Illumina MiSeq and iSeq platforms yield comparable results for viral genomic sequencing

Illumina MiSeq and iSeq are widely used short-read next-generation sequencing (NGS) platforms. The MiSeq instrument is specialized for mid-range throughput, while the iSeq instrument has lower throughput but is less expensive and simpler to operate. Several studies have compared Illumina platforms for sequencing of a variety of specimen types, but very few have quantified differences in sequencing quality, particularly for viruses. This study compared read quality, single nucleotide polymorphism (SNP) calling, and assembly metrics for SARS-CoV-2, norovirus, and poliovirus samples sequenced on both platforms. MiSeq and iSeq trimmed reads exhibited equivalent percentage of bases ≥ Q30 (% ≥ Q30) and equivalent reference mapping percentages. SNP concordance rates between the two platforms were 41 out of 43 (95.3 %) for SARS-CoV-2, 1628 out of 1633 (99.7 %) for norovirus, and 9 out of 11 (81.8 %) for poliovirus. Within each of the three virus groups, MiSeq and iSeq assemblies had equivalent N50 and maximum contig lengths. Despite platform-specific differences in the sequencing chemistry and flow cell design, MiSeq and iSeq offered comparable data quality, indicating that using either platform should produce concordant results for viral genomic sequencing.