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

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

The result of the phylogenetic and mutational analysis performed by AGA is available in a detailed report. This report contains an interactive phylogenetic tree and genome mapper (Supplementary Figure 1) . It also presents the virus species and cluster assignments and a detailed Table 4A ). Interestingly there were four amino acid insertions at position 237 (A237_F238insHRSY, genome NT position 22202_22203insCATAGAAGTTAT)), which is just upstream from a cleavage site. There is also a four amino acid insertion PRRA at the spike protein at positions 681 to 684.This is at the junction of S1 and S2 and creates a new polybase cleavage site. Our tool also allows us to compare mutations with other related sequences, such as the Pangolin, Bat RaTG13, the Bat SARS-CoV and SARS Sin940 (Picture 2 and supplementary table 2). The most diverse coding regions were the CDS Sars8a and Sars8b. In these two regions, only 30% of the amino acids were identical. Sars8b protein was truncated early and its CDS had four stop codons (Supplementary Table 4sA ). Our Coronavirus Typing Tool also allows a query sequence to be analysed against a sequence in the phylogenetic reference dataset. For example, the WH_Human1_China_2019Dec (GenBank: MN908947) the identity was 87.5% to the Bat sequence bat_SL_CoVZXC21 (Genbank: MG772934). This was one of the Bat-CoV sequences that were most related to n2019-CoV