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

• Published in: Journal of virological methods Vol. 280; no. C; p. 113865
• Main Authors: Marine, Rachel L., Magaña, Laura C., Castro, Christina J., Zhao, Kun, Montmayeur, Anna M., Schmidt, Alexander, Diez-Valcarce, Marta, Ng, Terry Fei Fan, Vinjé, Jan, Burns, Cara C., Nix, W. Allan, Rota, Paul A., Oberste, M. Steven
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.06.2020; Elsevier
• Subjects: Caliciviridae - genetics; Costs and Cost Analysis; Gene Library; Genome sequencing; Genome, Viral - genetics; High-Throughput Nucleotide Sequencing - economics; Humans; Next-generation sequencing platforms; Picornaviridae - genetics; RNA viruses; RNA, Viral - genetics; Whole Genome Sequencing - economics; Genome sequencing; RNA viruses; Next-generation sequencing platforms
• ISSN: 0166-0934; 1879-0984
• DOI: 10.1016/j.jviromet.2020.113865

•Sequencing results and cost were compared for three library kits and benchtop sequencers.•Breadth of coverage at genome termini was influenced by library preparation.•The Ion Torrent S5 generates more high-quality reads at lower cost than the PGM.•Indels in homopolymer regions were observed in Ion Torrent S5 consensus genomes.•Illumina MiSeq was the least expensive platform for low-throughput runs. 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.