SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV

BMC Infectious Diseases

Akihito Tsubota¹  Sumiko Nagoshi²  Tomokazu Matsuura³  Koichi Watashi⁴  Akio Miyasaka⁵  Kengo Usui⁶  Diane Delobel⁶  Yutaka Furutani⁷  Takaji Wakita⁸ 

[1] Core Research Facilities, Research Center for Medical Science, The Jikei University School of Medicine Minato-Ku;Department of Gastroenterology and Hepatology Saitama Medical Center, Saitama Medical University;Department of Laboratory Medicine, The Jikei University School of Medicine;Department of Virology II, National Institute of Infectious Diseases;Division of Hepatology, Department of Internal Medicine, Iwate Medical University, School of Medicine;Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Sciences;Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research;National Institute of Infectious Diseases;

关键词: Isothermal amplification;    Genotyping;    Hepatitis B virus;    High mutation rate;    Infectious diseases;   

DOI  :  10.1186/s12879-022-07458-4

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown