Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses

Abstract

28Next-generation sequencing is a powerful tool for virological surveillance. While 29 Illumina® and Ion Torrent® sequencing platforms are used extensively for generating 30 viral RNA genome sequences, there is limited data comparing different platforms. We 31 evaluated the Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5 platforms using a 32 panel of sixteen specimens containing picornaviruses and human caliciviruses 33 (noroviruses and sapoviruses). The specimens were processed, using combinations of 34 three library preparation and five sequencing kits, to assess the quality and 35 completeness of assembled viral genomes, and an estimation of cost per sample to 36 generate the data was calculated. The choice of library preparation kit and sequencing 37 platform was found to impact the breadth of genome coverage and accuracy of 38 consensus viral genomes. The Ion Torrent S5 outperformed the older Ion Torrent PGM 39 platform in data quality and cost, and generated the highest proportion of reads for 40 enterovirus D68 samples. However, indels at homopolymer regions impacted the 41 accuracy of consensus genome sequences. For lower throughput sequencing runs (i.e., 42 Ion Torrent 510 or Illumina MiSeq Nano V2), the cost per sample was lower on the 43 MiSeq platform, whereas with higher throughput runs (Ion Torrent 530 or Illumina MiSeq 44 V2) the cost per sample was comparable. These findings suggest that the Ion Torrent 45 S5 and Illumina MiSeq platforms are both viable options for genomic sequencing of 46 RNA viruses, each with specific advantages and tradeoffs.47 48Conventional Sanger sequencing has been the gold standard for genomic analysis of 49 pathogens in public health laboratories for over three decades. However, the expansion 50 of next-generation sequencing (NGS) technologies has increased demand for high-51 throughput sequencing of genomes at a lower cost (1). NGS has been used extensively 52 for routine surveillance and outbreak investigation of numerous viral RNA pathogens. 53The exponential growth of genomic information generated for important pathogens has 54 provided increased resolution for molecular epidemiology, as well as information 55 necessary for the design of clinical assays and therapeutics (2-5). NGS methods are 56 also useful for identifying pathogens in syndromes where etiologies often remain 57 unknown (e.g., encephalitis, febrile illness), complementing or even replacing current 58 diagnostic methods (2, 6, 7). 60Over the past several years, the suppliers of high-capacity short-read sequencers have 61 been reduced to two manufacturers: Illumina (sequencing-by-synthesis technology) and 62 Thermo Fisher Scientific (Ion Torrent semi-conductor sequencing technology) (3). 63 Illumina platforms have been used to generate nearly 90% of NGS data worldwide 64 (https://www.wired.com/2016/02/gene-sequencing-goliath-wants-get-bigger-still/). 65Illumina produces several benchtop and production-scale sequencers with data outputs 66 varying from 1.2 gigabases (Gb) to 6 terabases (Tb). In mic...

Method for quick DNA barcode reference library construction

“…Both platforms have been used on DNA metabarcoding of environmental samples (Deagle et al., 2013 ; Evans et al., 2016 ; Fantini et al., 2015 ; Schmidt et al., 2013 ). The operational taxonomic units (OTUs) from the environmental samples were much more than actual situations, and it is one major concern whether these two platforms are suitable for conventional DNA barcodes or not (Lahens et al., 2017 ; Marine et al., 2020 ; Quail et al., 2012 ; Speranskaya et al., 2018 ).…”