An ongoing challenge for SARS-CoV-2 detection and surveillance is capturing detailed genetic information, up to and including complete genomes, from samples of highly variable quality. While nasopharyngeal swabs are effective for collecting viral particles when they are present, the quantity of particles collected varies depending on a person’s viral load. A surveillance program must be able to generate usable data across that spectrum, and do so in a foolproof, highly automated fashion that can process huge numbers of these swabs in a short amount of time. Rachiglio et al1 published a study recently showing how this can be done with the Ion Torrent Genexus System.
Rachiglio et al collected RNA from nasopharyngeal swabs performed on 27 Italian citizens who had already tested positive for SARS-CoV-2. After viral RNA quantification, they sequenced these samples using the Ion AmpliSeq SARS-CoV-2 Research Panel on the Genexus Integrated Sequencer. They were able to obtain a complete viral genome for 21 of the 27 samples, including all 15 samples with high viral titer (> 200 copies/µl), for the two samples with a viral genome copy number less than 200 but greater than 20, and for 4/10 samples with a viral load below 20 viral copies. This enabled them to identify some samples as belonging to the B.1 and B.1.1 SARS-CoV-2 lineages and to flag and catalog numerous mutations relative to the reference genomes from Wuhan. With low viral titers particularly common among asymptomatic carriers, this sensitivity is critical for truly capturing the spread of SARS-CoV-2 in communities. Similarly, anything that can make SARS-CoV-2 variants of concern (VOCs) easier to detect and discover is a critical breakthrough for predicting their arrival in new locales and preparing accordingly.
The Genexus System effectively combines NGS library preparation, sequencing, and analysis into a single workflow with a single-day turnaround time. Able to process few or many samples at once and to generate complete genome sequences from samples with low viral titers, the Genexus System is an ideal solution for studying the spread of SARS-CoV-2 variants and the role of asymptomatic carriers in propagating this infection. Additionally, the Ion Torrent Genexus System’s highly automated workflow may help standardize SARS-CoV-2 sequencing protocols and improve the speed of novel variant identification, making sure other variants get detected and catalogued sooner and more effectively.
1. Rachiglio AM, L De Sabato, C Roma, et al. (2021) SARS-CoV-2 complete genome sequencing from the Italian Campania region using a highly automated next generation sequencing system. J. Transl. Med. 19(1):246.
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