In a recent work we showed that cellular RNA is massively degraded upon Sindbis virus infection, and this appears to apply to a broad range of cytopathic viruses. The goal of this project is to understand how cellular RNA degradation is triggered and what its consequences in infection are. We will focus on the exonuclease XRN1 that is stimulated upon the infection of several RNA viruses.
This project is a join effort between the Castello lab and the Pelechano‘s lab and combines cutting edge transcriptomic approaches with virology methods and computational biology.
If you are interested, you can apply to this project here:
The Castello lab will move to the Centre of Virus Research (CVR), in the University of Glasgow, between Nov 2020 and July 2021. The CVR is home to the UK’s largest critical mass of virology researchers, co-located in a purpose-built centre with state-of-the art facilities and infrastructure. New research activities will be based at the CVR, including new PhD and Msc projects.
The CVR research covers emerging viruses, chronic infections , innate and intrinsic immunity , viruses and cancer, structural virology, viral genomics and bioinformatics.
The CVR is a member of the COVID-19 genomics UK consortium, which is currying out critical research to follow the expansion of SARS-Cov-2 and the consequent evolution of its genome. The CVR contribution to combat COVID-19 pandemics spans different lines of research, including virus tracking, characterisation and surveillance, as well as development of critical toolkit to enable UK research in SARS-Cov-2.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causal agent of coronavirus disease 2019 (COVID-19). It has caused a global pandemic that is posing a major threat to millions of people’s health. Part of the reason that causes this pandemic is the lack of pre-existent adaptive immunity among the population. Before successful development and deployment of effective vaccine, the first line of defence against SARS-CoV-2 in our body is our innate immunity. Once the cell detects atypical signatures related to viruses, such as double-stranded RNA, it secrets signalling proteins to alarm its surrounding cells, known as cytokines . Secreted cytokines vary across cell types, and each has its own role in organizing the body’s defence against viruses. Some of the most important defences against viruses are the interferons (IFN), which recognise specific receptors in the surface of the cell as a key and a lock. The interaction of interferon with its receptor induces the expression of antiviral proteins in cytoplasm and nucleus of the cell to combat infection more effectively. Researchers has studied the functions of interferons for decades and developed recombinant proteins to be used in protein therapies, for example, to treat hepatitis C virus . The current COVID-19 pandemic raises the important questions about the role of individual cytokines and, in particular interferons, in body’s response to SARS-CoV-2.
As SARS-CoV-2 is a newly identified virus, researchers are still investigating the details about the importance of individual cytokines in COVID-19. However, we can infer their potential functions from its better studied relative SARS-CoV-1, the coronavirus that caused an outbreak in 2003. Cinatl and colleagues revealed that type I interferon (IFN-I), which includes IFN alpha and beta, can be used to effectively inhibit replication of SARS-CoV-1 in vitro . In vivo studies using human ACE-2 transgenic macaques confirmed the anti-SARS effect of IFN-I. Haagmans and colleagues tested the effect of pegylated IFN-alpha injection on macaques infected with SARS-Cov-1 and they showed lower viral titres in both throat swab and lung homogenate, and better histopathology results . The suppression of SARS-CoV-1 infection was even stronger when IFN was injected prior to the infection with the virus. Gao and colleagues conducted similar experiment in macaques using IFN-I nasal spray, which also showed protective effects . The preliminary clinical studies on SARS-CoV-1 patients treated with IFN-I showed improvement in oxygen saturation and symptoms , but larger scale clinical trials were inconclusive due to the lack of patients as the outbreak quickly ceased by summer .
Although IFN treatment sounds clinically promising for SARS-CoV-1 outbreak, we have also learnt that cytokines could be destructive when they go rampage. Typically, one week after SARS infection, patients that have arterial oxygen saturation (SO2) > 91% will recover within a week, while those that have SO2 < 91% enter a crisis phase that require access to ventilators, and have higher mortality rate. Cameron and colleagues discovered that patients that entered the crisis phase have naturally significantly higher levels of proinflammatory cytokines . Channappanavar and colleagues studied further the IFN-induced tissular damage using human ACE-2 transgenic mouse model . Surprisingly, mice lacking the receptor for IFN-I showed milder symptom (measured by body weight loss) and lower mortality rate when compared with wild-type mice after infected with lethal dose of SARS-CoV-1. Moreover, other studies have shown correlation between elevated levels of cytokines and severe symptoms in SARS-CoV-1 and MERS-CoV . Can we thus conclude that interferons do more harm than good? Using transgenic mice model, Channappanavar and colleagues discovered that multiple cytokines, including IFN-I, showed a 24-hour delay in expression level after SARS-CoV-1 infection. Early intervention of IFN-I treatment cured SARS in infected mice and had substantially milder symptoms than mice lacking the IFN-I receptor. Therefore, it appears that IFN-I response at the right timing effectively contains the virus, but at the wrong time is responsible for severe symptoms in SARS-CoV-1 infection (see figure ). It remains unclear how our understanding of SARS-CoV-1 could help us combat SARS-CoV-2, but these discoveries could be beneficial in the development of effective treatment or even to understand the battle between our immune system and the virus and its consequences.
Writen by Honglin Chen, DPhil student
 Kumar, H., Kawai, T. and Akira, S., 2011. Pathogen recognition by the innate immune system. International reviews of immunology, 30(1), pp.16-34.
 Feld, J.J. and Hoofnagle, J.H., 2005. Mechanism of action of interferon and ribavirin in treatment of hepatitis C. Nature, 436(7053), pp.967-972.
 Cinatl, J., Morgenstern, B., Bauer, G., Chandra, P., Rabenau, H. and Doerr, H.W., 2003. Treatment of SARS with human interferons. The Lancet, 362(9380), pp.293-294.
