![]() ![]() Similarly, the Ion Torrent technology is available in several models, producing data outputs from 30 megabases (Mb) to 25 Gb per chip. In microbial research laboratories, the MiSeq platform is convenient for sequencing small microbial genomes (i.e., viruses and bacteria) compared to the larger-output Illumina platforms, that are more appropriate for eukaryotic genomes or very large studies, due to the balance of system/reagent costs and required sequencing depth ( Glenn, 2011 Vincent et al., 2017). Illumina produces several benchtop and production-scale sequencers with data outputs varying from 0.144 gigabases (Gb) to 6 terabases (Tb) ( Kumar et al., 2019). Over the past several years, the suppliers of mainstream high-capacity short-read sequencers have been reduced to two manufacturers: Illumina (sequencing-by-synthesis technology) and Thermo Fisher Scientific (Ion Torrent semi-conductor sequencing technology) ( Heather and Chain, 2016). NGS methods are also useful for identifying pathogens in syndromes where etiologies often remain unknown (e.g., encephalitis, febrile illness), complementing or even replacing current diagnostic methods ( Perlejewski et al., 2015 Yozwiak et al., 2012). The exponential growth of genomic information generated for important pathogens has provided increased resolution for molecular epidemiology, as well as information necessary for the design of clinical assays and therapeutics ( Barzon et al., 2013 Koser et al., 2012 Lefterova et al., 2015). NGS has been used extensively for routine surveillance and outbreak investigation of numerous viral RNA pathogens. However, the expansion of next-generation sequencing (NGS) technologies has increased demand for high-throughput sequencing of genomes at a lower cost ( Metzker, 2010). These findings suggest that the Ion Torrent S5 and Illumina MiSeq platforms are both viable options for genomic sequencing of RNA viruses, each with specific advantages and tradeoffs.Ĭonventional Sanger sequencing has been the gold standard for genomic analysis of pathogens in public health laboratories for over three decades. ![]() For lower throughput sequencing runs (i.e., Ion Torrent 510 and Illumina MiSeq Nano V2), the cost per sample was lower on the MiSeq platform, whereas with higher throughput runs (Ion Torrent 530 and Illumina MiSeq V2) there is less of a difference in the cost per sample between the two sequencing platforms ($5.47-$10.25 more per sample for an Ion Torrent 530 chip run when multiplexing 24 samples). However, indels at homopolymer regions impacted the accuracy of consensus genome sequences. The Ion Torrent S5 510 chip runs produced more reads at a lower cost per sample than the highest output Ion Torrent PGM 318 chip run, and generated the highest proportion of reads for enterovirus D68 samples. The choice of library preparation kit and sequencing platform was found to impact the breadth of genome coverage and accuracy of consensus viral genomes. The specimens were processed, using combinations of three library preparation and five sequencing kits, to assess the quality and completeness of assembled viral genomes, and an estimation of cost per sample to generate the data was calculated. The Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5 platforms were evaluated using a panel of sixteen specimens containing picornaviruses and human caliciviruses (noroviruses and sapoviruses). While Illumina® and Ion Torrent® sequencing platforms are used extensively for generating viral RNA genome sequences, there is limited data comparing different platforms. Next-generation sequencing is a powerful tool for virological surveillance.
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