Primers and probe for this assay are designed using all available public and private genome databases.
The DENV1, DENV2, DENV3, and DENV4 RT-PCR assays were designed using all available whole genome DENV sequences in the NCBI nucleotide collection.
The DENV1, DENV2, DENV3, and DENV4 real-time RT-PCR assays were designed using all DENV1 (n = 1532), DENV2 (n = 1117), DENV3 (n = 832), and DENV4 (n = 145) whole genome sequences available in the NCBI nucleotide collection at the design stage.
The absence of any representative of these groups is unlikely to be a technical artifact since the group-specific primer pairs were designed using all known representatives in GenBank of the respective groups and given the elaborate amplification tests using several positive controls per group in Van Borm and Boomsma (2002).
The latter possibility, however, seems unlikely, since the goup-specific primer pairs were designed using all known representatives in GenBank of the respective groups, and were tested using several positive controls aimed to represent the whole diversity of the group in question [ 40].
Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp).
For transcript analyses of LUHMES, primers (Eurofins MWG Operon, Ebersberg, Germany) were designed using AiO (All in One) bioinformatics software and can be found in Supplementary Figure 11.
All primers were designed using OligoPerfect Designer (Invitrogen).
All primers were designed using Beacon Designer 7 (Premier BioSoft International, Palo Alto, CA, USA).
All primers were designed using Beacon Designer 3.0 (Premier Biosoft International, Palo Alto, CA).
