Computational protocol: Bat Caliciviruses and Human Noroviruses Are Antigenically Similar and Have Overlapping Histo-Blood Group Antigen Binding Profiles

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[…] Viral genomic sequences were identified as part of a previous study (). Briefly, bats were collected with harp traps at an abandoned railroad tunnel near Little Orleans, MD, and fresh guano was collected. Samples were stored on ice until processing. The BtCalV/A10 capsid sequence was isolated from Perimyotis subflavus (tri-colored bat) using the sequence-independent single-primer amplification technique and 454 next-generation sequencing platform. De novo contigs were assembled using three programs: Codon Code Aligner, Geneious, and DNAStar. Viral amino acid sequences were created using Vector NTI. Assembled contigs were analyzed using the basic local alignment search tool (BLAST) from the National Center for Biotechnology Information (NCBI) (). BLAST searches were conducted at the amino acid level using the protein-protein BLAST (blastp) function to query nonredundant protein sequences. [...] Maximum-likelihood cladograms of 50 known calicivirus VP1 amino acid sequences and 51 known calicivirus S domain amino acid sequences were generated using MEGA7. The cladograms were generated based on the JTT matrix-based amino acid substitution model and initially derived with the Neighbor-Join (NJ) and BioNJ algorithms followed by pairwise distance estimation by the use of the JTT amino acid replacement model. Bootstrapping was conducted by generating 500 bootstrapped replicates, and a consensus tree was developed using MEGA7. Consensus radial phylograms were generated in Geneious R11, employing the same sequences used to construct the cladograms, with the Jukes-Cantor genetic distance model, the NJ build method, no outgroup, and 100 bootstrap replicates. Phylograms were rendered for publication in Adobe Illustrator CC 2017. [...] The full-length BtCalV/A10, GII.4.1997.Lordsdale HuNoV, GI.1 human sapovirus, GV.1 MNV, and BtNoV capsid sequences () were submitted to the Protein Homology/analogy Recognition Engine V2.0 (PHYRE2) server () and analyzed using Intensive Mode. Homology modeling of the BtCalV/A10 and BtNoV sequences was based on the known HuNoV GII.4/VA387 (PDB ID: 2OBT) () and HuNoV GII.4.2012/NSW0514 bound to type A trisaccharide (PDB ID: 4WZT) () and MNV (PDB ID: 3LQE) structures from the Protein Data Bank. The amino acid sequences were aligned using the Clustal Omega platform on the Bioinformatics Toolkit from the Max Planck Institute (, ). The predicted tertiary structure of the aligned sequence was determined by the use of the Modeller platform from the Bioinformatics Toolkit from the Max Planck Institute using GII.4.2012/NSW0514 as the template (). Dimeric models were created using The PyMOL Molecular Graphics System, version (Schrödinger, LLC). […]

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