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

Rapid and accurate batch sequence retrieval is both the cornerstone and bottleneck for comparative gene or genome analysis. During the process of complete genome sequencing and comparative analysis of the various novel human and animal coronavirus genomes in the past 2 years, we have developed a comprehensive The first column is CoVDB gene id. In the Uniq column, 'Uniq' will be shown if there is no other identical sequence in CoVDB. Otherwise, gene id of the sequences identical to it will be shown. database, CoVDB, of annotated coronavirus genes and genomes, which offers efficient batch sequence retrieval and analysis. As shown by our experience in using CoVDB for comparative genome analysis of novel coronaviruses we have discovered (4, 13, 16, 18, 19) , we find that CoVDB is more rapid and efficient than other existing coronavirus databases for batch sequence retrieval for the following reasons. First, we have performed annotation on all non-structural proteins in the polyprotein encoded by orf1ab of every single sequence. Second, annotation was performed for the non-structural proteins encoded by ORFs downstream to orf1ab using a standardized system, with some exceptions given to some names that have been used for a long time so as to minimize confusion. Third, all sequences with identical nucleotide sequences were labeled where one can choose to show or not to show strains with identical sequences. Fourth, CoVDB contains not only complete coronavirus genome sequences, but also incomplete genomes and their genes. Some genes of coronaviruses, such as pol, spike and nucleocapsid are sequenced much more frequently than others because they are either most conserved or least conserved. These gene sequences are particularly important for evolutionary analysis, single nucleotide polymorphism studies and design of primers for RT-PCR or quantitative RT-PCR amplification.