Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2
Although next-generation sequencing technologies are advancing rapidly, many research topics often require selective sequencing of genomic regions of interest. In addition, sequencing low-titre viruses is challenging, especially for coronaviruses, which are the largest RNA viruses. Prior to sequenci...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2024-02-01
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| Series: | Virus Research |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0168170223002551 |
| _version_ | 1797387849189818368 |
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| author | Andres Ceballos-Garzon Sophie Comtet-Marre Pierre Peyret |
| author_facet | Andres Ceballos-Garzon Sophie Comtet-Marre Pierre Peyret |
| author_sort | Andres Ceballos-Garzon |
| collection | DOAJ |
| description | Although next-generation sequencing technologies are advancing rapidly, many research topics often require selective sequencing of genomic regions of interest. In addition, sequencing low-titre viruses is challenging, especially for coronaviruses, which are the largest RNA viruses. Prior to sequencing, enrichment of viral particles can help to significantly increase target sequence information as well as avoid large sequencing efforts and, consequently, can increase sensitivity and reduce sequencing costs. Targeting nucleic acids using capture by hybridization is another efficient method that can be performed by applying complementary probes (DNA or RNA baits) to directly enrich genetic information of interest while removing background non-target material. In studies where sequence capture by hybridization has been applied to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, most authors agree that this technique is useful to easily access sequence targets in complex samples. Furthermore, this approach allows for complete or near-complete sequencing of the viral genome, even in samples with low viral load or poor nucleic acid integrity. In addition, this strategy is highly efficient at discovering new variants by facilitating downstream investigations, such as phylogenetics, epidemiology, and evolution. Commercial kits, as well as in-house protocols, have been developed for enrichment of viral sequences. However, these kits have multiple variations in procedure, with differences in performance. This review compiles and describes studies in which hybridization capture has been applied to SARS-CoV-2 variant genomes. |
| first_indexed | 2024-03-08T22:31:02Z |
| format | Article |
| id | doaj.art-189f5a456520444fbf7bd0b3af6057d0 |
| institution | Directory Open Access Journal |
| issn | 1872-7492 |
| language | English |
| last_indexed | 2024-03-08T22:31:02Z |
| publishDate | 2024-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Virus Research |
| spelling | doaj.art-189f5a456520444fbf7bd0b3af6057d02023-12-18T04:24:00ZengElsevierVirus Research1872-74922024-02-01340199293Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2Andres Ceballos-Garzon0Sophie Comtet-Marre1Pierre Peyret2Université Clermont Auvergne, INRAE, MEDiS, 63000, Clermont-Ferrand, FranceUniversité Clermont Auvergne, INRAE, MEDiS, 63000, Clermont-Ferrand, FranceCorresponding author at: Centre Biomédical de Recherche et Valorisation, 28, place Henri Dunant, 63001, Clermont-Ferrand, France.; Université Clermont Auvergne, INRAE, MEDiS, 63000, Clermont-Ferrand, FranceAlthough next-generation sequencing technologies are advancing rapidly, many research topics often require selective sequencing of genomic regions of interest. In addition, sequencing low-titre viruses is challenging, especially for coronaviruses, which are the largest RNA viruses. Prior to sequencing, enrichment of viral particles can help to significantly increase target sequence information as well as avoid large sequencing efforts and, consequently, can increase sensitivity and reduce sequencing costs. Targeting nucleic acids using capture by hybridization is another efficient method that can be performed by applying complementary probes (DNA or RNA baits) to directly enrich genetic information of interest while removing background non-target material. In studies where sequence capture by hybridization has been applied to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, most authors agree that this technique is useful to easily access sequence targets in complex samples. Furthermore, this approach allows for complete or near-complete sequencing of the viral genome, even in samples with low viral load or poor nucleic acid integrity. In addition, this strategy is highly efficient at discovering new variants by facilitating downstream investigations, such as phylogenetics, epidemiology, and evolution. Commercial kits, as well as in-house protocols, have been developed for enrichment of viral sequences. However, these kits have multiple variations in procedure, with differences in performance. This review compiles and describes studies in which hybridization capture has been applied to SARS-CoV-2 variant genomes.http://www.sciencedirect.com/science/article/pii/S0168170223002551Hybridization captureSequence enrichmentProbesNext-generation sequencingSARS-CoV-2COVID-19 |
| spellingShingle | Andres Ceballos-Garzon Sophie Comtet-Marre Pierre Peyret Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2 Virus Research Hybridization capture Sequence enrichment Probes Next-generation sequencing SARS-CoV-2 COVID-19 |
| title | Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2 |
| title_full | Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2 |
| title_fullStr | Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2 |
| title_full_unstemmed | Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2 |
| title_short | Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2 |
| title_sort | applying targeted gene hybridization capture to viruses with a focus to sars cov 2 |
| topic | Hybridization capture Sequence enrichment Probes Next-generation sequencing SARS-CoV-2 COVID-19 |
| url | http://www.sciencedirect.com/science/article/pii/S0168170223002551 |
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