Validation of a new strategy for the identification of SARS-CoV-2 variants by sequencing the spike gene by Sanger
© 2022 The Authors..
Introduction: The emergence of multiple variants of SARS-CoV-2 during the COVID-19 pandemic is of great world concern. Until now, their analysis has mainly focused on next-generation sequencing. However, this technique is expensive and requires sophisticated equipment, long processing times, and highly qualified technical personnel with experience in bioinformatics. To contribute to the analysis of variants of interest and variants of concern, increase the diagnostic capacity, and process samples to carry out genomic surveillance, we propose a quick and easy methodology to apply, based on Sanger sequencing of 3 gene fragments that code for protein spike.
Methods: Fifteen positive samples for SARS-CoV-2 with a cycle threshold below 25 were sequenced by Sanger and next-generation sequencing methodologies. The data obtained were analyzed on the Nextstrain and PANGO Lineages platforms.
Results: Both methodologies allowed the identification of the variants of interest reported by the WHO. Two samples were identified as Alpha, 3 Gamma, one Delta, 3 Mu, one Omicron, and 5 strains were close to the initial Wuhan-Hu-1 virus isolate. According to in silico analysis, key mutations can also be detected to identify and classify other variants not evaluated in the study.
Conclusion: The different SARS-CoV-2 lineages of interest and concern are classified quickly, agilely, and reliably with the Sanger sequencing methodology.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:41 |
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| Enthalten in: |
Enfermedades infecciosas y microbiologia clinica - 41(2023), 5 vom: 16. Mai, Seite 284-289 |
| Sprache: |
Spanisch |
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| Weiterer Titel: |
Validación de una nueva estrategia para la identificación de variantes de SARS-CoV-2 mediante secuenciación del gen espiga por Sanger |
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| Beteiligte Personen: |
Murillo, Enderson [VerfasserIn] |
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| Links: |
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| Themen: |
English Abstract |
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| Anmerkungen: |
Date Revised 03.05.2023 published: Print-Electronic Citation Status PubMed-not-MEDLINE |
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| doi: |
10.1016/j.eimc.2022.04.014 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
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| 245 | 1 | 0 | |a Validation of a new strategy for the identification of SARS-CoV-2 variants by sequencing the spike gene by Sanger |
| 246 | 3 | 3 | |a Validación de una nueva estrategia para la identificación de variantes de SARS-CoV-2 mediante secuenciación del gen espiga por Sanger |
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| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status PubMed-not-MEDLINE | ||
| 520 | |a © 2022 The Authors. | ||
| 520 | |a Introduction: The emergence of multiple variants of SARS-CoV-2 during the COVID-19 pandemic is of great world concern. Until now, their analysis has mainly focused on next-generation sequencing. However, this technique is expensive and requires sophisticated equipment, long processing times, and highly qualified technical personnel with experience in bioinformatics. To contribute to the analysis of variants of interest and variants of concern, increase the diagnostic capacity, and process samples to carry out genomic surveillance, we propose a quick and easy methodology to apply, based on Sanger sequencing of 3 gene fragments that code for protein spike | ||
| 520 | |a Methods: Fifteen positive samples for SARS-CoV-2 with a cycle threshold below 25 were sequenced by Sanger and next-generation sequencing methodologies. The data obtained were analyzed on the Nextstrain and PANGO Lineages platforms | ||
| 520 | |a Results: Both methodologies allowed the identification of the variants of interest reported by the WHO. Two samples were identified as Alpha, 3 Gamma, one Delta, 3 Mu, one Omicron, and 5 strains were close to the initial Wuhan-Hu-1 virus isolate. According to in silico analysis, key mutations can also be detected to identify and classify other variants not evaluated in the study | ||
| 520 | |a Conclusion: The different SARS-CoV-2 lineages of interest and concern are classified quickly, agilely, and reliably with the Sanger sequencing methodology | ||
| 650 | 4 | |a English Abstract | |
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Mutations | |
| 650 | 4 | |a Next generation sequencing | |
| 650 | 4 | |a SARS-CoV-2 | |
| 650 | 4 | |a Sanger sequencing | |
| 650 | 4 | |a Spike protein | |
| 650 | 4 | |a Variants of concern | |
| 650 | 4 | |a Variants of interest | |
| 700 | 1 | |a Palacio-Rua, Katherine |e verfasserin |4 aut | |
| 700 | 1 | |a Afanador-Ayala, Carlos |e verfasserin |4 aut | |
| 700 | 1 | |a García-Correa, Juan Felipe |e verfasserin |4 aut | |
| 700 | 1 | |a Zuluaga, Andrés F |e verfasserin |4 aut | |
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