A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing

• DOI: 10.1371/journal.pone.0294283
• Publication Date: 2023-11-30T18:51:27Z
• Authors: Per A. Adastra; Neva C. Durand; Namita Mitra; Saul Godinez Pulido; Ragini Mahajan; Alyssa Blackburn; Zane L. Colaric; Joshua W. M. Theisen; David Weisz; Olga Dudchenko; Andreas Gnirke; Suhas S. P. Rao; Parwinder Kaur; Erez Lieberman Aiden; Aviva Presser Aiden
• Keywords: Pandemic

Early detection of SARS-CoV-2 infection is key to managing the current global pandemic, as evidence shows virus most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this amplifies entirety genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only few loci. To achieve goal, combine enrichment developed by ARTIC Network ( https://artic.network/ ) short-read DNA sequencing de novo genome assembly. Using method, can reliably (>95% accuracy) detect at concentration 84 equivalents per milliliter (GE/mL). The vast majority methods meeting our analytical criteria that are currently authorized use United States Food Drug Administration Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require higher concentrations degree sensitivity specificity. In addition, assemble in sample, often no gaps perfect accuracy given sufficient viral load. genotypic data these assemblies enable more effective analysis disease spread than possible an ordinary binary diagnostic. These also help identify vaccine drug targets. Finally, show diagnoses obtained using POLAR positive negative clinical nasal mid-turbinate swab samples 100% match those lab Center Control’s 2019-Novel test. POLAR, single person manually process 192 over 8-hour experiment cost ~$36 patient (as December 7 th , 2022), enabling 24-hour turnaround time. We anticipate further testing refinement will allow greater approach.