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class="content-sidebar-wrap"><main class="content"><article class="post-16470 post type-post status-publish format-standard has-post-thumbnail category-infectious-diseases tag-covid-19 tag-csd tag-popular tag-sars-cov-2 entry" aria-label="Variant Surveillance with Single-Day NGS"><header class="entry-header"><h1 class="entry-title">Variant Surveillance with Single-Day NGS</h1> <span class="post-info-author"> By <a href="https://www.thermofisher.com/blog/author/behind-the-bench-staff/" title="Posts by Behind The Bench Staff" rel="author">Behind The Bench Staff</a> </span> <span class="post-info-date"> 04.29.2022 </span> </header><div class="entry-content"><p style="text-align: left"><img decoding="async" class="alignright wp-image-16488 size-full" src="https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2022/04/COL019453-Blog-Shutterstock-Download-resize-Global-F_450x450.jpg" alt="Variant Surveillance with Single-Day NGS" width="450" height="450" srcset="https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2022/04/COL019453-Blog-Shutterstock-Download-resize-Global-F_450x450.jpg 450w, https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2022/04/COL019453-Blog-Shutterstock-Download-resize-Global-F_450x450-300x300.jpg 300w, https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2022/04/COL019453-Blog-Shutterstock-Download-resize-Global-F_450x450-150x150.jpg 150w, https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2022/04/COL019453-Blog-Shutterstock-Download-resize-Global-F_450x450-80x80.jpg 80w" sizes="(max-width: 450px) 100vw, 450px" />As SARS-CoV-2 continues to circulate and evolve, so too does our ability to study it. It’s now clear that <a href="https://www.nature.com/articles/s41467-021-27881-6" target="_blank" rel="noopener">multiple strains of SARS-CoV-2 can co-exist in different tissues</a> and that <a href="https://www.nejm.org/doi/full/10.1056/NEJMc2120219" target="_blank" rel="noopener">the virus can evolve resistance to monoclonal antibodies during an infection</a>. New <a href="https://www.npr.org/sections/goatsandsoda/2022/03/23/1088236568/when-2-coronavirus-variants-meet-inside-1-person-a-frankenstein-hybrid-can-be-bo" target="_blank" rel="noopener">recombinants like “deltacron”</a> have also been discovered that mix-and-match genomic segments from circulating variants. With this many complexities to navigate and world case counts still in the millions, it’s more important than ever to deploy robust tools like full-genome sequencing for variant surveillance.</p> <p style="text-align: left">Microbiology labs can now submit SARS-CoV-2-positive samples for full-genome sequencing instead of using PCR assays for variant detection. Full-genome sequencing can detect novel mutations—eliminating the need for revalidation when a new variant emerges.</p> <p style="text-align: left">In a recent report<sup>1</sup>, Dr. Jennifer Dien Bard describes how her microbiology lab at Children’s Hospital Los Angeles (CHLA) <a href="https://journals.asm.org/doi/pdf/10.1128/jcm.02569-21" target="_blank" rel="noopener">implemented variant surveillance during the emergence of the Omicron variant</a>. All SARS-CoV-2-positive qPCR samples with a viral titer of Ct < 30 were <a href="https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-torrent-genexus-system/infectious-disease-research-solutions/coronavirus-research.html?cid=csd_ngs_sbu_r01_co_cp1507_pjt8468_colchla_0so_blg_il_lgn_at_s00_VarCHLA" target="_blank" rel="noopener">genotyped with NGS</a>. These samples were run in batches of 14 performed twice weekly. With this method, CHLA reported variants within 30 hours of initial qPCR detection, all with a workflow that required only 10 minutes of wet-lab hands-on time. This workflow also required minimal training thanks to on-board library preparation and sequencing with a complete <a href="https://www.thermofisher.com/us/en/home/life-science/sequencing/dna-sequencing/microbial-sequencing/microbial-identification-ion-torrent-next-generation-sequencing/viral-typing/coronavirus-research.html?cid=csd_ngs_sbu_r01_co_cp1507_pjt8468_colchla_0so_blg_il_lgn_at_s00_VarCHLA" target="_blank" rel="noopener">SARS-CoV-2 NGS assay</a> and integrated data analysis with built-in software that automatically listed mutations and calls SARS-CoV-2 variants. With minimal hands-on time, flexible throughput, and rapid sequencing, an integrated sequencer was a great fit for routine SARS-CoV-2 genomic sequencing at CHLA, delivering actionable results in a single day.</p> <p style="text-align: left">All-in-one NGS systems make it easy to implement <a href="https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-torrent-genexus-system/infectious-disease-research-solutions.html?cid=csd_ngs_sbu_r01_co_cp1507_pjt8468_colchla_0so_blg_il_lgn_at_s00_VarCHLA" target="_blank" rel="noopener">full-genome sequencing for microbial and infectious disease research applications</a>, including pathogen identification, <a href="https://www.thermofisher.com/blog/behindthebench/rapid-highly-sensitive-mumps-genotyping-with-ngs/?cid=csd_ngs_sbu_r01_co_cp1507_pjt8468_colchla_0so_blg_il_edu_at_s00_VarCHLA" target="_blank" rel="noopener">epidemiological investigations</a>, <a href="https://www.thermofisher.com/blog/behindthebench/profiling-antimicrobial-resistance-with-next-generation-sequencing/?cid=csd_ngs_sbu_r01_co_cp1507_pjt8468_colchla_0so_blg_il_edu_at_s00_VarCHLA" target="_blank" rel="noopener">antimicrobial resistance profiling</a>, and <a href="https://www.thermofisher.com/blog/behindthebench/easy-rapid-and-routine-sars-cov-2-sequencing/?cid=csd_ngs_sbu_r01_co_cp1507_pjt8468_colchla_0so_blg_il_edu_at_s00_VarCHLA" target="_blank" rel="noopener">variant surveillance</a> – all within as little as one-day turnaround time.</p> <p style="text-align: left">For Research Use Only. Not for use in diagnostic procedures.</p> <p style="text-align: left">1. Fissel, J. A., Mestas, J., Chen, P. Y., Flores-Vazquez, J., Truong, T. T., Bootwalla, M., Maglinte, D. T., Gai, X., & Dien Bard, J. (2022). Implementation of a Streamlined SARS-CoV-2 Whole-Genome Sequencing Assay for Expeditious Surveillance during the Emergence of the Omicron Variant. 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} $.each(elems, function(index, elem) { var inElementsArray = $.inArray(elem, options.elements); var inCacheArray = $.inArray(elem, cache); if (inElementsArray != -1) { options.elements.splice(inElementsArray, 1); } if (inCacheArray != -1) { cache.splice(inCacheArray, 1); } }); }; /* * Throttle function borrowed from: * Underscore.js 1.5.2 * http://underscorejs.org * (c) 2009-2013 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors * Underscore may be freely distributed under the MIT license. */ function throttle(func, wait) { var context, args, result; var timeout = null; var previous = 0; var later = function() { previous = new Date; timeout = null; result = func.apply(context, args); }; return function() { var now = new Date; if (!previous) previous = now; var remaining = wait - (now - previous); context = this; args = arguments; if (remaining <= 0) { clearTimeout(timeout); timeout = null; previous = now; result = func.apply(context, args); } else if (!timeout) { timeout = setTimeout(later, remaining); 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