MERS-CoV-3D: integrating whole-genome variation, proteome mapping, and structural annotation of MERS-CoV mutations

Middle East respiratory syndrome coronavirus (MERS-CoV) remains a high-consequence zoonotic pathogen with recurrent outbreak potential and substantially higher reported case fatality than many other human coronaviruses. Although increasing numbers of MERS-CoV genomes and protein structures are available, these data remain distributed across independent sequence, proteome, and structural repositories, limiting systematic interpretation of viral mutations in their functional and three-dimensional contexts. Here, we present an integrated and automated MERS-CoV structural mutation database that connects whole-genome variation, mature viral protein coordinates, experimentally available structures, and residue-level structural annotations. The genome-wide pipeline curates complete or near-complete good-quality MERS-CoV genomes, performs whole-genome alignment, phylogenetic clade and lineage assignment, and identifies amino-acid mutations relative to the reference genome. Replicase mutations are further converted from ORF1a/ORF1ab polyprotein coordinates into mature non-structural protein positions. In parallel, the proteome-wide pipeline automatically retrieves MERS-CoV-related structural records, extracts coordinate-derived chain sequences, performs strict chain-level mapping to the reference proteome, and generates structure-specific mutation mappings. The resulting database contains 1715 unique protein-level mutations, 35 995 cumulative genome-level mutation observations, 456 mapped structure-chain records, 213 unique structures, and 13 542 residue-level structural annotations. The web interface (https://merscov3d.org/version 1.0) lets users browse mutation frequencies, clade distributions, mapped structures, and structural annotations, and inspect mutation positions interactively in a three-dimensional molecular context. Therefore, integrating automated genome surveillance with proteome-scale structural mapping, this resource provides a platform for prioritizing biologically relevant mutations, supporting public health and national surveillance interpretation of emerging MERS-CoV variants, identifying structurally important viral regions, and assisting antiviral-development organizations in drug-target prioritization and resistance-monitoring studies.