Updated on 26th October
As the COVID-19 pandemic continues to rage all over the world, members of LMB have been finding ways to help. From scientifically untangling the virus’s inner workings to providing equipment to hospitals, from volunteering for the NHS or as an experienced scientist at a testing centre, our staff and students are staying involved.
Here is a current summary of our efforts towards the COVID-19 fight. We will keep updating this as we go along / till all this is over.
This model of an authentic virus particle reveals positions, conformations and orientations of the spike proteins on the virion membrane (blue). RBD = Receptor Binding Domain.
Image available to download and use under a CC-BY-NC-ND 4.0 International license.
Copyright MRC Laboratory of Molecular Biology.
Collaborative scientific efforts
LMB’s scientific efforts towards the pandemic are strongly cross-linked, in line with the collaborative ethos that underpins LMB day-to-day research, and how science progresses.
The SARS-CoV-2 is the virus responsible for COVID-19, and it has several protein parts and interactions.
Opening of LMB Containment Level 3 lab fast-tracked to enable rapid responsive COVID-19 research using live SARS-CoV-2 virus
To enable vital research using live SARS-CoV-2 virus by Leo James’s group and others, a team including those with expertise in research safety, building management systems and virus research was rapidly assembled to fast-track opening of the LMB’s Containment Level 3 lab.
After a mammoth team effort, the LMB’s CL3 laboratory was opened within just three months. The first virus samples arrived from Cambridge University Hospital on the very same day, and results from experiments using live virus have already contributed to two research publications, with more in the pipeline. Read more here.
LMB joins UK-wide COVID-19 Protein Portal
In response to the urgent need for COVID-19 therapeutics, vaccines and diagnostics, many expert UK scientists, including several at the LMB, are working to understand the fundamental biology of SARS-CoV-2. Reliable protein reagents are crucial to such research, but can be challenging and time consuming to produce, especially under restricted working conditions. To facilitate vital research on SARS-CoV-2, Wellcome and UKRI have brought together a consortium of leading centres of protein engineering and production to launch the COVID-19 Protein Portal. Read more here…
Making pseudoviruses to study infection and use in functional assays
The SARS-CoV-2 virus is membrane-enclosed but exposes trimeric protein ‘spikes’ on the outside that are immunogenic. These spikes allow the virus to enter cells by binding to ACE2 receptors on cells. We are making several disabled ‘pseudotyped’ versions of the virus in order to study its infection and for use in virus neutralisation tests (functional assays). These viruses just contain the SARS-CoV-2 spikes on the outside (and hence, are not pathogenic).
Groups: Leo James, John Briggs, Andrew Carter, Harvey McMahon, Sean Munro
Outputs: Pseudotyped SARS-CoV-2 virus-like particles (mammalian expression system) <2 months
Furin cleavage of SARS-CoV-2 Spike promotes but is not essential for infection and cell-cell fusion. Papa, G., Mallery, D.L., Albecka, A., Welch, L., Cattin-Ortola, J., Luptak, J., Paul, D., McMahon, H., Goodfellow, I.G., Carter, A., Munro, S., James, L.C. bioRxiv (pre-print – not yet peer reviewed)
Antigens as vaccine candidates and for serological testing
We are developing effective antigens based on viral spike proteins and nucleoprotein. We are making soluble trimeric spikes and also receptor binding domains (RBDs) that are a small part of the spike. RBD binds to ACE2 on the target cell, and is the part that is most different from other coronaviruses.
The antigens are made for two reasons: they can be injected into animals and humans to produce an immune response as a vaccine candidate or to make antibodies and their libraries. Secondly, these antigens are needed to run serological tests that would determine if patients have been infected with SARS-CoV-2 already. At the moment, these tests are not very good and we are developing ideas on how to make better antigens, for example, by turning them into multimers to exploit avidity.
Groups: Radu Aricescu, John Briggs, Andrew Carter, Leo James, Jan Löwe, Yorgo Modis, Sjors Scheres
Outputs: SARS-CoV-2 RBD protein (bacterial, yeast and mammalian expression systems) <2 months
SARS-CoV-2 multimerised RBD protein (bacterial, yeast and mammalian expression systems) <2 months
SARS-CoV-2 Spike protein (mammalian expression system) <2 months
A thermostable, closed SARS-CoV-2 spike protein trimer. Xiong, X., Qu, K., Ciazynska, KA., Hosmillo, M., Carter, AP., Ebrahimi, S., Ke, Z., Scheres, SHW., Bergamaschi, L., Grice, GL., Zhang, Y., The CITIID-NIHR COVID-19 BioResource Collaboration, Nathan, JA., Baker, S., James, LC., Baxendale, HE., Goodfellow, I., Doffinger, R., Briggs, JAG. Nature Structural & Molecular Biology 27, 934–941. doi:10.1038/s41594-020-0478-5.
