DOI: 10.6084/m9.figshare.29316056
title: Nucleotide analogue tolerant synthetic RdRp mutant construct for Surveillance and Therapeutic Resistance Monitoring in SARS-CoV-2

description: This dataset comprises a synthetic construct specifically designed to facilitate the development of primers and probes capable of detecting emerging resistant strains of SARS-CoV-2. It serves as a robust reference for genomic surveillance pipelines and provides valuable insights to guide next-generation antiviral design and therapeutic strategies.The main data contributions come from GVAtlas (tahirhb.com/GVAtlas) platform. It has SARS-CoV-2 genomes processed either fully or processed for specific region of SARS-CoV-2. From that massive dataset all publicly available sequences were extracted then a representative consensus genome was built.A local custom AI model was trained on 10 Million historical genomes and data for Q1 of 2025 simulating remdesivir pressure to predict which mutations are likely to emerge under therapeutic selection.Using the output of this locally trained AI model a synthetic RdRp region was generated incorporating those predicted mutations and was inserted into the consensus backbone.This gave me a model-based remdesivir-resistant candidate genome. It is derived from real-world trends and AI-guided evolution.<b>Summary of Mutation Impacts </b>The RdRp (nsp12) mutations introduced into the consensus genome reflect evolutionary pressures simulated using AI model trained under remdesivir-like conditions. These mutations are located in functionally important regions of the polymerase and may collectively influence the enzyme's interaction with <b>nucleotide analogs</b> and its overall fidelity.The <b>P323S</b> mutation, found in motif <b>F</b>, is a known polymorphic site often linked to increased fitness under treatment pressure. It resides at the interface with nsp7 and nsp8, suggesting potential impacts on complex formation or dynamic movement during RNA synthesis.At position 680 (<b>S680N</b>) , the mutation is in proximity to the active site, and while not directly interacting with the incoming nucleotides, it may influence the structural flexibility of the enzyme, allowing the RdRp to better <b>tolerate nucleotide analogs</b> or maintain activity under drug pressure.<b>A685G</b> replaces an alanine with glycine, increasing local flexibility. While alanine is structurally rigid, glycine can induce turns or bends in secondary structures. If this change occurs within a helical region, it may alter the positioning of nearby residues, possibly reducing the affinity of remdesivir during RNA synthesis.The <b>C861K</b> and <b>N866K</b> mutations are notable for their chemical nature. Cysteine plays a crucial role in maintaining tertiary structure via disulfide bridges, and replacing it with a large, positively charged lysine could disrupt local folding or interactions. Similarly, <b>N866K</b> introduces a bulky residue in a region critical for RNA template binding or enzyme dynamics, potentially influencing elongation efficiency or fidelity .Finally, <b>R897K</b>, though a conservative substitution, could modify protein-protein interactions with cofactors or even affect host factor recruitment, indirectly influencing replication efficiency.<b>Files included:</b>3k_consensus_modified.fasta : Final mutant genomemutations_summary.csv : Mutation table for 8 genesremde_resistance_mutations.csv : RdRp-specific mutationsproteins/*.fasta : Translated protein sequences<b>Refrences:</b><b>1</b>- Chen, L., Zhang, Z., Wu, M., & Xiao, J. (2021). Machine learning applications in virus-related research: A review. Briefings in Bioinformatics, 22 (1), 1 14. https://doi.org/10.1093/bib/bbaa104 <br><b>2</b>- Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., & de Hoon, M. J. (2009). 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Nature Genetics, 53 (1), 1 8. https://doi.org/10.1038/s41588-020-00766-z <br><b>11</b>- Agostini, M. L., Pruijssers, A. J., Chappell, J. D., Gribble, J., Lu, X., Andres, S., & Denison, M. R. (2022). Small molecule inhibitors targeting replication enzymes of RNA viruses. Annual Review of Pharmacology and Toxicology, 62 , 253 273. https://doi.org/10.1146/annurev-pharmtox-051221-114943 <br><b>12</b>- Figshare. (2024). Digital repository for research. https://figshare.com <br><b>13</b>- NCBI Resource Coordinators. (2023). GenBank database. National Center for Biotechnology Information . https://www.ncbi.nlm.nih.gov/genbank/ <br><b>Note:</b>This genome represents a candidate for surveillance and vaccine preparedness.Novel mutations include <b>P323S, A685G, R897K</b> in <b>nsp12</b> (RdRp).For any query / related data / files i can be contacted at tahirhb@hotmail.com