The Ion AmpliSeq SARS-CoV-2 Insight Research Assay, which effectively identifies SARS-CoV-2 variants with >99% genome coverage, has been used to sequence the Omicron variant (B.1.1.529), providing fast, accurate genomic surveillance in under a day.
Omicron, the newly designated SARS-CoV-2 variant of concern, was first reported to the World Health Organization on November 24, 2021. Among the first to detect this new variant were clinical virologist Dr. Allison Glass and her team at Lancet Laboratories in Gauteng, South Africa. According to Dr. Glass, PCR results hinted at the virus’ potential evolution. “We first detected the possibility of a new variant in early November after noticing an S-gene dropout on our SARS-CoV-2 detection using Thermo Fisher’s COVID-19 PCR testing kits,” said Dr. Glass. “By then sequencing these samples in-house with the Ion Torrent Genexus Integrated Sequencer, we were able to analyze and identify the specific virus mutations in less than 24 hours and alert the South African national surveillance program for confirmation and swift action. This speed of testing and sequencing is critical to help inform public health decisions and keep our populations safe through this new variant and those that are yet to emerge.”
Omicron has since been detected in over 20 countries, including the United States, Hong Kong, Australia, Israel, and multiple European nations. While Delta is still the dominant variant in circulation, Omicron’s larger number of mutations (over 30 in Omicron’s spike protein versus 13 in Delta) and potentially greater transmissibility are concerning, causing a wave of new lockdowns and travel restrictions. As we learn more about Omicron’s mutations in the weeks ahead—and how they potentially impact the virus’ ability to escape detection by the immune system—rapid genomic surveillance will be crucial for identifying new mutations and monitoring the spread of this emerging variant.
With highly automated next-generation sequencing (NGS) on the Genexus system, SARS-CoV-2 samples can be fully sequenced in as little as a day, providing detailed information to quickly inform public health initiatives and support local, regional, and global surveillance efforts. Ion Torrent NGS also includes the Ion GeneStudio S5 system, a cost-effective, scalable solution for high-throughput SARS-CoV-2 sequencing. With the intelligent panel design of the Ion AmpliSeq SARS-CoV-2 Insight Research Assay, which is available on both Genexus and GeneStudio S5 systems, emerging and yet unknown variants can be detected with high sensitivity for a variety of samples, including those with low viral loads.
Dr. Iva Dolinová of Liberec regional hospital describes her experience using the Ion AmpliSeq SARS-CoV-2 Insight Research Assay for the Genexus system to detect the first case of the Omicron variant in the Czech Republic. “We have been able to confirm the new Omicron strain in a female patient within less than 24 hours using the very sensitive Ion AmpliSeq SARS-CoV-2 Insight Research Assay,” said Dr. Dolinová, head of the Department of Genetics and Molecular Diagnostics. ‘’This would have not been possible without the fast, automated Ion Torrent Genexus Integrated Sequencer, our committed team and thanks to our collaboration with Thermo Fisher Scientific.”
In addition to rapid turnaround times, SARS-CoV-2 surveillance on Ion Torrent systems provides the scalability and precision to confidently detect emerging SARS-CoV-2 variants, from Delta to Omicron and beyond.
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