Whole genome sequencing of SARS-CoV-2 for Canada's COVID-19 genomic surveillance

Simple item page
dc.contributor.authorSeo, Grace
dc.contributor.examiningcommitteeVan Domselaar, Gary (Medical Microbiology and Infectious Diseases)
dc.contributor.examiningcommitteeBooth, Stephanie (Medical Microbiology and Infectious Diseases)
dc.contributor.examiningcommitteeMajer, Anna (Medical Microbiology and Infectious Diseases)
dc.contributor.supervisorBooth, Tim
dc.contributor.supervisorKnox, Natalie
dc.date.accessioned2024-01-12T18:29:28Z
dc.date.available2024-01-12T18:29:28Z
dc.date.issued2023-12-29
dc.date.submitted2023-12-29T16:06:00Zen_US
dc.degree.disciplineMedical Microbiology and Infectious Diseasesen_US
dc.degree.levelMaster of Science (M.Sc.)
dc.description.abstractAt the onset of the COVID-19 pandemic, researchers around the globe joined forces to study the evolutionary biology of SARS-CoV-2 and identify approaches to minimize its spread in the population. Whole genome sequencing (WGS) quickly became the gold standard for monitoring SARS-CoV-2 viral evolution and how it may impact disease severity, transmission, and vaccine efficacy. As a result, researchers demonstrated concerted efforts to develop, optimize, and validate methods for WGS of the novel virus. This research herein optimized wet-lab sequencing protocols developed by the international research group using reverse transcription PCR-tiling and nanopore sequencing technologies to sequence the whole genome of SARS-CoV-2. As a part of the Canadian COVID Genomics Network (CanCOGeN), the work presented in this thesis outlines materials, methods, and results that contributed to the optimization and validation of a Canadian-specific SARS-CoV-2 WGS approach. To achieve this goal, the investigation included identifying the most economical reverse transcriptase, DNA polymerase, PCR primer schemes, library preparation conditions, and comparison of Nanopore and Illumina sequencing platforms. The optimized WGS protocol was shared with the CanCOGeN partners across Canada to increase Canada’s SARS-CoV-2 sequencing capacity towards a sustainable national genomic surveillance program. Throughout this project, the WGS protocol was validated to ensure that emerging variants of concern were detectable. In summary, the current research contributed to operationalizing the first national genomic surveillance program for viral pathogens in Canada. The developed protocol remains in use across Canadian partners and contributes data to support evidence-based decisions for implementing public health measures. Thanks to our work through the CanCOGeN project and its network of expertise, Canada is well-positioned and prepared to perform genomic surveillance of emerging and re-emerging pathogens should a new public health threat arise.
dc.description.noteFebruary 2024
dc.description.sponsorshipResearch Manitoba Master's Studentship (http://dx.doi.org/10.13039/100008794) - https://researchmanitoba.ca/wp-content/uploads/2021/07/ANN_2021-WEB_2021-Trainees-and-NI_Awardees_23Jul21.pdf
dc.identifier.urihttp://hdl.handle.net/1993/37979
dc.language.isoeng
dc.rightsopen accessen_US
dc.subjectCOVID-19 Genomic Surveillance
dc.subjectCanCOGeN
dc.subjectCanada COVID Genomics Network
dc.subjectSARS-CoV-2
dc.subjectSevere Acute Respiratory Syndrome Coronavirus 2
dc.subjectReverse transcription
dc.subjectPolymerase chain reaction
dc.subjectOxford Nanopore Technologies
dc.subjectCanadian Public Health Laboratory Network
dc.subjectGridION
dc.titleWhole genome sequencing of SARS-CoV-2 for Canada's COVID-19 genomic surveillance
dc.typemaster thesisen_US
local.subject.manitobano
oaire.awardNumber498021-2017
oaire.awardTitleNSERC CREATE Visual and Automated Disease Analytics Program Fellowship
oaire.awardURIhttps://vada.cs.umanitoba.ca/profiles/grace-seo
project.funder.identifierhttps://doi.org/10.13039/501100000038
project.funder.nameNatural Sciences and Engineering Research Council of Canada
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Seo, Grace.pdf
Size:
4.59 MB
Format:
Adobe Portable Document Format
Description:
Download
License bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
770 B
Format:
Item-specific license agreed to upon submission
Description:
Download
Collections
FGS - Electronic Theses and Practica