Development and validation of four one-step real-time RT-LAMP assays for specific detection of each dengue virus serotype

摘要

Author summary The co-existence of several dengue virus (DENV) serotypes within the same location and/or individuals as well as a single mosquito being able to carry multiple DENV serotypes highlight the necessity of specific diagnostic tools capable of detect and serotype DENV strains circulating worldwide. In addition, these methodologies must be highly sensitive in order to detect the genome at low levels (i.e., before the onset of clinical symptoms) and not cross-detect other flaviviruses. Isothermal amplification methods (such as reverse transcription loop-mediated isothermal amplification, RT-LAMP) are affordable for laboratories with limited resources and do not need expensive equipment. Because of the increasing number of publicly available full DENV genome sequences, traditional primer design tools are not able to handle such huge amount of information. Therefore, to be able to cover all the diversity documented, we developed 4 complicated oligonucleotide mixes for the individual detection of DENV1-4 serotypes by RT-LAMP. This approach combined Principal Component Analysis, phylogenetic analysis and LAVA algorithm. Our assays are specific and do not cross-react with other arboviruses and DNA pathogens included in this study, they are sensitive and have been validated with samples from Tanzania, Senegal, Sudan, Mauritania and Cambodia, showing very good performance parameters.