The position will focus on a COVID-19 rapid response project aimed at characterizing SARS-CoV-2 viral mutations in vaccinated populations. The proposed research will generate critical data on the interplay between virus evolution and vaccine effectiveness, by identifying and studying potential vaccine escape/resistant mutants. This work will be based at the British Columbia Centre for Disease Control (BCCDC) Public Health Laboratory (PHL). BCCDC is the lead public health organization for surveillance, modelling, research and evaluation, guidelines and policy development for COVID-19 response in British Columbia. BCCDC has continuously been a national leader in building comprehensive COVID-19 linked datasets, operationalizing SARS-CoV-2 sequencing and characterizing the immune response following infection/vaccination. At BCCDC, we have a strong interdisciplinary group scientists, clinicians, and policymakers working in a data-rich environment with many learning and development opportunities. The Department of Pathology is active in many fields of translational research, providing trainees with a broad exposure to projects that improve patient care and outcomes.
The Department of Pathology and Laboratory Medicine at UBC is a hybrid, academically intensive Department within the UBC Faculty of Medicine whose activities span a broad spectrum of teaching, research, and academic service, often performed in the milieu of clinical practice, and are ultimately devoted to improving the care, treatment, and well-being of patients. The Department offers academic degrees at the bachelor’s (Bachelor of Medical Laboratory Science (BMLSc)) and graduate (MSc, PhD) levels with the graduate program, one of the largest in the Faculty of Medicine, which has been recognized by UBC for its quality. The Department plays a major role in the MD undergraduate program and offers an accredited residency-training program. Faculty members participate across a spectrum of research from basic investigative to translational to clinical applied research and are recognized locally, nationally and internationally for their excellence.
The successful candidate will characterize novel SARS-CoV-2 variants that have the potential to escape the vaccine response. The primary responsibility will be analysis of genomic data from whole genome sequencing of SARS-CoV-2 positive diagnostic samples to determine lineage and mutation compositions. The overarching role is to support the genomics/bioinformatics program at the BCCDC PHL. Results will need to be categorized based on vaccine history and potentially other epidemiological metadata, as well as antibody neutralization studies, requiring interdisciplinary teamwork. The candidate will also be involved in data sharing with collaborators outside of BCCDC. Other specific duties include, but are not limited to: developing a plan for analysis with quality measures, writing or updating Research Ethics Board applications, writing reports and manuscripts, communicating results internally as well as with collaborators and stakeholders, and writing grants. The candidate may mentor graduate and undergraduate students.
The successful candidate will work under the supervision of PIs, BCCDC PHL Microbiologists, and Pathology Assistant Professors Drs Agatha Jassem and Natalie Prystajecky as well as with BCCDC PHL Genomics Senior Scientist Dr John Tyson and BCCDC Senior Epidemiologist Dr Hind Sbihi.
- PhD in microbiology, infectious disease, genomics, bioinformatics
- Has basic experience in data analysis pipeline development
- Has experience in genomic data analysis relating to protein structure and function
- Experience with tools such as samtools, bcftools, spades, Unix, BLAST, shovill, prokka, pubMLST, Docker, NextFlow/Cromwell/WDL/Snakemake, Git and GitHub, CI/CD, etc.
- Documented proficiency in sequence data analysis and experience in building biological databases based on SQL
- Documented proficiency in at least one of: Python (preferred), Java, Perl, Shell, R and other modern computer languages
- Experience with data standards including XML is desirable
- Has the ability to integrate various data sources for comparative analyses, keeps meticulous records of data analyses, reports on research progress and outcomes openly, and reviews methodologies in response to feedback
- Has a proven track-record of research accomplishments (i.e. publication record)
- Works well in a goal-oriented team environment
- Possesses excellent communication skills – both verbal and written
- Has the ability to work independently and organize their own workload.
- Works collaboratively with external collaborators and stakeholders
- Has the ability to update knowledge in their specialized area and implements relevant technologies to advance the project
Consequence of Error
Any successful candidate is required to conduct all activities in an ethical manner. Any procedures or data recorded must be accurate and must accurately reflect the work performed. All activities are accountable to the PIs. As data from this effort will be made widely available to a range of data users for surveillance, epidemiological, and policy research, consequences of error could result in erroneous information with negative implications for all of these activities. Confidentiality of highly personal health information and identifiers present in datasets must be protected at all costs.
Start Date and Stipend
This position is available from July 1, 2021 and will initially be for a one-year term with the possibility of extension subject to funding availability, work performance and compliance with UBC policies. Salary will be commensurate with qualifications and experience. Candidates are strongly encouraged to apply for competitive fellowship awards.