{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T10:37:26Z","timestamp":1792751846177,"version":"4.5.0"},"reference-count":40,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:00:00Z","timestamp":1792713600000},"content-version":"vor","delay-in-days":295,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100019725","name":"Deanship of Scientific Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100019725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004054","name":"King Abdulaziz University","doi-asserted-by":"publisher","award":["1288-130-2026"],"award-info":[{"award-number":["1288-130-2026"]}],"id":[{"id":"10.13039\/501100004054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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\u2009995 cumulative genome-level mutation observations, 456 mapped structure-chain records, 213 unique structures, and 13\u2009542 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.<\/jats:p>","DOI":"10.1093\/database\/baag065","type":"journal-article","created":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T09:37:26Z","timestamp":1792748246000},"source":"Crossref","is-referenced-by-count":0,"title":["MERS-CoV-3D: integrating whole-genome variation, proteome mapping, and structural annotation of MERS-CoV mutations"],"prefix":"10.1093","volume":"2026","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6696-7770","authenticated-orcid":false,"given":"Ali F","family":"Alsulami","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Faculty of Science, King Abdulaziz University , Jeddah 21589 ,","place":["Saudi Arabia"]},{"name":"The Centre for Artificial Intelligence Research & Innovation in Precision Medicines (CAIPM), King Abdulaziz University , Jeddah 21589 ,","place":["Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,23]]},"reference":[{"key":"2026102305372040400_bib1","doi-asserted-by":"publisher","first-page":"1814","DOI":"10.1056\/NEJMoa1211721","article-title":"Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia","volume":"367","author":"Zaki","year":"2012","journal-title":"N Engl J Med"},{"key":"2026102305372040400_bib2","doi-asserted-by":"publisher","first-page":"408","DOI":"10.1038\/s41586-021-04188-6","article-title":"The emergence, genomic diversity and global spread of SARS-CoV-2","volume":"600","author":"Li","year":"2021","journal-title":"Nature"},{"key":"2026102305372040400_bib3","doi-asserted-by":"publisher","first-page":"e0183850","DOI":"10.1371\/journal.pone.0183850","article-title":"Occurrence of the Middle East respiratory syndrome coronavirus (MERS-CoV) across the Gulf Corporation Council countries: four years update","volume":"12","author":"Aly","year":"2017","journal-title":"PLoS One"},{"key":"2026102305372040400_bib4","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/s44298-024-00080-y","article-title":"Middle East respiratory syndrome coronavirus (MERS-CoV) internalization does not rely on DPP4 cytoplasmic tail signaling","volume":"2","author":"Thankamani","year":"2024","journal-title":"Npj Viruses"},{"key":"2026102305372040400_bib5","doi-asserted-by":"publisher","first-page":"101520","DOI":"10.1016\/j.tmaid.2019.101520","article-title":"MERS-CoV as an emerging respiratory illness: a review of prevention methods","volume":"32","author":"Baharoon","year":"2019","journal-title":"Travel Med Infect Dis"},{"key":"2026102305372040400_bib6","doi-asserted-by":"publisher","first-page":"2988","DOI":"10.1038\/s41467-022-30698-6","article-title":"Transmission of SARS-CoV-2 from humans to animals and potential host adaptation","volume":"13","author":"Tan","year":"2022","journal-title":"Nat Commun"},{"key":"2026102305372040400_bib7","doi-asserted-by":"publisher","first-page":"5324","DOI":"10.1038\/s41467-021-25519-1","article-title":"Functional comparison of MERS-coronavirus lineages reveals increased replicative fitness of the recombinant lineage 5","volume":"12","author":"Schroeder","year":"2021","journal-title":"Nat Commun"},{"key":"2026102305372040400_bib8","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/nrmicro.2016.81","article-title":"SARS and MERS: recent insights into emerging coronaviruses","volume":"14","author":"de\u00a0Wit","year":"2016","journal-title":"Nat Rev Micro"},{"key":"2026102305372040400_bib9","doi-asserted-by":"publisher","first-page":"e181","DOI":"10.1038\/emm.2015.76","article-title":"Middle East respiratory syndrome coronavirus: transmission, virology and therapeutic targeting to aid in outbreak control","volume":"47","author":"Durai","year":"2015","journal-title":"Exp Mol Med"},{"key":"2026102305372040400_bib10","doi-asserted-by":"publisher","first-page":"e88716","DOI":"10.1371\/journal.pone.0088716","article-title":"Distinct immune response in two MERS-CoV-infected