Genome characterization and receptor-binding protein identification of a newly discovered Klebsiella phage vB_VIPKPNMC05, a member of a novel viral family Pituviridae

Genome characterization and receptor-binding protein identification of a newly discovered Klebsiella phage vB_VIPKPNMC05, a member of a novel viral family Pituviridae | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Genome characterization and receptor-binding protein identification of a newly discovered Klebsiella phage vB_VIPKPNMC05, a member of a novel viral family Pituviridae Michael Angelou L Nada, Arra B Asejo, Marel Jan G Joloro, Ruth Antoinette D Chin, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7522797/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 10 Mar, 2026 Read the published version in Archives of Virology → Version 1 posted 5 You are reading this latest preprint version Abstract Klebsiella pneumoniae is an opportunistic pathogen and a leading cause of antimicrobial-resistant infections in the Philippines. Here, we report the genome sequence of Klebsiella phage vB_VIPKPNMC05, which targets a multidrug-resistant (MDR) K. pneumoniae strain with capsule type K8. VIPKPNMC05 has a siphovirus morphology and exhibits a broad lytic activity against several strains of K. pneumoniae, K. quasipneumoniae, Pseudomonas aeruginosa, and Escherichia coli. The linear double-stranded DNA genome (34,476 bp; 51.0% GC content) encodes 58 protein-coding sequences (CDS), 37 of which are involved in phage morphogenesis, DNA replication, transcription regulation, and host lysis. Notably, a receptor-binding protein (RBP) with a putative depolymerase (Dpo) was identified. Structural prediction using AlphaFold 3 showed that the tailspike protein (TSP) forms a homotrimer structure with a conserved C-terminal pectin lyase domain. The TSP module is conserved among Enterobacteriaceae-infecting phages and may have been acquired through horizontal gene transfer. Whole-genome comparisons revealed 52-54% similarity to known phages, suggesting that VIPKPNMC05 represents a distinct lineage. Based on taxonomic analysis, we propose that VIPKPNMC05 belongs to a novel phage family, Pituviridae. The absence of virulence, toxin, and antimicrobial resistance genes, along with its broad host range and lytic lifestyle, supports the potential of VIPKPNMC05 as a promising candidate for phage therapy and other biotechnology applications. To our knowledge, this is the first report of a newly discovered phage family from the Philippines, underscoring the importance of local phage bioprospecting for therapeutic applications. Klebsiella pneumoniae phage antimicrobial resistance whole genome sequencing tailspike protein Pituviridae Philippines Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Full Text Supplementary Files SupplementaryDataS1.fasta Supplementary Data S1. Multiple sequence alignment of Klebsiella phage vB_VIPKPNMC05 TSP with other phage tailspike proteins. SupplementaryDataS2.pdb Supplementary Data S2. Constructed structural model of Klebsiella phage vB_VIPKPNMC05 tailspike protein (TSP19) using AlphaFold 3. SupplementaryFigureS1.tiff Supplementary Information Supplementary Figure S1. Recombination breakpoint analysis of Klebsiella vB_VIPKPNMC05 tailspike protein. GARD analysis identified three breakpoints, with position 287 likely being the recombination site (ΔAICc = 1039.49). SupplementaryFigureS2.tiff Supplementary Figure S2. Phylogenetic tree based on the breakpoint coordinate (position 287-541) clustering TSP19 with other K. pneumoniae, K. quasipneumoniae, K. variicola, and E. coli prophage tailspike proteins. SupplementaryFigureS3.tif Supplementary Figure S3. Viral proteomic tree consisting of 3,724 genome sequences. The closest relatives of Klebsiella vB_VIPKPNMC05 (highlighted in blue) were identified using mash and INPHARED at 0.20 distance cutoff. Closely related genomes marked in red. Sequences were obtained from NCBI GenBank and viewed using VIPTree. The tree is based on a dissimilarity matrix generated by pairwise tBLASTx scores between each of the genomes. SupplementaryFigureS4.tif Supplementary Figure S4. Phylogenomic tree of Klebsiella vB_VIPKPNMC05 (highlighted in blue) and other Enterobacteriaceae-infecting phages using VICTOR phylogeny. Branch numbers indicate bootstrap support values inferred from 100 iterations with lengths scaled (scale bar=0.1) in terms of GBDP distance formula. The tree was rooted at midpoint and bootstrap values >60% are shown. SupplementaryFigureS5.tif Supplementary Figure