{"id":14662,"date":"2020-10-23T19:13:52","date_gmt":"2020-10-23T19:13:52","guid":{"rendered":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/?p=14662"},"modified":"2021-04-09T16:13:11","modified_gmt":"2021-04-09T16:13:11","slug":"sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/","title":{"rendered":"Sequencing dominant SARS-CoV-2 strain in suburban, southern U.S. region"},"content":{"rendered":"

<\/p>\n

While many technologies can be used to determine presence or absence of the SARS-CoV-2 virus in a sample, there is also an immediate need for epidemiological research to track viral transmission patterns, including identification of mutations within the viral genome. One key mutation is found in the SARS-CoV-2 spike protein gene, which influences cell entry and is a key target for vaccine development research. Identifying all variants in a SARS-CoV-2 genome in a given sample from a collection of samples can be accomplished by targeted next-generation sequencing (NGS), which enables sequencing of the complete SARS-CoV-2 viral genome and provides variant-level information that other molecular methods cannot.<\/p>\n

Dr. Dirk Dittmer, Professor and Director of Virology and Global Oncology Programs at the UNC Lineberger Comprehensive Cancer Center and UNC Viral Genomics Core facility at UNC-Chapel Hill, is leveraging NGS for his research that focuses on the discovery of new viruses. Initially, his lab worked to discover viruses associated with cancers and most recently in respiratory infections, which enabled him to quickly pivot to SARS-CoV-2 research as the virus moved from urban travel centers into less densely populated areas in North Carolina.<\/p>\n

In SARS-CoV-2 and infectious disease applications, molecular methodologies like qPCR and NGS are complementary tools and equally vital as each serves a unique purpose. Because qPCR focuses on detecting specific key targets, such as the spike protein for SARS-CoV-2, this technology is regularly used in healthcare settings to determine the presence of a viral pathogen.<\/p>\n

On the other hand, Dr. Dittmer says NGS can provide more information of critical scientific value, as it enabling sequencing of the entire viral genome to identify critical viral genome variants that inform viral evolution, disease risk and severity, and host response. He explains that the idea of sequencing viruses is a well-established and proven method to track infections and person-to-person transmission patterns for other viral pathogens like influenza and HIV.<\/p>\n

Dr. Dittmer applies the same principles for his studies in immunodeficiency and HIV\/AIDS to his research of the SARS-CoV-2 virus, leveraging targeted NGS to identify super-spreaders and super-spreading events.<\/p>\n

“We need to know if the virus spreads and evolves differently in different communities that differ by geography, race, ethnicity, preferred mode of transport and congregation. Sequencing an entire viral genome does not make any assumptions about which genes are important in any particular situation, allowing us to discover regions of the SARS-CoV-2 virus that no one has ever considered [and] gives us a footprint of evolutionary forces,” he says.<\/p>\n

He hopes the insights gleaned from sequencing the entire viral genome will generate new insights about the biology of SARS-CoV-2 and novel drug targets that could inform vaccine development research.<\/p>\n

Dr. Dittmer and his team have been studying a specific strain of the SARS-CoV-2 virus most commonly found in North Carolina<\/a> since the beginning of the global crisis[1]. This particular strain has a mutation in its spike protein called D614G that appears to be more contagious than the original strain from Asia. Since NGS enables analysis of specific viral strains and can be used to identify potential mutations that may occur in the spike protein, the data collected can be crucial for vaccine research. Any potential mutation in the spike protein will need to be taken into consideration during vaccine development research, or else it may render a vaccine candidate less effective as the virus continues to evolve.<\/p>\n

For his research, Dr. Dittmer and his team use the highly automated Ion Torrent Genexus System<\/a>, which makes NGS accessible to almost any lab. He describes it as “a closed system that takes care of even the bioinformatics for pre-defined assays” like the Ion AmpliSeq SARS-CoV-2 Research Panel<\/a>. When used together, the Ion Torrent Genexus Integrated Sequencer and Ion AmpliSeq SARS-CoV-2 Research Panel<\/a> enables automated sample-to-variant report NGS in under a single day.<\/p>\n

