Our group
RNA viruses are the source of numerous outbreaks over the past few years. We focus on the evolution of these viruses in the host and between hosts. However, we primarily focus on the viral diversity produced by RNA viruses and its interaction with the host. The RNA virus evolution group uses standard virological techniques combined with sequencing and large data analysis including machine learning to develop a greater insight into the evolution and transmission of these viruses.
Our aims
The aim of my group is to understand the complex interplay of RNA viruses in the host. We focus on all levels, the interaction of the RNA virus in the host cell, at the molecular level, the tissue level and at the organism level.
At every point we are focused on the role of the ability of RNA viruses to produce mutations that function as a single entity, working together to produce an environment in which the virus can replicate and transmit. We look to understand what happens when we perturb this environment and reduce the amount of mutations or increase the amount of mutations. We are also interested in how this affects the host cell responses and use machine learning to interrogate the interactions between the host and the virus.
Our research
Our research focuses on the ways in which RNA viruses replicate and interact within the host cell, and how this impacts the transmission and emergence of the virus. We focus primarily on the diversity produced as a result of replication by the RNA-dependent RNA-polymerase which generates a cloud of mutations. We are looking at this from several perspectives.
Identifying the role that these minority variants play in affecting the host cell and providing a successful environment for the cell. Some of these mutations are found repeatedly even after severe bottlenecks that reduce the likelihood of these mutations being found. It is likely therefore, that they have some function that aids the virus.
What is the role of these mutations in the secondary structure of the RNA genome. Do the mutations influence the secondary structure or is the secondary structure influenced by the RNA genomes.
How do viruses account and manage the number of non-functional genomes? Are they using cell processes to eliminate non0functional genomes. We have some evidence that when we alter the mutation rate, we alter the number of productive genomes and this maybe what leads to attenuation. We are investigating this.
Additionally, we are interested in the bigger picture, how the diversity allows the virus to successfully complete its transmission cycle, particularly for mosquito-borne viruses, when the virus must infect two hosts. Additionally, how the early replication in the host sets the stage for later infection.
Our impact
Our research will provide a better understanding of the emergence of viruses from the environment. We focus on endemic viruses and look to see how often and what mechanisms they use to emerge from the environment. In addition, understanding these mechanisms provides scope for identifying key viral mutations that facilitate the switch to epidemic states and understand the drivers that sustain endemic transmission, currently an understudied part of virus transmission and emergence. Given that most viruses emerge from endemic cycles, it is imperative to understand these cycles to be able to prevent the emergence of novel viruses from the environment for both animal and human pandemics.