S5. Constructed maximum-likelihood phylogenetic tree of the large terminase subunit (terL) gene of Klebsiella vB_VIPKPNMC05 (highlighted in blue) with 1,000 iterations. The tree was rooted at midpoint and bootstrap support of ≥60% are shown. SupplementaryFigureS6.tif Supplementary Figure S6. Multiple whole-genome sequence alignment of Klebsiella vB_VIPKPNMC05 (highlighted in blue) and other Enterobacteriaceae phages. The genomic position of TSP19 is marked by the red asterisk. The colors indicate percent (%) sequence similarly between sequences (blue=low, red=high) with VIPKPNMC05 exhibiting strong collinearity with Klebsiella phages Kp4872 and 1 LV-2017 and a conserved gene order across major functional modules, including structural, replication, and lysis genes. Arrowheads indicate the direction of transcription. Scale bar=4 Kbp. SupplementaryTableS1.pdf Supplementary Table S1. Host range of Klebsiella phage vB_VIPKPNMC05. SupplementaryTableS2.pdf Supplementary Table S2. Predicted hosts according to iPHoP tool. SupplementaryTableS3.pdf Supplementary Table S3. Protein functional annotation of Klebsiella phage vB_VIPKPNMC05. SupplementaryTableS4.pdf Supplementary Table S4. Prediction of receptor-binding proteins (RBP) and depolymerases (Dpo) of Klebsiella phage vB_VIPKPNMC05. SupplementaryTableS5.xlsx Supplementary Table S5. Functional domain analysis of tailspike proteins using InterPro. SupplementaryTableS6.xlsx Supplementary Table S6. Taxonomic classification and accession numbers of closely related genomes. Cite Share Download PDF Status: Published Journal Publication published 10 Mar, 2026 Read the published version in Archives of Virology → Version 1 posted Editorial decision: Major Revision 22 Oct, 2025 Reviewers agreed at journal 14 Sep, 2025 Reviewers invited by journal 08 Sep, 2025 Editor assigned by journal 03 Sep, 2025 First submitted to journal 02 Sep, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7522797","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":512098387,"identity":"c9d66577-7ae7-4a45-aa41-9e7738b5043e","order_by":0,"name":"Michael Angelou L Nada","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABBElEQVRIiWNgGAWjYDACZjYIzQcm2RjkQNSBB8RoYYOSxmAtCXitQdOS2ACi8WnRbWdLfPBzR60cG3uP2YMfZXbp88MOPwTaYien24Bdi9lhtsOGvWeOG7PxnDE37DmXnLvxdpoBUEuysdkBXFrY2yR4244ltknkmAEZzLkbZyeAtBxI3IZbS/vPv23H6kFaJP+21acbzk7/QEAL2zFm3raaBDagFmnetsMJ8tI5hGxhS5aWbTtg2MZzrExa5txxww3SOQUHEgzw+OX8McOPb9vq5PnZm7dJvimrlpefnb75w4cKOzlcWqDgMIJpAFZpgFc5CNQhmPINBFWPglEwCkbBCAMAg3peowFXkB0AAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0002-3466-3465","institution":"Industrial Technology Development Institute, Department of Science and Technology","correspondingAuthor":true,"prefix":"","firstName":"Michael","middleName":"Angelou L","lastName":"Nada","suffix":""},{"id":512098388,"identity":"2999fd4d-e032-4d58-8228-cc0c74b18f0d","order_by":1,"name":"Arra B Asejo","email":"","orcid":"","institution":"Industrial Technology Development Institute, Department of Science and 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Institute, Department of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Mark","middleName":"Christian C","lastName":"Reterta","suffix":""},{"id":512098392,"identity":"354b67be-d31b-498f-862c-4b12e77b9b53","order_by":5,"name":"Anton Roi G Collado","email":"","orcid":"","institution":"Industrial Technology Development Institute, Department of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Anton","middleName":"Roi G","lastName":"Collado","suffix":""},{"id":512098393,"identity":"27c8ef91-671c-4c6b-8164-67d6fa6d33a3","order_by":6,"name":"Janna Ysabelle O Casidsid","email":"","orcid":"","institution":"Industrial Technology Development Institute, Department of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Janna","middleName":"Ysabelle O","lastName":"Casidsid","suffix":""},{"id":512098394,"identity":"98ac5cfa-6860-4618-9deb-17ce15c78264","order_by":7,"name":"Aubrey Joy P Tejada","email":"","orcid":"","institution":"Industrial Technology Development Institute, Department of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Aubrey","middleName":"Joy P","lastName":"Tejada","suffix":""},{"id":512098395,"identity":"a971bc15-116c-4115-b44e-b28e573bd32a","order_by":8,"name":"Joseph B Ancla","email":"","orcid":"","institution":"Industrial Technology Development Institute, Department of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Joseph","middleName":"B","lastName":"Ancla","suffix":""},{"id":512098396,"identity":"c86a0f0a-b06c-48a9-b15b-5445d52449a7","order_by":9,"name":"Rommel