– Insight on Research: Studying the Spike protein of SARS-CoV-2
Combined point of care nucleic acid and antibody testing for SARS-CoV-2 following emergence of D614G Spike Variant. Mlcochova, P., Collier, D., Ritchie, A., Assennato, S.M., Hosmillo, M., Goel, N., Meng, B., Chatterjee, K., Mendoza, V., Temperton, N., Kiss, L., James, L.C., Ciazynska, K.A., Xiong, X., Briggs, J.A.G., Nathan, J.A., Mescia, F., Bergamaschi, L., Zhang, H., Barmpounakis, P., Demeris, N., Skells, R., Lyons, P.A., Bradley, J., Baker, S., Allain, J.P., Smith, K.G.C., Bousfield, R., Wilson, M., Sparkes, D., Amoroso, G., Gkrania-Klotsas, E., Hardwick, S., Boyle, A., Goodfellow, I., Gupta, R.K., The CITIID-NIHR COVID BioResource Collaboration. Cell Reports Medicine doi:10.1016/j.xcrm.2020.100099
ACE2 decoys
As an alternative to antibodies – evolving the region of the ACE2 receptor to which SARS-CoV-2 binds to make it bind more effectively to the virus and less well to its natural ligand, Angiotensin II, could produce a soluble protein that reduces the ability of the virus to enter cells without disturbing the Angiotensin system, which plays an important role in blood pressure control. We will use hypermutating cells lines and in vitro selection to rapidly evolve human ACE2 with the aim of producing these candidate viral decoys. This approach is highly innovative and is directly targeted towards an emergency therapy.
Groups: Nick Brindle (University of Leicester), Julian Sale
Outputs: Evolved ACE2 viral decoys; chicken cell line expression & selection system; mutational scanning of the ACE2-COVID-19 spike protein interaction. 3-6 months
The structure of the virus
We are using electron tomography to obtain structures of parts of the SARS-CoV-2 virus from virus particles. We are also aiming to study the structure of the S protein on virus-like particles in complex with receptors and neutralising antibodies. Structures are available for isolated proteins, but some interactions with antibodies and the membrane fusion event that the virus triggers can only be understood when structures of these complexes and events are available at high-enough resolutions in the context of the virus.
Groups: John Briggs, Andrew Carter, Leo James, Sjors Scheres
Outputs: Images of the virus and of virus-like particles, structures of viral proteins in the context of the virus, and structures with ACE2 domain and antibodies bound. 3-6 months
Structures and distributions of SARS-CoV-2 spike proteins on intact virions. Ke, Z., Oton, J., Qu, K., Cortese, M., Zila, V., McKeane, L., Nakane, T., Zivanov, J., Neufeldt, CJ., Cerikan, B., Lu, JM., Peukes, J., Xiong, X., Kräusslich, H-G., Scheres, SHW., Bartenschlager, R., Briggs, JAG. Nature doi:10.1038/s41586-020-2665-2.
– Insight on Research: Studying the Spike protein of SARS-CoV-2
Inhibiting the SARS-CoV-2 polymerase
In order to replicate, the SARS-CoV-2 virus needs to transcribe and replicate its RNA into more strands of RNA. For this it uses its own RNA-dependent RNA polymerase (RdRp). We are making the polymerase (nsp12 + nsp7 and 8) and it is planned to image it by cryo-EM in complex with a primed RNA substrate while it is being transcribed, and then to add known inhibitors such as the antiviral drugs Avigan and Remdesivir. We have access to the highest-resolution cryo-EM instrument in the world and aim to exploit that machine for this study since only true atomic resolution will help with the ongoing efforts to find drugs that are more active against SARS-CoV-2.
Groups: David Barford, Jan Löwe, Chris Russo, Sjors Scheres, John Sutherland
Outputs: SARS-CoV-2 RdRp with RNA substrate and small-molecule inhibitors. Cryo-EM structure at atomic resolution (better than 2.0 Å). 3-6 months
Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP. Naydenova, K., Muir, K.W., Wu, L-F., Zhang, Z., Coscia, F., Peet, M.J., Castro-Hartmann, P., Qian, P., Sader, K., Dent, K., Kimanius, D., Sutherland, J.D., Löwe, J., Barford, D., Russo, C.J. bioRxiv (pre-print: not yet peer reviewed)
S2m RNA elements
One mystery of SARS-CoV-2 is how its genes are translated. All its genes contain a 48 bp stem-loop RNA element in their 3’ UTR. We will help find whether this particular element helps the virus to hijack the cell’s translation machinery (ribosomes to make protein) through these elements, by making reporter strains. We will also find proteins that bind to this RNA element as that might enable us to find inhibitors that are truly specific for this type of virus. Since it is an RNA element, it is not entirely inconceivable that an RNAi-type approach could be used to develop an emergency therapy very quickly.
