Next-Generation Sequencing (NGS) is the cutting edge of genome sequencing technology, but expanding this technology beyond academic research centers and large institutions has been challenging. Some labs may lack the staffing or expertise to perform traditional NGS workflows, or they want to run smaller, more frequent batches than existing solutions can offer. This need for broader access to easy, rapid, and routine NGS has only intensified with the SARS-CoV-2 pandemic, as genomic surveillance relies on a wide sequencing network to detect new variants and monitor changes in viral composition across regions. Implementing SARS-CoV-2 surveillance across more labs continues to be a slow and difficult process. But as Dr. Paul Hofman of the Laboratory of Clinical and Experimental Pathology at the Centre Hospitalier Universitaire of Nice, France, demonstrates, the Genexus Integrated Sequencer is an all-in-one NGS solution designed for frequent, low-volume use, making it ideal for SARS-CoV-2 genomic surveillance in smaller labs around the world.
“Complete genomic sequencing needs to be accessible to a large number of laboratories and not only a few referent centers of expertise.” – Dr. Paul Hofman
Easily add SARS-CoV-2 surveillance to your workflow
All-in-one solutions like the Genexus system are ideal for laboratories that are just getting started with next-generation sequencing and do not want to, or cannot, invest in a large amount of expensive equipment and additional staffing to serve it. Genexus requires far fewer personnel than typical NGS systems, making it a good fit for smaller labs where people often serve many different roles as needed and lab space is at a premium.
Rapidly report SARS-CoV-2 variants
The core strength of the Genexus system for epidemiological surveillance is its speed. Genexus provides a swift turnaround time for SARS-CoV-2 sequencing and can perform sequencing runs on a daily basis, allowing users to rapidly analyze samples and build a picture of the viral genomes in their region. In his recent publication1, Dr. Hofman shares his workflow for daily SARS-CoV-2 sequencing on the Genexus system. His lab found that on average, they can go from sample collection to report in 30 hours, with only five minutes of hands-on time to set up the sequencing run. With its automated cDNA synthesis, library prep, template prep, and sequencing, the Genexus workflow removed the need for dedicated operators and enabled responses to collected samples within days.
Routinely sequence a wide range of SARS-CoV-2 samples
Epidemiological surveillance at the scale needed to stay ahead of the SARS-CoV-2 pandemic requires being able to sequence samples from patients with low viral loads, including asymptomatic patients, since these vastly outnumber hospitalizations. If only hospital-level samples are sequenced, this provides a skewed reading of the viral strains circulating in the larger population. The Genexus system is not only sensitive enough to generate robust sequences from samples taken from patients with low viral loads, it can do so from multiple sample types, including nasopharyngeal swabs and saliva. For example, Dr. Hofman’s team found excellent concordance in SARS-CoV-2 sequencing results for matched nasopharyngeal swabs and saliva samples, supporting more widespread use of saliva samples as a convenient collection method for SARS-CoV-2 surveillance.
With these strengths, it is now feasible to rapidly set up NGS in any academic hospital using the Ion AmpliSeq SARS-CoV-2 Assay and the Genexus system. The Genexus system’s rapid turnaround time, extensive workflow automation, and seamless informatics and data upload can help more investigators obtain epidemiological insights and contribute them to public SARS-CoV-2 data repositories, helping lawmakers and public health officials make informed decisions.
Watch a webinar by Dr. Paul Hofman on Pivoting from cancer to COVID-19 in a global pandemic
1. Hofman P, O Bordone, E Chamorey, et al. (2022) Setting-Up a Rapid SARS-CoV-2 Genome Assessment by Next-Generation Sequencing in an Academic Hospital Center (LPCE, Louis Pasteur Hospital, Nice, France). Front. Med. 8.
For Research Use Only. Not for use in diagnostic procedures.