Analysis code for: Lineage-Restricted Reassortment and Glycoprotein Stability in Crimean-Congo Hemorrhagic Fever Virus, 36 Countries, 1956–2025
Abstract
Analysis code and derived results for “Lineage-Restricted Reassortment and Glycoprotein Stability in Crimean-Congo Hemorrhagic Fever Virus, 36 Countries, 1956–2025” This deposit contains the analysis code and the derived result files supporting the above manuscript (EID-26-1962, submitted to Emerging Infectious Diseases). The study assembled every publicly available Crimean-Congo hemorrhagic fever virus (CCHFV) isolate for which the S, M and L genome segments were sequenced to near-completeness (429 isolates, 36 countries, 1956–2025), retrieved from GenBank, and asked whether segment reassortment is distributed evenly across the major lineages of the virus. The code reproduces: retrieval of the records from GenBank and assembly of the tri-segment isolate set; per-segment alignment (MAFFT) and maximum-likelihood phylogenies (FastTree 2, GTR+Γ); lineage and sublineage delimitation by clustering of pairwise p-distances; the sublineage-level test of intra-lineage segment exchange; simulation of the false-positive rate and of the probability that planted segment exchanges are detected; tests of the regional contrast at the level of independent ancestries under three counting rules and three definitions of lineage exposure; the amino-acid divergence analysis of the M-segment glycoprotein precursor by functional region; and the figures. No new sequence data are generated. All sequences analysed are publicly available in GenBank, and their accession numbers are listed in Appendix Table 1 of the manuscript. Contents: Python scripts (*.py), a README describing the run order and software requirements, and a results/ folder holding the output of every analysis in JSON so that the values reported in the manuscript text, tables and figures can be checked without re-running the pipeline. Requirements: Python 3 with numpy, scipy, biopython, matplotlib and openpyxl; MAFFT v7 and FastTree 2 on the path.