J Gestuveo","email":"","orcid":"","institution":"S\u0026T Fellows Program, Department of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Rommel","middleName":"J","lastName":"Gestuveo","suffix":""}],"badges":[],"createdAt":"2025-09-03 04:58:03","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7522797/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7522797/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s00705-026-06542-3","type":"published","date":"2026-03-10T15:59:23+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":91375408,"identity":"e9a55f1b-08a0-4b6e-a08d-aa32ced01106","added_by":"auto","created_at":"2025-09-15 20:03:09","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":26138814,"visible":true,"origin":"","legend":"\u003cp\u003eBiological characterization of Klebsiella phage vB_VIPKPNMC05. (a) Plaque morphology in a double layer agar plate. Clear zones indicate areas where VIPKPNMC05 has lysed K. pneumoniae cells. (b) Virion morphology under transmission electron microscopy (scale bar=100 nm). (c) The head-neck-tail modules of VIPKPNMC05 according to Virfam. (d) Representative spot assays performed showing the host range of VIPKPNMC05 (see Supplementary Table S1).\u003c/p\u003e","description":"","filename":"Fig1.png","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/8616170df4fc9f0eb23778f2.png"},{"id":91375233,"identity":"a9b2480f-b357-4f5e-939f-8507f11e78e8","added_by":"auto","created_at":"2025-09-15 19:55:09","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":5867462,"visible":true,"origin":"","legend":"\u003cp\u003eGenome map of Klebsiella phage vB_VIPKPNMC05. The large terminase (terL) gene serves as the start site. The inner and middle circle indicate the GC skew and GC content, respectively. The outermost circle shows the protein-coding sequences (CDS) and their predicted functions with the colors representing Prokaryotic Virus Remote Homologous Groups (PHROGs) categories. The arrowheads indicate the direction of transcription. Abbreviations: VF=virulence factor, AMR=antimicrobial resistance, ACR=anti-CRISPR protein, DF=defense finder.\u003c/p\u003e","description":"","filename":"Fig2.png","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/13e4b01b7c73f38a0a87748c.png"},{"id":91375238,"identity":"1fd01894-3801-4c8d-868f-7fa6306806dc","added_by":"auto","created_at":"2025-09-15 19:55:09","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":28074360,"visible":true,"origin":"","legend":"\u003cp\u003eTailspike protein (TSP19) of Klebsiella phage vB_VIPKPNMC05. (a) Predicted 3D model of the TSP19 using AlphaFold3 showing a homotrimeric structure with an N- terminus head and C-terminus receptor binding domain. (b) Individual protein monomer of TSP19 showing a putative pectin lyase along its central β-helical structure. (c) Top, (d) cutaway top-down, (e) bottom, and (f) cutaway bottom-up views of TSP19 showing a central pore formed from the assembled monomers. (g) Superimposition of aligned regions of VIPKPNMC05 TSP19 in blue and GH-K3 in yellow (PDB ID=7VYV).\u003c/p\u003e","description":"","filename":"Fig3.png","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/38fba3d759431d94154e1943.png"},{"id":91375244,"identity":"fcd73d9b-84f5-4787-b8be-15f420905422","added_by":"auto","created_at":"2025-09-15 19:55:09","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":2044675,"visible":true,"origin":"","legend":"\u003cp\u003eClustering of viral proteins showing Klebsiella phage vB_VIPKPNMC05 relative to other Klebsiella phages using VirClust. Viral proteins are grouped into protein superclusters (PSC) based on their hidden Markov model (HMM) similarities. The top and bottom groups were phages identified by VIPTree and mash, respectively. VIPKPNMC05 (highlighted in blue) is grouped together with Klebsiella phage 1 LV-2017 and Klebsiella phage Kp4872.\u003c/p\u003e","description":"","filename":"Fig4.png","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/bfa7c880e76ba206b9ffadb7.png"},{"id":91375252,"identity":"e6e6e5cf-6e3b-437f-a181-c5faa42f01fa","added_by":"auto","created_at":"2025-09-15 19:55:10","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":4493123,"visible":true,"origin":"","legend":"\u003cp\u003eIntergenomic similarity between Klebsiella phage vB_VIPKPNMC05 (highlighted in blue) to other phage genomes. The heat map shows the percent (%) similarities (yellow=low, red=high), fraction of aligned genomes (beige bars), and genome length and ratios (gray bars) according to VIRIDIC.