[Monkeypox] Rapid Research Response
Lead Research Organisation:
University of Cambridge
Department Name: Cambridge Institute for Medical Research
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The 200 kb MPXV genome is a challenging sequencing target due to repeated sequences near each genomic terminus and low GC (33%) content. A fast, reliable and low-cost method will be developed that can accurately reconstruct the genome for evolutionary analysis, genomic epidemiology and functional character-isation.
A panel of cell lines from a range of rodent and livestock species available at Pirbright will be used to examine the host range of MPXV. Virus growth in cell culture will be measured using classical methods and live-cell analysis systems.
We will determine MPXV evolution of tropism and hIFN-I antagonism, to predict virus human-to-human transmission.
We will evaluate the long-term immunity induced by MPXV infection in humans and define differences between vaccine-induced responses: immunodominance pattern, functional immunophenotype and if T cell responses to MPXV viral immediate early proteins exhibit better viral control than other specificities. Also, associations with antibody responses and clinical outcome will be evaluated.
We will establish and optimise antiviral screening pipelines to assess the antiviral efficacy of tecovirimat and brincidofovir, drugs with known activity against orthopoxviruses. We assess 26 FDA-approved drugs and a novel cyclosporine A derivative that inhibit VACV in vitro. Also, current MPXV isolates will be tested in cell culture for the rapid testing of circulating strains of MPXV for tecovirimat-resistance.
We will develop two rapid point of care diagnostic tests. Lateral flow Assay (LFA). An orthopoxvirus (OPV) LFA has been developed at Dstl, comprising 4 Mabs all reactive with old world OPVs. Making use of novel bead types we will provide data packs to enable rapid progress through regulatory pathways for licensure.
Loop-mediated isothermal amplification (LAMP)-based assay. LAMP is a rapidly maturing technology providing PCR levels of sensitivity and specificity without the need for thermal cycling.
A panel of cell lines from a range of rodent and livestock species available at Pirbright will be used to examine the host range of MPXV. Virus growth in cell culture will be measured using classical methods and live-cell analysis systems.
We will determine MPXV evolution of tropism and hIFN-I antagonism, to predict virus human-to-human transmission.
We will evaluate the long-term immunity induced by MPXV infection in humans and define differences between vaccine-induced responses: immunodominance pattern, functional immunophenotype and if T cell responses to MPXV viral immediate early proteins exhibit better viral control than other specificities. Also, associations with antibody responses and clinical outcome will be evaluated.
We will establish and optimise antiviral screening pipelines to assess the antiviral efficacy of tecovirimat and brincidofovir, drugs with known activity against orthopoxviruses. We assess 26 FDA-approved drugs and a novel cyclosporine A derivative that inhibit VACV in vitro. Also, current MPXV isolates will be tested in cell culture for the rapid testing of circulating strains of MPXV for tecovirimat-resistance.
We will develop two rapid point of care diagnostic tests. Lateral flow Assay (LFA). An orthopoxvirus (OPV) LFA has been developed at Dstl, comprising 4 Mabs all reactive with old world OPVs. Making use of novel bead types we will provide data packs to enable rapid progress through regulatory pathways for licensure.
Loop-mediated isothermal amplification (LAMP)-based assay. LAMP is a rapidly maturing technology providing PCR levels of sensitivity and specificity without the need for thermal cycling.
Organisations
- University of Cambridge (Lead Research Organisation)
- Defence Science & Technology Laboratory (DSTL) (Collaboration)
- UK Health Security Agency (Collaboration)
- Guy's and St Thomas' NHS Foundation Trust (Collaboration)
- University of Surrey (Collaboration)
- THE PIRBRIGHT INSTITUTE (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- University of Oxford (Collaboration)
- UNIVERSITY OF BIRMINGHAM (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- University of Glasgow (Collaboration)
- Animal and Plant Health Agency (Collaboration)
Publications
Albarnaz JD
(2023)
Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection.
in Nature communications
Goodrum F
(2023)
Virology under the Microscope-a Call for Rational Discourse.
in mBio
Goodrum F
(2023)
Virology under the Microscope-a Call for Rational Discourse.
in mSphere
Goodrum F
(2023)
Virology under the Microscope-a Call for Rational Discourse.