Groups: Ben Luisi (Cambridge University), Helena Maier (Pirbright Institute), Chris Oubridge, Felix Randow, Bill Scott (University of California at Santa Cruz)
Outputs: Insights into RNA element s2m’s role in translation of SARS-CoV-2 proteins: a potentially entirely new drug / RNAi target. 3-12 months
Antisense oligonucleotides target a nearly invariant structural element from the SARS-CoV-2 genome and drive RNA degradation. Lulla, V., Wandel, M.P., Bandyra, K.J., Dendooven, T., Yang, X., Doyle, N., Oerum, S., O’Rourke, S., Randow, F., Maier, H.J., Scott, W., Ding, Y., Firth, A.E., Bloznelyte, K.B., Luisi, B.F. bioRxiv (pre-print – not yet peer reviewed).
Traffic and processing of SARS-CoV-2 membrane proteins
The membrane proteins that surround the SARS-CoV-2 virus are made in the endoplasmic reticulum (ER) and then trafficked to the Golgi when the virus is assembled. In the Golgi the proteins are processed further by carbohydrate modification and proteolytic cleavage. In addition, some of the Spike protein travels beyond the Golgi to the cell surface where it can cause fusion to adjacent cells. We are investigating how the viral proteins recruit host cell proteins to direct their traffic, and why it may be advantageous to the virus for some Spike to go beyond the Golgi to enable cell fusion and the formation of multinuclear syncytia.
Groups: Sean Munro, Leo James
Output: Identification of host cell factors required for viral replication and an understanding of the significance of syncytia formation.
Sequences in the cytoplasmic tail of SARS-CoV-2 spike facilitate syncytia formation. Cattin-Ortola, J., Welch, L., Maslen, S.L., Skehel, J.M., Papa, G., James, L.C., Munro, S. bioRxiv (pre-print – not yet peer reviewed).
Control of poly(A) tails by SARS-CoV-2
It has recently been found that the virus’ mRNA has poly(A) tails of defined length, suggesting inhibition of deadenylation activities to stabilise the viral RNAs. It is planned to investigate the role of the 3’ UTR in this and to clarify the role of Pan2-Pan3 and Ccr4-Not complexes in these processes. It is possible that the N protein protects poly(A) tails and this will be investigated in vitro, as well as the role of nsp8 in the process which might be extending the poly(A) tails.
Groups: Lori Passmore
Output: An understanding of the role of viral RNA and proteins in RNA deadenylation/stability. 3-6 months
Drug screening platform
The efficient generation of SARS-CoV2 Viral Like Particles (VLPs) is a fundamental step for the study of the molecular mechanisms of viral entry and for the identification of drugs that might interfere with it. We have re-purposed our line of research in order to develop novel methods for the generation of recombinant VLPs and for monitoring their infectivity. Our aim is to generate an efficient screening platform on which to test FDA approved drugs with the potential to interfere with viral uptake.
Group: Marco Tripodi
Output: Generation and distribution of an efficient drug screening platform for inhibitors of SARS-CoV2 cell entry. 3 months.
Phage-based SARS-CoV-2 assay
Will patients (and how many) infected with SARS-CoV-2 develop an antibody response and how widespread will this response be in the population as a whole? These are critical questions for understanding the spread of SARS-CoV-2 and informing policy response to the pandemic. However, current antibody assays are expensive, unreliable and poorly scalable. As an alternative, we propose a phage-based approach to probe patient sera. Filamentous phage can be viewed as a self-assembling nanoparticle detection reagent, which can be cheaply prepared and propagated simply by growth in a bacterial culture. Our approach is fast, cheap and easily scalable to >10E4 assays per day at a cost <1p per assay.
Groups: Phil Holliger, Willem H. Ouwehand (University of Cambridge)
Output: A phage-based assay for detection and analysis of patient anti-SARS-CoV-2 antibody responses. 3-6 months.
Investigating SARS-CoV-2 entry into the CNS
There are increasing reports of some patients with COVID-19 experiencing neurological symptoms. However, it is not yet clear whether the virus actually crosses into the brain, or causes these effects indirectly. We are using neural organoids to investigate the expression patterns of viral entry factors, such as ACE2, and to test whether pseudotyped viruses with SARS-CoV-2 spike protein can enter neural tissues.
Groups: Madeline Lancaster, Leo James
Outputs: Expression analysis of viral entry factors in CNS tissues. 1-2 months.
Testing viral uptake of pseudotyped virus in neural cell types. 2-3 months.
