The Univeristy of Melbourne The Royal Melbourne Hopspital

A joint venture between The University of Melbourne and The Royal Melbourne Hospital

EDUCATION

Research Projects

Project: Direct whole genome sequencing of respiratory syncytial virus using nanopore third generation sequencing technology

WHO Collaborating Centre for Reference and Research on Influenza

The WHO Collaborating Centre for Reference and Research on Influenza is also one of the Reference Laboroatories for the WHO Global Respiratory Syncytial Virus (RSV) surveillance program. Human RSV causes severe acute respiratory infection (ARI) in the young and elderly with an estimated 3.2 million hospitalizations and over 100,000 deaths globally each year. Travel restrictions and other non-pharmaceutical interventions (NPIs) for controlling COVID-19 have suppressed many respiratory virus circulations, including RSV.  However, since late 2020, RSV outbreaks have occurred widely in many states of Australia.

Sequencing of RSV is important for monitoring and controlling RSV. RSV is a negative sense, single stranded RNA virus, with a genome of about 15 kb, and there are two subtypes RSV-A and RSV-B. We routinely use Illumina iSeq 100 to sequence the RSV whole genomes which involves multiple RT-PCR reactions and library preparation, which is quite labor and time-intensive. Nanopore technology is the third generation sequencing technology that offers a simpler workflow, long reads, real-time data calling, and the possibility of direct RNA sequencing. The aim for this project is to compare the use of Nanopore MinION against the Illumina iSeq100 for RSV WGS, with a focus on, sensitivity, specificity and accuracy as well as speed and ease of use. In addition, we will explore a novel direct RNA sequencing approach for RSV sequencing. This project offers a unique opportunity to learn a broad range of molecular biology techniques including RNA extraction, RT-PCR, NGS for both MinION and iSeq100, NGS data analysis using pipelines, etc.

Contact project supervisor for further
information and application enquiries

Project Supervisor

Dr Yi-Mo Deng

Project Co-supervisor

Xiaomin Dong

Project availability
Honours

WHO Collaborating Centre for Reference and Research on Influenza

Annette.Fox@influenzacentre.org

2 vacancies

Themes
Immunology
Viral Infectious Diseases
Cross Cutting Disciplines
Discovery Research
Genomics
Epidemiology
Translational and Clinical Research

The WHO Collaborating Centre for Reference and Research on Influenza (WHOCCRI) is a world-class influenza virus surveillance laboratory. A key goal of our work is to identify strategies to improve the immunogenicity and, therefore, effectiveness of influenza vaccines.  It can be challenging to induce immunity against rapidly evolving viruses such as influenza. This is in part due to virus escape from immune recognition, but may also be due to a propensity for vaccines to induce more antibodies against past than current strains.