Development and validation of oligonucleotide sets for real time RT-PCR detection and next generation sequencing, of re-emerged sylvatic Dengue virus 2 strains

Dengue virus (DENV) is one of the most prevalent arboviral threats worldwide. The virus is associated with a high health and economic burden mainly in tropical and subtropical regions. Available molecular tools however fail to correctly serotype and sequence sylvatic DENV-2 (DENV-2/GVI) which in known to circulate in forests in West Africa and Malaysia. The recent emergence of human case linked to this virus variant in Southern Senegal raises concerns about the correct detection and characterization of the virus for public health purposes. Here we developed and validate new sets of oligonucleotides for DENV-2 (DENV-2/GVI) detection, and next generation sequencing. Validations were carried out using epidemic DENV and sylvatic DENV-2 strains from the biobank of the WHO collaborating Center for Arboviruses and Haemorrhagic fevers. The presented approaches showed good performance to specifically detect sylvatic DENV-2 in both singleplex and multiplex PCR with other DENV serotypes respectively with a limit of detection of 68.85 and 133.21 RNA copies/reaction at 0.95 probability in a probit analysis. Additionally, tilling PCR primers were developed which yield a better genome coverage ranging from 93.9 % to 95.1 % for all processed DENV-2/GVI strains both on Illumina and Nanopore platforms and outperform previous schemes to efficiently amplified DENV-2/GVI strains. In summary the developed oligonucleotides will contribute to improving DENV surveillance and genomic epidemiology in endemic areas.