Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes

Sara Cleemput; Wim Dumon; Vagner Fonseca; Wasim Abdool Karim; Marta Giovanetti; Luiz Carlos Alcantara; Koen Deforche; Tulio de Oliveira

reference sequences from VIPR and 47 public 2019-nCoV sequences). The sensitivity, specificity and accuracy of our method was calculated for both species assignment and phylogenetic clustering of SARSr-CoV. Sensitivity was computed by the formula Classifying query sequences in an automated fashion involves two steps. The first step enables virus species assignments and the second, which is restricted to SARSr-CoV, includes phylogenetic analysis. The first classification analysis subjects a query sequence to BLAST and AGA analysi. AGA is a novel alignment method for nucleic acid sequences against annotated genomes from NCBI RefSeq Virus Database. AGA (Deforche 2017) expands the optimal alignment algorithms of Smith-Waterman (Smith & Waterman 1981) and Gotoh (Gotoh 1982) based on an induction state with additional parameters. The result is a more accurate aligner, as it takes into account both nucleotide and protein scores and identifies all of the polymorphisms at nucleotide and amino acid levels. In the second step, a query sequence is aligned against the phylogenetic reference dataset using -add alignment option in the MAFFT software (Katoh & Standley 2013) . In addition, a Neighbor Joining phylogenetic tree is constructed using the HKY distance metric with gamma among-site rate variation with 1,000 bootstrap replicates using PAUP* (Swofford) . The query sequence is assigned to a particular phylogenetic cluster if it clusters monophyletically with that clade or a subset of it with bootstrap support >70%. If the bootstrap support is <70%, the genotype is reported to be unassigned.