SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV
Abstract Background SmartAmp-Eprimer Binary code (SEB) Genotyping is a novel isothermal amplification method for rapid genotyping of any variable target of interest. Methods After in silico alignment of a large number of sequences and computational analysis to determine the smallest number of region...
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| Format: | Article |
| Language: | English |
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BMC
2022-06-01
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| Series: | BMC Infectious Diseases |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12879-022-07458-4 |
| _version_ | 1817968666893877248 |
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| author | Diane Delobel Yutaka Furutani Sumiko Nagoshi Akihito Tsubota Akio Miyasaka Koichi Watashi Takaji Wakita Tomokazu Matsuura Kengo Usui |
| author_facet | Diane Delobel Yutaka Furutani Sumiko Nagoshi Akihito Tsubota Akio Miyasaka Koichi Watashi Takaji Wakita Tomokazu Matsuura Kengo Usui |
| author_sort | Diane Delobel |
| collection | DOAJ |
| description | Abstract Background SmartAmp-Eprimer Binary code (SEB) Genotyping is a novel isothermal amplification method for rapid genotyping of any variable target of interest. Methods After in silico alignment of a large number of sequences and computational analysis to determine the smallest number of regions to be targeted by SEB Genotyping, SmartAmp primer sets were designed to obtain a binary code of On/Off fluorescence signals, each code corresponding to a unique genotype. Results Applied to HBV, we selected 4 targets for which fluorescence amplification signals produce a specific binary code unique to each of the 8 main genotypes (A–H) found in patients worldwide. Conclusions We present here the proof of concept of a new genotyping method specifically designed for complex and highly variable targets. Applied here to HBV, SEB Genotyping can be adapted to any other pathogen or disease carrying multiple known mutations. Using simple preparation steps, SEB Genotyping provides accurate results quickly and will enable physicians to choose the best adapted treatment for each of their patients. |
| first_indexed | 2024-04-13T20:11:02Z |
| format | Article |
| id | doaj.art-b4316f00b8bc4108a045926d5cbd7edd |
| institution | Directory Open Access Journal |
| issn | 1471-2334 |
| language | English |
| last_indexed | 2024-04-13T20:11:02Z |
| publishDate | 2022-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Infectious Diseases |
| spelling | doaj.art-b4316f00b8bc4108a045926d5cbd7edd2022-12-22T02:31:50ZengBMCBMC Infectious Diseases1471-23342022-06-012211910.1186/s12879-022-07458-4SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBVDiane Delobel0Yutaka Furutani1Sumiko Nagoshi2Akihito Tsubota3Akio Miyasaka4Koichi Watashi5Takaji Wakita6Tomokazu Matsuura7Kengo Usui8Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical SciencesLiver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering ResearchDepartment of Gastroenterology and Hepatology Saitama Medical Center, Saitama Medical UniversityCore Research Facilities, Research Center for Medical Science, The Jikei University School of Medicine Minato-KuDivision of Hepatology, Department of Internal Medicine, Iwate Medical University, School of MedicineDepartment of Virology II, National Institute of Infectious DiseasesNational Institute of Infectious DiseasesDepartment of Laboratory Medicine, The Jikei University School of MedicineGenetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical SciencesAbstract Background SmartAmp-Eprimer Binary code (SEB) Genotyping is a novel isothermal amplification method for rapid genotyping of any variable target of interest. Methods After in silico alignment of a large number of sequences and computational analysis to determine the smallest number of regions to be targeted by SEB Genotyping, SmartAmp primer sets were designed to obtain a binary code of On/Off fluorescence signals, each code corresponding to a unique genotype. Results Applied to HBV, we selected 4 targets for which fluorescence amplification signals produce a specific binary code unique to each of the 8 main genotypes (A–H) found in patients worldwide. Conclusions We present here the proof of concept of a new genotyping method specifically designed for complex and highly variable targets. Applied here to HBV, SEB Genotyping can be adapted to any other pathogen or disease carrying multiple known mutations. Using simple preparation steps, SEB Genotyping provides accurate results quickly and will enable physicians to choose the best adapted treatment for each of their patients.https://doi.org/10.1186/s12879-022-07458-4Isothermal amplificationGenotypingHepatitis B virusHigh mutation rateInfectious diseases |
| spellingShingle | Diane Delobel Yutaka Furutani Sumiko Nagoshi Akihito Tsubota Akio Miyasaka Koichi Watashi Takaji Wakita Tomokazu Matsuura Kengo Usui SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV BMC Infectious Diseases Isothermal amplification Genotyping Hepatitis B virus High mutation rate Infectious diseases |
| title | SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV |
| title_full | SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV |
| title_fullStr | SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV |
| title_full_unstemmed | SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV |
| title_short | SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV |
| title_sort | seb genotyping smartamp eprimer binary code genotyping for complex highly variable targets applied to hbv |
| topic | Isothermal amplification Genotyping Hepatitis B virus High mutation rate Infectious diseases |
| url | https://doi.org/10.1186/s12879-022-07458-4 |
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