Detection of a Novel Tick-Associated Papillomavirus Related to Bovine Papillomaviruses in Northeastern China

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Abstract Papillomaviruses (PVs) are diverse DNA viruses infecting vertebrates. Using viral metagenomics, we identified a novel PV genome in Haemaphysalis longicornis ticks from northeastern China. The virus, 7,426 bp in length, encoded six canonical papillomavirus ORFs. Phylogenetic analysis of the L1 gene revealed a close relationship with bovine papillomavirus type 7 but sufficient divergence to represent a new species within Dyoxipapillomavirus. PCR screening of 80 cattle and 60 human blood samples showed viral DNA in 3 cattle but none in humans. This is the first report of a complete mammalian papillomavirus genome associated with ticks.
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Using viral metagenomics, we identified a novel PV genome in Haemaphysalis longicornis ticks from northeastern China. The virus, 7,426 bp in length, encoded six canonical papillomavirus ORFs. Phylogenetic analysis of the L1 gene revealed a close relationship with bovine papillomavirus type 7 but sufficient divergence to represent a new species within Dyoxipapillomavirus. PCR screening of 80 cattle and 60 human blood samples showed viral DNA in 3 cattle but none in humans. This is the first report of a complete mammalian papillomavirus genome associated with ticks. Figures Figure 1 Full Text Papillomaviruses (PVs) are non-enveloped, double-stranded circular DNA viruses approximately 8 kb in size that infect a wide range of vertebrate species including mammals, birds, reptiles, and fish. They are well known for inducing epithelial proliferations such as papillomas and carcinomas in their hosts. Most PVs exhibit strict species and tissue tropism, typically infecting stratified squamous epithelia. However, bovine papillomaviruses (BPVs) belonging to Deltapapillomavirus and Dyoxipapillomavirus can infect both epithelial and mesenchymal cells, and have been implicated in cross-species infections (1). To explore potential viral diversity in blood-feeding arthropods, we conducted viral metagenomic screening of ticks from northeastern China. In 2015, 300 adult Haemaphysalis longicornis ticks were collected from a forested region using flagging techniques. Ticks were grouped into six pools of 50 each. Surface decontamination was performed by three washes with sterile phosphate-buffered saline (PBS). The samples were homogenized, subjected to freeze-thaw cycles, and centrifuged to remove debris. Supernatants were filtered through 0.45-μm membranes to remove cell-sized particles (2). To enrich for viral particles, each filtrate was treated with a cocktail of nucleases (DNase and RNase) to eliminate host and bacterial nucleic acids unprotected by viral capsids (3). Viral nucleic acids were extracted using the QIAamp MinElute Virus Spin Kit (Qiagen) . Reverse transcription was performed using SuperScript III reverse transcriptase, followedby second-strand synthesis using Klenow fragment. Libraries were constructed with Nextera XT kits (Illumina) and sequenced on the MiSeq platform using 250-bp paired-end reads (3). Sequence reads were trimmed for quality, deduplicated based on identical 5–55 bp signatures, and filtered for adapters. De novo assembly was carried out using SOAPdenovo2. Contigs and singlets were queried using BLASTx against an in-house viral proteome database, and false positives were excluded by comparison to a non-viral protein database. Candidate contigs were further analyzed using the vFam database and HMMER3 for remote homology detection (4). Among the assembled sequences, 49 reads from one pool showed significant similarity (E-value <10⁻⁵) to bovine papillomaviruses. These were assembled into eight contigs spanning different genomic regions. PCR primers were designed to bridge sequence gaps, and Sanger sequencing was used to confirm and complete the circular genome. The final genome was 7,426 bp with a GC content of 41.5%. It encoded six typical papillomavirus ORFs: early genes