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NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges

Identification of SARS-CoV-2 lineages has shown to provide invaluable information regarding treatment efficacy, viral transmissibility, disease severity, and immune evasion. These benefits provide institutions with an expectation of high informational upside with little insight in regards to practic...

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Autores principales: Tartanian, Aileen C., Mulroney, Nicole, Poselenzny, Kelly, Akroush, Michael, Unger, Trevor, Helseth, Donald L., Sabatini, Linda M., Bouma, Michael, Larkin, Paige M.K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10157391/
https://www.ncbi.nlm.nih.gov/pubmed/37151582
http://dx.doi.org/10.3389/fpubh.2023.1177695
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author Tartanian, Aileen C.
Mulroney, Nicole
Poselenzny, Kelly
Akroush, Michael
Unger, Trevor
Helseth, Donald L.
Sabatini, Linda M.
Bouma, Michael
Larkin, Paige M.K.
author_facet Tartanian, Aileen C.
Mulroney, Nicole
Poselenzny, Kelly
Akroush, Michael
Unger, Trevor
Helseth, Donald L.
Sabatini, Linda M.
Bouma, Michael
Larkin, Paige M.K.
author_sort Tartanian, Aileen C.
collection PubMed
description Identification of SARS-CoV-2 lineages has shown to provide invaluable information regarding treatment efficacy, viral transmissibility, disease severity, and immune evasion. These benefits provide institutions with an expectation of high informational upside with little insight in regards to practicality with implementation and execution of such high complexity testing in the midst of a pandemic. This article details our institution’s experience implementing and using Next Generation Sequencing (NGS) to monitor SARS-CoV-2 lineages in the northern Chicagoland area throughout the pandemic. To date, we have sequenced nearly 7,000 previously known SARS-CoV-2 positive samples from various patient populations (e.g., outpatient, inpatient, and outreach sites) to reduce bias in sampling. As a result, our hospital was guided while making crucial decisions about staffing, masking, and other infection control measures during the pandemic. While beneficial, establishing this NGS procedure was challenging, with countless considerations at every stage of assay development and validation. Reduced staffing prompted transition from a manual to automated high throughput workflow, requiring further validation, lab space, and instrumentation. Data management and IT security were additional considerations that delayed implementation and dictated our bioinformatic capabilities. Taken together, our experience highlights the obstacles and triumphs of SARS-CoV-2 sequencing.
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spelling pubmed-101573912023-05-05 NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges Tartanian, Aileen C. Mulroney, Nicole Poselenzny, Kelly Akroush, Michael Unger, Trevor Helseth, Donald L. Sabatini, Linda M. Bouma, Michael Larkin, Paige M.K. Front Public Health Public Health Identification of SARS-CoV-2 lineages has shown to provide invaluable information regarding treatment efficacy, viral transmissibility, disease severity, and immune evasion. These benefits provide institutions with an expectation of high informational upside with little insight in regards to practicality with implementation and execution of such high complexity testing in the midst of a pandemic. This article details our institution’s experience implementing and using Next Generation Sequencing (NGS) to monitor SARS-CoV-2 lineages in the northern Chicagoland area throughout the pandemic. To date, we have sequenced nearly 7,000 previously known SARS-CoV-2 positive samples from various patient populations (e.g., outpatient, inpatient, and outreach sites) to reduce bias in sampling. As a result, our hospital was guided while making crucial decisions about staffing, masking, and other infection control measures during the pandemic. While beneficial, establishing this NGS procedure was challenging, with countless considerations at every stage of assay development and validation. Reduced staffing prompted transition from a manual to automated high throughput workflow, requiring further validation, lab space, and instrumentation. Data management and IT security were additional considerations that delayed implementation and dictated our bioinformatic capabilities. Taken together, our experience highlights the obstacles and triumphs of SARS-CoV-2 sequencing. Frontiers Media S.A. 2023-04-20 /pmc/articles/PMC10157391/ /pubmed/37151582 http://dx.doi.org/10.3389/fpubh.2023.1177695 Text en Copyright © 2023 Tartanian, Mulroney, Poselenzny, Akroush, Unger, Helseth, Sabatini, Bouma and Larkin. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Public Health
Tartanian, Aileen C.
Mulroney, Nicole
Poselenzny, Kelly
Akroush, Michael
Unger, Trevor
Helseth, Donald L.
Sabatini, Linda M.
Bouma, Michael
Larkin, Paige M.K.
NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges
title NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges
title_full NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges
title_fullStr NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges
title_full_unstemmed NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges
title_short NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges
title_sort ngs implementation for monitoring sars-cov-2 variants in chicagoland: an institutional perspective, successes and challenges
topic Public Health
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10157391/
https://www.ncbi.nlm.nih.gov/pubmed/37151582
http://dx.doi.org/10.3389/fpubh.2023.1177695
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