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 biolayer_interferometry.zip file contains Bio-Layer Interferometry (BLI) data generated as part of the study. The following folder is included: Reference_subtracted_BLI_data: 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 isothermal_titration_calorimetry.zip file contains Isothermal Titration Calorimetry (ITC) data generated as part of the study. The following data are included: ITC_raw_data: 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); ITC_data_table.pdf: summary table listing syringe and cell contents, in addition to fitted values where relevant. 3 Western Blot The western_blot.zip file contains: aCoV_original_immunoblots.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 raw_data_analysis.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: Raw_data_analysis_Main_figures.xlsx: raw data used to construct figures presented in the main text; Raw_data_analysis_Extended_data.xlsx: raw data used to construct figures included as extended data; Raw_data_analysis_SI.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/aCoV_sequences 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: aCoV_spikeAA_seqs_n2714.fasta: fasta unaligned set of alphacoronavirus whole spike protein sequences, n=2714; aCoV_spikeCDS_seqsa_n2714.xlsx: fasta unaligned set of alphacoronavirus whole spike coding DNA sequences, n=2714; aCoV_spikeAA_meta_n2714.xlsx: metadata associated with the n=2714 alphacoronavirus whole spike protein sequences; aCoV_spikeAA_seqs_GMMD_n40.fasta: fasta unaligned set of alphacoronavirus whole spike protein sequences selected using the greedy algorithm procedure, n=40; aCoV_spikeCDS_seqs_GMMD_n40.fasta: fasta unaligned set of alphacoronavirus whole spike coding DNA sequences selected using the greedy algorithm procedure, n=40; aCoV_spikeCDS_seqs_tree_n48.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; aCoV_spikeCDS_meta_tree_n48.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/greedy_mmd 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: greedy_mmd.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/ML_trees 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: aCov_spikeAA_treeML_n2714.nexus: maximum-likelihood estimation of the full alphacoronavirus spike protein phylogeny including the n=2714 protein sequences; aCoV_spikeCDS_treeML_n2714.nexus: maximum-likelihood estimation of the full alphacoronavirus spike protein phylogeny including the n=2714 coding DNA sequences; aCoV_spikeCDS_treeML_n40.nexus: maximum-likelihood estimation of the alphacoronavirus spike protein phylogeny including the n=40 coding DNA sequences selected using the greedy algorithm procedure; aCoV_spikeAA_treeML_n48.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; aCoV_spikeCDS_treeML_n48.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/BEAST_trees 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/BEAST_trees/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: aCoV_spike_WAG_n48.xml: XML file generated in BEAUti for the WAG protein model analysis; aCoV_spike_WAG_n48.trees.txt: full posterior tree space generated from BEAST using the WAG protein model; aCoV_spike_Y96_n48.xml: XML file generated in BEAUti for the Y96 codon model analysis; aCoV_spike_Y96_n48.trees.txt: full posterior tree space generated from BEAST using the Y96 codon model; aCoV_spike_SRD06_n48.xml: XML file generated in BEAUti for the SRD06 codon-aware model analysis; aCoV_spike_SRD096_n48.trees.txt: full posterior tree space generated from BEAST using the SRD06 codon-aware model. 5.3.2.2 CEACAM6 The analysis/BEAST_trees/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: aCoV_spike_SRD06_ceacam6_n48.xml: XML file generated in BEAUti; aCoV_spike_SRD06_ceacam6_n48.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