When cellular proteins meet SARS-CoV-2 RNA: a story of protein-RNA interactions

I our recent work we comprehensively and systematically identify the complement of cellular RNA-binding proteins that are involved in SARS-CoV-2 infection. We discover that the cellular RNA-binding proteome (RBPome) is pervasively remodelled upon SARS-CoV-2 infection, affecting a broad range of RNA metabolism and antiviral pathways. We also apply a new method to uncover the composition of SARS-CoV-2 RNPs, revealing a dozens of cellular RBPs and seven viral proteins. Our study reveals a new universe of host-virus interactions awaiting to be characterised and with great potential for novel therapies againt COVID-19.

This work is a synergistic collaboration between the Castello, Mohammed, Bartenschlager, Martinez and Lilley labs. See full publication in BioRxiv below:

Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection | bioRxiv

How SARS-Cov-2 enters in the host cell?

The recent pandemic explosion of the “severe acute respiratory syndrome coronavirus 2” (SARS-CoV-2), firstly originated in the Hubei province of China and subsequently spread all over the word, reached officially over three million detected cases and caused the death of more than two hundred thousand people. Scientists have begun a race toward the understanding of the mechanisms at the basis of SARS-CoV-2 viral cycle and unique features. This virus belongs to the betacoronavirus genus, together with SARS-CoV-1 and Middle East respiratory syndrome (MERS-CoV), which caused outbreaks in the last two decades.

Researches across the globe are leading to the discovery of pivotal characteristics of SARS-Cov-2, some of which shared with its ‘cousins’ SARS-Cov-1 and MERS. One of these achievements is the documentation of the mechanism of entrance into the host cell. This involves the interaction between the transmembrane viral spike glycoprotein and the angiotensin-converting enzyme 2 (ACE2) receptor on the host cell surface. The spike is a homotrimeric glycoprotein complex, in which each monomer is composed by two subunits. The S1 subunit comprises the receptor binding motif (RBM) and is responsible for the first attachment to the host receptor, while the S2 subunit mediates the membrane fusion, and requires a proteolytic cleavage executed by the host transmembrane serine protease 2 (TMPRSS2). Exciting biochemical and structural analysis of the virus-host interacting surfaces, revealed a very high binding affinity of these proteins and the occurrence of conformational changes in the complex which allow the entry of the virus. The interaction of the spike with its receptor is a key step in virus infection, which can be explained as the intimate relation of a key and its lock opening the doors to the intracellular environment. 

Advanced knowledge on the interaction between the virus and the target cells is extremely valuable and has been object of innovative studies aiming to develop vaccines and antiviral drugs, which could potentially be beneficial in our long-lasting fight against coronavirus, endowing us with potent tools and advantage in the battlefield.  

Written by Dr. Vincenzo Ruscica, Marie Sklodowska-Curie fellow


  • Hoffmann et al., 2020, Cell 181, 271-280 April 16, 2020
  • Walls et al., 2020, Cell 181, 281-292, April 16, 2020
  • Shang et al., 2020, Nature, March 30, 2020
  • Lan et al., 2020, Nature, March 30, 2020

The importance of serological test to understand SARS-Cov2 pandemic

There are many things that we do not yet understand about the new coronavirus that has driven us all inside and stretched health systems across the globe to breaking point. One of its most fundamental aspects that remains obscure is how many people are actually infected. While official case numbers rise to 2 million, a frequently repeated maxim is that the confirmed cases represent just ‘the tip of the iceberg’. Part of the reason that the number of confirmed cases is so much lower than the actual number of cases is that many people are asymptomatic or present(ed) mild symptoms and have not been tested. Indeed, since testing capacity has been limited across the globe, only people who experience severe illness, or even who end up in hospital, are usually tested for SARS-Cov2 (the virus responsible for COVID-19) with RT-PCR assays. A proposed implication of these asymptomatic or mild-symptom infections is that we could be close to reaching, or even have already reached, a state of ‘herd immunity’. In this state, the immunized population acts as a firewall that protects those individuals that have not been exposed to the virus, disrupting the host-to-host transmission chain.

“Herd immunity is a form of indirect protection from an infectious disease that occurs when a large percentage of a population has become immune to the pathogen. Immunized individuals act as firewalls that disrupt pathogen spreading from host to host. Herd immunity can be reached when the pathogen has infected a large proportion of the population (typically 2/3) or by the generalised use of effective vaccines.”