“For SARS-CoV-2 and any other scenario that has the purpose of informing decision-making, any turnaround time greater than twenty-four hours is a non-starter,” he says.<\/p>\n

In addition to rapid turnaround time, an added benefit of the Genexus System is sample flexibility, to help keep running costs low in his other research efforts.<\/p>\n

“When we perform NGS in cancer clinical trials, the samples are collected over months and run together in batches. In this scenario, cost, precision and accuracy is more important than speed.”<\/p>\n

The automation capabilities of Ion Torrent NGS allow Dr. Dittmer’s team to eliminate all hand pipetting steps for the SARS-CoV-2 assay, allowing them to “track every error which makes all the difference in reporting actionable information.”<\/p>\n

Finally, Dr. Dittmer highlights the use of the Ion GeneStudio S5 series system<\/a> as a complement to the Genexus System, primarily as a discovery and training platform as they develop workflows to study other infectious diseases. This scalable NGS system enables higher throughput and is flexible to run a broad range of infectious disease research applications, including host and immune response, microbiome analysis and transcriptome studies<\/a>.<\/p>\n

Contributions from researchers like Dr. Dittmer increase our understanding of the SARS-CoV-2 biology and transmission patterns, enabling more confidence in approaches to potential vaccine development and therapeutics to help minimize the impact of the virus.<\/p>\n

Request a virtual demo to experience the Ion Torrent Genexus System> <\/a><\/p>\n

Read the press release featuring Dr. Dittmer’s research><\/a><\/p>\n

For Research Use Only. Not for use in diagnostic procedures.<\/p>\n

Reference:
[1] McNamara, R.P., Caro-Vegas, C., Landis, J.T., Moorad, R., Pluta, L.J., Eason, A.B., Thompson, C., Bailey, A., Villamor, F.C.S., Lange, P.T., Wong, J.P., Seltzer, T., Seltzer, J., Zhou, Y., Vahrson, W., Juarez, A., Meyo, J.O., Calabre, T., Broussard, G., Rivera-Soto, R., Chappell, D.L., Baric, R.S., Damania, B., Miller, M.B., Dittmer, D.P., High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States, Cell Reports (2020), doi: https:\/\/doi.org\/10.1016\/j.celrep.2020.108352<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"

