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Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the causal agent of the COVID-19 pandemic that emerged in late 2019. The outbreak of variants with mutations in the region encoding the spike protein S1 sub-unit that can make them more resistant to neutralizing or monoclonal antib...

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Autores principales: Lhomme, Sébastien, Latour, Justine, Jeanne, Nicolas, Trémeaux, Pauline, Ranger, Noémie, Migueres, Marion, Salin, Gérald, Donnadieu, Cécile, Izopet, Jacques
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8707593/
https://www.ncbi.nlm.nih.gov/pubmed/34960813
http://dx.doi.org/10.3390/v13122544
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author Lhomme, Sébastien
Latour, Justine
Jeanne, Nicolas
Trémeaux, Pauline
Ranger, Noémie
Migueres, Marion
Salin, Gérald
Donnadieu, Cécile
Izopet, Jacques
author_facet Lhomme, Sébastien
Latour, Justine
Jeanne, Nicolas
Trémeaux, Pauline
Ranger, Noémie
Migueres, Marion
Salin, Gérald
Donnadieu, Cécile
Izopet, Jacques
author_sort Lhomme, Sébastien
collection PubMed
description The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the causal agent of the COVID-19 pandemic that emerged in late 2019. The outbreak of variants with mutations in the region encoding the spike protein S1 sub-unit that can make them more resistant to neutralizing or monoclonal antibodies is the main point of the current monitoring. This study examines the feasibility of predicting the variant lineage and monitoring the appearance of reported mutations by sequencing only the region encoding the S1 domain by Pacific Bioscience Single Molecule Real-Time sequencing (PacBio SMRT). Using the PacBio SMRT system, we successfully sequenced 186 of the 200 samples previously sequenced with the Illumina COVIDSeq (whole genome) system. PacBio SMRT detected mutations in the S1 domain that were missed by the COVIDseq system in 27/186 samples (14.5%), due to amplification failure. These missing positions included mutations that are decisive for lineage assignation, such as G142D (n = 11), N501Y (n = 6), or E484K (n = 2). The lineage of 172/186 (92.5%) samples was accurately determined by analyzing the region encoding the S1 domain with a pipeline that uses key positions in S1. Thus, the PacBio SMRT protocol is appropriate for determining virus lineages and detecting key mutations.
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spelling pubmed-87075932021-12-25 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing Lhomme, Sébastien Latour, Justine Jeanne, Nicolas Trémeaux, Pauline Ranger, Noémie Migueres, Marion Salin, Gérald Donnadieu, Cécile Izopet, Jacques Viruses Article The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the causal agent of the COVID-19 pandemic that emerged in late 2019. The outbreak of variants with mutations in the region encoding the spike protein S1 sub-unit that can make them more resistant to neutralizing or monoclonal antibodies is the main point of the current monitoring. This study examines the feasibility of predicting the variant lineage and monitoring the appearance of reported mutations by sequencing only the region encoding the S1 domain by Pacific Bioscience Single Molecule Real-Time sequencing (PacBio SMRT). Using the PacBio SMRT system, we successfully sequenced 186 of the 200 samples previously sequenced with the Illumina COVIDSeq (whole genome) system. PacBio SMRT detected mutations in the S1 domain that were missed by the COVIDseq system in 27/186 samples (14.5%), due to amplification failure. These missing positions included mutations that are decisive for lineage assignation, such as G142D (n = 11), N501Y (n = 6), or E484K (n = 2). The lineage of 172/186 (92.5%) samples was accurately determined by analyzing the region encoding the S1 domain with a pipeline that uses key positions in S1. Thus, the PacBio SMRT protocol is appropriate for determining virus lineages and detecting key mutations. MDPI 2021-12-18 /pmc/articles/PMC8707593/ /pubmed/34960813 http://dx.doi.org/10.3390/v13122544 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lhomme, Sébastien
Latour, Justine
Jeanne, Nicolas
Trémeaux, Pauline
Ranger, Noémie
Migueres, Marion
Salin, Gérald
Donnadieu, Cécile
Izopet, Jacques
Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing
title Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing
title_full Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing
title_fullStr Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing
title_full_unstemmed Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing
title_short Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing
title_sort prediction of sars-cov-2 variant lineages using the s1-encoding region sequence obtained by pacbio single-molecule real-time sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8707593/
https://www.ncbi.nlm.nih.gov/pubmed/34960813
http://dx.doi.org/10.3390/v13122544
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