeta Dutta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Gavin J D Smith
- Duke-NUS Medical School, Singapore, Singapore.,Duke Global Health Institute, Duke University, Durham, NC, United States
| | | | | | | | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Masato Hatta
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| |
Collapse
|
35
|
Davis CW, Jackson KJL, McElroy AK, Halfmann P, Huang J, Chennareddy C, Piper AE, Leung Y, Albariño CG, Crozier I, Ellebedy AH, Sidney J, Sette A, Yu T, Nielsen SCA, Goff AJ, Spiropoulou CF, Saphire EO, Cavet G, Kawaoka Y, Mehta AK, Glass PJ, Boyd SD, Ahmed R. Longitudinal Analysis of the Human B Cell Response to Ebola Virus Infection. Cell 2019; 177:1566-1582.e17. [PMID: 31104840 PMCID: PMC6908968 DOI: 10.1016/j.cell.2019.04.036] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 02/11/2019] [Accepted: 04/16/2019] [Indexed: 01/12/2023]
Abstract
Ebola virus (EBOV) remains a public health threat. We performed a longitudinal study of B cell responses to EBOV in four survivors of the 2014 West African outbreak. Infection induced lasting EBOV-specific immunoglobulin G (IgG) antibodies, but their subclass composition changed over time, with IgG1 persisting, IgG3 rapidly declining, and IgG4 appearing late. Striking changes occurred in the immunoglobulin repertoire, with massive recruitment of naive B cells that subsequently underwent hypermutation. We characterized a large panel of EBOV glycoprotein-specific monoclonal antibodies (mAbs). Only a small subset of mAbs that bound glycoprotein by ELISA recognized cell-surface glycoprotein. However, this subset contained all neutralizing mAbs. Several mAbs protected against EBOV disease in animals, including one mAb that targeted an epitope under evolutionary selection during the 2014 outbreak. Convergent antibody evolution was seen across multiple donors, particularly among VH3-13 neutralizing antibodies specific for the GP1 core. Our study provides a benchmark for assessing EBOV vaccine-induced immunity. Ebola virus infection causes massive recruitment of naive B cells Virus-specific antibodies continue to class-switch and mutate for months after acute infection Protective antibodies can be neutralizing or non-neutralizing and can appear early Convergent, protective antibody rearrangements are seen in multiple donors
Collapse
Affiliation(s)
- Carl W Davis
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Katherine J L Jackson
- Department of Pathology, Stanford University, Stanford, CA, USA; Immunology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Anita K McElroy
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA; Division of Pediatric Infectious Disease, Emory University, Atlanta, GA, USA; Division of Pediatric Infectious Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI, USA
| | - Jessica Huang
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Chakravarthy Chennareddy
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Ashley E Piper
- Virology Division, United States Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, USA
| | | | - César G Albariño
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ian Crozier
- Integrated Research Facility at Fort Detrick, Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institutes, Frederick, MD, USA
| | - Ali H Ellebedy
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA; Division of Immunobiology, Department of Pathology and Immunology Washington University School of Medicine, St. Louis, MO, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA; Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | | | - Arthur J Goff
- Virology Division, United States Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Erica Ollman Saphire
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA; La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI, USA; Division of Virology, Department of Microbiology and Immunology, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Aneesh K Mehta
- Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA, USA
| | - Pamela J Glass
- Virology Division, United States Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rafi Ahmed
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA.
| |
Collapse
|
36
|
Norris MJ, Bornholdt ZA, Noda T, Abelson DM, Halfmann P, Wood M, Kawaoka Y, Saphire EO. Structural transformation begets multiple functions in the viral life cycle. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318096137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
37
|
Westhoff Smith D, Hill-Batorski L, N'jai A, Eisfeld AJ, Neumann G, Halfmann P, Kawaoka Y. Ebola Virus Stability Under Hospital and Environmental Conditions. J Infect Dis 2016; 214:S142-S144. [PMID: 27279525 DOI: 10.1093/infdis/jiw167] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The West African outbreak of Ebola virus (EBOV) is largely contained, but sporadic new cases continue to emerge. To assess the potential contribution of fomites to human infections with EBOV, we tested EBOV stability in human blood spotted onto Sierra Leonean banknotes and in syringe needles under hospital and environmental conditions. Under some of these conditions, EBOV remained infectious for >30 days, indicating that EBOV-contaminated items may pose a serious risk to humans.
