SARS2Mutant: SARS-CoV-2 amino-acid mutation atlas database

Abstract

The coronavirus disease 19 (COVID-19) is a highly pathogenic viral infection of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulted in the global pandemic of 2020. A lack of therapeutic and preventive strategies has quickly posed significant threats to world health. A comprehensive understanding of SARS-CoV-2 evolution and natural selection, how it impacts host interaction, and phenotype symptoms is vital to develop effective strategies against the virus. The SARS2Mutant database (http://sars2mutant.com/) was developed to provide valuable insights based on millions of high-quality, high-coverage SARS-CoV-2 complete protein sequences. Users of this database have the ability to search for information on three amino acid substitution mutation strategies based on gene name, geographical zone, or comparative analysis. Each strategy is presented in five distinct formats which includes: (i) mutated sample frequencies, (ii) heat maps of mutated amino acid positions, (iii) mutation survivals, (iv) natural selections and (v) details of substituted amino acids, including their names, positions, and frequencies. GISAID is a primary database of genomics sequencies of influenza viruses updated daily. SARS2Mutant is a secondary database developed to discover mutation and conserved regions from the primary data to assist with design for targeted vaccine, primer, and drug discoveries.

Figure 1.

Schematic view of the SARS-CoV-2 particles, genome arrangement, and proteome organization. SARS-CoV-2 is an enveloped positive-sense single-stranded RNA beta coronavirus with a ∼30 kb polycistronic genome that encodes non-structural proteins (ORF1a and ORF1b, that are processed into Nsp1-16) at the 5′-end, and structural proteins (S, E, M and N), and several other accessory factors (ORF3a, 6, 7a, 7b, 8 and 10) at the 3′-end. Wild type of 3D structural models of protein were retrieved from I-TASSER (40).

Figure 2.

Database architecture and workflow. Request mechanisms from users to the database.

Figure 3.

Database structure. (A) The homepage, services and facilities. (B) The quick access part of the database that helps the user find the results quickly and clearly.

Figure 4.

Database data representation structure. (A) Protein description, functions, and official sequence. (B) mutation frequency among all analyzed samples. (C) Hotspot genome positions versus conserved. (D) Mutation detection trend during the month. (E) Mutation frequencies and Substitution amino acids.

Figure 5.

Database search strategy. (A) Mutant Search allows the user to search based on the candidate gene. (B) Comparative analysis enables user to search and compare the candidate gene between two different areas.