in mSphere
| Description | There are two outputs from this award; one published, and the other pending publication. For the published output: Modified vaccinia Ankara (MVA) immunisation is being deployed to curb the current outbreak of mpox in multiple countries. Originally authorized for vaccination against smallpox, MVA is a vaccinia virus (VACV) that does not replicate in human cells or cause serious adverse events. Here, we conducted a highly multiplexed proteomic analysis to quantify >9,000 cellular proteins and ~80% of viral proteins at five time points throughout MVA infection of human cells. >690 human proteins were down-regulated >2-fold by MVA, revealing a substantial remodelling of the host proteome. >25% of these MVA targets, including multiple components of the nuclear pore complex, were not shared with VACV-Western Reserve, which is derived from a first generation smallpox vaccine associated with serious adverse events. Using pharmacological inhibition of viral DNA replication and heat-inactivated virions, we discovered that post-replicative gene expression is necessary for the downregulation of nucleoporins and for elements of MVA antagonism of innate immune sensing. Furthermore, viral suppression of effectors of the interferon response such as ISG20 potentiated virus gene expression. Proteomic changes specific to MVA infection of macrophages indicated extensive modulation of mediators of the inflammatory response. MVA-induced inflammasome activation and caspase-1-mediated pyroptosis were confirmed experimentally. Our approach thus provided the first global view of the impact of MVA infection on the host proteome, offered insights into how MVA interacts with the antiviral defences and identified cellular mechanisms that may underpin the abortive infection of human cells. These discoveries will prove vital to the rational design of future generations of vaccines. For the unpublished output: we have conducted a similar comprehensive proteomic / transcriptomic analysis of infection with monkeypox virus (MPXV). This has revealed key proteins that the virus targets for destruction, and has additionally analysed the individual effects of ~50% of all MPXV proteins on the host. Publication is pending. |
| Exploitation Route | In addition to researchers interested in virology and immunology, our data will be of broad interest to laboratories studying elements of basic cell biology (for example nucleoporin biology). Virologists will derive clear, substantial benefit from these studies, particularly because of our comprehensive databases published not only as part of this award, but on other poxviruses (e.g. vaccinia virus), and other viruses (e.g. various herpesviruses). Significant benefit can be gained by learning about what diverse viruses commonly do in order to understand critical, targetable cellular processes. It is a characteristic of our proteomic and transcriptomic studies that more hypotheses are generated than can be tested in any one grant award, and I anticipate that the resources generated will be of broad benefit in hypothesis generation about cellular manipulation by poxviruses specifically, and intracellular pathogens more generally. Additionally, plasmids and cell lines individually expressing each mpox protein have been generated, which I have already started sharing upon request. There is a clear potential for significant health impact, in particular with regards (a) to new vaccines from the information generated about the MVA vaccine and (b) with regards to new therapeutics for mpox, particularly with regard to inhibitors of critical interactions between certain viral factors and their cellular targets. |
| Sectors | Healthcare Pharmaceuticals and Medical Biotechnology |
| Title | Quantitative temporal proteomic analysis of modified vaccinia Ankara, a mpox vaccine |
| Description | Modified vaccinia Ankara (MVA) immunisation is being deployed to curb the current outbreak of mpox in multiple countries1. Originally authorized for vaccination against smallpox, MVA is a vaccinia virus (VACV) strain that does not replicate in human cells or cause serious adverse events. Here, we conducted a highly multiplexed proteomic analysis2 to quantify >9,000 cellular proteins and ~80% of viral proteins at five time points throughout MVA infection of human cells3. 