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Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform

Many SARS-CoV-2 variants have emerged during the course of the COVID-19 pandemic. These variants have acquired mutations conferring phenotypes such as increased transmissibility or virulence, or causing diagnostic, therapeutic, or immune escape. Detection of Alpha and the majority of Omicron subline...

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Autores principales: Stanhope, Bryce J., Peterson, Brittany, Knight, Brittany, Decadiz, Ray Nobles, Pan, Roger, Davis, Phillip, Fraser, Anne, Nuth, Manunya, vanWestrienen, Jesse, Wendlandt, Erik, Goodwin, Bruce, Myers, Christopher, Stone, Jennifer, Sozhamannan, Shanmuga
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9798920/
https://www.ncbi.nlm.nih.gov/pubmed/36590003
http://dx.doi.org/10.3389/fpubh.2022.1042647
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author Stanhope, Bryce J.
Peterson, Brittany
Knight, Brittany
Decadiz, Ray Nobles
Pan, Roger
Davis, Phillip
Fraser, Anne
Nuth, Manunya
vanWestrienen, Jesse
Wendlandt, Erik
Goodwin, Bruce
Myers, Christopher
Stone, Jennifer
Sozhamannan, Shanmuga
author_facet Stanhope, Bryce J.
Peterson, Brittany
Knight, Brittany
Decadiz, Ray Nobles
Pan, Roger
Davis, Phillip
Fraser, Anne
Nuth, Manunya
vanWestrienen, Jesse
Wendlandt, Erik
Goodwin, Bruce
Myers, Christopher
Stone, Jennifer
Sozhamannan, Shanmuga
author_sort Stanhope, Bryce J.
collection PubMed
description Many SARS-CoV-2 variants have emerged during the course of the COVID-19 pandemic. These variants have acquired mutations conferring phenotypes such as increased transmissibility or virulence, or causing diagnostic, therapeutic, or immune escape. Detection of Alpha and the majority of Omicron sublineages by PCR relied on the so-called S gene target failure due to the deletion of six nucleotides coding for amino acids 69–70 in the spike (S) protein. Detection of hallmark mutations in other variants present in samples relied on whole genome sequencing. However, whole genome sequencing as a diagnostic tool is still in its infancy due to geographic inequities in sequencing capabilities, higher cost compared to other molecular assays, longer turnaround time from sample to result, and technical challenges associated with producing complete genome sequences from samples that have low viral load and/or high background. Hence, there is a need for rapid genotyping assays. In order to rapidly generate information on the presence of a variant in a given sample, we have created a panel of four triplex RT-qPCR assays targeting 12 mutations to detect and differentiate all five variants of concern: Alpha, Beta, Gamma, Delta, and Omicron. We also developed an expanded pentaplex assay that can reliably distinguish among the major sublineages (BA.1–BA.5) of Omicron. In silico, analytical and clinical testing of the variant panel indicate that the assays exhibit high sensitivity and specificity. This panel can help fulfill the need for rapid identification of variants in samples, leading to quick decision making with respect to public health measures, as well as treatment options for individuals. Compared to sequencing, these genotyping PCR assays allow much faster turn-around time from sample to results—just a couple hours instead of days or weeks.
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spelling pubmed-97989202022-12-30 Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform Stanhope, Bryce J. Peterson, Brittany Knight, Brittany Decadiz, Ray Nobles Pan, Roger Davis, Phillip Fraser, Anne Nuth, Manunya vanWestrienen, Jesse Wendlandt, Erik Goodwin, Bruce Myers, Christopher Stone, Jennifer Sozhamannan, Shanmuga Front Public Health Public Health Many SARS-CoV-2 variants have emerged during the course of the COVID-19 pandemic. These variants have acquired mutations conferring phenotypes such as increased transmissibility or virulence, or causing diagnostic, therapeutic, or immune escape. Detection of Alpha and the majority of Omicron sublineages by PCR relied on the so-called S gene target failure due to the deletion of six nucleotides coding for amino acids 69–70 in the spike (S) protein. Detection of hallmark mutations in other variants present in samples relied on whole genome sequencing. However, whole genome sequencing as a diagnostic tool is still in its infancy due to geographic inequities in sequencing capabilities, higher cost compared to other molecular assays, longer turnaround time from sample to result, and technical challenges associated with producing complete genome sequences from samples that have low viral load and/or high background. Hence, there is a need for rapid genotyping assays. In order to rapidly generate information on the presence of a variant in a given sample, we have created a panel of four triplex RT-qPCR assays targeting 12 mutations to detect and differentiate all five variants of concern: Alpha, Beta, Gamma, Delta, and Omicron. We also developed an expanded pentaplex assay that can reliably distinguish among the major sublineages (BA.1–BA.5) of Omicron. In silico, analytical and clinical testing of the variant panel indicate that the assays exhibit high sensitivity and specificity. This panel can help fulfill the need for rapid identification of variants in samples, leading to quick decision making with respect to public health measures, as well as treatment options for individuals. Compared to sequencing, these genotyping PCR assays allow much faster turn-around time from sample to results—just a couple hours instead of days or weeks. Frontiers Media S.A. 2022-12-15 /pmc/articles/PMC9798920/ /pubmed/36590003 http://dx.doi.org/10.3389/fpubh.2022.1042647 Text en Copyright © 2022 Stanhope, Peterson, Knight, Decadiz, Pan, Davis, Fraser, Nuth, vanWestrienen, Wendlandt, Goodwin, Myers, Stone and Sozhamannan. 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 authors grant nonexclusive right to copy, distribute, adapt, and transmit the published Work for commercial or non-commercial use with proper attribution under the Creative Commons Attribution 4.0 International license (CC-BY). No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Public Health
Stanhope, Bryce J.
Peterson, Brittany
Knight, Brittany
Decadiz, Ray Nobles
Pan, Roger
Davis, Phillip
Fraser, Anne
Nuth, Manunya
vanWestrienen, Jesse
Wendlandt, Erik
Goodwin, Bruce
Myers, Christopher
Stone, Jennifer
Sozhamannan, Shanmuga
Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform
title Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform
title_full Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform
title_fullStr Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform
title_full_unstemmed Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform
title_short Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform
title_sort development, testing and validation of a sars-cov-2 multiplex panel for detection of the five major variants of concern on a portable pcr platform
topic Public Health
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9798920/
https://www.ncbi.nlm.nih.gov/pubmed/36590003
http://dx.doi.org/10.3389/fpubh.2022.1042647
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