patients: can we go from bench to bedside?","volume":"9","author":"Faure","year":"2014","journal-title":"PLoS One"},{"key":"2026102305372040400_bib11","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1038\/nrd.2015.37","article-title":"Coronaviruses\u2014drug discovery and therapeutic options","volume":"15","author":"Zumla","year":"2016","journal-title":"Nat Rev Drug Discovery"},{"key":"2026102305372040400_bib12","doi-asserted-by":"publisher","first-page":"e217","DOI":"10.1016\/S1473-3099(18)30127-0","article-title":"Middle East respiratory syndrome coronavirus: risk factors and determinants of primary, household, and nosocomial transmission","volume":"18","author":"Hui","year":"2018","journal-title":"Lancet Infect Dis"},{"key":"2026102305372040400_bib13","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1016\/j.idc.2019.08.001","article-title":"The Middle East respiratory syndrome (MERS)","volume":"33","author":"Azhar","year":"2019","journal-title":"Infect Dis Clin North Am"},{"key":"2026102305372040400_bib14","doi-asserted-by":"publisher","first-page":"20210008","DOI":"10.1098\/rsfs.2021.0008","article-title":"The SARS-CoV-2 pandemic: remaining uncertainties in our understanding of the epidemiology and transmission dynamics of the virus, and challenges to be overcome","volume":"11","author":"Anderson","year":"2021","journal-title":"Interface Focus"},{"key":"2026102305372040400_bib15","doi-asserted-by":"publisher","first-page":"117367","DOI":"10.1016\/j.diagmicrobio.2026.117367","article-title":"Middle East respiratory syndrome coronavirus (MERS-CoV): an underestimated betacoronavirus with pandemic potential","volume":"115","author":"Asokan","year":"2026","journal-title":"Diagn Microbiol Infect Dis"},{"key":"2026102305372040400_bib16","doi-asserted-by":"crossref","first-page":"1342","DOI":"10.1016\/j.jiph.2020.04.007","article-title":"Demographic, clinical, and outcomes of confirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) in Najran, Kingdom of Saudi Arabia (KSA); A retrospective record based study","volume":"13","author":"Al\u00a0Sulayyim","year":"2020","journal-title":"J Infect Public Health"},{"key":"2026102305372040400_bib17","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1038\/s44360-026-00098-x","article-title":"Human MERS-CoV cases are falling but pose an ongoing pandemic threat","volume":"1","author":"Subissi","year":"2026","journal-title":"Nat Health"},{"key":"2026102305372040400_bib18","doi-asserted-by":"publisher","first-page":"101704","DOI":"10.1016\/j.nmni.2026.101704","article-title":"Persistent signals from MERS-CoV in 2025: surveillance gaps, clinical heterogeneity, and preparedness priorities","volume":"70","author":"Al-Tawfiq","year":"2026","journal-title":"New Microbes New Infect"},{"key":"2026102305372040400_bib19","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1038\/s44298-024-00028-2","article-title":"Study of key residues in MERS-CoV and SARS-CoV-2 main proteases for resistance against clinically applied inhibitors nirmatrelvir and ensitrelvir","volume":"2","author":"Krismer","year":"2024","journal-title":"Npj Viruses"},{"key":"2026102305372040400_bib20","doi-asserted-by":"publisher","first-page":"e01381","DOI":"10.1128\/jvi.01381-18","article-title":"Mutations in the spike protein of Middle East respiratory syndrome coronavirus transmitted in Korea increase resistance to antibody-mediated neutralization","volume":"93","author":"Hannah","year":"2019","journal-title":"J Virol"},{"key":"2026102305372040400_bib21","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s12985-021-01563-7","article-title":"Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012\u20132019","volume":"18","author":"Farrag","year":"2021","journal-title":"Virol J"},{"key":"2026102305372040400_bib22","doi-asserted-by":"publisher","first-page":"e00309","DOI":"10.1128\/genomea.00309-16","article-title":"Complete genome sequence of Middle East respiratory syndrome coronavirus isolated from a dromedary camel in Egypt","volume":"4","author":"Kandeil","year":"2016","journal-title":"Genome Announc"},{"key":"2026102305372040400_bib23","doi-asserted-by":"publisher","first-page":"15092","DOI":"10.1038\/ncomms15092","article-title":"Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains","volume":"8","author":"Yuan","year":"2017","journal-title":"Nat Commun"},{"key":"2026102305372040400_bib24","doi-asserted-by":"publisher","first-page":"E7348","DOI":"10.1073\/pnas.1707304114","article-title":"Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen","volume":"114","author":"Pallesen","year":"2017","journal-title":"Proc Natl Acad Sci"},{"key":"2026102305372040400_bib25","doi-asserted-by":"publisher","first-page":"1102","DOI":"10.1107\/S1399004715003521","article-title":"Structures