Collapse
Affiliation(s)
- Danielle Westhoff Smith
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison
| | - Lindsay Hill-Batorski
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison
| | - Alhaji N'jai
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison Department of Biological Sciences, Fourah Bay College College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown
| | - Amie J Eisfeld
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison
| | - Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison
| | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison Division of Virology, Department of Microbiology and Immunology, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Japan
| |
Collapse
|
38
|
Pécheur EI, Borisevich V, Halfmann P, Morrey JD, Smee DF, Prichard M, Mire CE, Kawaoka Y, Geisbert TW, Polyak SJ. The Synthetic Antiviral Drug Arbidol Inhibits Globally Prevalent Pathogenic Viruses. J Virol 2016; 90:3086-92. [PMID: 26739045 PMCID: PMC4810626 DOI: 10.1128/jvi.02077-15] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 12/25/2015] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Arbidol (ARB) is a synthetic antiviral originally developed to combat influenza viruses. ARB is currently used clinically in several countries but not in North America. We have previously shown that ARB inhibits in vitro hepatitis C virus (HCV) by blocking HCV entry and replication. In this report, we expand the list of viruses that are inhibited by ARB and demonstrate that ARB suppresses in vitro infection of mammalian cells with Ebola virus (EBOV), Tacaribe arenavirus, and human herpesvirus 8 (HHV-8). We also confirm suppression of hepatitis B virus and poliovirus by ARB. ARB inhibited EBOV Zaire Kikwit infection when added before or at the same time as virus infection and was less effective when added 24 h after EBOV infection. Experiments with recombinant vesicular stomatitis virus (VSV) expressing the EBOV Zaire glycoprotein showed that infection was inhibited by ARB at early stages, most likely at the level of viral entry into host cells. ARB inhibited HHV-8 replication to a similar degree as cidofovir. Our data broaden the spectrum of antiviral efficacy of ARB to include globally prevalent viruses that cause significant morbidity and mortality. IMPORTANCE There are many globally prevalent viruses for which there are no licensed vaccines or antiviral medicines. Some of these viruses, such as Ebola virus or members of the arenavirus family, rapidly cause severe hemorrhagic diseases that can be fatal. Other viruses, such as hepatitis B virus or human herpesvirus 8 (HHV-8), establish persistent infections that cause chronic illnesses, including cancer. Thus, finding an affordable, effective, and safe drug that blocks many viruses remains an unmet medical need. The antiviral drug arbidol (ARB), already in clinical use in several countries as an anti-influenza treatment, has been previously shown to suppress the growth of many viruses. In this report, we expand the list of viruses that are blocked by ARB in a laboratory setting to include Ebola virus, Tacaribe arenavirus, and HHV-8, and we propose ARB as a broad-spectrum antiviral drug that may be useful against hemorrhagic viruses.
