Data from: Heart-nosed bat alphacoronaviruses use human CEACAM6 to enter cells

This data repository contains supplementary information, data and output files from analyses performed and accompanying the Gallo et al. (2026), Heart-nosed bat alphacoronaviruses use human CEACAM6 to enter cells Nature publication (10. 1038/s41586-026-10394-x). A description of the deposited files with their folder structured is provided below. __________________________________________________ 1 Biolayer Interferometry The biolayerᵢnterferometry. zip file contains Bio-Layer Interferometry (BLI) data generated as part of the study. The following folder is included: ReferenceₛubtractedBLIdata: data in CSV format describing reference sensor substracted response (nm) versus time for binding of various CEACAM protein analytes (at five different concentrations: 37. 5, 75, 150, 300 and 600 nM) to ligands CcCoV|KY43 or CcCoV|2B RBD. Binding of analyte to a control reference biosensor is also shown (CEACAM6 for first replicate experiments, CEACAM5 for second replicate experiments). 2 Isothermal Titration Calorimetry The isothermalₜitrationcalorimetry. zip file contains Isothermal Titration Calorimetry (ITC) data generated as part of the study. The following data are included: ITCᵣawdata: folder containing compressed. zip file including data in CSV format describing raw ITC data (differential power versus time) and integrated enthalpy as a function of molar ratio (where binding was observd) ; ITCdataₜable. pdf: summary table listing syringe and cell contents, in addition to fitted values where relevant. 3 Western Blot The westernblot. zip file contains: aCoVₒriginalᵢmmunoblots. pdf: original immunoblot used to validate the incorporation of alphaCoV S on pseudovirus particles, with or without treatment with trypsin before purification __________________________________________________ 4 Raw Data Analysis The rawdataₐnalysis. zip file contains raw and analysed data supporting the figures presented in the main text, extended data and supplementary information. The following data are inlcuded: RawdataₐnalysisMainfigures. xlsx: raw data used to construct figures presented in the main text; RawdataₐnalysisExtendeddata. xlsx: raw data used to construct figures included as extended data; RawdataₐnalysisSI. xlsx: raw data used to construct figures included as supplementary informatio. __________________________________________________ 5 Phylogenetics The phylogenetics. zip file is structured into data, code and analysis folders, as detailed below. 5. 1 Data 5. 1. 1 aCoV Sequences The data/aCoVₛequences folder contains all publicly available alphacoronavirus sequences encoding for the whole spike protein region retrieved from the Virus Pathogen Database and Analysis Resource (ViPR) platform hosted by the Bioinformatics Resource Center (BRC) at the National Institute of Allergy and Infectious Diseases (NIAID) https: //www. bv-brc. org/ n=2714, as of May 2021. The following files are included: aCoVₛpikeAAₛeqsₙ2714. fasta: fasta unaligned set of alphacoronavirus whole spike protein sequences, n=2714; aCoVₛpikeCDSₛeqsaₙ2714. xlsx: fasta unaligned set of alphacoronavirus whole spike coding DNA sequences, n=2714; aCoVₛpikeAAₘetaₙ2714. xlsx: metadata associated with the n=2714 alphacoronavirus whole spike protein sequences; aCoVₛpikeAAₛeqsGMMDₙ40. fasta: fasta unaligned set of alphacoronavirus whole spike protein sequences selected using the greedy algorithm procedure, n=40; aCoVₛpikeCDSₛeqsGMMDₙ40. fasta: fasta unaligned set of alphacoronavirus whole spike coding DNA sequences selected using the greedy algorithm procedure, n=40; aCoVₛpikeCDSₛeqsₜreeₙ48. fasta: fasta unaligned set of alphacoronavirus whole spike coding DNA sequences used for reconstructing the phylogenetic tree in Fig. 5A, n=48. This include the set of greedy-selected alphacoronavirus spike sequences plus sequences representing the 'local phylogeny' of CcCoV|KY43; aCoVₛpikeCDSₘetaₜreeₙ48. xlsx: metadata associated with the n=48 alphacoronavirus whole spike coding DNA sequences used for reconstructing the phylogenetic tree in Fig. 5A, n=48. 