SARS-CoV-2 infects the brain choroid plexus and disrupts the blood-CSF-barrier. Pellegrini, L., Albecka, A., Mallery, DL., Kellner, MJ., Paul, D., Carter, AP., James, LC., Lancaster, MA. Cell Stem Cell doi:10.1016/j.stem.2020.10.001
– Insight on Research: SARS-CoV-2 disrupts the brain barrier in human organoids
Identification of COVID-19 genetic risk factors
We are applying our novel phenotype prediction algorithm to DNA data from direct-to-consumer tests collected via online participation from volunteers from around the world. In addition to a personalised questionnaire selecting a few questions from over 6,000 phenotypes, we are asking every participant a few questions on their COVID-19 status. This early data, with our unique algorithm applied, has the potential to detect different genetic factors to traditional human genetics approaches, and possibly much sooner.
We are also applying our novel phenotype prediction algorithm to participants from the UK Biobank who have tested positive for the coronavirus and have discovered some preliminary candidates for risk variants which could affect chances of survival (results deposited as a preprint on medRxiv). These preliminary findings are unconfirmed, because the datasets are too small, and so efforts now are focused on securing additional data sources, e.g. from other European biobanks.
Groups: Julian Gough
Outputs: Outside chance of a new discovery. If a COVID-19 discovery is made, results will be published rapidly. <2 months
Genetic risk factors for death with SARS-CoV-2 from the UK Biobank. Lu, C., Gam, R., Pandurangan, A.P., Gough, J. medRxiv (pre-print – not yet peer reviewed).
Positive results have the potential to impact healthcare and may lead to development of a genetic risk test by others.
SARS-CoV-2 entry into the cytosol
SARS-CoV-2 enters the cells from endocytic compartments and a pH-raising agent, chloroquine, has shown effectiveness against the virus in vitro. Unfortunately, the results from COVID-19 patients suggest chloroquine might not be protective in vivo. Better understanding of factors that control the mechanism of viral entry could point us towards more effective compounds that could inhibit infection in patients. We will investigate whether SARS-CoV-2 entry can be prevented by manipulating endolysosomal permeability.
Groups: Patrycja Kozik, Leo James
Outputs: Candidate small molecule tools or genetic targets for manipulating SARS-CoV-2 entry. 6 months
Volunteer calls
In addition to contributing scientific research, numerous members of LMB have volunteered to help the NHS and local communities:
- The LMB assisted with a Cambridge-wide call for volunteers, coordinated by Professor Ian Goodfellow at the Department of Pathology, University of Cambridge.
- 15 LMB-based scientists volunteered at COVID-19 testing centres:
- Tobias Wauer, Elyse Fischer, Hasan Al-Habib, Nadia Cummins, Antonio Galindo, Ewa Gogola, Samuel Lacey, Andrei Mihut, Jack Munns and James Rhodes volunteered as experienced scientists at the COVID-19 National Testing Centre set up by the National Institute of Health Research in Milton Keynes. The 10 volunteers completed 12-hour shifts to help in the national effort to increase COVID-19 testing capacity.
- Tobias Wauer shared his experience of volunteering at the UK Biocentre Lighthouse Lab in The Conversation: ‘My new life as a coronavirus tester’
- Lorena Boquete Vilarino, Shabih Shakeel, Laura Whitworth, Conny Yu and Eszter Zavodszky volunteered as experienced scientists helping to increase local testing capacity for NHS staff at a COVID-19 testing facility located near the LMB on the Cambridge Biomedical Campus.
- The testing volunteers shared details of their experience – see: Putting science skills to new use during the pandemic
- Nina Rzechorzek has enrolled as an NHS volunteer and a biomedical researcher on the Cambridge call for volunteers.
- LMB’s Health and Safety department has been busy coordinating donations of personal protective equipment (PPE) to Addenbrookes Hospital in Cambridge. Following a request from the University of Cambridge, LMB staff assembled a large donation of essential PPE including gloves, disposable aprons and coveralls, safety glasses and overshoes. The collection was coordinated by Jillian Deans, Head of LMB Health and Safety. Jillian said: “It was amazing how quickly LMB staff responded to the request and we hope that the PPE goes some way to help front line NHS staff.”
- Lesley Drynan and Matt Coleman of Biological Services Group coordinated another large effort in getting over 1,500 masks to the COVID response team, University of Cambridge, that is working with the NHS. The LMB has lent its PortaCount mask-fit testing machine to Addenbrookes Hospital and Liam Bray is training NHS staff on how to use it.
- Several members of LMB are helping out their communities in their personal capacities, such as Freda Chapman from our Domestic Services department. Freda has signed up to be an NHS volunteer responder and is also assisting her neighbour, who is an essential health worker, by providing hot meals.