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Conquering COVID-19 with novel sequencing technologies in clinical settings

Genome sequencing technologies have played an integral role in helping us understand the COVID-19 pandemic. Australia has played a leading role in implementing these technologies in public health settings. While this was effective during prior phases of the epidemic, the ongoing spread of COVID-19 has made it increasingly challenging to continue using a public health-based approach. Furthermore, understanding pathogen characteristics will play an increasingly important role in allowing us to personalise COVID therapies for patients, while detecting emergence of resistance to these therapies. Finally, healthcare-associated transmission remains a significant challenge and the ability to detect hospital outbreaks will play an important role in guiding our infection prevention approaches as COVID-19 becomes an endemic disease. In light of this, we are starting a research program that will aim to use the flexibility of Oxford Nanopore sequencing to understanding SARS-CoV-2 in the clinical microbiology laboratory at Alfred Health. We are seeking students to help lead these endeavours. The broad aims of the project are: 1) Implement existing pipelines for whole genome sequencing for SARS-CoV-2 variant detection in the clinical microbiology laboratory 2) Develop a prospective surveillance program that uses whole genome sequencing to detect emergence of resistance to COVID-19 therapies following treatment 3) Use whole genome sequencing to detect hospital-based outbreaks of COVID-19 Students would be expected to develop skills in computational biology approaches (including command-line programs) to analyse and interpret large datasets. Prior experience using the Unix operating system and the R and Python programming languages is preferred but not essential.
Essential criteria: 
Minimum entry requirements can be found here:
COVID-19; viral genomics; SARS-CoV-2; whole genome sequencing; Nanopore; genomics
Available options 
Masters by research
Time commitment 
Top-up scholarship funding available 
Physical location 
Alfred Centre
Anton Peleg
Jane Hawkey

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