Collapse
Affiliation(s)
| | - Viktoriya Borisevich
- Galveston National Laboratory, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Peter Halfmann
- Department of Pathobiological Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - John D Morrey
- Institute for Antiviral Research, Utah State University, Logan, Utah, USA
| | - Donald F Smee
- Institute for Antiviral Research, Utah State University, Logan, Utah, USA
| | - Mark Prichard
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, Alabama, USA
| | - Chad E Mire
- Galveston National Laboratory, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin, Madison, Wisconsin, USA International Research Center for Infectious Diseases and Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Thomas W Geisbert
- Galveston National Laboratory, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Stephen J Polyak
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA Department of Global Health, University of Washington, Seattle, Washington, USA
| |
Collapse
|
39
|
Hill-Batorski L, Halfmann P, Marzi A, Lopes TJS, Neumann G, Feldmann H, Kawaoka Y. Loss of Interleukin 1 Receptor Antagonist Enhances Susceptibility to Ebola Virus Infection. J Infect Dis 2015. [PMID: 26209680 DOI: 10.1093/infdis/jiv335] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The current outbreak of Ebola virus (EBOV) infection in West Africa is unprecedented, with nearly 26 000 confirmed cases and >10 000 deaths. Comprehensive data on the pathogenesis of EBOV infection are lacking; however, recent studies suggested that fatal EBOV infections are characterized by dysregulation of the innate immune response and a subsequent cytokine storm. Specifically, several studies suggested that hypersecretion of interleukin 1 receptor antagonist (IL-1Ra) correlates with lethal EBOV infections. To examine the significance of IL-1Ra in EBOV infections, we infected mice that lack the gene encoding IL-1Ra, Il1rn (IL-1RN-KO), and mice with wild-type Il1rn (IL-1RN-WT) with a mouse-adapted EBOV (MA-EBOV). Infected IL-1RN-KO mice lost more weight and had a lower survival rate than IL-1RN-WT mice infected with MA-EBOV. In addition, IL-1RN-KO mice infected with wild-type EBOV, which does not cause lethal infection in adult immunocompetent mice, such as C57BL/6 mice, experienced greater weight loss than IL-1RN-WT mice infected with wild-type EBOV. Further studies revealed that the levels of 6 cytokines in spleens-IL-1α, IL-1β, interleukin 12p40, interleukin 17, granulocyte colony-stimulating factor, and regulated on activation, normal T-cell expressed and secreted-were significantly different between IL-1RN-KO mice and IL-1RN-WT mice infected with MA-EBOV. Collectively, our data suggest that IL-1Ra may have a protective effect upon EBOV infection, likely by damping an overactive proinflammatory immune response.
Collapse
Affiliation(s)
- Lindsay Hill-Batorski
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison
| | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Tiago J S Lopes
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison Division of Virology, Department of Microbiology and Immunology, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo
| | - Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison Division of Virology, Department of Microbiology and Immunology, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo ERATO Infection-Induced Host Responses Project, Japan Science and Technology Agency, Saitama, Japan
| |
Collapse
|
40
|
Chin AWH, Perera RAPM, Guan Y, Halfmann P, Kawaoka Y, Peiris M, Poon LLM. Pseudoparticle neutralization assay for detecting ebola- neutralizing antibodies in biosafety level 2 settings. Clin Chem 2015; 61:885-6. [PMID: 25829407 PMCID: PMC7108194 DOI: 10.1373/clinchem.2015.238204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alex W H Chin
- Centre of Influenza Research School of Public Health and
| | | | - Yi Guan
- Centre of Influenza Research School of Public Health and
| | - Peter Halfmann
- Department of Pathobiological Sciences School of Veterinary Medicine University of Wisconsin Madison, WI
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences School of Veterinary Medicine University of Wisconsin Madison, WI Division of Virology Department of Microbiology and Immunology Institute of Medical Science University of Tokyo, Tokyo, Japan
| | - Malik Peiris
- Centre of Influenza Research School of Public Health and HKU-Pasteur Pole The University of Hong Kong Hong Kong, China
| | - Leo L M Poon
- Centre of Influenza Research School of Public Health and
| |
Collapse
|
41
|
Marzi A, Halfmann P, Hill-Batorski L, Feldmann F, Shupert WL, Neumann G, Feldmann H, Kawaoka Y. Vaccines. An Ebola whole-virus vaccine is protective in nonhuman primates. Science 2015; 348:439-42. [PMID: 25814063 DOI: 10.1126/science.aaa4919] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 03/13/2015] [Indexed: 12/25/2022]
Abstract
Zaire ebolavirus is the causative agent of the current outbreak of hemorrhagic fever disease in West Africa. Previously, we showed that a whole Ebola virus (EBOV) vaccine based on a replication-defective EBOV (EBOVΔVP30) protects immunized mice and guinea pigs against lethal challenge with rodent-adapted EBOV. Here, we demonstrate that EBOVΔVP30 protects nonhuman primates against lethal infection with EBOV. Although EBOVΔVP30 is replication-incompetent, we additionally inactivated the vaccine with hydrogen peroxide; the chemically inactivated vaccine remained antigenic and protective in nonhuman primates. EBOVΔVP30 thus represents a safe, efficacious, whole-EBOV vaccine candidate that differs from other EBOV vaccine platforms in that it presents all viral proteins and the viral RNA to the host immune system, which might contribute to protective immune responses.