5. 2 Code 5. 2. 1 Greedy MMD The code/greedyₘmd folder contains the R script used to select the k=40 representative among the n=2714 alphaCoV full-length S sequences retrieved from the ViPR database. The following file is included: greedyₘmd. R: implementation of the Bordewich et al. (2008) algorithm for selecting a k subset of taxa/sequences that maximise phylogenetic spread based on their minimum pairwise distance. 5. 3 Analysis 5. 3. 1 ML Trees The analysis/MLₜrees folder contains. nexus files of maximum-likelihood phylogenies reconstructed in IQTREE 2. 3. 4 and using alphacoronavirus whole spike sequences. The following files are included: aCovₛpikeAAₜreeMLₙ2714. nexus: maximum-likelihood estimation of the full alphacoronavirus spike protein phylogeny including the n=2714 protein sequences; aCoVₛpikeCDSₜreeMLₙ2714. nexus: maximum-likelihood estimation of the full alphacoronavirus spike protein phylogeny including the n=2714 coding DNA sequences; aCoVₛpikeCDSₜreeMLₙ40. nexus: maximum-likelihood estimation of the alphacoronavirus spike protein phylogeny including the n=40 coding DNA sequences selected using the greedy algorithm procedure; aCoVₛpikeAAₜreeMLₙ48. nexus: maximum-likelihood estimation of the alphacoronavirus spike protein phylogeny including the n=48 protein sequences representing the set of greedy-selected alphacoronavirus spike sequences plus sequences those representing the 'local phylogeny' of CcCoV|KY43; aCoVₛpikeCDSₜreeMLₙ48. nexus: maximum-likelihood estimation of the full alphacoronavirus spike protein phylogeny including the n=48 coding DNA sequences representing the set of greedy-selected alphacoronavirus spike sequences plus sequences those representing the 'local phylogeny' of CcCoV|KY43; 5. 3. 2 BEAST Trees The analysis/BEASTₜrees folder contains XML files generated in BEAST 1. 10. 5 and used to run the time-stamped phylodynamic reconstruction of the n=48 alphacoronavirus whole spike coding DNA sequences. 5. 3. 2. 1 Codon The analysis/BEASTₜrees/codon folder contains the XML file generated in BEAST 1. 10. 5 and used to reconstruct the evolutionary history of alphacoronavirus by modelling evolution either using protein or codon-aware models with and characterising the whole spike sequences presented in Fig. 5a. The following files are included: aCoVₛpikeWAGₙ48. xml: XML file generated in BEAUti for the WAG protein model analysis; aCoVₛpikeWAGₙ48. trees. txt: full posterior tree space generated from BEAST using the WAG protein model; aCoVₛpikeY96ₙ48. xml: XML file generated in BEAUti for the Y96 codon model analysis; aCoVₛpikeY96ₙ48. trees. txt: full posterior tree space generated from BEAST using the Y96 codon model; aCoVₛpikeSRD06ₙ48. xml: XML file generated in BEAUti for the SRD06 codon-aware model analysis; aCoVₛpikeSRD096ₙ48. trees. txt: full posterior tree space generated from BEAST using the SRD06 codon-aware model. 5. 3. 2. 2 CEACAM6 The analysis/BEASTₜrees/ceacam6 folder contains the XML file generated in BEAST 1. 10. 5 and used to run discrete traits Markov Jump reconstructions to investigate the potential acquisition (or loss) of the CEACAM6 usage along the full evolutionary history of alphacoronavirus, using the whole spike coding DNA sequences presented in Supplementary Fig. 18. The following files are included: aCoVₛpikeSRD06ceacam6ₙ48. xml: XML file generated in BEAUti; aCoVₛpikeSRD06ceacam6ₙ48. trees. txt: full posterior tree space generated from BEAST analysis. __________________________________________________ References 1. Bordewich M, Rodrigo AG, Semple C (2008). Selecting Taxa to Save or Sequence: Desirable Criteria and a Greedy Solution. Systematic Biology, 57 (6): 825–834. https: //doi. org/10. 1080/10635150802552831 2. Olson D, et al. (2023). Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. Nucleic Acids Research, 51 (D1): D678–D689. https: //doi. org/10. 1093/nar/gkac1003