Laboratory-based high throughput methods and compositions (e.g., kits) for the detection of pathogen mRNA, including in particular, for the detection of SARS-CoV-2 RNA from up to 85,000 samples in one Illumina NovaSeq sequencing run. These methods may include barcoding cDNA, indexing pools of libraries and intensive use of automatic liquid handling, providing a ready-to-sequence library mix. These methods and compositions may allow a very inexpensive per sample cost and an assay that may be performed in about one day or less.