\u003c/p\u003e","description":"","filename":"Fig5.png","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/37ec2527de4ea67476a74fe9.png"},{"id":104739574,"identity":"0f83fe34-3e0a-481a-8c8b-69ee60286eb6","added_by":"auto","created_at":"2026-03-16 16:09:37","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":7342016,"visible":true,"origin":"","legend":"","description":"","filename":"Manuscriptv1.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1_covered_c51fc3f6-f1db-47f0-a696-ac059f511b90.pdf"},{"id":91375231,"identity":"5c95da6b-78d7-4b93-8c9c-f57669d5dadf","added_by":"auto","created_at":"2025-09-15 19:55:09","extension":"fasta","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":18739,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Data S1. Multiple sequence alignment of Klebsiella phage vB_VIPKPNMC05 TSP with other phage tailspike proteins.\u003c/p\u003e","description":"","filename":"SupplementaryDataS1.fasta","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/70d0aba6040d178994b082c4.fasta"},{"id":91375234,"identity":"407534ec-704c-4f0c-a880-046a86d08505","added_by":"auto","created_at":"2025-09-15 19:55:09","extension":"pdb","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":1535785,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Data S2. Constructed structural model of Klebsiella phage vB_VIPKPNMC05 tailspike protein (TSP19) using AlphaFold 3.\u003c/p\u003e","description":"","filename":"SupplementaryDataS2.pdb","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/3b918234ffd7c9477fd0ec68.pdb"},{"id":91375243,"identity":"d0a15f79-a12e-436d-b12d-93b54b3acd56","added_by":"auto","created_at":"2025-09-15 19:55:09","extension":"tiff","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":327598,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Information\u003c/p\u003e\n\u003cp\u003eSupplementary Figure S1. Recombination breakpoint analysis of Klebsiella vB_VIPKPNMC05 tailspike protein. GARD analysis identified three breakpoints, with position 287 likely being the recombination site (ΔAICc = 1039.49).\u003c/p\u003e","description":"","filename":"SupplementaryFigureS1.tiff","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/17d79334421b1865a1aa189f.tiff"},{"id":91375236,"identity":"5381454d-d3c8-428e-a8f8-5de5d82775c7","added_by":"auto","created_at":"2025-09-15 19:55:09","extension":"tiff","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":8202355,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Figure S2. Phylogenetic tree based on the breakpoint coordinate (position 287-541) clustering TSP19 with other K. pneumoniae, K. quasipneumoniae, K. variicola, and E. coli prophage tailspike proteins.\u003c/p\u003e","description":"","filename":"SupplementaryFigureS2.tiff","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/21c0cba7a3b8d05aee6a8dde.tiff"},{"id":91375251,"identity":"c2b6113f-49f5-488a-8a55-a41ef3ec27e1","added_by":"auto","created_at":"2025-09-15 19:55:10","extension":"tif","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":68949840,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Figure S3. Viral proteomic tree consisting of 3,724 genome sequences. The closest relatives of Klebsiella vB_VIPKPNMC05 (highlighted in blue) were identified using mash and INPHARED at 0.20 distance cutoff. Closely related genomes marked in red. Sequences were obtained from NCBI GenBank and viewed using VIPTree. The tree is based on a dissimilarity matrix generated by pairwise tBLASTx scores between each of the genomes.\u003c/p\u003e","description":"","filename":"SupplementaryFigureS3.tif","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/f6160e1cd9608f05074a242b.tif"},{"id":91375255,"identity":"7abd8c67-22e7-44b0-9e8f-70f0e173ecc1","added_by":"auto","created_at":"2025-09-15 19:55:10","extension":"tif","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":777304,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Figure S4. Phylogenomic tree of Klebsiella vB_VIPKPNMC05 (highlighted in blue) and other Enterobacteriaceae-infecting phages using VICTOR phylogeny. Branch numbers indicate bootstrap support values inferred from 100 iterations with lengths scaled (scale bar=0.1) in terms of GBDP distance formula. The tree was rooted at midpoint and bootstrap values \u0026gt;60% are shown.