Project Outline

Zoonotic diseases, like influenza and SARS-CoV-2, can move from animals into humans causing pandemics. However, once zoonotic viruses begin circulating in humans, they adapt to their new environment. For example, a well-defined change leading to adaptation of avian influenza viruses to human cells is the PB2 E627K mutation in the influenza polymerase, which enhances transcription in human vs bird cells [1].

Whilst some of these changes have been documented, it is unclear how the overall morphology of viruses like influenza and SARS-CoV-2 changes as viruses adapt to their new host species, and if any change is maintained as a virus evolves to evade host immunity. This question is not purely academic, but also has profound implications on the accessibilities of epitopes that might be targeted by universal vaccines, which attempt to produce a vaccine that protects against all viral strains, or how virulent a potential new viral strain could be [2].

In this project, we aim to answer this question for influenza, which is a virus that has previously caused several pandemics and will cause pandemics in the future. Influenza has two major glycoproteins on its surface; haemagglutinin (HA) and neuraminidase (NA). There are approximately 300-400 HA and 40-50 NA proteins on the surface of each virion [3]. The aim of this project is to determine how the distribution of HA and NA changes pre and post zoonotic transfers and then through subsequent evolution. It will involve using an array of advanced techniques; protein cross-linking followed by mass spectrometry, super-resolution microscopy and qRT-PCR will be used to determine how the distribution of these proteins changes over time in relation to virus genome copy number [4]. Influenza viruses will be grown in the University of Warick’s new CL3 laboratory. Sialic acid binding assays will also be used to determine how the affinity of HA and NA proteins change as influenza moves host and evolves. Phenotypic changes will also be bioinformatically related to sequence change via the use of association studies.

This is an almost unexplored area of virology – by studying it we hope to elucidate understand how viruses evolve, why they are virulent, and how to make better vaccines to combat them.

References

Techniques

• CL2 and CL3 virus culture
• Bioinformatics
• Molecular Biology (e.g. cloning, PCR, plasmid digestion, western blotting, qRT-PCR, RNA synthesis, protein cross-linking)
• Mass spectroscopy
• Super-resolution imaging