While many technologies can be used to determine presence or absence of the SARS-CoV-2 virus in a sample, there is also an immediate need for epidemiological research to track viral transmission patterns, including identification of mutations within the viral genome. One key mutation is found in the SARS-CoV-2 spike protein gene, which influences cell entry<\/p>\n","protected":false},"author":120,"featured_media":14666,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[172,67],"tags":[1353,2221,2126,1352,2125],"division":[],"class_list":{"0":"post-14662","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-general","8":"category-infectious-diseases","9":"tag-covid-19","10":"tag-csd","11":"tag-ion-sarscov2","12":"tag-sars-cov-2","13":"tag-sarscov2-ngs-edu","14":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"\nSequencing dominant SARS-CoV-2 strain in suburban in southern U.S. region<\/title>\n<meta name=\"description\" content=\"Dr. Dittmer and his team at UNC leveraged targeted NGS to find that the dominant SARS-CoV-2 strain in their region has a mutation in the spike protein gene.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Sequencing dominant SARS-CoV-2 strain in suburban, southern U.S. region\" \/>\n<meta property=\"og:description\" content=\"Dr. Dittmer and his team at UNC leveraged targeted NGS to find that the dominant SARS-CoV-2 strain in their region has a mutation in the spike protein gene.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/\" \/>\n<meta property=\"og:site_name\" content=\"Behind the Bench\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/thermofisher\" \/>\n<meta property=\"article:published_time\" content=\"2020-10-23T19:13:52+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2021-04-09T16:13:11+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2020\/10\/unc-dittmer-2.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"450\" \/>\n\t<meta property=\"og:image:height\" content=\"253\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Behind The Bench Staff\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@thermofisher\" \/>\n<meta name=\"twitter:site\" content=\"@thermofisher\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Behind The Bench Staff\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"5 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\\\/\"},\"author\":{\"name\":\"Behind The Bench Staff\",\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#\\\/schema\\\/person\\\/9bbb2d67616274d3d4a21a584f7f4a0c\"},\"headline\":\"Sequencing dominant SARS-CoV-2 strain in suburban, southern U.S. region\",\"datePublished\":\"2020-10-23T19:13:52+00:00\",\"dateModified\":\"2021-04-09T16:13:11+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\\\/\"},\"wordCount\":1000,\"image\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2020\\\/10\\\/unc-dittmer-2.jpg\",\"keywords\":[\"covid-19\",\"csd\",\"ion-sarscov2\",\"sars-cov-2\",\"sarscov2-ngs-edu\"],\"articleSection\":[\"General\",\"Infectious Diseases\"],\"inLanguage\":\"en-US\"},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\\\/\",\"url\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\\\/\",\"name\":\"Sequencing dominant SARS-CoV-2 strain in suburban in southern U.S. region\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\\\/#primaryimage\"},\"image\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2020\\\/10\\\/unc-dittmer-2.jpg\",\"datePublished\":\"2020-10-23T19:13:52+00:00\",\"dateModified\":\"2021-04-09T16:13:11+00:00\",\"author\":{\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#\\\/schema\\\/person\\\/9bbb2d67616274d3d4a21a584f7f4a0c\"},\"description\":\"Dr. Dittmer and his team at UNC leveraged targeted NGS to find that the dominant SARS-CoV-2 strain in their region has a mutation in the spike protein gene.\",\"breadcrumb\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\\\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\\\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\\\/#primaryimage\",\"url\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2020\\\/10\\\/unc-dittmer-2.jpg\",\"contentUrl\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2020\\\/10\\\/unc-dittmer-2.jpg\",\"width\":450,\"height\":253},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\\\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Sequencing dominant SARS-CoV-2 strain in suburban, southern U.S. region\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#website\",\"url\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/\",\"name\":\"Behind the Bench\",\"description\":\"\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"},{\"@type\":\"Person\",\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#\\\/schema\\\/person\\\/9bbb2d67616274d3d4a21a584f7f4a0c\",\"name\":\"Behind The Bench Staff\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\\\/\\\/secure.gravatar.com\\\/avatar\\\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g\",\"url\":\"https:\\\/\\\/secure.gravatar.com\\\/avatar\\\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g\",\"contentUrl\":\"https:\\\/\\\/secure.gravatar.com\\\/avatar\\\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g\",\"caption\":\"Behind The Bench Staff\"},\"url\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/author\\\/behind-the-bench-staff\\\/\"}]}<\/script>\n<!