This is a very enticing prospect, and one that has received a lot of attention in recent weeks. If not backed up by sufficient evidence, however, taking actions based on the principle of herd immunity has the potential to do more harm than good. Slackening of public health measures too early could potentially lead to catastrophic second, and even third, waves of infections, and an overconfidence in herd immunity could detract from ongoing efforts to generate a vaccine or an effective antiviral. Even if herd immunity is achieved through natural infection, we do not yet have convincing evidence that this immunity will keep the virus at bay for long enough and consistently enough to end this pandemic. Before we make any decisions based on this principle, it will, therefore, be important to understand precisely what proportion of the population has been infected, and whether infection confers long-term protection.

“Implementation of systematic serological tests is critical to determine the proportion of the population that has been exposed to the virus.”

 The first necessary step will be to develop an accurate serology test to detect antibodies against SARS-CoV2 in our blood. Antibodies are one of our most effective tools in fighting viral infection and are generated as a result of a highly specific adaptive immune response. Hence, the presence of antibodies against SARS-Cov2 is in an unequivocal sign that someone has been infected and recovered from the virus. Once such a test is systematically applied, we will have a better idea on how close we are to threshold for herd immunity to be effective. These analyses will only provide information about the proportion of people exposed to the virus, but will not answer two critical questions: are these antibodies effective at combating the virus, and can they provide long-term protection?

One way in which antibodies can stop being protective is if the virus mutates into a form that is no longer recognised. Unlike other viruses, SARS-CoV2 has a relatively low mutation rate due to a proof-reading enzyme encoded in its genome, which corrects errors introduced by the RNA polymerase during replication. While this does not mean that the virus never mutates, comparisons made between common cold coronavirus strains from 30 years ago and those in circulation today indicate that changes in the viral genome are minimal, and that these do not substantially affect the viral proteins known to be the targets of antibodies. This is important and heartening evidence that a vaccine designed against this virus is likely to confer lasting protection. However, it also poses another question. If the viruses that cause up to a third of common cold cases in the human population are not undergoing significant mutation over time, how is it that people can be re-infected with them every couple of years?

Part of the answer to this likely lies in the quality and longevity of antibody response mounted against these viruses. A study published 30 years ago in which volunteers were infected with common cold coronaviruses found that antibodies declined soon after infection. More worrying is that after a year people could be reinfected when challenged with the same virus. One possibility is that the low pathogenicity of these viruses (most cases of the common cold are relatively mild) results in a half-hearted immune response that is sufficient to clear the virus but fails to generate lasting protection. Evidence that this might be a common problem with coronaviruses comes from a study performed in healthcare workers who recovered from MERS. In this study, authors found that the longevity of the antibody response against MERS was far more variable among individuals who had had mild symptoms than those having severe illness. Since so many cases of SARS-Cov2 infection are thought to be asymptomatic or entailing mild-severity, it is a possibility that a large proportion of infected people lack robust or long-lasting antibody response against the virus.

“Two critical questions remain unanswered: Are antibodies generated against SARS-Cov2 effective at combating the infection? and if so, is the immunization long-lasting?

In a recent pre-print looking at serology of 175 patients who experienced mild symptoms, almost 50% of people had medium or low antibody levels, and 10 patients showed no neutralising antibodies at all. The ability of the antibodies to block infection were assessed through an in vitro neutralisation assay. However, the extent to which this assay correlates with protection in vivo remains unclear. An important aspect that has not been possible to assess yet is how long-lasting this antibody response will be. Hence, whether exposure to SARS-Cov2 will lead to long-term protection is uncertain. Studies with patients infected with SARS-Cov1 (which is closely related to SARS-Cov2) during the outbreak in 2003, indicated that antibody levels declined after 2 years. The risk that natural infection might not provide sufficient long-term protection is an important justification for focusing resources on the development of an effective vaccine and antiviral drugs. By training our immune system with the ‘right’ antigen and following a robust immunization regimen, it might be possible to induce long-term and dependable immunity across the population. Whilst the antibody test will be important in informing policy decisions and epidemiological models in the short term, evidence about the efficacy of natural immunity will critical to identify a long-term solution for this pandemic.

Written by Louise Iselin, DTP rotation student in the Castello lab

Uncovering the human proteins targeted by COVID-19

New research published by the University of California has revealed over 230 interactions that COVID-19 proteins establish with human proteins. This work offers insights into how COVID-19 infection occurs and identifies almost 70 potential drug-targets.

