CPS-Guided Nucleocapsid Haplotype Atlas of MERS-CoV (2013 - 2019): A Genome-Constrained, CPS-Informed Dataset for Anticipatory Surveillance

This dataset comprises 67 high-quality, codon-resolved nucleocapsid (N) gene coding sequences from global MERS-CoV clinical isolates (2013 - 2019), aligned to the RefSeq reference (YP_009047211.1). It includes: A CPS-informed consensus sequence derived from empirical codon usage,27 observed haplotypes at evolutionarily permissive sites,Full metadata (collection date, country, host, passage history),Quality-controlled CDS files ready for synthetic genomics or evolutionary modeling.Generated using the Codon-Permissiveness Score (CPS) framework (Bhatti, Preprints 2025, doi:10.20944/preprints202510.0285.v1), this resource enables anticipatory surveillance, viability screening of emerging lineages, and extension of codon-resolution evolutionary analysis beyond Spike and SARS-CoV-2. All data are open, reproducible, and compatible with forward-looking pathogen genomics pipelines. Study by: Tahir Bhatti