CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes

Huang, Yi; Lau, Susanna K. P.; Woo, Patrick C. Y.; Yuen, Kwok-yung

In CoVDB, with the aim of facilitating gene retrieval, we tried to unify the naming of these non-structural proteins from different groups of coronaviruses. On the other hand, we have also tried to avoid radical changes in the names that may lead to confusion. In CoVDB, these non-structural proteins are named as NS2a, NS3x, NS4x, NS5x and NS7x (x = a, b, c,. . .). NS2a denotes the ORF between orf1ab and HE of group 2a coronaviruses. NS3x denotes the ORFs between S and E of groups 1, 2c, 2d and 3 coronaviruses. In most of these coronaviruses, there are two NS3x, named NS3a and NS3b. However, in group 1 coronaviruses, the genomes of some members (e.g. HCoV-NL63, PEDV) contain only one ORF between S and E. When we compared their putative amino acid sequences to the corresponding ones in other group 1 coronavirus genomes using BLAST, as well as searching for conserved domains using motifscan, results showed that the putative proteins encoded by these ORFs belonged to a protein family in Pfam originally assigned as 'Corona_NS3b' (accession number PF03053). Therefore, we named these ORFs as NS3b. NS4x denotes the ORFs between S and E of group 2a coronaviruses. NS5x denotes the ORFs between M and N of group 3 coronaviruses. One exception is NS5a of group 2a coronaviruses. Traditionally, this name denotes an ORF upstream of E in group 2a coronaviruses. Therefore, we have kept this name for that ORF in CoVDB. NS7x denotes the ORFs downstream of N gene. It is important to note that due to variations in genome organizations among different groups of coronaviruses (Table 1) , NS genes with the same name in different coronavirus groups may not be orthologs of each other. The complete genome gene search page of CoVDB contains a link to a Gene synonyms page, which includes a list of synonymous names of the various genes in the coronavirus genomes.