Coronavirus Disease-2019 (COVID-19) has infected over 1,030,000 people in more than 100 countries (data 03/04/2020), but due to a lack of known molecular detail, there are no current antiviral compounds available to combat the virus. Interactions between host cell proteins and viral proteins are at the forefront of infection, where viruses such as COVID-19 hijack host resources to propagate. There is an ever-developing arms race between host antiviral factors, which aim to hinder infection, and viral antagonistic factors, which aim to counteract host defences. Revealing this complex network of interactions can help us understand how viral infection occurs and can reveal therapeutic targets to combat infection.

The Krogan labrevealed the interactions of 26 of the 29 COVID-19 proteins in human cells using a technique known as affinity purification followed by mass spectroscopy (AP-MS, Figure A), which allowed them to probe protein-protein complexes with high sensitivity. The researchers identified over 230 human interactors which participate in a wide array of key cellular pathways such as innate immunity and the protein unfolded response (Figure B). Using bioinformatic analysis, they reveal almost 70 compounds which target key parts of the network and may represent potential antiviral drugs. Current tests for antiviral activity are ongoing. The work also reveals many common interaction partners between COVID-19 and other viruses also associated with pulmonary conditions such as West Nile Virus and Mycobacterium tuberculosis, suggesting that they may have similar mechanisms of infection.

This work contributes significantly to our current understanding of COVID-19 and furthers our efforts to find compounds which may combat infection. 

Written by Catherine Truman, DTP DPhil student

Original publication:

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug Repurposing. David E. Gordon, Gwendolyn M. Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Matthew J. O’Meara, […], Pedro Beltrao, Kevan Shokat, Brian K. Shoichet, Nevan J. Krogan,. BioRxiv. DOI: https://doi.org/10.1101/2020.03.22.002386

Oxford Vaccine Effort Towards COVID-19

Oxford University has joined the global effort to fight COVID-19 (also referred to as SARS-Cov2) and is recruiting healthy volunteers to test a new vaccine. This comes after both the USA and China announced that they were starting clinical trials of COVID-19 vaccines. The team from the University’s Jenner Institute is working in collaboration with the Oxford Vaccine Group to conduct the trial which has been approved by UK regulators.

The team, led by Prof. Sarah Gilbert, Prof. Andrew Pollard, Prof. Teresa Lambe, Dr. Sandy Douglas and Prof. Adrian Hill, started designing the vaccine on the 10th of January as soon as the first genome sequence of COVID-19 was made publicly available. The vaccine candidate put forward for the trial uses a chimpanzee adenovirus vector (ChAdOx1) previously developed by the Jenner Institute. It was chosen as the most suitable vaccine technology as only one dose is required to generate a strong immune response and the adenovirus vector is defective so cannot cause an infection in the vaccinated individual. So far, the ChAdOx1 vector technology has been successfully used in vaccines targeting over 10 different diseases.

Coronaviruses (including COVID-19. SARS and MERS) have a club-shaped protein on their surfaces called spike protein. Previous studies of coronavirus vaccines suggested that the spike protein is a good vaccine target. The genetic sequence of the COVID-19 surface spike protein is introduced inside the ChAdOx1 vector. Once the ChAdOx1 vector enters a cell, the host machinery transcribes and translates the genetic sequence and the COVID-19 spike protein is expressed. The spike protein then serves as a training tool for B cells, leading to the production of antibodies against the spike protein. Antibodies work as tailored weapons targeting a specific pathogen, in this case, COVID-19. A vaccinated individual is expected to develop an effective immunological arsenal against COVID-19 which will be instrumental to fight and prevent the infection or, at least, reduce its severity.

Due to the urgent need for means to fight the COVID-19 pandemic, the production of the vaccine is already being scaled up to produce enough stock for large clinical trials and potentially future deployment. This will ensure that as soon as the vaccine is proven safe and effective, it can be available for the people that need it the most, including frontline healthcare workers, the elderly and those with underlying health conditions.

Writen by Kate Dicker, WT IITM DPhil student


  1. Clinical Trials Arena. Covid-19: China to launch clinical trials for coronavirus vaccine, (2020).
  2. Clinical Trials Arena. First US clinical trial of Covid-19 vaccine candidate begins, (2020).
  3. University of Oxford. Oxford COVID-19 vaccine programme opens for clinical trial recruitment, (2020).
  4. University of Oxford. About the COVID-19 vaccine trials ,(2020).