\u003c/p\u003e","description":"","filename":"SupplementaryFigureS4.tif","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/42a407e81ecf0ee3cb77d65f.tif"},{"id":91375241,"identity":"2004cf97-08b4-446e-96e5-1c5553826b62","added_by":"auto","created_at":"2025-09-15 19:55:09","extension":"tif","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":965848,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Figure S5. Constructed maximum-likelihood phylogenetic tree of the large terminase subunit (terL) gene of Klebsiella vB_VIPKPNMC05 (highlighted in blue) with 1,000 iterations. The tree was rooted at midpoint and bootstrap support of ≥60% are shown.\u003c/p\u003e","description":"","filename":"SupplementaryFigureS5.tif","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/7e02f5164c43c4e476ae1f2d.tif"},{"id":91375256,"identity":"cac03420-ece1-4f7d-806f-68180da7f178","added_by":"auto","created_at":"2025-09-15 19:55:10","extension":"tif","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":71059804,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Figure S6. Multiple whole-genome sequence alignment of Klebsiella vB_VIPKPNMC05 (highlighted in blue) and other Enterobacteriaceae phages. The genomic position of TSP19 is marked by the red asterisk. The colors indicate percent (%) sequence similarly between sequences (blue=low, red=high) with VIPKPNMC05 exhibiting strong collinearity with Klebsiella phages Kp4872 and 1 LV-2017 and a conserved gene order across major functional modules, including structural, replication, and lysis genes. Arrowheads indicate the direction of transcription. Scale bar=4 Kbp.\u003c/p\u003e","description":"","filename":"SupplementaryFigureS6.tif","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/3ebc75617a00ea1ff88196aa.tif"},{"id":91375409,"identity":"7ff02981-02b4-44e7-88f1-85f2705a46ce","added_by":"auto","created_at":"2025-09-15 20:03:10","extension":"pdf","order_by":9,"title":"","display":"","copyAsset":false,"role":"supplement","size":117479,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table S1. Host range of Klebsiella phage vB_VIPKPNMC05.\u003c/p\u003e","description":"","filename":"SupplementaryTableS1.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/baf2d76fb980f3b06d3ee5b2.pdf"},{"id":91375245,"identity":"30551793-9086-4d6e-9ee5-29fb25b4f6f3","added_by":"auto","created_at":"2025-09-15 19:55:10","extension":"pdf","order_by":10,"title":"","display":"","copyAsset":false,"role":"supplement","size":104499,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table S2. Predicted hosts according to iPHoP tool.\u003c/p\u003e","description":"","filename":"SupplementaryTableS2.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/23036724b101e6e562ec2120.pdf"},{"id":91375254,"identity":"8689ab6c-271e-4eb4-9e3c-8fa14bfaf6e8","added_by":"auto","created_at":"2025-09-15 19:55:10","extension":"pdf","order_by":11,"title":"","display":"","copyAsset":false,"role":"supplement","size":142501,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table S3. Protein functional annotation of Klebsiella phage vB_VIPKPNMC05.\u003c/p\u003e","description":"","filename":"SupplementaryTableS3.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/48947b999854547e8e9c1d44.pdf"},{"id":91375248,"identity":"e396feec-3c32-484e-bc51-2277e69cf4f9","added_by":"auto","created_at":"2025-09-15 19:55:10","extension":"pdf","order_by":12,"title":"","display":"","copyAsset":false,"role":"supplement","size":127894,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table S4. Prediction of receptor-binding proteins (RBP) and depolymerases (Dpo) of Klebsiella phage vB_VIPKPNMC05.\u003c/p\u003e","description":"","filename":"SupplementaryTableS4.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/6c08449ea329f94b1de924eb.pdf"},{"id":91375253,"identity":"3a12cf0e-7bad-4511-9c91-719ff78d976d","added_by":"auto","created_at":"2025-09-15 19:55:10","extension":"xlsx","order_by":13,"title":"","display":"","copyAsset":false,"role":"supplement","size":11428,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table S5. Functional domain analysis of tailspike proteins using InterPro.\u003c/p\u003e","description":"","filename":"SupplementaryTableS5.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/674d0110f1159cc7236618b9.xlsx"},{"id":91375410,"identity":"04c733cd-834f-44fa-9843-28c2665d87b2","added_by":"auto","created_at":"2025-09-15 20:03:10","extension":"xlsx","order_by":14,"title":"","display":"","copyAsset":false,"role":"supplement","size":20892,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table S6. Taxonomic classification and accession numbers of closely related genomes.\u003c/p\u003e","description":"","filename":"SupplementaryTableS6.