Updated on 26th May
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.
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.
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…
Antigens as vaccine candidates and for serological testing
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 versions of viruses (pseudotyped viruses) and antigens that are based on the spikes. These viruses just contain the SARS-CoV-2 spikes on the outside (and hence, are not pathogenic).
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.
Outputs: Pseudotyped SARS-CoV-2 virus-like particles (mammalian expression system) <2 months
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
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.
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
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.
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
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.
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
Endocytosis of SARS-Cov-2
After the spikes on the surface have engaged ACE2 receptors on the surface of the target cell, the virus enters the cell through a well-known and non-disease process called endocytosis. We have started to investigate which of the known endocytosis pathways is engaged in this process. Since a number of these pathways have known inhibitors and very good genetic tools, we expect this to be clarified quickly. It is not inconceivable that a locally applied inhibitor of the correct endocytic pathways could be developed into a therapeutic tool, at least as an emergency measure.
Groups: Leo James, Harvey McMahon
Output: Insight into the precise cell entry mechanism of SARS-CoV-2, possibly known pathways that have small molecule inhibitors already. 6 months
Processing of SARS-CoV-2 multiproteins
All proteins of the SARS-CoV-2 virus are first made as part of long polyproteins that are cleaved during trafficking through the ER and Golgi by proteases. We are investigating the fact that chloroquine is affecting the retention of furin in the Golgi. Furin is known to cleave some of the polyproteins of the virus and this might explain the reported activity of chloroquine against the COVID-19 infection.
Groups: John Briggs, Sean Munro
Output: Clarification of the role of chloroquine, a SARS-CoV-2 drug candidate, in the processing of polyproteins. 3-6 months
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
Suppression of host translation by SARS-CoV-2 nsp1
One of the first consequences of invasion of a host cell by coronaviruses is suppression of host translation at the expense of viral translation, which is accomplished by non-structural protein 1 (Nsp1), which is coded by the viral genome. The main aim of this project is to understand the molecular mechanism underlying how SARS-CoV-2 Nsp1 represses host translation.
Groups: Venki Ramakrishnan
Output: Molecular mechanism underlying SARS-CoV-2 Nsp1 suppression of host translation. 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.
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.
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.
Groups: Julian Gough
Outputs: Outside chance of a new discovery. If a COVID-19 discovery is made, results will be published rapidly. <2 months
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
In addition to contributing scientific research, numerous members of LMB have volunteered to help the NHS and local communities:
- The LMB has assisted with a Cambridge-wide call for volunteers, coordinated by Professor Ian Goodfellow at the Department of Pathology, University of Cambridge.
- Tobias Wauer, Elyse Fischer, Hasan Al-Habib, Nadia Cummins, Antonio Galindo, Ewa Gogola, Samuel Lacey, Andrei Mihut, Jack Munns and James Rhodes are volunteering 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 are completing 12-hour shifts to help in the national effort to increase COVID-19 testing capacity.
- Shabih Shakeel, Conny Yu, Lorena Boquete Vilarino and Eszter Zavodszky are volunteer experienced scientists helping to increase local testing capacity at a COVID-19 testing facility located near the LMB on the Cambridge Biomedical Campus.
- 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.