E6, E7, E1, E2, and late genes L2, L1. The L1 gene, the most conserved region for papillomavirus classification, was analyzed. Multiple sequence alignments and maximum-likelihood phylogenetic trees were constructed using MEGA7 with 1,000 bootstrap replicates. The virus, designated lnzw-lsx, showed 65.7% nucleotide and 64.8% amino acid identity with BPV7, the closest known relative in the Dyoxipapillomavirus genus. These values fall below the 70% species demarcation threshold defined by the International Committee on Taxonomy of Viruses, confirming lnzw-lsx as a new species. To investigate the host distribution of lnzw-lsx, we performed PCR screening on 80 cattle and 60 human blood samples collected from the same region. A semi-nested PCR targeting the L1 gene amplified a 333-bp fragment in three bovine samples. No human samples tested positive. Sanger sequencing of the amplicons revealed >99% identity among the three cattle-derived sequences, and 97% identity to the original lnzw-lsx genome, suggesting strain-level variation. The co-detection of this virus in ticks and bovine blood suggests a possible host-vector interaction. However, PVs are typically epitheliotropic, and their presence in blood may reflect contamination from skin or hair follicles during sample collection. BPVs have previously been detected in peripheral blood mononuclear cells, but replication in blood remains unclear (5). Since H. longicornis ticks commonly parasitize cattle and other livestock, it is plausible that ticks acquired the virus through feeding on infected hosts (6). Although papillomaviruses have been reported in mosquitoes and biting midges, this study represents the first identification of a full-length mammalian papillomavirus genome in a tick species. It remains to be determined whether ticks can transmit PVs or if they serve merely as mechanical carriers. Future studies are needed to assess viral replication, tropism, and transmission potential in both arthropods and vertebrate hosts. The discovery of lnzw-lsx expands the known genetic diversity and host range of papillomaviruses and raises new questions about their ecology and evolution. It also highlights the utility of metagenomic approaches for uncovering cryptic viral infections in understudied vectors and environments. Declarations Acknowledgements This work was supported by the National Key Research and Development Program of China (2023YFD1801302). Competing Interests The authors declare no competing interests. Data Availability The genome sequence of lnzw-lsx and three partial sequences from cattle blood have been submitted to GenBank (accession numbers MK124618–MK124621). References Mlynarczyk-Bonikowska B, Rudnicka L. HPV Infections-Classification, Pathogenesis, and Potential New Therapies. Int J Mol Sci. 2024;25(14).https://doi.org/10.3390/ijms25147616 Yang Z, Zhang J, Yang S, Wang X, Shen Q, Sun G, et al. Virome analysis of ticks in a forest region of Liaoning, China: characterization of a novel hepe-like virus sequence. Virol J. 2021;18(1):163.https://doi.org/10.1186/s12985-021-01632-x Ogunbayo AE, Sabiu S, Nyaga MM. Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach. J Virol Methods. 2023;314:114677.https://doi.org/10.1016/j.jviromet.2023.114677 Vibin J, Chamings A, Klaassen M, Bhatta TR, Alexandersen S. Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian wild ducks. Sci Rep. 2020;10(1):12800.https://doi.org/10.1038/s41598-020-69557-z Melo TC, Araldi RP, Pessoa NS, de-Sa-Junior PL, Carvalho RF, Becak W, Stocco RC. Bos taurus papillomavirus activity in peripheral blood mononuclear cells: demonstrating a productive infection. Genet Mol Res. 2015;14(4):16712-27.https://doi.org/10.4238/2015.December.11.19 Luo LM, Zhao L, Wen HL, Zhang ZT, Liu JW, Fang LZ, et al. Haemaphysalis longicornis Ticks as Reservoir and Vector of Severe Fever with Thrombocytopenia Syndrome Virus in China. Emerg Infect Dis. 2015;21(10):1770-6.https://doi.org/10.3201/eid2110.150126 Cite Share Download PDF Status: Posted Version 1 posted 