School of Science Department of Chemistry 7 The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU, Haibin / CHEM Student: CHANG, Ka Pui / CHEM Course: UROP2100, Fall UROP3100, Spring The recent emergence of the XBB.1.16 variant, also known as Arcturus, demonstrates the COVID-19-causing virus SARS-CoV-2 is still frequently mutating, particularly in its spike glycoprotein. The virus is constantly finetuning its virulence and transmissibility by different modes of mutations such as SAP, deletion, insertion, and N-linked glycosylation. Here, the refined dynamic expedition of leading mutations (deLemus) method, leading mutations by composite metric, a promising method for identifying mutations of interests in the spike and predicting viral evolution, and the online deLemus platform, which is developed to illustrate the mutation landscape and the evolving structure of the spike, both crucial information for monitoring the viral evolutionary dynamics, are introduced. The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU, Haibin / CHEM Student: LEUNG, Cheuk Fung Alvin / BCB Course: UROP2100, Fall UROP3100, Spring UROP4100, Summer The co-translational transfers of carbohydrate moieties onto proteins contribute to their unique physical and biochemical properties. These regiments of sugars regulate various physiological processes, including the lifecycles of viruses. For one, the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) bears a glycan shield which modulates its infectivity and immune escape capability. Even though slight perturbations of the native glycosylation pattern may pose significant impacts on viral fitness, the evolutionary trajectory of potential N-glycosylation sites (PNGSs) remains poorly understood. In this report, PNGS evolution on the SARS-CoV-2 spike would be unravelled. Interestingly, attempts to quantify the spatial geometry of PNGSs on the N-terminal domain suggest that glycan evolution directs their redistributions differentially in the open and closed conformations. The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU, Haibin / CHEM Student: LIN, Sijia / CHEM Course: UROP1000, Summer The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made a great impact on humans in the past few years. Studying the evolution of the SARS-CoV-2 spike (S) protein may help us understand the virus in depth, which could benefit global public health. Different variants of SARS-CoV-2 were analysed in order of priority. Clade assignment, consensus sequence selection, mutation rate calculation and other analyses were performed on the Alpha variant. At the protein level, the pattern of mutation rates obtained using consensus sequences with different thresholds did not match the trend of the number of all Alpha sequences against time. Further analysis will be continued to find out the insight of viral evolution.
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