690 human proteins were down-regulated >2-fold by MVA, revealing a substantial remodelling of the host proteome. >25% of these MVA targets, including multiple components of the nuclear pore complex (NPC), were not shared with VACV-Western Reserve4, which is derived from a first generation smallpox vaccine associated with serious adverse events. Using pharmacological inhibition of viral DNA replication and heat-inactivated virions, we discovered that post-replicative gene expression is necessary for the downregulation of NPC proteins and for elements of MVA antagonism of innate immune sensing. Our approach thus provides the first global view of the impact of MVA infection on the host proteome, offers insights into how MVA interacts with the antiviral defences and identifies cellular mechanisms that may underpin the abortive infection of human cells. These discoveries will prove vital to the rational design of future generations of vaccines. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | In addition to researchers interested in virology and immunology, our data will be of broad interest to laboratories studying elements of basic cell biology (for example nucleoporin biology). Virologists will derive clear, substantial benefit from these studies. Significant benefit can be gained by learning about what diverse viruses commonly do in order to understand critical, targetable cellular processes. It is a characteristic of our proteomic and transcriptomic studies that more hypotheses are generated than can be tested in any one grant award, and I anticipate that the resources generated will be of broad benefit in hypothesis generation about cellular manipulation by poxviruses specifically, and intracellular pathogens more generally. There is a clear potential for significant health impact, in particular with regards to new vaccines from the information generated about the MVA vaccine. |
| URL | https://www.ebi.ac.uk/pride/archive/projects/PXD039034 |
| Description | Monkeypox rapid research response |
| Organisation | Animal and Plant Health Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Part of mpox consortium - our Workpackage is part of the UKRI consortium funding. We are investigating particular proteomic aspects of mpox infection (specifically, interactions of viral proteins and host targets of the virus). |
| Collaborator Contribution | Consortium systematically investigating multiple different aspects of mpox. We gain access to data via regular meetings, access to generation of samples (Pirbright) and access to analysis (Edinburgh, RNAseq). |
| Impact | Nat Commun. 2023 Dec 8;14(1):8134. doi: 10.1038/s41467-023-43299-8. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection Jonas D Albarnaz # 1 2 3, Joanne Kite # 4 5, Marisa Oliveira # 4 5, Hanqi Li 4 5, Ying Di 4 5, Maria H Christensen 6, Joao A Paulo 7, Robin Antrobus 4 5, Steven P Gygi 7, Florian I Schmidt 6, Edward L Huttlin 7, Geoffrey L Smith 8 9, Michael P Weekes 10 11 PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8 |
| Start Year | 2022 |
| Description | Monkeypox rapid research response |
| Organisation | Defence Science & Technology Laboratory (DSTL) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Part of mpox consortium - our Workpackage is part of the UKRI consortium funding. We are investigating particular proteomic aspects of mpox infection (specifically, interactions of viral proteins and host targets of the virus). |
| Collaborator Contribution | Consortium systematically investigating multiple different aspects of mpox. We gain access to data via regular meetings, access to generation of samples (Pirbright) and access to analysis (Edinburgh, RNAseq). |
| Impact | Nat Commun. 2023 Dec 8;14(1):8134. doi: 10.1038/s41467-023-43299-8. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection Jonas D Albarnaz # 1 2 3, Joanne Kite # 4 5, Marisa Oliveira # 4 5, Hanqi Li 4 5, Ying Di 4 5, Maria H Christensen 6, Joao A Paulo 7, Robin Antrobus 4 5, Steven P Gygi 7, Florian I Schmidt 6, Edward L Huttlin 7, Geoffrey L Smith 8 9, Michael P Weekes 10 11 PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8 |
| Start Year | 2022 |
| Description | Monkeypox rapid research response |
| Organisation | Guy's and St Thomas' NHS Foundation Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Part of mpox consortium - our Workpackage is part of the UKRI consortium funding. We are investigating particular proteomic aspects of mpox infection (specifically, interactions of viral proteins and host targets of the virus). |
| Collaborator Contribution | Consortium systematically investigating multiple different aspects of mpox. We gain access to data via regular meetings, access to generation of samples (Pirbright) and access to analysis (Edinburgh, RNAseq). |