-- \/ Yoast SEO Premium plugin. -->","yoast_head_json":{"title":"Sequencing dominant SARS-CoV-2 strain in suburban in southern U.S. region","description":"Dr. Dittmer and his team at UNC leveraged targeted NGS to find that the dominant SARS-CoV-2 strain in their region has a mutation in the spike protein gene.","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/","og_locale":"en_US","og_type":"article","og_title":"Sequencing dominant SARS-CoV-2 strain in suburban, southern U.S. region","og_description":"Dr. Dittmer and his team at UNC leveraged targeted NGS to find that the dominant SARS-CoV-2 strain in their region has a mutation in the spike protein gene.","og_url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/","og_site_name":"Behind the Bench","article_publisher":"https:\/\/www.facebook.com\/thermofisher","article_published_time":"2020-10-23T19:13:52+00:00","article_modified_time":"2021-04-09T16:13:11+00:00","og_image":[{"width":450,"height":253,"url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2020\/10\/unc-dittmer-2.jpg","type":"image\/jpeg"}],"author":"Behind The Bench Staff","twitter_card":"summary_large_image","twitter_creator":"@thermofisher","twitter_site":"@thermofisher","twitter_misc":{"Written by":"Behind The Bench Staff","Est. reading time":"5 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/#article","isPartOf":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/"},"author":{"name":"Behind The Bench Staff","@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#\/schema\/person\/9bbb2d67616274d3d4a21a584f7f4a0c"},"headline":"Sequencing dominant SARS-CoV-2 strain in suburban, southern U.S. region","datePublished":"2020-10-23T19:13:52+00:00","dateModified":"2021-04-09T16:13:11+00:00","mainEntityOfPage":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/"},"wordCount":1000,"image":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/#primaryimage"},"thumbnailUrl":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2020\/10\/unc-dittmer-2.jpg","keywords":["covid-19","csd","ion-sarscov2","sars-cov-2","sarscov2-ngs-edu"],"articleSection":["General","Infectious Diseases"],"inLanguage":"en-US"},{"@type":"WebPage","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/","url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/","name":"Sequencing dominant SARS-CoV-2 strain in suburban in southern U.S. region","isPartOf":{"@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/#primaryimage"},"image":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/#primaryimage"},"thumbnailUrl":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2020\/10\/unc-dittmer-2.jpg","datePublished":"2020-10-23T19:13:52+00:00","dateModified":"2021-04-09T16:13:11+00:00","author":{"@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#\/schema\/person\/9bbb2d67616274d3d4a21a584f7f4a0c"},"description":"Dr. Dittmer and his team at UNC leveraged targeted NGS to find that the dominant SARS-CoV-2 strain in their region has a mutation in the spike protein gene.","breadcrumb":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/#primaryimage","url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2020\/10\/unc-dittmer-2.jpg","contentUrl":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2020\/10\/unc-dittmer-2.jpg","width":450,"height":253},{"@type":"BreadcrumbList","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sequencing-dominant-sars-cov-2-strain-in-suburban-southern-u-s-region\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/admin.acceleratingscience.com\/behindthebench\/"},{"@type":"ListItem","position":2,"name":"Sequencing dominant SARS-CoV-2 strain in suburban, southern U.S. region"}]},{"@type":"WebSite","@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#website","url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/","name":"Behind the Bench","description":"","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/admin.acceleratingscience.com\/behindthebench\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"},{"@type":"Person","@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#\/schema\/person\/9bbb2d67616274d3d4a21a584f7f4a0c","name":"Behind The Bench Staff","image":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/secure.gravatar.com\/avatar\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g","url":"https:\/\/secure.gravatar.com\/avatar\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g","caption":"Behind The Bench Staff"},"url":"https:\/\/admin.acceleratingscience.com\/author\/behind-the-bench-staff\/"}]}},"taxonomy_info":{"category":[{"value":172,"label":"General"},{"value":67,"label":"Infectious Diseases"}],"post_tag":[{"value":1353,"label":"covid-19"},{"value":2221,"label":"csd"},{"value":2126,"label":"ion-sarscov2"},{"value":1352,"label":"sars-cov-2"},{"value":2125,"label":"sarscov2-ngs-edu"}]},"featured_image_src_large":["https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2020\/10\/unc-dittmer-2.jpg",450,253,false],"author_info":{"display_name":"Behind The Bench