 Haagmans, B.L., Kuiken, T., Martina, B.E., Fouchier, R.A., Rimmelzwaan, G.F., Van Amerongen, G., van Riel, D., De Jong, T., Itamura, S., Chan, K.H. and Tashiro, M., 2004. Pegylated interferon-α protects type 1 pneumocytes against SARS coronavirus infection in macaques. Nature medicine, 10(3), pp.290-293.
 Gao, H., Zhang, L.L., Wei, Q., Duan, Z.J., Tu, X.M., Yu, Z.A., Deng, W., Zhang, L.P., Bao, L.L., Zhang, B. and Tong, W., 2005. Preventive and therapeutic effects of recombinant IFN-alpha2b nasal spray on SARS-CoV infection in Macaca mulata. Zhonghua shi yan he lin chuang bing du xue za zhi= Zhonghua shiyan he linchuang bingduxue zazhi= Chinese journal of experimental and clinical virology, 19(3), pp.207-210.
 Loutfy, M.R., Blatt, L.M., Siminovitch, K.A., Ward, S., Wolff, B., Lho, H., Pham, D.H., Deif, H., LaMere, E.A., Chang, M. and Kain, K.C., 2003. Interferon alfacon-1 plus corticosteroids in severe acute respiratory syndrome: a preliminary study. Jama, 290(24), pp.3222-3228.
 Stockman, L.J., Bellamy, R. and Garner, P., 2006. SARS: systematic review of treatment effects. PLoS medicine, 3(9).
 Cameron, M.J., Ran, L., Xu, L., Danesh, A., Bermejo-Martin, J.F., Cameron, C.M., Muller, M.P., Gold, W.L., Richardson, S.E., Poutanen, S.M. and Willey, B.M., 2007. Interferon-mediated immunopathological events are associated with atypical innate and adaptive immune responses in patients with severe acute respiratory syndrome. Journal of virology, 81(16), pp.8692-8706.
 Channappanavar, R., Fehr, A.R., Vijay, R., Mack, M., Zhao, J., Meyerholz, D.K. and Perlman, S., 2016. Dysregulated type I interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in SARS-CoV-infected mice. Cell host & microbe, 19(2), pp.181-193.
 Channappanavar, R. and Perlman, S., 2017, July. Pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology. In Seminars in immunopathology (Vol. 39, No. 5, pp. 529-539). Springer Berlin Heidelberg.
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in December 2019 and is the virus responsible for the COVID-19 pandemic. Recent serological data from Spain and Germany have smashed the hopes of the scientific community on herd immunity in the mid-term, as only 10-15% of the people analysed presented antibodies against SARS-CoV-2. Hence, the development of a vaccine is urgently required. Oxford University scientists working at The Jenner Institute have developed a chimpanzee adenoviral vector vaccine encoding the SARS-CoV-2 spike glycoprotein, the club-shaped protein on the surface of the virus (visit our recent comments on the spike and the Oxford vaccine effort for more information). The vaccine, ChAdOx1 nCoV-19 is based on an adenoviral vector, a strategy previously used for the middle eastern respiratory syndrome coronavirus (MERS-CoV) vaccine that showed protection in non-human primates.
Initial testing of ChAdOx1 nCoV-19 in mice showed that injection of the vaccine into muscle tissue produced a strong antibody response against both subunits of the spike glycoprotein, mainly driven by T helper cells (Th1 type). These cells produce cytokines which are chemical messengers that signal to other immune cells in the body and generate a specific type of immune response. The antibodies produced in immunised mice were neutralising. This means that the binding of the antibody interferes with the ability of the viral spike glycoprotein to interact with the cell’s surface and enter into the cytoplasm.
Following the success in mice, the ChAdOx1 nCoV-19 vaccine was tested in rhesus macaques, which are closer to humans. 6 animals were vaccinated followed by challenge with a very high dose of SARS-CoV-2 28 days later. As quickly as 14 days later, neutralising antibodies against the spike glycoprotein were detected in the monkeys’ blood. When challenged with SARS-CoV-2, vaccinated monkeys showed very little respiratory stress symptoms when compared to unvaccinated controls. Viruses were produced in the nose of vaccinated and unvaccinated monkeys at a similar level. However, this is possibly due to the high virus dosage that they were exposed to, which does not reflect the levels a human would encounter in natural infection. The RNA genome of SARS-CoV-2 was detected in all control monkeys, but only in 2 out of 6 vaccinated monkeys. After 3 days, SARS-CoV-2 replication was detected in unvaccinated controls through the measurement of sub-genomic RNAs. However, replication was undetectable in vaccinated monkeys as no sub-genomic RNA was detected. Conversely to unvaccinated macaques, neither pneumonia nor immune-enhanced inflammatory disease was detected in vaccinated animals after 7 days post virus inoculum.
These results show that a single vaccination with ChAdOx1 nCoV-19 effectively prevents SARS-cov2-derived lung damage in monkeys despite high doses of virus inoculum. This data is very promising and will complement the results from the phase 1 clinical trials that began in Oxford on April 23rd 2020 and involve 1000 human volunteers. These results are a promising step towards the development of a safe and effective vaccine against SARS-CoV-2.
Written by Kate Dicker, WT IITM DPhil student
Original work: ChAdOx1 nCoV-19 vaccination prevents SARS-CoV-2 pneumonia in rhesus macaques. van Doremalen, N., Lambe, T., […], Gilbert, S.C., and Munster, V.J., 2020 BioRxiv. doi: https://doi.org/10.1101/2020.05.13.093195
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