Multiplex logic processing isothermal diagnostic assays for an evolving virus

Sanchita Bhadra; Miguel A. Saldaña; Hannah Grace Han; Grant L. Hughes; Andrew D. Ellington

To ensure readout specificity, individual hemiduplex OSD probes 12 were designed for each of the four ZIKV LAMP amplicons ( Figure 1B) . To facilitate detection of LAMP amplicons from different viral lineages, probe nucleotide positions corresponding to polymorphic target loci were substituted with degenerate bases (Supplementary Table T2 ). The NS3 OSD probe was the least degenerate with only two positions in the long and the short probe strands varying between two bases. The capsid OSD probe contained two nucleotide variations at four and two positions in the long and the short strand, respectively. Three positions in both the long and the short strands of the NS5 OSD probe varied between two bases. The NS1 OSD probes displayed the greatest degeneracy with four positions in both the long and the short strands varying between two bases.