Collapse
Affiliation(s)
- Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Lindsay Hill-Batorski
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - W Lesley Shupert
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA. Department of Microbiology and Immunology, Division of Virology, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo. ERATO Infection-Induced Host Responses Project, Japan Science and Technology Agency, Saitama, Japan.
| |
Collapse
|
42
|
Halfmann P, Neumann G, Feldmann H, Kawaoka Y. Ebola Conquers West Africa - More to Come? EBioMedicine 2014; 1:2-3. [PMID: 26137502 PMCID: PMC4457411 DOI: 10.1016/j.ebiom.2014.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin, Madison, WI 53711, United States
| | - Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin, Madison, WI 53711, United States
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT 59840, United States
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin, Madison, WI 53711, United States ; Department of Microbiology and Immunology, Division of Virology, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| |
Collapse
|
43
|
Saphire EO, Bornholdt ZA, Abelson DM, Halfmann P, Noda T, Wood M, Kawaoka Y. Structural Rearrangement of the Ebola Virus VP40 Protein Begets Multiple Functions in the Virus Life Cycle. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
44
|
Bornholdt ZA, Noda T, Abelson DM, Halfmann P, Wood MR, Kawaoka Y, Saphire EO. Structural rearrangement of ebola virus VP40 begets multiple functions in the virus life cycle. Cell 2013; 154:763-74. [PMID: 23953110 DOI: 10.1016/j.cell.2013.07.015] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 05/13/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
Proteins, particularly viral proteins, can be multifunctional, but the mechanisms behind multifunctionality are not fully understood. Here, we illustrate through multiple crystal structures, biochemistry, and cellular microscopy that VP40 rearranges into different structures, each with a distinct function required for the ebolavirus life cycle. A butterfly-shaped VP40 dimer traffics to the cellular membrane. Once there, electrostatic interactions trigger rearrangement of the polypeptide into a linear hexamer. These hexamers construct a multilayered, filamentous matrix structure that is critical for budding and resembles tomograms of authentic virions. A third structure of VP40, formed by a different rearrangement, is not involved in virus assembly but instead uniquely binds RNA to regulate viral transcription inside infected cells. These results provide a functional model for ebolavirus matrix assembly and the other roles of VP40 in the virus life cycle and demonstrate how a single wild-type, unmodified polypeptide can assemble into different structures for different functions.
Collapse
Affiliation(s)
- Zachary A Bornholdt
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | | | | | | | | |
Collapse
|
45
|
Nanbo A, Watanabe S, Halfmann P, Kawaoka Y. The spatio-temporal distribution dynamics of Ebola virus proteins and RNA in infected cells. Sci Rep 2013; 3:1206. [PMID: 23383374 PMCID: PMC3563031 DOI: 10.1038/srep01206] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 10/31/2012] [Indexed: 12/16/2022] Open
Abstract
Here, we used a biologically contained Ebola virus system to characterize the spatio-temporal distribution of Ebola virus proteins and RNA during virus replication. We found that viral nucleoprotein (NP), the polymerase cofactor VP35, the major matrix protein VP40, the transcription activator VP30, and the minor matrix protein VP24 were distributed in cytoplasmic inclusions. These inclusions enlarged near the nucleus, became smaller pieces, and subsequently localized near the plasma membrane. GP was distributed in the cytoplasm and transported to the plasma membrane independent of the other viral proteins. We also found that viral RNA synthesis occurred within the inclusions. Newly synthesized negative-sense RNA was distributed inside the inclusions, whereas positive-sense RNA was distributed both inside and outside. These findings provide useful insights into Ebola virus replication.