Staff","author_link":"https:\/\/admin.acceleratingscience.com\/author\/behind-the-bench-staff\/"},"comment_info":0,"category_info":[{"term_id":172,"name":"General","slug":"general","term_group":0,"term_taxonomy_id":172,"taxonomy":"category","description":"","parent":0,"count":161,"filter":"raw","meta":[],"cat_ID":172,"category_count":161,"category_description":"","cat_name":"General","category_nicename":"general","category_parent":0},{"term_id":67,"name":"Infectious Diseases","slug":"infectious-diseases","term_group":0,"term_taxonomy_id":67,"taxonomy":"category","description":"","parent":0,"count":82,"filter":"raw","meta":[],"cat_ID":67,"category_count":82,"category_description":"","cat_name":"Infectious Diseases","category_nicename":"infectious-diseases","category_parent":0}],"tag_info":[{"term_id":1353,"name":"covid-19","slug":"covid-19","term_group":0,"term_taxonomy_id":1353,"taxonomy":"post_tag","description":"","parent":0,"count":40,"filter":"raw","meta":[]},{"term_id":2221,"name":"csd","slug":"csd","term_group":0,"term_taxonomy_id":2221,"taxonomy":"post_tag","description":"Posts from the Clinical Next-Generation Sequencing Division","parent":0,"count":57,"filter":"raw","meta":[]},{"term_id":2126,"name":"ion-sarscov2","slug":"ion-sarscov2","term_group":0,"term_taxonomy_id":2126,"taxonomy":"post_tag","description":"","parent":0,"count":9,"filter":"raw","meta":[]},{"term_id":1352,"name":"sars-cov-2","slug":"sars-cov-2","term_group":0,"term_taxonomy_id":1352,"taxonomy":"post_tag","description":"","parent":0,"count":46,"filter":"raw","meta":[]},{"term_id":2125,"name":"sarscov2-ngs-edu","slug":"sarscov2-ngs-edu","term_group":0,"term_taxonomy_id":2125,"taxonomy":"post_tag","description":"","parent":0,"count":16,"filter":"raw","meta":[]}],"jetpack-related-posts":[{"id":19883,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/building-a-better-sample-qc-workflow-from-extraction-to-sequencing\/","url_meta":{"origin":14662,"position":0},"title":"Building a Better Sample QC Workflow: From Extraction to Sequencing","author":"Marlene Gasdia-Cochrane","date":"August 25, 2026","format":false,"excerpt":"Article Summary Successful genomics experiments don't begin with sequencing\u2014they begin with sample quality. Every downstream application, from PCR to next-generation sequencing (NGS), depends on starting with nucleic acids that are accurately quantified and free from contaminants that could compromise results. Establishing a consistent quality control workflow helps laboratories improve reproducibility\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"A pipette drops a liquid into a petri dish with a dna sequence background, science concept. It suggests medical or genetic research.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":20004,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/a-guide-to-nucleic-acid-quality-control-dna-and-rna-purity\/","url_meta":{"origin":14662,"position":1},"title":"A Guide to Nucleic Acid Quality Control: DNA and RNA Purity","author":"Marlene Gasdia-Cochrane","date":"September 22, 2026","format":false,"excerpt":"Article Summary Nucleic acid quality control helps researchers evaluate DNA and RNA concentration and purity before downstream applications such as PCR, qPCR, and next-generation sequencing (NGS). A standardized workflow combining reliable extraction, concentration and purity assessment, application-appropriate quantification, and consistent laboratory practices can help identify sample issues early, improve reproducibility,\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"Close-up shot of a dna sequence on a screen, a digital representation of genetic code, used for analysis.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19810,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/integration-site-analysis-gene-therapy-safety\/","url_meta":{"origin":14662,"position":2},"title":"Genotoxicity, vectors, and the power of integration site analysis","author":"Ashleigh Barlow","date":"June 23, 2026","format":false,"excerpt":"Article Summary In this episode of Absolute Gene-ius, Michael Stump, PhD, President of ProtaGene, and Matteo Franco, Lead Scientist at ProtaGene, discuss how integration site analysis is helping researchers evaluate genotoxicity risks in cell and gene therapy workflows. Their conversation explores how viral vectors integrate into the genome, why integration\u2026","rel":"","context":"In "Gene Editing"","block_context":{"text":"Gene Editing","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/gene-editing\/"},"img":{"alt_text":"Matteo Franco, Lead Scientist at ProtaGene, discussing integration site analysis and genotoxicity assessment","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/FRANCO-headshot_Jordan-Ruggieri.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/FRANCO-headshot_Jordan-Ruggieri.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/FRANCO-headshot_Jordan-Ruggieri.png?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/FRANCO-headshot_Jordan-Ruggieri.png?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/FRANCO-headshot_Jordan-Ruggieri.png?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/FRANCO-headshot_Jordan-Ruggieri.png?