Massively paralleled multi-patient assay for pathogenic infection diagnosis and host physiology surveillance using nucleic acid sequencing

Abstract

Although this invention as disclosed herein is not limited to specific advantages or functionalities (such for example, detection of severe acute respiratory syndrome coronavirus using next generation sequencing), the invention provides a scalable and massively paralleled screening for infectious pathogens using nucleic acid sequencing. In this approach, biological samples collected from donor are used to assemble agnostic libraries of nucleic acids, each one artificially appended with a prescribed, distinct, and donor-specific barcode, which capture underlying gene expression information from the donor and any infectious pathogens present in the biological sample. Then, to enhance detection of pathogen infection status, donor libraries are subjected to selective enrichment of pathogen-derived nucleic acids via targeted amplification anchored to interspersed, repetitive, evolutionarily conserved and/or genetically functional consensus sequences found across nucleic acids originating from one or many infectious pathogens. Next, nucleic acid libraries from many donors, each flagged with donor-specific barcodes and carrying copies of donor and/or any underlying pathogen-derived gene expression templates, are sequenced in a bolus. After, the collective of sequences read are assigned back to their respective donors based on their synthetic barcodes and bioinformatically aligned to reference host and pathogen genomes. Finally, using machine-learning methods, donors are parsed by their detected infection status and classified under prognostic, evolving or concomitant pathology groups based on sequences read from their respective specimens.