Collapse
Affiliation(s)
- Asuka Nanbo
- Influenza Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711, USA.
| | | | | | | |
Collapse
|
46
|
Iwasa A, Halfmann P, Noda T, Oyama M, Kozuka-Hata H, Watanabe S, Shimojima M, Watanabe T, Kawaoka Y. Contribution of Sec61α to the life cycle of Ebola virus. J Infect Dis 2011; 204 Suppl 3:S919-26. [PMID: 21987770 DOI: 10.1093/infdis/jir324] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Similar to other viruses, the viral proteins of Ebola virus (EBOV) interact with a variety of host proteins for its replication. Of the 7 structural proteins encoded in the EBOV genome, VP24 is the smallest and is multifunctional. METHODS To identify host factors that interact with VP24 and are required for EBOV replication, we transfected 293 cells with plasmid expressing FLAG- and HA-tagged VP24, immunoprecipitated the host proteins that bound to VP24, and analyzed the immunoprecipitants with use of mass spectrometry. RESULTS Of the 68 candidate host proteins identified, we selected Sec61α because of its similar intracellular localization to that of VP24 (ie, perinuclear region), its involvement in various biological functions, and its roles in pathogenesis, such as type 2 diabetes and hepatosteatosis, and investigated its possible role in the EBOV life cycle. Our results suggest that Sec61α is not involved in EBOV entry, interferon antagonism by VP24, nucleocapsid formation, or budding. However, Sec61α colocalized with VP24 contributed to the ability of VP24 to inhibit EBOV genome transcription and reduced the polymerase activity of EBOV. CONCLUSIONS The present study indicates that Sec61α is a host protein involved in EBOV replication, specifically in EBOV genome transcription and replication.
Collapse
Affiliation(s)
- Ayaka Iwasa
- Division of Virology, Department of Microbiology and Immunology, University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Halfmann P, Neumann G, Kawaoka Y. The Ebolavirus VP24 protein blocks phosphorylation of p38 mitogen-activated protein kinase. J Infect Dis 2011; 204 Suppl 3:S953-6. [PMID: 21987775 DOI: 10.1093/infdis/jir325] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Type I interferon (IFN) signaling is mediated through several signaling pathways, including the Janus kinase and signal transducer and activator (JAK-STAT) and p38 mitogen-activated protein (MAP) kinase pathways. The VP24 protein of Ebolavirus is an IFN antagonist, blocking type I IFN signaling through the JAK-STAT pathway. Here, we show that, in 293 cells, VP24 also interferes with the p38 MAP kinase pathway by blocking IFN-β-stimulated phosphorylation of p38-α. Similar inhibition was not observed in HeLa cells, suggesting cell type-specific differences in signal transduction.
Collapse
Affiliation(s)
- Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, WI, USA
| | | | | |
Collapse
|
48
|
Dias JM, Kuehne AI, Abelson DM, Bale S, Wong AC, Halfmann P, Muhammad MA, Fusco ML, Zak SE, Kang E, Kawaoka Y, Chandran K, Dye JM, Saphire EO. A shared structural solution for neutralizing ebolaviruses. Nat Struct Mol Biol 2011; 18:1424-7. [PMID: 22101933 PMCID: PMC3230659 DOI: 10.1038/nsmb.2150] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 09/06/2011] [Indexed: 11/09/2022]
Abstract
Sudan virus (genus Ebolavirus) is lethal, yet no monoclonal antibody is known to neutralize it. We here describe antibody 16F6 that neutralizes Sudan virus and present its structure bound to the trimeric viral glycoprotein. Unexpectedly, the 16F6 epitope overlaps that of KZ52, the only other antibody against the GP(1,2) core to be visualized to date. Furthermore, both antibodies against this crucial epitope bridging GP1-GP2 neutralize at a post-internalization step--probably fusion.
