{"id":14302,"date":"2020-08-24T18:19:07","date_gmt":"2020-08-24T18:19:07","guid":{"rendered":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/?p=14302"},"modified":"2021-04-09T16:12:44","modified_gmt":"2021-04-09T16:12:44","slug":"targeted-ngs-or-serology-for-sars-cov-2-epidemiology-research","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/targeted-ngs-or-serology-for-sars-cov-2-epidemiology-research\/","title":{"rendered":"Targeted NGS or Serology for SARS-CoV-2 Epidemiology Research?"},"content":{"rendered":"<p><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-content\/uploads\/sites\/9\/2020\/08\/shutterstock_179112709420-20blog-3.jpg\" style=\"float: right;margin: 5px\" title=\"Targeted NGS or Serology for SARS-CoV-2 Research\" width=\"480\" height=\"333\" alt=\"Epidemiology Research\" class=\"alignright\" \/>Mapping out the spread SARS-CoV-2 virus to determine if new strains are emerging in a population or geographic region requires rapid, variant-level detection and analysis, and results from serology tests used for the detection of SARS-CoV-2 antibodies may not be sufficient for these types of studies. The immune system is our body&rsquo;s defense mechanism, which is made up of <a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/sequencing\/dna-sequencing\/microbial-sequencing\/microbial-identification-ion-torrent-next-generation-sequencing\/immune-response-targeted-ngs.html?cid=csd_ngs_ngs_r01_co_cp1347_pjt5732_colblog_0so_blg_op_edu_at_s00_NGSSERO\" target=\"_blank\" rel=\"noopener noreferrer\">armies of B cells and T cells.<\/a> While we know the function of B cells is to create antibodies with specific markers to ward off foreign invaders like the SARS-CoV-2 virus, there&rsquo;s still a lot to learn about what role T cells may play in <a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/sequencing\/dna-sequencing\/microbial-sequencing\/microbial-identification-ion-torrent-next-generation-sequencing\/immune-response-targeted-ngs.html?cid=csd_ngs_ngs_r01_co_cp1347_pjt5732_colblog_0so_blg_op_edu_at_s00_NGSSERO\" target=\"_blank\" rel=\"noopener noreferrer\">SARS-CoV-2 immunity[1].<\/a> Serology tests are used to detect the presence of antibodies in the blood, however antibodies may not always be detectable during early-stage infection when the immune system is still in the process of responding. An added challenge is the factor of the varying degrees of infection severity for SARS-CoV-2, since there are asymptomatic carriers of the virus.<\/p>\n<p>The results of a recent serological survey in Spain[2], one of the countries more severely impacted by SARS-CoV-2, suggests that a majority of the Spanish population is sero-negative to antibodies for SARS-CoV-2, even in hotspot areas. This implies that immunity to SARS-CoV-2 may not be easily achieved as previously thought. Without a clear timeframe for a vaccine in view, there is a need for alternative ways to track SARS-CoV-2 prevalence in a population, since there are still questions regarding how long someone can remain immune to the virus, and how quickly reinfection could occur.<\/p>\n<p>Alternatively, environmental monitoring could be a faster way to track the prevalence of SARS-CoV-2 in a particular region. <a href=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/ngs-based-wastewater-sequencing-may-provide-clues-to-sars-cov-2-prevalence-and-spread\/?cid=csd_ngs_ngs_r01_co_cp1347_pjt5732_colblog_0so_blg_op_edu_at_s00_NGSSERO\" target=\"_blank\" rel=\"noopener noreferrer\">Wastewater-based epidemiology (WBE)<\/a> has been used in locations like Italy, Spain, UK and US, as the virus is detectable in sewage samples. Rapid detection of the virus down to the variant-level would be crucial for the prediction of potential hotspots and tracking new emerging strains in real time, as the results could help inform public health measures and containment strategies.