In early 2020 the World Health Organization (WHO) declared a COVID-19 pandemic outbreak. As of March 2023, the Kingdom of Saudi Arabia has reported over 829 thousand cases and over 9 thousand deaths. Due to the public health emergency, the wild-type SARS-CoV-2 genome was fully sequenced early on the pandemic course. Afterward, different viral variants emerged around the world. The variant prevalence fluctuates over time, with some strains presenting increased transmissibility, changes in disease severity, and decreased efficacy of containment measures. In this respect, genomic surveillance and timely data sharing to public repositories represent a tool to track and detect emerging changes that require addressing with public health measurements. However, the Kingdom's genome contribution to the GISAID database represents merely 0.27% of the reported cases. To address this gap, we incorporated whole genome sequencing and the available metadata, to track the circulating viral lineages and identify the variants of concern (VOC) and variants of interest (VOI) over 14 months, from December 2021 to January 2023. We sequenced 581 genomes using the MinION MK1C platform of Oxford Nanopore Technologies (ONT) and assigned the viral lineages, the data primarily derived from COVID-19-positive patients from the city of Jeddah. The VOC Omicron was the principal circulating variant in the country (~99%), which aligns with the global trend. Our report included the sublineages BA.2.75, BQ.1, CH.1.1, XBB, and XBB.1.5, which are under WHO monitoring. We also reported the VOC Delta and the recombinant strains XF, XZ, and XPB. Finally, to validate the use of ONT for genomic surveillance, we compared the data quality of 93 samples sequenced in both ONT MinION and Illumina NaovaSeq platforms. There was 90% correspondence in the Nextstrain clade assignment (84/93) and 78% correspondence in the Pangolin sublineage assignment (73/93). MinION offered a shorter turnaround time, while Illumina produced a consistently higher breadth of genome coverage. In conclusion, the continued viral evolution patterns are reflected in the Kingdom's variant prevalence, where only Omicron circulated by January 2023. Likewise, current Variants Under Monitoring (VUM) were already identified in KSA, highlighting the need for increased genomic surveillance.
| Identifer | oai:union.ndltd.org:kaust.edu.sa/oai:repository.kaust.edu.sa:10754/691532 |
| Date | 04 1900 |
| Creators | Trejos Vidal, Danna |
| Contributors | Pain, Arnab, Biological and Environmental Science and Engineering (BESE) Division, Shuaib, Muhammad, Schmidt, Fabian, Moradigaravand, Danesh |
| Source Sets | King Abdullah University of Science and Technology |
| Language | English |
| Detected Language | English |
| Type | Thesis |
| Rights | 2024-05-07, At the time of archiving, the student author of this thesis opted to temporarily restrict access to it. The full text of this thesis will become available to the public after the expiration of the embargo on 2024-05-07. |
| Relation | N/A |
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