Project: Capturing influenza virus with enrichment probes for next generation sequencing
WHO Collaborating Centre for Reference and Research on Influenza
A key function of the WHO Collaborating Centre for Reference and Research on Influenza is to antigenically characterise influenza viruses from patient samples collected across our regions to determine whether they can escape immunity induced by current vaccine, and, if so, select new candidate strains for incorporation into new vaccine formulation.
We routinely carry out next generation sequencing (NGS) of thousands influenza viruses each year. This involves PCR amplification of influenza viruses genomes followed by NGS using Illumina iSeq100. However, this routine approach sometimes fails to generate satisfactory results due to low amounts of virus or RNA degradation in some original samples. One effective way to sequence viruses with low levels or degraded RNA is by using influenza virus specific probes to capture and enrich influenza sequences. Although there are some commercial viral enrichment kits available for respiratory viruses, they are very expensive.
We plan to develop our own probes for influenza virus enrichment. Therefore, the aim of this project is to design and optimize sets of probes specific for various influenza subtypes, to capture influenza virus fragments from original specimens with different viral loads. Once multiple sets of probes for different influenza A and B types are validated to work well, they can be combined as a panel for influenza virus enrichment and NGS. This project offers a unique opportunity to learn broad techniques in bioinformatics and molecular biology, including the use of programs for probe designing and pipelines for NGS data analysis; RNA extraction, RT-PCR and NGS with Illumina iSeq100.
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WHO Collaborating Centre for Reference and Research on Influenza
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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.
WHO Collaborating Centre for Reference and Research on Influenza Current Projects
Research degrees at the Doherty Institute are administered by the University of Melbourne.