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

The Genome Detective Coronavirus Typing Tool correctly classified all of the 175 SARSr-CoV sequences at species level, i.e. specificity, sensitivity and accuracy of 100%. Furthermore, all of the 47 2019-nCoV WGS that were isolated in China (n=36), USA (n=5), France (n=2), Thailand (n=2), Japan (n=1) and Taiwan (n=1) were correctly classified at phylogenetic cluster level as 2019-nCoV, which may be renamed as SARS-B. In addition, we classified with very high specificity, sensitivity and accuracy (i.e. 100%) all of the 112 SARS outbreak WGS of 2002 and 2003. We also achieved perfect classification (i.e. specificity, sensitivity and accuracy of 100%) for all of Beta coronavirus, Human_coronavirus_HKU1, MERS-CoV, Rousettus_bat_coronavirus_HKU9 and Tylonycteris_bat_coronavirus_HKU4 at species level. For a detailed overview of assignment performance, please refer to the Supplementary Table 3. Our tool also allows detailed analysis of coding regions and proteins for each of the coronavirus species. For example, the analysis of the first released 2019-nCoV sequence, the WH_Human1_China_2019Dec (GenBank: MN908947) demonstrated at genome level , the nucleotide (NT) identity was 79.0% to the reference strain of SARSr-CoV (ACCESSION: NC_004718.3) and that the Envelop Small Membrane Protein (protein E) is the most similar protein. In total, 94.8% (73/77) of the amino acids were identical; the four amino acid differences were located at positions 55 (T55S), 56 (V56F), 69 (69deletion) and 70 (G70R). The spike protein (protein S), which can be associated with virulence, was 76.2% identical to the reference strain of SARSr-CoV (Supplementary 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. 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 ).