Sub-project 1 – March 2019
What is Next Generation Sequencing and how is it relevant to disease control?
Next-generation sequencing (NGS) is a novel method to determine the genome sequence of any living organism with high accuracy and at speeds that were not previously thought possible. Using NGS techniques, scientists can extract more, and better, information of viruses in samples collected from infected animals. In the case of FMD, the accurate virus sequence can be used to trace where the virus might have come from and where it has spread to and help disease control teams plan their response tactics during an outbreak.
In collaboration with Duke-National University Singapore, SP1 has developed a method for processing samples taken from the nose and mouth of infected animals, and use these samples to determine the virus sequence directly, without the need to first isolate and grow the virus. This results in a much faster turnaround from sample collection to result, and also a more accurate reflection of the field virus, as we know that mutations occur in the viral genome during adaption to cell culture. Swabs are easier to collect than samples from lesions and the project has shown that saliva and nasal secretions remain positive for virus before lesions are observed and also after they have started healing. There is therefore a better chance of finding virus (if it is there) and ensuring improved investigations during an outbreak.
After generating these sequences, the challenge is then to compute the large amounts of data that result from NGS into information that could be used to assist in control decisions. The SPREAD application developed in SP4 will use the sequence data to trace the movement of the disease with forensic accuracy.
These developments will help guarantee Australia’s successful response to an outbreak and could be used as evidence to help prove when the country has eliminated the disease so exports can resume.
Jacquelyn Horsington left the project at the end of 2018 to take up a position at MSD Animal Health in Boxmeer, the Netherlands. The team wish her well in her new career in pig vaccine development. CSIRO is in the process of filling this vacancy.
Nagendra Singanallur visited the University of Bern in Switzerland to undertake a 3 month sabbatical funded by the Endeavour Executive Fellowships, Department of Education and Training, Government of Australia from 5 August – 26 October 2018. Nagendra underwent training in immunological techniques at the Department of Infectious Diseases and Pathobiology under Professor (Dr) Artur Summerfield. This training will assist the project with new approaches for vaccination in sheep and pigs, assessing the vaccine response by systems immunology-based approach to identify vaccine responders from non-responders.
The SP1 team has represented Australia at various international meetings, with several talks and posters presented at the biennial Open Session of the EUFMD, one of the largest international FMD related conferences.
The Global FMD Research Alliance will hold their biennial FMD conference in Bangkok, Thailand, 29–31 October 2019. More information on this conference and the scientific programme is here.