Genomic Characterization of a Post-Omicron Recombinant SARS-CoV-2 Strain: Transition from BA.1 to BA.5 Using Public Data (SRR32480181)

This study presents computational analysis of a recombinant SARS-CoV-2 isolate derived from publicly available FASTQ data (SRR32480181) submitted by Ginkgo Bioworks. The genome shows evidence of recombination between Omicron BA.1 and BA.5 subvariants based on RDP5 and MAFFT alignment. Sample SRR32480181 Strain hCoV-19/USA/VA-GBW-GKISBBBF25035/2025 Clade (Nextclade) 24H (LF.7) Pango Lineage LF.7.3 Recombinant Signal BA.1 + BA.5 hybrid pattern Breakpoint Region ~Position 11,200–11,300 GenBank Submission Submitted via NCBI Portal Key Mutations Identified Unique mutations detected using iVar variant calling at ≥5% allele frequency threshold. RdRp (nsp12): C14408T → P323L– May affect remdesivir binding nsp14: A23403G → A762V– Located near proofreading domain Spike Protein: C241T– UTR mutation A502G → T19R– Antigenic site change T23014C → L452R– Immune escape signal G22578A → T478K– Common in Omicron C23604G → P681H – Enhances cell entry T23599G → S371F– Part of antigenic supersite C23603T → S373P– Strong immune evasion potential C23604A → S375F– Extended Spike motif Recombination Detected Based on RDP5 analysis, this isolate shows mosaic structure between BA.1 and BA.5 subvariants. Detected Breakpoints: Start End Parental Sequences 11288 11296 BA.1 → BA.5 28254 28254 BA.5 → BA.1 Supporting Methods: RDP BootScan Chimaera GeneConv Supporting Files Included File Description SRR32480181_consensus_5.0.fasta Reconstructed genome aligned.fasta MAFFT alignment for RDP5 nextclade.csv Mutation and lineage classification SRR32480181_coverage.png Coverage depth across genome run_full_pipeline.sh Script used for processing README.md This document LICENSE CC-BY 4.0 Notes This work was conducted independently using open-source tools and public data. No institutional funding involved. Recombination patterns suggest ongoing evolution within Omicron descendants. Hybrid strains like this may have altered ACE2 binding and immune evasion profiles. The isolate has been submitted to GenBank for formal classification and will be updated upon acceptance. License This work is licensed under a Creative Commons Attribution 4.0 International License. You are free to share and adapt the material, even commercially, provided you give appropriate credit. Author & Contact Tahir Hussain Bhatti 📧 Email: [e-mail] 🌐 Website: tahirhb.com/reports 🧬 ORCID: 0009-0003-6042-1616