| Impact | Nat Commun. 2023 Dec 8;14(1):8134. doi: 10.1038/s41467-023-43299-8. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection Jonas D Albarnaz # 1 2 3, Joanne Kite # 4 5, Marisa Oliveira # 4 5, Hanqi Li 4 5, Ying Di 4 5, Maria H Christensen 6, Joao A Paulo 7, Robin Antrobus 4 5, Steven P Gygi 7, Florian I Schmidt 6, Edward L Huttlin 7, Geoffrey L Smith 8 9, Michael P Weekes 10 11 PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8 |
| Start Year | 2022 |
| Description | Monkeypox rapid research response |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Part of mpox consortium - our Workpackage is part of the UKRI consortium funding. We are investigating particular proteomic aspects of mpox infection (specifically, interactions of viral proteins and host targets of the virus). |
| Collaborator Contribution | Consortium systematically investigating multiple different aspects of mpox. We gain access to data via regular meetings, access to generation of samples (Pirbright) and access to analysis (Edinburgh, RNAseq). |
| Impact | Nat Commun. 2023 Dec 8;14(1):8134. doi: 10.1038/s41467-023-43299-8. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection Jonas D Albarnaz # 1 2 3, Joanne Kite # 4 5, Marisa Oliveira # 4 5, Hanqi Li 4 5, Ying Di 4 5, Maria H Christensen 6, Joao A Paulo 7, Robin Antrobus 4 5, Steven P Gygi 7, Florian I Schmidt 6, Edward L Huttlin 7, Geoffrey L Smith 8 9, Michael P Weekes 10 11 PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8 |
| Start Year | 2022 |
| Description | Monkeypox rapid research response |
| Organisation | The Pirbright Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Part of mpox consortium - our Workpackage is part of the UKRI consortium funding. We are investigating particular proteomic aspects of mpox infection (specifically, interactions of viral proteins and host targets of the virus). |
| Collaborator Contribution | Consortium systematically investigating multiple different aspects of mpox. We gain access to data via regular meetings, access to generation of samples (Pirbright) and access to analysis (Edinburgh, RNAseq). |
| Impact | Nat Commun. 2023 Dec 8;14(1):8134. doi: 10.1038/s41467-023-43299-8. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection Jonas D Albarnaz # 1 2 3, Joanne Kite # 4 5, Marisa Oliveira # 4 5, Hanqi Li 4 5, Ying Di 4 5, Maria H Christensen 6, Joao A Paulo 7, Robin Antrobus 4 5, Steven P Gygi 7, Florian I Schmidt 6, Edward L Huttlin 7, Geoffrey L Smith 8 9, Michael P Weekes 10 11 PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8 |
| Start Year | 2022 |
| Description | Monkeypox rapid research response |
| Organisation | UK Health Security Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Part of mpox consortium - our Workpackage is part of the UKRI consortium funding. We are investigating particular proteomic aspects of mpox infection (specifically, interactions of viral proteins and host targets of the virus). |
| Collaborator Contribution | Consortium systematically investigating multiple different aspects of mpox. We gain access to data via regular meetings, access to generation of samples (Pirbright) and access to analysis (Edinburgh, RNAseq). |
| Impact | Nat Commun. 2023 Dec 8;14(1):8134. doi: 10.1038/s41467-023-43299-8. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection Jonas D Albarnaz # 1 2 3, Joanne Kite # 4 5, Marisa Oliveira # 4 5, Hanqi Li 4 5, Ying Di 4 5, Maria H Christensen 6, Joao A Paulo 7, Robin Antrobus 4 5, Steven P Gygi 7, Florian I Schmidt 6, Edward L Huttlin 7, Geoffrey L Smith 8 9, Michael P Weekes 10 11 PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8 |
| Start Year | 2022 |
| Description | Monkeypox rapid research response |
| Organisation | University of Birmingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Part of mpox consortium - our Workpackage is part of the UKRI consortium funding. We are investigating particular proteomic aspects of mpox infection (specifically, interactions of viral proteins and host targets of the virus). |
| Collaborator Contribution | Consortium systematically investigating multiple different aspects of mpox. We gain access to data via regular meetings, access to generation of samples (Pirbright) and access to analysis (Edinburgh, RNAseq). |
| Impact | Nat Commun. 2023 Dec 8;14(1):8134. doi: 10.1038/s41467-023-43299-8. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection Jonas D Albarnaz # 1 2 3, Joanne Kite # 4 5, Marisa Oliveira # 4 5, Hanqi Li 4 5, Ying Di 4 5, Maria H Christensen 6, Joao A Paulo 7, Robin Antrobus 4 5, Steven P Gygi 7, Florian I Schmidt 6, Edward L Huttlin 7, Geoffrey L Smith 8 9, Michael P Weekes 10 11 PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8 |