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-6872969","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":470408736,"identity":"3b61994a-8623-41cd-9ecc-e9cbe15ae60f","order_by":0,"name":"Bin Ni","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAtElEQVRIiWNgGAWjYDACZh6GAwwVDMwgtgQJWs6QpIWBh4GBsQ3CJE6LOTvvwcOF8w6zyzcwH7zNw2CXR1CLZTNfwuGZ2w4zGxxgS7bmYUguJqjF4DCPwWFekBYGHjNpoL8SG4jTMucws3wD/zdStDQcZmY4wMNGrBagX3iOpTMbHGYztpxjkEyElvNnD3/mqbFOlm9vfnjjTYUdYS0wkAyJTANi1QOBHQlqR8EoGAWjYKQBANkiNPF+okdGAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0003-3975-0602","institution":"Jiangsu University","correspondingAuthor":true,"prefix":"","firstName":"Bin","middleName":"","lastName":"Ni","suffix":""},{"id":470408737,"identity":"84a8d5b8-22d4-47c8-9108-82dc0577b87a","order_by":1,"name":"Jing Gao","email":"","orcid":"","institution":"Jiangsu University","correspondingAuthor":false,"prefix":"","firstName":"Jing","middleName":"","lastName":"Gao","suffix":""},{"id":470408738,"identity":"e7944726-918f-4fcd-82d8-79470605c533","order_by":2,"name":"Chun mei Wang","email":"","orcid":"","institution":"Shanghai Veterinary Research Institute Chinese Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Chun","middleName":"mei","lastName":"Wang","suffix":""},{"id":470408739,"identity":"5ee1d04b-11c5-44dd-97c0-d710a37958b7","order_by":3,"name":"Shou xin Li","email":"","orcid":"","institution":"Shenyang Normal University","correspondingAuthor":false,"prefix":"","firstName":"Shou","middleName":"xin","lastName":"Li","suffix":""},{"id":470408740,"identity":"2c5ee797-9271-459b-b3a6-0b4ef7ee18ae","order_by":4,"name":"Shi xing Yang","email":"","orcid":"","institution":"Jiangsu University","correspondingAuthor":false,"prefix":"","firstName":"Shi","middleName":"xing","lastName":"Yang","suffix":""},{"id":470408741,"identity":"41da1d53-888c-40de-b7e6-464d78629b46","order_by":5,"name":"Xu tao Deng","email":"","orcid":"","institution":"University of California San Francisco","correspondingAuthor":false,"prefix":"","firstName":"Xu","middleName":"tao","lastName":"Deng","suffix":""},{"id":470408742,"identity":"155699b4-7766-4496-844a-a92fe38d3342","order_by":6,"name":"Wen Zhang","email":"","orcid":"","institution":"Jiangsu University","correspondingAuthor":false,"prefix":"","firstName":"Wen","middleName":"","lastName":"Zhang","suffix":""}],"badges":[],"createdAt":"2025-06-11 14:41:21","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6872969/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6872969/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":84703633,"identity":"1a7c9b90-aefc-4be5-92b6-e08def05624b","added_by":"auto","created_at":"2025-06-16 11:57:25","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":958189,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eGenomic organization and phylogenetic analysis of the novel papillomavirus identified in ticks.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e(A) Genomic organization of the novel papillomavirus identified in ticks. (B) Phylogenetic analysis was performed based on the amino acid sequence of L1 protein. The sequence alignments included lnzw-lsx, all the 4 known papillomavirus strains with complete genome in genus \u003cem\u003eDyoxipapillomavirus\u003c/em\u003e, the 15 representative bovine papillomaviruses, and 66 representative species from each of the currently recognized genera. Previously identified bovine papillomaviruses were labeled with black dots, and the tick-associated papillomavirus lnzw-lsx identified in this study was labeled with a solid triangle. (C) L1 protein sequence pairwise comparison between lnzw-lsx and the other 4 strains in genus \u003cem\u003eDyoxipapillomavirus.\u003c/em\u003e (D) Phylogenetic tree based on the 333bp sequences generated in PCR screening.\u003c/p\u003e","description":"","filename":"floatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-6872969/v1/49eee8b996aa9140d19d62dd.png"},{"id":86109318,"identity":"3212fd29-8fa5-4770-be9f-75c6ea1df19a","added_by":"auto","created_at":"2025-07-06 18:29:30","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1213479,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6872969/v1/b4cc6bed-0e84-439a-a2cc-b911345151a0.pdf"}],"financialInterests":"","formattedTitle":"Detection of a Novel Tick-Associated Papillomavirus Related to Bovine Papillomaviruses in Northeastern China","fulltext":[{"header":"Full Text","content":"\u003cp\u003ePapillomaviruses (PVs) are non-enveloped, double-stranded circular DNA viruses approximately 8 kb in size that infect a wide range of vertebrate species including mammals, birds, reptiles, and fish. They are well known for inducing epithelial proliferations such as papillomas and carcinomas in their hosts. Most PVs exhibit strict species and tissue tropism, typically infecting stratified squamous epithelia. However, bovine papillomaviruses (BPVs) belonging to \u003cem\u003eDeltapapillomavirus\u003c/em\u003e and \u003cem\u003eDyoxipapillomavirus\u003c/em\u003e can infect both epithelial and mesenchymal cells, and have been implicated in cross-species infections (1).\u003c/p\u003e\n\u003cp\u003eTo explore potential viral diversity in blood-feeding arthropods, we conducted viral metagenomic screening of ticks from northeastern China. In 2015, 300 adult Haemaphysalis longicornis ticks were collected from a forested region using flagging techniques. Ticks were grouped into six pools of 50 each. Surface decontamination was performed by three washes with sterile phosphate-buffered saline (PBS). The samples were homogenized, subjected to freeze-thaw cycles, and centrifuged to remove debris. Supernatants were filtered through 0.45-\u0026mu;m membranes to remove cell-sized particles (2). To enrich for viral particles, each filtrate was treated with a cocktail of nucleases (DNase and RNase) to eliminate host and bacterial nucleic acids unprotected by viral capsids (3). Viral nucleic acids were extracted using the QIAamp MinElute Virus Spin Kit (Qiagen) . Reverse transcription was performed using SuperScript III reverse transcriptase, followedby second-strand synthesis using Klenow fragment. Libraries were constructed with Nextera XT kits (Illumina) and sequenced on the MiSeq platform using 250-bp paired-end reads (3). Sequence reads were trimmed for quality, deduplicated based on identical 5\u0026ndash;55 bp signatures, and filtered for adapters. De novo assembly was carried out using SOAPdenovo2. Contigs and singlets were queried using BLASTx against an in-house viral proteome database, and false positives were excluded by comparison to a non-viral protein database. Candidate contigs were further analyzed using the vFam database and HMMER3 for remote homology detection (4).\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eAmong the assembled sequences, 49 reads from one pool showed significant similarity (E-value \u0026lt;10⁻⁵) to bovine papillomaviruses. These were assembled into eight contigs spanning different genomic regions. PCR primers were designed to bridge sequence gaps, and Sanger sequencing was used to confirm and complete the circular genome. The final genome was 7,426 bp with a GC content of 41.5%. It encoded six typical papillomavirus ORFs: early genes E6, E7, E1, E2, and late genes L2, L1. The L1 gene, the most conserved region for papillomavirus classification, was analyzed. Multiple sequence alignments and maximum-likelihood phylogenetic trees were constructed using MEGA7 with 1,000 bootstrap replicates. The virus, designated lnzw-lsx, showed 65.7% nucleotide and 64.8% amino acid identity with BPV7, the closest known relative in the Dyoxipapillomavirus genus. These values fall below the 70% species demarcation threshold defined by the International Committee on Taxonomy of Viruses, confirming lnzw-lsx as a new species. To investigate the host distribution of lnzw-lsx, we performed PCR screening on 80 cattle and 60 human blood samples collected from the same region. A semi-nested PCR targeting the L1 gene amplified a 333-bp fragment in three bovine samples. No human samples tested positive. Sanger sequencing of the amplicons revealed \u0026gt;99% identity among the three cattle-derived sequences, and 97% identity to the original lnzw-lsx genome, suggesting strain-level variation. The co-detection of this virus in ticks and bovine blood suggests a possible host-vector interaction. However, PVs are typically epitheliotropic, and their presence in blood may reflect contamination from skin or hair follicles during sample collection. BPVs have previously been detected in peripheral blood mononuclear cells, but replication in blood remains unclear (5). Since H. longicornis ticks commonly parasitize cattle and other livestock, it is plausible that ticks acquired the virus through feeding on infected hosts (6).