UROP Proceedings 2021-22

School of Science Department of Chemistry 5 The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU Haibin / CHEM Student: CHANG Ka Pui / CHEM Course: UROP1100, Summer The COVID-19-causing virus SARS-CoV-2 have mutated frequently since its debut in December 2019, mainly in its spike glycoprotein. By having the combination of different types of amino acid mutations in the spike, for example, amino acids substitution on a site (SAP) which may have altering chemical properties, deletion and glycosylation, commonly N-linked glycosylation, the emerged variants have quite distinct viral properties such as a change in virulence or transmissibility. Here, sequence tracking is used to detect a pattern of mutations using representative sequences found before the emergence of VoC/VoI, to account for their viral properties, effects to the pandemic and to have a more accurate prediction for the next VoC/VoI. The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU Haibin / CHEM Student: JUSMIN Frederick Gabriel / CHEM Course: UROP1000, Summer The rapid mutation of SARS-CoV-2 leads to the emergence of new variants and numerous key mutations which are conserved in the viral genome. The positive selection of these mutations produce evolutionary adaptations allowing the virus to be more infectious and more virulent. As a way to track new mutations appearing in future sequences, a moving reference chosen from past sequences with highest genetic similarity is used instead of the original strain. Through observation of monthly plots, leading counts in mutated sites reveal some insights to key mutations which later appear in SARS-CoV-2 variants while counts of reference sequences shows the previous key mutations. Additionally, further analysis of these mutated sites will definitely be a contributing factor to determine the evolutionary trajectory of SARS-CoV-2. The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU Haibin / CHEM Student: LAM Chak Fai / CHEM Course: UROP1100, Spring UROP2100, Summer COVID-19 pandemic has been affecting the world for almost 3 years, continuous records of mutations of the acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were made. Spikes proteins in the new variants are mutated with improvements in both transmissibility and immune escape, leaving the lives of billions in danger. Investigations and predictions of the spike glycoproteins of SARS-CoV-2 mutation, which is the key to the entrance into target cells, are done worldwide. Using the data from January 2022 to June 2022 in the GISAID hCoV-19 database, this report aims to compare different approaches that assist the tracking of emerging variants. Data of dynamic expedition of leading mutations (deLemus) and escape fraction are the two methods used to compare with the results of this report for further analysis.