| Start Year | 2022 |
| Description | Monkeypox rapid research response |
| Organisation | University of Edinburgh |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Part of mpox consortium - our Workpackage is part of the UKRI consortium funding. We are investigating particular proteomic aspects of mpox infection (specifically, interactions of viral proteins and host targets of the virus). |
| Collaborator Contribution | Consortium systematically investigating multiple different aspects of mpox. We gain access to data via regular meetings, access to generation of samples (Pirbright) and access to analysis (Edinburgh, RNAseq). |
| Impact | Nat Commun. 2023 Dec 8;14(1):8134. doi: 10.1038/s41467-023-43299-8. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection Jonas D Albarnaz # 1 2 3, Joanne Kite # 4 5, Marisa Oliveira # 4 5, Hanqi Li 4 5, Ying Di 4 5, Maria H Christensen 6, Joao A Paulo 7, Robin Antrobus 4 5, Steven P Gygi 7, Florian I Schmidt 6, Edward L Huttlin 7, Geoffrey L Smith 8 9, Michael P Weekes 10 11 PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8 |
| Start Year | 2022 |
| Description | Monkeypox rapid research response |
| Organisation | University of Glasgow |
| Department | MRC - University of Glasgow Centre for Virus Research |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Part of mpox consortium - our Workpackage is part of the UKRI consortium funding. We are investigating particular proteomic aspects of mpox infection (specifically, interactions of viral proteins and host targets of the virus). |
| Collaborator Contribution | Consortium systematically investigating multiple different aspects of mpox. We gain access to data via regular meetings, access to generation of samples (Pirbright) and access to analysis (Edinburgh, RNAseq). |
| Impact | Nat Commun. 2023 Dec 8;14(1):8134. doi: 10.1038/s41467-023-43299-8. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection Jonas D Albarnaz # 1 2 3, Joanne Kite # 4 5, Marisa Oliveira # 4 5, Hanqi Li 4 5, Ying Di 4 5, Maria H Christensen 6, Joao A Paulo 7, Robin Antrobus 4 5, Steven P Gygi 7, Florian I Schmidt 6, Edward L Huttlin 7, Geoffrey L Smith 8 9, Michael P Weekes 10 11 PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8 |
| Start Year | 2022 |
| Description | Monkeypox rapid research response |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Part of mpox consortium - our Workpackage is part of the UKRI consortium funding. We are investigating particular proteomic aspects of mpox infection (specifically, interactions of viral proteins and host targets of the virus). |
| Collaborator Contribution | Consortium systematically investigating multiple different aspects of mpox. We gain access to data via regular meetings, access to generation of samples (Pirbright) and access to analysis (Edinburgh, RNAseq). |
| Impact | Nat Commun. 2023 Dec 8;14(1):8134. doi: 10.1038/s41467-023-43299-8. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection Jonas D Albarnaz # 1 2 3, Joanne Kite # 4 5, Marisa Oliveira # 4 5, Hanqi Li 4 5, Ying Di 4 5, Maria H Christensen 6, Joao A Paulo 7, Robin Antrobus 4 5, Steven P Gygi 7, Florian I Schmidt 6, Edward L Huttlin 7, Geoffrey L Smith 8 9, Michael P Weekes 10 11 PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8 |
| Start Year | 2022 |
| Description | Monkeypox rapid research response |
| Organisation | University of Surrey |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Part of mpox consortium - our Workpackage is part of the UKRI consortium funding. We are investigating particular proteomic aspects of mpox infection (specifically, interactions of viral proteins and host targets of the virus). |
| Collaborator Contribution | Consortium systematically investigating multiple different aspects of mpox. We gain access to data via regular meetings, access to generation of samples (Pirbright) and access to analysis (Edinburgh, RNAseq). |
| Impact | Nat Commun. 2023 Dec 8;14(1):8134. doi: 10.1038/s41467-023-43299-8. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection Jonas D Albarnaz # 1 2 3, Joanne Kite # 4 5, Marisa Oliveira # 4 5, Hanqi Li 4 5, Ying Di 4 5, Maria H Christensen 6, Joao A Paulo 7, Robin Antrobus 4 5, Steven P Gygi 7, Florian I Schmidt 6, Edward L Huttlin 7, Geoffrey L Smith 8 9, Michael P Weekes 10 11 PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8 |
| Start Year | 2022 |