An integrated bioinformatics and computational biophysics approach to enterovirus surveillance and research
Creators: name: Roberts, Jason
Publisher: name: RMIT University
Year: 2024

description: This PhD thesis examines the integration of complex computational methodologies with the surveillance and research of a genus of viruses implicated in a wide variety of clinical conditions, ranging from asymptomatic infection to death. These viruses, known as the enteroviruses, are some of the most studied viruses in history and as a result are represented by a vast body of literature. The fact that enterovirus research and surveillance rests upon such an extensive foundation of published material, makes enteroviruses a perfect candidate for the experimental application of modern computational methods, or in-silico experimentation. The hypothesis that computational power currently available can be utilised for multiple stages of virus study incorporating identification, epidemiology and atomic structure prediction forms the basis of this thesis. Fundamental to the understanding of virus behaviour is the determination of molecular structure and function, a fact which applies not only to viruses, but to biological entities in general. Extensive work was performed during the course of this thesis in adapting classical molecular dynamics techniques to the large scale simulation of a prototype poliovirus, using millions of simulated atoms. The successful application of these techniques has resulted in microsecond-timescale, atomistic simulations of complete virus particles. These simulations represent the first published instance of the simulation of a biologically complete pathogenic microorganism, incorporating the encoding genetic information. This thesis also examines the use of bioinformatics methods in the development and application of an advanced quantitative multiplex real-time reverse-transcription polymerase chain reaction (qRT-PCR) methodology, for the primary screening of samples from patients suffering acute flaccid paralysis (AFP), which is one of the most debilitating presentations of enterovirus infection. The application of this novel qRT-PCR method reduces the initial screening time of samples derived from a symptomatic patient from 4-5 days using virus culture, to four hours using the novel qRT-PCR. This novel qRT-PCR method can be rapidly scaled-up in response to an outbreak situation. The ability to screen large numbers of samples during an outbreak situation is important and is hampered when using virus culture methods exclusively. In Australia and the Western Pacific region over the last decade, the rate at which non-polio enteroviruses in cases of AFP have been identified, is on average 18%. With the introduction of PCR screening methods, a number of non-cultivable enteroviruses were identified, along with newly described and a previously undescribed enterovirus. Little is known about these newly described and novel enteroviruses. This thesis aimed to investigate the identification of viruses that may represent a significant public health threat and to then use their genetic sequence information to recreate major virus structural components in-silico. This reconstruction process was achieved by exploiting advances in comparative protein modelling and molecular dynamics simulation methods. In order to apply these methods to the reconstruction of previously undescribed viruses for which no structural data exist, validation of different comparative protein modelling techniques was required. The predictive in-silico methods generated reliable atomic coordinates, representing structures suitable for the reconstruction of virus capsid models for further study.