of the Middle East respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity","volume":"71","author":"Needle","year":"2015","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"2026102305372040400_bib26","doi-asserted-by":"publisher","first-page":"D564","DOI":"10.1093\/nar\/gkae1091","article-title":"Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank","volume":"53","author":"Burley","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026102305372040400_bib27","doi-asserted-by":"publisher","first-page":"D36","DOI":"10.1093\/nar\/gks1195","article-title":"GenBank","volume":"41","author":"Benson","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2026102305372040400_bib28","doi-asserted-by":"publisher","first-page":"D480","DOI":"10.1093\/nar\/gkaa1100","article-title":"UniProt: the universal protein knowledgebase in 2021","volume":"49","author":"Consortium, T. U.","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026102305372040400_bib29","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1093\/bib\/bbaa404","article-title":"SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets","volume":"22","author":"Alsulami","year":"2021","journal-title":"Briefings Bioinf"},{"key":"2026102305372040400_bib30","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1038\/s41588-020-0693-3","article-title":"Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource","volume":"52","author":"Portelli","year":"2020","journal-title":"Nat Genet"},{"key":"2026102305372040400_bib31","doi-asserted-by":"publisher","first-page":"3703","DOI":"10.1111\/febs.15366","article-title":"Ligand-centered assessment of SARS-CoV-2 drug target models in the Protein Data Bank","volume":"287","author":"Wlodawer","year":"2020","journal-title":"FEBS J"},{"key":"2026102305372040400_bib32","doi-asserted-by":"publisher","first-page":"D715","DOI":"10.1093\/nar\/gkaf1254","article-title":"BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration","volume":"54","author":"Shukla","year":"2026","journal-title":"Nucleic Acids Res"},{"key":"2026102305372040400_bib33","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1038\/s41597-024-03571-y","article-title":"Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets","volume":"11","author":"O\u2019Leary","year":"2024","journal-title":"Sci Data"},{"key":"2026102305372040400_bib34","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2026102305372040400_bib35","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1038\/s41588-023-01368-0","article-title":"Maximum likelihood pandemic-scale phylogenetics","volume":"55","author":"De\u00a0Maio","year":"2023","journal-title":"Nat Genet"},{"key":"2026102305372040400_bib36","doi-asserted-by":"publisher","first-page":"bbae514","DOI":"10.1093\/bib\/bbae514","article-title":"Mut-Map: comprehensive computational pipeline for structural mapping and analysis of cancer-associated mutations","volume":"25","author":"Alsulami","year":"2024","journal-title":"Briefings Bioinf"},{"key":"2026102305372040400_bib37","doi-asserted-by":"publisher","first-page":"W431","DOI":"10.1093\/nar\/gkab314","article-title":"Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures","volume":"49","author":"Sehnal","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026102305372040400_bib38","doi-asserted-by":"publisher","first-page":"7385","DOI":"10.1038\/s41598-019-43586-9","article-title":"Comparative analysis of eleven healthcare-associated outbreaks of Middle East respiratory syndrome coronavirus (Mers-Cov) from 2015 to 2017","volume":"9","author":"Bernard-Stoecklin","year":"2019","journal-title":"Sci Rep"},{"key":"2026102305372040400_bib39","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1586\/17512433.2014.890515","article-title":"What are our pharmacotherapeutic options for MERS-CoV?","volume":"7","author":"Al-Tawfiq","year":"2014","journal-title":"Expert Rev Clin Pharmacol"},{"key":"2026102305372040400_bib40","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1007\/s40506-015-0048-2","article-title":"Therapeutic options for Middle East respiratory syndrome coronavirus (MERS-CoV) infection: how close are we?","volume":"7","author":"Omrani","year":"2015","journal-title":"Curr Treat Options Infect Dis"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baag065\/72427227\/baag065.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baag065\/72427227\/baag065.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T09:37:28Z","timestamp":1792748248000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baag065\/8991263"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":40,"URL":"https:\/\/doi.org\/10.1093\/database\/baag065","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2026]]},"article-number":"baag065"}}