Collapse
Affiliation(s)
- João M Dias
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Nanbo A, Imai M, Watanabe S, Noda T, Takahashi K, Neumann G, Halfmann P, Kawaoka Y. Ebolavirus is internalized into host cells via macropinocytosis in a viral glycoprotein-dependent manner. PLoS Pathog 2010; 6:e1001121. [PMID: 20886108 PMCID: PMC2944813 DOI: 10.1371/journal.ppat.1001121] [Citation(s) in RCA: 325] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 08/25/2010] [Indexed: 12/12/2022] Open
Abstract
Ebolavirus (EBOV) is an enveloped, single-stranded, negative-sense RNA virus that causes severe hemorrhagic fever with mortality rates of up to 90% in humans and nonhuman primates. Previous studies suggest roles for clathrin- or caveolae-mediated endocytosis in EBOV entry; however, ebolavirus virions are long, filamentous particles that are larger than the plasma membrane invaginations that characterize clathrin- or caveolae-mediated endocytosis. The mechanism of EBOV entry remains, therefore, poorly understood. To better understand Ebolavirus entry, we carried out internalization studies with fluorescently labeled, biologically contained Ebolavirus and Ebolavirus-like particles (Ebola VLPs), both of which resemble authentic Ebolavirus in their morphology. We examined the mechanism of Ebolavirus internalization by real-time analysis of these fluorescently labeled Ebolavirus particles and found that their internalization was independent of clathrin- or caveolae-mediated endocytosis, but that they co-localized with sorting nexin (SNX) 5, a marker of macropinocytosis-specific endosomes (macropinosomes). Moreover, the internalization of Ebolavirus virions accelerated the uptake of a macropinocytosis-specific cargo, was associated with plasma membrane ruffling, and was dependent on cellular GTPases and kinases involved in macropinocytosis. A pseudotyped vesicular stomatitis virus possessing the Ebolavirus glycoprotein (GP) also co-localized with SNX5 and its internalization and infectivity were affected by macropinocytosis inhibitors. Taken together, our data suggest that Ebolavirus is internalized into cells by stimulating macropinocytosis in a GP-dependent manner. These findings provide new insights into the lifecycle of Ebolavirus and may aid in the development of therapeutics for Ebolavirus infection. Ebolavirus (EBOV) is an enveloped, single-stranded, negative-sense RNA virus that causes severe hemorrhagic fever with high mortality rates in humans and nonhuman primates. Previous studies suggest roles for clathrin- or caveolae-mediated endocytosis in EBOV entry; however, questions remain regarding the mechanism of EBOV entry. Here, we demonstrate that internalization of EBOV particles is independent of clathrin- or caveolae-mediated endocytosis. Specifically, we show that internalized EBOV particles co-localize with macropinocytosis-specific endosomes (macropinosomes) and that their entry is negatively affected by treatment with macropinocytosis inhibitors. Moreover, the internalization of Ebola virions accelerated the uptake of a macropinocytosis-specific cargo, was associated with plasma membrane ruffling, and was dependent on cellular GTPases and kinases involved in macropinocytosis. We further demonstrate that a pseudotyped vesicular stomatitis virus possessing the EBOV glycoprotein (GP) also co-localizes with macropinosomes and its internalization is similarly affected by macropinocytosis inhibitors. Our results indicate that EBOV uptake into cells involves the macropinocytic pathway and is GP-dependent. These findings provide new insights into the lifecycle of EBOV and may aid in the development of therapeutics for EBOV infection.
Collapse
Affiliation(s)
- Asuka Nanbo
- Influenza Research Institute, Department of Pathological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Noda T, Halfmann P, Sagara H, Kawaoka Y. Regions in Ebola virus VP24 that are important for nucleocapsid formation. J Infect Dis 2008; 196 Suppl 2:S247-50. [PMID: 17940956 DOI: 10.1086/520596] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Ebola virus (EBOV) VP24, together with nucleoprotein and VP35, is an essential component of viral RNA-protein complexes called "nucleocapsids." In this study, using a series of deletion mutants of VP24, we identified regions within VP24 that are important for the formation of nucleocapsid-like structures and determined that both termini of VP24 are essential for nucleocapsid formation. This finding advances our knowledge of both EBOV morphogenesis and the nature of VP24 molecules in nucleocapsid formation, which will be useful for the development of antiviral compounds.
Collapse
Affiliation(s)
- Takeshi Noda
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan.
| | | | | | | |
Collapse
|