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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| Format: | Article |
| Language: | English |
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MDPI AG
2021-12-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/12/2544 |
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| author | Sébastien Lhomme Justine Latour Nicolas Jeanne Pauline Trémeaux Noémie Ranger Marion Migueres Gérald Salin Cécile Donnadieu Jacques Izopet |
| author_facet | Sébastien Lhomme Justine Latour Nicolas Jeanne Pauline Trémeaux Noémie Ranger Marion Migueres Gérald Salin Cécile Donnadieu Jacques Izopet |
| author_sort | Sébastien Lhomme |
| collection | DOAJ |
| 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 (<i>n</i> = 11), N501Y (<i>n</i> = 6), or E484K (<i>n</i> = 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. |
| first_indexed | 2024-03-10T03:54:05Z |
| format | Article |
| id | doaj.art-5730af35e40144438f805673a8831718 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T03:54:05Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-5730af35e40144438f805673a88317182023-11-23T10:59:27ZengMDPI AGViruses1999-49152021-12-011312254410.3390/v13122544Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time SequencingSébastien Lhomme0Justine Latour1Nicolas Jeanne2Pauline Trémeaux3Noémie Ranger4Marion Migueres5Gérald Salin6Cécile Donnadieu7Jacques Izopet8Infinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, FranceLaboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, FranceLaboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, FranceLaboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, FranceLaboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, FranceInfinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, FranceINRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, FranceINRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, FranceInfinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, FranceThe 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 (<i>n</i> = 11), N501Y (<i>n</i> = 6), or E484K (<i>n</i> = 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.https://www.mdpi.com/1999-4915/13/12/2544SARS-CoV-2PacBio SMRT sequencingIllumina sequencingS1 domaincladelineage |
| spellingShingle | Sébastien Lhomme Justine Latour Nicolas Jeanne Pauline Trémeaux Noémie Ranger Marion Migueres Gérald Salin Cécile Donnadieu Jacques Izopet Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing Viruses SARS-CoV-2 PacBio SMRT sequencing Illumina sequencing S1 domain clade lineage |
| 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 | SARS-CoV-2 PacBio SMRT sequencing Illumina sequencing S1 domain clade lineage |
| url | https://www.mdpi.com/1999-4915/13/12/2544 |
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