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19223,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/innovations-in-qpcr-technology\/","url_meta":{"origin":14662,"position":3},"title":"Innovations in qPCR Technology: What Researchers Need to Know","author":"Ashleigh Barlow","date":"October 29, 2025","format":false,"excerpt":"https:\/\/youtu.be\/z9Kb1xAnNcg?si=TVUIc8rUxZUOhCqA Real-time PCR, also known as quantitative polymerase chain reaction (qPCR) technology, has been a cornerstone of molecular biology research for decades. With continuous advancements, qPCR remains a critical tool for researchers worldwide. Damien Luk, Senior Director of Product Management at Thermo Fisher Scientific, shared his insights on the future\u2026","rel":"","context":"In "Developmental Biology"","block_context":{"text":"Developmental Biology","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/developmental-biology\/"},"img":{"alt_text":"A lineup of Thermo Fisher Scientific QuantStudio real-time PCR systems, including QuantStudio 3, 5, 6 Pro, 7 Pro, and 12K Flex instruments, displayed against a blue gradient background.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/qPCR-Blog-Cover-Image.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/qPCR-Blog-Cover-Image.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/qPCR-Blog-Cover-Image.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/qPCR-Blog-Cover-Image.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/qPCR-Blog-Cover-Image.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/qPCR-Blog-Cover-Image.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":20019,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/qpcr-dpcr-ngs-cancer-research\/","url_meta":{"origin":14662,"position":4},"title":"From tumor heterogeneity to low-frequency variants: How qPCR, dPCR, and NGS work together in cancer research","author":"Ashleigh Barlow","date":"September 26, 2026","format":false,"excerpt":"Dr. Javier Hernandez Losa explains how combining broad genomic profiling with targeted, sensitive confirmation can help researchers address some of cancer biology\u2019s most difficult analytical challenges. A Q&A with Dr. Javier Hernandez Losa, Director of the Molecular Biology Laboratory, Department of Pathology, Hospital Universitario Vall d\u2019Hebron, Barcelona Cancer research increasingly\u2026","rel":"","context":"In "Cancer Research"","block_context":{"text":"Cancer Research","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/cancer-research\/"},"img":{"alt_text":"Dr. Javier Hernandez Losa, Director of the Molecular Biology Laboratory at Hospital Universitario Vall d'Hebron in Barcelona.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Picture133.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Picture133.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Picture133.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Picture133.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Picture133.jpg?resize=1050%2C600&ssl=1 3x"},"classes":[]},{"id":19805,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/liquid-biopsy-workflow-standardization\/","url_meta":{"origin":14662,"position":5},"title":"Improving the Reliability of Liquid Biopsy in Real-World Settings Through Workflow Standardization: A Discussion with Dr. Matteo Allegretti","author":"Ashleigh Barlow","date":"June 18, 2026","format":false,"excerpt":"Liquid biopsy offers a powerful, noninvasive way to detect and track cancer, but ensuring reliability in real-world settings remains a key hurdle. Variability in workflows and the need for robust verification steps limit widespread adoption. Dr. Matteo Allegretti, Senior Researcher at the Translational Oncology Research Unit at the IRCCS Regina\u2026","rel":"","context":"In "Cancer Research"","block_context":{"text":"Cancer Research","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/cancer-research\/"},"img":{"alt_text":"Research scientist operating laboratory equipment during liquid biopsy and biomarker research.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/Allegretti-Header.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/Allegretti-Header.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/Allegretti-Header.png?resize=525%2C300&ssl=1 1.5x"},"classes":[]}],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2020\/10\/unc-dittmer-2.jpg","_links":{"self":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts\/14662","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/users\/120"}],"replies":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/comments?post=14662"}],"version-history":[{"count":0,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts\/14662\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/media\/14666"}],"wp:attachment":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/media?parent=14662"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/categories?post=14662"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/tags?post=14662"},{"taxonomy":"division","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/division?post=14662"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}