<\/p>\n<p>Since the beginning of the crisis, researchers in over 34 countries have been using <a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/products-and-services\/promotions\/life-science\/ngs-solutions-sars-cov-2-research.html?cid=csd_ngs_ngs_r01_co_cp1347_pjt5732_colblog_0so_blg_op_edu_at_s00_NGSSERO\" target=\"_blank\" rel=\"noopener noreferrer\">Ion Torrent&trade; targeted next-generation sequencing (NGS) solution<\/a> for SARS-CoV-2 research and epidemiological investigations. The <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_ngs_r01_co_cp1347_pjt5732_colblog_0so_blg_op_edu_at_s00_NGSSERO\" target=\"_blank\" rel=\"noopener noreferrer\">Ion AmpliSeq&trade; SARS-CoV-2 Research Panel<\/a> is a rapid, automated and accurate solution that enables variant-level analysis and &gt;99% coverage of SARS-CoV-2 genome, including all serotypes. This assay is part of a complete nucleic acid-to-analysis workflow that includes powerful yet intuitive analysis tools, allowing NGS to be accessible to any user regardless of their informatics experience.<\/p>\n<p><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_ngs_r01_co_cp1347_pjt5732_colblog_0so_blg_op_edu_at_s00_NGSSERO\" target=\"_blank\" rel=\"noopener noreferrer\">Learn more about simple, practical NGS for SARS-CoV-2 epidemiology research<\/a><\/p>\n<p><a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/products-and-services\/promotions\/life-science\/ngs-solutions-sars-cov-2-research.html?cid=csd_ngs_ngs_r01_co_cp1347_pjt5732_colblog_0so_blg_op_edu_at_s00_NGSSERO\" target=\"_blank\" rel=\"noopener noreferrer\">Explore the comprehensive portfolio of Targeted NGS solutions for studying SARS-CoV-2 viral research, vaccine development research, host genetics and immune response<\/a><\/p>\n<p>Reference: <br \/>[1] Braun, J., Loyal, Lucie. Et al. Presence of SARS-CoV-2 reactive T cells in COVID-19 patients and healthy donors. medRxiv, 2020.04.17.20061440. <a href=\"https:\/\/www.medrxiv.org\/content\/10.1101\/2020.04.17.20061440v1?cid=csd_ngs_ngs_r01_co_cp1347_pjt5732_colblog_0so_blg_op_edu_at_s00_NGSSERO\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/doi.org\/10.1101\/2020.04.17.20061440<\/a><\/p>\n<p>[2] Pollan, M., Perez-Gomez, B. et al. Prevalence of SARS-CoV-2 in Spain (ENE-COVID): a nationwide, population-based seroepidemiological study. The Lancet, 2020.07.06. <a href=\"https:\/\/www.thelancet.com\/journals\/lancet\/article\/PIIS0140-6736(20)31483-5\/fulltext?cid=csd_ngs_ngs_r01_co_cp1347_pjt5732_colblog_0so_blg_op_edu_at_s00_NGSSERO\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/doi.org\/10.1016\/S0140-6736(20)31483-5<\/a><\/p>\n<p><strong>For Research Use Only. Not for use in diagnostic procedures.<\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Mapping out the spread SARS-CoV-2 virus to determine if new strains are emerging in a population or geographic region requires rapid, variant-level detection and analysis, and results from serology tests used for the detection of SARS-CoV-2 antibodies may not be sufficient for these types of studies. The immune system is our body&rsquo;s defense mechanism, which<\/p>\n","protected":false},"author":120,"featured_media":14308,"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":[185,172,67,84,106],"tags":[1353,2221,2126,1352,2125],"division":[],"class_list":{"0":"post-14302","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-complex-diseases","8":"category-general","9":"category-infectious-diseases","10":"category-metagenomics","11":"category-population-studies","12":"tag-covid-19","13":"tag-csd","14":"tag-ion-sarscov2","15":"tag-sars-cov-2","16":"tag-sarscov2-ngs-edu","17":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"<!-- 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