Next-generation sequencing is a powerful tool for virological surveillance. While Illumina® and Ion Torrent® sequencing platforms are used extensively for generating viral RNA genome sequences, there is limited data comparing different platforms. 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). 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 choice of library preparation kit and sequencing platform was found to impact the breadth of genome coverage and accuracy of consensus viral genomes. 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. However, indels at homopolymer regions impacted the accuracy of consensus genome sequences. 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). 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.

中文翻译：

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Illumina MiSeq 与 Ion Torrent PGM 和 S5 平台对小核糖核酸病毒和杯状病毒进行全基因组测序的比较。

下一代测序是病毒学监测的强大工具。虽然 Illumina® 和 Ion Torrent® 测序平台广泛用于生成病毒 RNA 基因组序列，但比较不同平台的数据有限。使用一组包含小核糖核酸病毒和人类杯状病毒（诺如病毒和沙波病毒）的 16 个样本对 Illumina MiSeq、Ion Torrent PGM 和 Ion Torrent S5 平台进行了评估。使用三个文库制备和五个测序试剂盒的组合对样本进行处理，以评估组装的病毒基因组的质量和完整性，并计算每个样本生成数据的成本估计。研究发现文库制备试剂盒和测序平台的选择会影响基因组覆盖的广度和共有病毒基因组的准确性。与最高输出的 Ion Torrent PGM 318 芯片运行相比，Ion Torrent S5 510 芯片运行以更低的每个样本成本产生了更多的读数，并且为肠道病毒 D68 样本生成了最高比例的读数。然而，同聚物区域的插入缺失影响了共有基因组序列的准确性。对于较低通量的测序运行（即 Ion Torrent 510 和 Illumina MiSeq Nano V2），MiSeq 平台上每个样品的成本较低，而对于较高通量的运行（Ion Torrent 530 和 Illumina MiSeq V2），每个样品的成本差异较小两个测序平台之间每个样本的成本（当复用 24 个样本时，Ion Torrent 530 芯片运行每个样本的成本要高出 5.47-10.25 美元）。这些发现表明，Ion Torrent S5 和 Illumina MiSeq 平台都是 RNA 病毒基因组测序的可行选择，各自具有特定的优势和权衡。