GESS: a database of global evaluation of SARS-CoV-2/hCoV-19 sequences

Abstract

The COVID-19 outbreak has become a global emergency since December 2019. Analysis of SARS-CoV-2 sequences can uncover single nucleotide variants (SNVs) and corresponding evolution patterns. The Global Evaluation of SARS-CoV-2/hCoV-19 Sequences (GESS, https://wan-bioinfo.shinyapps.io/GESS/) is a resource to provide comprehensive analysis results based on tens of thousands of high-coverage and high-quality SARS-CoV-2 complete genomes. The database allows user to browse, search and download SNVs at any individual or multiple SARS-CoV-2 genomic positions, or within a chosen genomic region or protein, or in certain country/area of interest. GESS reveals geographical distributions of SNVs around the world and across the states of USA, while exhibiting time-dependent patterns for SNV occurrences which reflect development of SARS-CoV-2 genomes. For each month, the top 100 SNVs that were firstly identified world-widely can be retrieved. GESS also explores SNVs occurring simultaneously with specific SNVs of user's interests. Furthermore, the database can be of great help to calibrate mutation rates and identify conserved genome regions. Taken together, GESS is a powerful resource and tool to monitor SARS-CoV-2 migration and evolution according to featured genomic variations. It provides potential directive information for prevalence prediction, related public health policy making, and vaccine designs.

Figure 1.

Overview of GESS database. (A) The infrastructure of GESS database. The central part is individual SNV analysis and concurrence of SNVs. (B) Home page of GESS database. Besides a brief description of the website, the ‘Home’ page includes distributions of viral genome numbers around the world, or in the USA, or within each month. Several subpages contain different functions under the ‘Home’ page, in addition to the ‘Tutorial’ with the introduction to the use of GESS.

Figure 2.

An example to show the process of data mining via GESS. (A) World map of distribution of the mutation A23403G (S:D614G). (B) Table including event counts of A23403G in different counties/areas. (C) Temporal occurrence ratios of A23403G along the time. (D) SNVs in concurrence with A23403G (identified in at least 1,000 samples with the ratio larger than 0.9).

Figure 3.

Function of ‘SNV birth query’. (A) Word cloud of new SNVs in March 2020. (B) Table listing corresponding information for new SNVs in March 2020. (C) Word cloud of new SNVs and (D) information of new SNVs in June 2020.

Figure 4.

Examples to use GESS to calibrate sequence conservation for vaccine design. (A) Helper T lymphocyte-based epitope LLLQYGSFCTQLNRA on the genomic region: 23 816 – 23 860 (Spike). The y-axis in the dot plot represents the numbers (base-10 log scale) of viral genomes with point mutations at each position. Nucleotides and amino acids are marked, respectively, under the dot plot at corresponding genomic locations. (B) B lymphocyte epitope, QGEIKDATPSDF, within the viral genome: 25 441 – 25 476 (ORF3a). The screenshots were taken from GESS.