Optimising the laboratory response to outbreaks caused by novel viruses

This thesis has 3 related aims that are linked to experiences working in the Virus Identification Laboratory at the Victorian infectious diseases reference laboratory (VIDRL) in Melbourne, Australia. This laboratory provides diagnostic services to major Victorian hospitals and specialised infectious diseases clinics, as well as a reference service to the Victorian Health Department. The aims of the thesis relate to practical issues experienced during the 2009 influenza A H1N1 pandemic (chapter 3) and to the area of public health involving the capacity to detect novel viruses that may emerge and cause morbidity and mortality at significant levels (chapters 4 and 5). In the first experimental chapter (Chapter 3) I present the results of a study investigating optimal swab types and transport media and the role of specimen transport conditions on the results of polymerase chain reaction (PCR) testing. This is followed in Chapter 4 by a description of the validation and design of a large number of consensus PCR assays to detect viruses across a wide range of virus families. The strategy of using multiple consensus PCR assays provides an alternative to existing virus isolation cell-culture systems when a novel virus may not grow or high throughput sequencing methods involving cloning of nucleic acids of viruses directly from clinical material which may take too long. When confronted with a novel virus or zoonotic syndrome causing significant community disruption, the panel of consensus PCRs could be rapidly employed, along with virus isolation methods as a primary screening tool to identify the agent responsible. In Chapter 5, several specimen panels, including one containing a large number of CSF samples from patients with encephalitis of unknown aetiology were tested in the developed PCR assays with the aims of demonstrating the utility of the assays, and possibly identifying novel viruses in one such targeted syndrome