Bioinformatic analysis to design subtype-agnostic RT-LAMP primers.

<p>A) Conservation of sequence in HIV. HIV genomes (n = 1340) from the Los Alamos National Laboratory collection (file HIV1_ALL_2012_genome_DNA.fasta; <a href="http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html#web" target="_blank">http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html#web</a>) were aligned and conservation calculated. The x-axis shows the coordinate on the HIV genome, the y-axis shows the proportion of sequences matching the consensus for each 21 base segment of the genome (red points). The black line shows a 101 base sliding average over these proportions. The vertical red shading shows the region targeted for LAMP primer design that was used as input into the EIKEN primer design tool. Numbering is relative to the HIV_89.6 sequence. B) Aligned genomes, showing the locations of the ACeIN-26 primers. Sequences in the red shaded region in A are shown, with DNA bases color-coded as shown at the lower right. Each row indicates an HIV sequence and each column a base in that sequence. Horizontal lines separate the HIV subtypes (labeled at right). Arrows indicate the strand targeted by each primer. Primers targeting the negative strand of the virus are shown as reverse compliments for ease of viewing.