Viral Typing Research
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.
Table 1. The Ion AmpliSeq Ebola Research Panel targets 99.49% of the Ebola virus (EBOV) genome with 145 amplicons.
|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)|
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
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 semiconductor sequencing has been paired with PathAmp™ FluA reagents to provide a streamlined research workflow for complete influenza A genome sequencing. PathAmp™ FluA reagents are a set of highly specific, universal influenza primers combined with a high-fidelity master mix for the amplification of all eight influenza A genomic segments in a single tube. The reaction produces DNA amplicons which can then be used for Ion Torrent™ System sequencing to deliver highly accurate influenza A typing in under a day.
Viral typing research literature
Briese T, et al. 2014. Middle East respiratory syndrome coronavirus quasispecies that include homologues of human isolates revealed through whole-genome analysis and virus cultured from dromedary camels in Saudi Arabia. mBio 5(3):e01146-14.