Viral sequencing on Ion Torrent sequencing systems

Fastest targeted sequencing workflow for viral genomes and gene panels

Ion AmpliSeq™ technology is an easy-to-use enrichment method for targeted sequencing of archived biological samples that have not been cultured. Based on ultrahigh-multiplex PCR, Ion AmpliSeq technology requires as little as 1 ng of input nucleic acid to target sets of genes, making sequencing of limited-quantity or degraded samples more accessible on Ion Torrent™ sequencing systems. You can get data from your precious samples in less than 24 hours.

Creating your own custom panel is simple with the Ion AmpliSeq Designer—a free, online assay design tool that connects you directly to our assay design pipeline. You can upload your own FASTA file reference sequence to have a panel designed for any viral genome. Or browse our Community Panels for infectious disease research, including a panel for Ebola virus (Table 1).


Figure 1. Ion AmpliSeq workflow. Ion AmpliSeq libraries are prepared manually or with the Ion Chef System. Libraries are then placed in the Ion Chef System for emulsion PCR, enrichment, and loading onto Ion S5™ Chips.

Organism EBOV
No. of amplicons 145
No. of pools 2
Genes targeted 99.49% of the EBOV genome
Input required 10 ng RNA
Recommended no. of samples for multiplexing 13 per Ion 520 Chip (2,000x coverage)

Table 1. The Ion AmpliSeq Ebola Research Panel targets 99.49% of the Ebola virus (EBOV) genome with 145 amplicons.

Boots on the ground—sequencing Ebola in Sierra Leone

We needed a workflow that is robust and is relatively straightforward, so the Ion AmpliSeq Ebola Research Panel was perfect for what we wanted to do.
Professor Ian Goodfellow University of Cambridge

Sequencing Ebola in Sierra Leone

Influenza A typing on the Ion Torrent sequencing system

A major challenge for microbiologists and virologists is the prediction of patterns of evolution and emergence of disease agents. RNA viruses like influenza A share the biological feature of high genetic variability, which causes them to appear as clouds of mutants. Influenza A variants also emerge through antigenic shift within animal reservoirs, such as pigs and birds. The World Health Organization estimates that seasonal influenza A is responsible for epidemics that cause approximately three to five million cases of severe illness, and 250,000 to 300,000 deaths annually.

Ion Torrent sequencing enables a streamlined research workflow for complete influenza A genome sequencing. Through use of a set of highly specific, universal influenza primers in combination with a high-fidelity master mix, all eight influenza A genomic segments are amplified in a single tube. The reaction produces DNA amplicons which can then be sequenced on any Ion Torrent™ System to deliver highly accurate influenza A typing in under a day.

Viral typing research literature