Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design

Jacob Kames; David Dillon Holcomb; Ofer Kimchi; Michael DiCuccio; Nobuko Hamasaki-Katagiri; Tony Wang; Anton A Komar; Aikaterini Alexaki; Chava Kimchi-Sarfaty

Sequence alignment was measured using MatLab's Needleman-Wunsch sequence alignment implemented on the 100 nts following the frameshift using default parameters. The parameters employed were the defaults: the NUC44 scoring matrix and a gap penalty of 8 for all gaps. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.30.016832 doi: bioRxiv preprint Structure alignment was measured using a method similar to our previously-studied "per-base topology" score [29] . Taking the dot-bracket representation of each secondary structure, we summed the number of positions containing identical elements. Employing an alignment model allowing for gaps, with a gap penalty and a misalignment penalty of -1, did not change our results [42] . The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.30.016832 doi: bioRxiv preprint Table 1 -Euclidean distance (scaled /1000) between codon pair usage frequencies of SARS-CoV-2, Coronaviridae (All CoV), Homo sapiens (genomic), lung, kidney (cortex), small intestine (terminal ileum), Pholidota (pangolins), Chiroptera (bats) and Canis lupus familiaris. TTA TTG AAA AAG ATG TTC TTT CCA CCC CCG CCT AGC AGT TCA TCC TCG TCT TAA TAG TGA ACA ACC ACG ACT TGG TAC TAT