\u003c/p\u003e\n\u003cp\u003eAlthough papillomaviruses have been reported in mosquitoes and biting midges, this study represents the first identification of a full-length mammalian papillomavirus genome in a tick species. It remains to be determined whether ticks can transmit PVs or if they serve merely as mechanical carriers. Future studies are needed to assess viral replication, tropism, and transmission potential in both arthropods and vertebrate hosts. The discovery of lnzw-lsx expands the known genetic diversity and host range of papillomaviruses and raises new questions about their ecology and evolution. It also highlights the utility of metagenomic approaches for uncovering cryptic viral infections in understudied vectors and environments.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003eAcknowledgements\u003c/p\u003e\n\u003cp\u003eThis work was supported by the National Key Research and Development Program of China (2023YFD1801302).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting Interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData Availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe genome sequence of lnzw-lsx and three partial sequences from cattle blood have been submitted to GenBank (accession numbers MK124618\u0026ndash;MK124621).\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eMlynarczyk-Bonikowska B, Rudnicka L. HPV Infections-Classification, Pathogenesis, and Potential New Therapies. Int J Mol Sci. 2024;25(14).https://doi.org/10.3390/ijms25147616\u003c/li\u003e\n\u003cli\u003eYang Z, Zhang J, Yang S, Wang X, Shen Q, Sun G, et al. Virome analysis of ticks in a forest region of Liaoning, China: characterization of a novel hepe-like virus sequence. Virol J. 2021;18(1):163.https://doi.org/10.1186/s12985-021-01632-x\u003c/li\u003e\n\u003cli\u003eOgunbayo AE, Sabiu S, Nyaga MM. Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach. J Virol Methods. 2023;314:114677.https://doi.org/10.1016/j.jviromet.2023.114677\u003c/li\u003e\n\u003cli\u003eVibin J, Chamings A, Klaassen M, Bhatta TR, Alexandersen S. Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian wild ducks. Sci Rep. 2020;10(1):12800.https://doi.org/10.1038/s41598-020-69557-z\u003c/li\u003e\n\u003cli\u003eMelo TC, Araldi RP, Pessoa NS, de-Sa-Junior PL, Carvalho RF, Becak W, Stocco RC. Bos taurus papillomavirus activity in peripheral blood mononuclear cells: demonstrating a productive infection. Genet Mol Res. 2015;14(4):16712-27.https://doi.org/10.4238/2015.December.11.19\u003c/li\u003e\n\u003cli\u003eLuo LM, Zhao L, Wen HL, Zhang ZT, Liu JW, Fang LZ, et al. Haemaphysalis longicornis Ticks as Reservoir and Vector of Severe Fever with Thrombocytopenia Syndrome Virus in China. Emerg Infect Dis. 2015;21(10):1770-6.https://doi.org/10.3201/eid2110.150126\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-6872969/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6872969/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003ePapillomaviruses (PVs) are diverse DNA viruses infecting vertebrates. Using viral metagenomics, we identified a novel PV genome in Haemaphysalis longicornis ticks from northeastern China. The virus, 7,426 bp in length, encoded six canonical papillomavirus ORFs. Phylogenetic analysis of the L1 gene revealed a close relationship with bovine papillomavirus type 7 but sufficient divergence to represent a new species within Dyoxipapillomavirus. PCR screening of 80 cattle and 60 human blood samples showed viral DNA in 3 cattle but none in humans. 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