How does virus shape relate to infectivity?

Lead Research Organisation: University College London
Department Name: MRC Laboratory of Molecular Cell Biology

Abstract

Viruses are responsible for many important infectious diseases, e.g. AIDS, smallpox and Ebola but also the common cold and the seasonal flu. It is important to understand how they replicate in our bodies to develop effective treatments such as vaccines or antiviral therapies. However, the shape and composition of the virus itself cannot be easily studied because its structure cannot be resolved by standard microscopes. In my research I develop novel high-resolution microscopy technologies called super-resolution microscopy (SRM) to decipher the way viruses replicate in the cells of our bodies with details previously unachievable. In fact, the nanoscale shape and the molecular composition of a virus largely determine how it infects a cell, what types of cells it infects and how efficiently it does it, critical to the development of the disease.

One particularly important virus is the Influenza A Virus (IAV), responsible for the seasonal flu and the flu pandemics that have been regularly occurring since the end of the 19th century. When an IAV infects an organism, it can take a very large range of shapes and compositions. This suggests that it is able to infect and replicate in many different ways, making it rather elusive and complex to study, but also that IAV needs to be considered as an heterogenous population rather than a group of individual viruses. Indeed, this heterogeneity may be highly advantageous for the virus population as a whole, despite some shapes and compositions not being as infectious as others. However, researchers have not had the right tools to study this important aspect of influenza until very recently. A novel set of microscopy tools available today, especially those that I have developed, can now enable the study IAV at the level of individual molecules and therefore provide a wealth of information about what it is made of and how it assembles.

The research that I am carrying out here is focused on understanding the relationship between the heterogeneity of IAV strains, including the current seasonal strains, and their capability to infect. This is an incredibly complex and multi-disciplinary project that involves cell and virus biology, microscopy and big data analysis. In order to ensure that I use and develop the best tools possible, I have assembled a team of experts in virology, next-generation microscopy developments, high-content screening and Artificial Intelligence. This team spans across multiple research centres of excellence, such as UCL and the Francis Crick Institute in London. Additionally, two other important partners have joined our efforts: the Flu vaccine development team from AstraZeneca, Liverpool and bioengineers from Berkeley University, in California, USA.

In more details, the first stage of the study involves understanding the structural and biochemical make-up of a large number of viruses from several IAV strains to understand their variability at the population level. We can combine this analysis with a genetic analysis that will allow us to ask what viral genes each virus shape contains, which will in turn inform on what each shape can do. Second, we want to study their respective capabilities to infect cells from the human respiratory tract, which is the natural host for the virus in our bodies. This is possible using fast automated SRM, that are able to generate large quantitative datasets and therefore correlate the results from infectivity assays with what each virus is made of. We will finally follow the virus in real time as it enters the cell and replicates, informing us on the dynamics of the virus replication with unprecedented details.

This research pipeline will allow us to test the effect of chemical and genetic influencers on the virus behaviour and shape variability. In turn it will allow a deeper understanding into how it infects and support pharmaceutical companies in the design of better drugs against influenza.

Technical Summary

The influenza A virus (IAV) is responsible for the seasonal flu as well as the recurring global flu pandemics. The WHO has identified the risk of global influenza pandemic as one of the 10 most serious threats to global health in 2019, placing the study of influenza as a high priority for biomedical research. One particularity of IAV is its heterogeneity in shapes and composition suggesting a highly adaptable phenotype in vivo. The importance of this large variability for the virus however remains poorly understood, in part due to the lack of imaging technologies capable of studying the virus at the nanoscale.

My research focusses on exploiting and developing novel imaging technologies, by combining super-resolution microscopy (SRM), high-content screening (HCS) and machine learning, to study the virus from the single molecule, single cell to the population level, essential to understand the role of viral heterogeneity.

Initially, I will develop quantitative structural and genetic analysis to inform on the architecture of the virus assembly and genome at the single virus level. Then, by correlating this high-content data with infectivity assay at the nanoscale, I will explore how modulation of this heterogeneity affects the infectivity of the virus in primary respiratory epithelial cells, the virus' host in vivo. This combination of SRM and HCS has large potentials for its drug screening capabilities. Finally, by following the virus' replication in real time at the entry and assembly stages, I will be able to understand the effect of shape and composition heterogeneity on its mechanisms.

This research is jointly supported by an industrial partner, developing Live Attenuated Influenza Viruses (LAIV) as a vaccine technology, so not only it has the potential to highlight the importance of the virus variability for its replication mechanisms, it will also inform the design of vaccines, joining the global effort to tackle influenza's health and economic burden.

Planned Impact

The World Health Organisation (WHO) has identified the risk of global influenza pandemic as one of the 10 most serious threats to global health in 2019, placing the study of influenza dissemination as a high priority for biomedical research. Currently, the effect of virus shape heterogeneity on the infection fitness of influenza, therapy and vaccines is poorly understood, yet understanding their relations is necessary to provide a complete view of the biology of this virus, and develop new therapeutic approach to tackle influenza's burden.

This research aims at exploiting and developing new imaging methodologies to study the importance of the heterogeneity to influenza's replication, evolution and dissemination. The major societal impact therefore is on enabling the design and development of new therapeutics to prevent or treat influenza infection, mitigating its health and economic burden globally.

My close involvement with the pharmaceutical industry, especially with Astra-Zeneca, on the development of influenza vaccines, using Live Attenuated Influenza Viruses (LAIV), will give me a direct translational avenue, through studying the structural content and replication fitness of the LAIV and therefore directly informing on the efficacy of these vaccines and their modes of production. Further, this research has the potential to establish novel targets against viral entry based on the deep understanding of the influence of structural heterogeneity that will be obtained. Although I will focus on influenza virus, the approach can be applied to the studies of many other important viral pathogens, especially those involved in respiratory diseases.

More fundamentally, this research will generate knowledge about the biology of influenza infection as well as providing a new set of research tools that the research community at large will benefit from. Microscopy remains a central tool to biomedical research and the quantitative high-resolution, high-content microscopy developed here has great potentials for the study of biomolecular and cellular mechanisms in health and disease. Many fields of research will therefore benefit from these developments.

Additionally, this research involves multiple partners from diverse fields that will provide their expertise with a unique focus on the replication of influenza. This network of world-renown experts will foster further collaborations and multi-disciplinary works across universities, research institutes and borders. In particular, this research involves the pharmaceutical industry, the Worldwide influenza centre (located at the Francis Crick Institute), the LMCB labs at UCL as well as bioengineers from the University of California Berkeley.
Finally, we are committed to high-quality education and democratization of our research, involving teaching students at multiple levels as well as engaging with the public about our research and scientific outcomes. We hope that this approach will help generating passion from the next generation of scientists for this important field of research.

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