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7522797/v1/bf1d4a7a3eb34d973b3070b2.xlsx"}],"financialInterests":"","formattedTitle":"Genome characterization and receptor-binding protein identification of a newly discovered Klebsiella phage vB_VIPKPNMC05, a member of a novel viral family Pituviridae","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"archives-of-virology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"arvi","sideBox":"Learn more about [Archives of Virology](https://www.springer.com/journal/705)","snPcode":"705","submissionUrl":"https://submission.nature.com/new-submission/705/3","title":"Archives of Virology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Klebsiella pneumoniae phage, antimicrobial resistance, whole genome sequencing, tailspike protein, Pituviridae, Philippines","lastPublishedDoi":"10.21203/rs.3.rs-7522797/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7522797/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Klebsiella pneumoniae is an opportunistic pathogen and a leading cause of antimicrobial-resistant infections in the Philippines. Here, we report the genome sequence of Klebsiella phage vB_VIPKPNMC05, which targets a multidrug-resistant (MDR) K. pneumoniae strain with capsule type K8. VIPKPNMC05 has a siphovirus morphology and exhibits a broad lytic activity against several strains of K. pneumoniae, K. quasipneumoniae, Pseudomonas aeruginosa, and Escherichia coli. The linear double-stranded DNA genome (34,476 bp; 51.0% GC content) encodes 58 protein-coding sequences (CDS), 37 of which are involved in phage morphogenesis, DNA replication, transcription regulation, and host lysis. Notably, a receptor-binding protein (RBP) with a putative depolymerase (Dpo) was identified. Structural prediction using AlphaFold 3 showed that the tailspike protein (TSP) forms a homotrimer structure with a conserved C-terminal pectin lyase domain. The TSP module is conserved among Enterobacteriaceae-infecting phages and may have been acquired through horizontal gene transfer. Whole-genome comparisons revealed 52-54% similarity to known phages, suggesting that VIPKPNMC05 represents a distinct lineage. Based on taxonomic analysis, we propose that VIPKPNMC05 belongs to a novel phage family, Pituviridae. The absence of virulence, toxin, and antimicrobial resistance genes, along with its broad host range and lytic lifestyle, supports the potential of VIPKPNMC05 as a promising candidate for phage therapy and other biotechnology applications. To our knowledge, this is the first report of a newly discovered phage family from the Philippines, underscoring the importance of local phage bioprospecting for therapeutic applications.","manuscriptTitle":"Genome characterization and receptor-binding protein identification of a newly discovered Klebsiella phage vB_VIPKPNMC05, a member of a novel viral family Pituviridae","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-15 19:55:04","doi":"10.21203/rs.3.rs-7522797/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Major Revision","date":"2025-10-22T13:43:49+00:00","index":"","fulltext":""},{"type":"reviewerAgreed","content":"","date":"2025-09-15T03:33:35+00:00","index":0,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-09-08T18:45:45+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-09-03T09:15:19+00:00","index":"","fulltext":""},{"type":"submitted","content":"Archives of Virology","date":"2025-09-03T00:57:42+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"archives-of-virology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"arvi","sideBox":"Learn more about [Archives of Virology](https://www.springer.com/journal/705)","snPcode":"705","submissionUrl":"https://submission.nature.com/new-submission/705/3","title":"Archives of Virology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"caef4150-d882-43ea-9c31-3e45eda426b4","owner":[],"postedDate":"September 15th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2026-03-16T16:04:28+00:00","versionOfRecord":{"articleIdentity":"rs-7522797","link":"https://doi.org/10.1007/s00705-026-06542-3","journal":{"identity":"archives-of-virology","isVorOnly":false,"title":"Archives of Virology"},"publishedOn":"2026-03-10 15:59:23","publishedOnDateReadable":"March 10th, 2026"},"versionCreatedAt":"2025-09-15 19:55:04","video":"","vorDoi":"10.1007/s00705-026-06542-3","vorDoiUrl":"https://doi.org/10.1007/s00705-026-06542-3","workflowStages":[]},"version":"v1","identity":"rs-7522797","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7522797","identity":"rs-7522797","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}