A method of assaying a polio virus-derived therapeutic for a polio viral sequence variant, comprising: extracting RNA from a master viral bank or a working cell bank, wherein the master viral bank or the working cell bank comprises host cells containing the polio virus-derived therapeutic; contacting the extracted RNA with 4 U of DNase at 2 U /μl for 20 - 40 minutes at 37°C under conditions that substantially digest host cell genomic DNA and host cell mitochondrial DNA, but do not substantially digest viral RNA molecules, thereby generating enriched viral RNA; inactivating the DNase; producing double-stranded cDNA from the enriched viral RNA using oligo(dT) x primers, thereby generating viral double-stranded cDNA; amplifying the viral double-stranded cDNA; quantifying the viral double-stranded cDNA; producing a sequencing library from 500 pg to 1 ng of the viral double-stranded cDNA by randomly fragmenting the double-stranded cDNA to produce cDNA fragments, ligating 5' adaptors and 3' adaptors to the cDNA fragments to produce adaptor-ligated cDNA fragments, and amplifying the adaptor-ligated cDNA fragments to produce the sequencing library; clonally amplifying the sequencing library using surface-bound oligonucleotides complementary to the 5' adaptors and the 3' adaptors to produce a clonally amplified sequencing library; sequencing the clonally amplified sequencing library using parallel single-end or paired-end sequencing to produce a raw sequence dataset comprising a plurality of sequence reads; aligning the plurality of sequence reads with a reference polio sequence for the polio virus-derived therapeutic to produce an aligned sequence containing a plurality of aligned sequence reads; and determining polio viral sequence variants from the aligned sequence. extracting RNA from a master viral bank or a working cell bank, wherein the master viral bank or the working cell bank comprises host cells containing the polio virus-derived therapeutic; contacting the extracted RNA with 4 U of DNase at 2 U /μl for 20 - 40 minutes at 37°C under conditions that substantially digest host cell genomic DNA and host cell mitochondrial DNA, but do not substantially digest viral RNA molecules, thereby generating enriched viral RNA; inactivating the DNase; producing double-stranded cDNA from the enriched viral RNA using oligo(dT) x primers, thereby generating viral double-stranded cDNA; amplifying the viral double-stranded cDNA; quantifying the viral double-stranded cDNA; producing a sequencing library from 500 pg to 1 ng of the viral double-stranded cDNA by randomly fragmenting the double-stranded cDNA to produce cDNA fragments, ligating 5' adaptors and 3' adaptors to the cDNA fragments to produce adaptor-ligated cDNA fragments, and amplifying the adaptor-ligated cDNA fragments to produce the sequencing library; clonally amplifying the sequencing library using surface-bound oligonucleotides complementary to the 5' adaptors and the 3' adaptors to produce a clonally amplified sequencing library; sequencing the clonally amplified sequencing library using parallel single-end or paired-end sequencing to produce a raw sequence dataset comprising a plurality of sequence reads; aligning the plurality of sequence reads with a reference polio sequence for the polio virus-derived therapeutic to produce an aligned sequence containing a plurality of aligned sequence reads; and determining polio viral sequence variants from the aligned sequence.