{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T23:33:23Z","timestamp":1779320003645,"version":"3.51.4"},"reference-count":92,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2024,12,5]],"date-time":"2024-12-05T00:00:00Z","timestamp":1733356800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Spanish Ministerio de Ciencia e Innovaci\u00f3n (MICINN)","award":["PID2020-118602RB-I00"],"award-info":[{"award-number":["PID2020-118602RB-I00"]}]},{"name":"Spanish Ministerio de Ciencia e Innovaci\u00f3n (MICINN)","award":["CIAICO\/2022\/110"],"award-info":[{"award-number":["CIAICO\/2022\/110"]}]},{"name":"Conselleria de Educaci\u00f3n, Universidades y Empleo (Generalitat Valenciana)","award":["PID2020-118602RB-I00"],"award-info":[{"award-number":["PID2020-118602RB-I00"]}]},{"name":"Conselleria de Educaci\u00f3n, Universidades y Empleo (Generalitat Valenciana)","award":["CIAICO\/2022\/110"],"award-info":[{"award-number":["CIAICO\/2022\/110"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Viromics studies are allowing us to understand not only the enormous diversity of the virosphere, but also the potential threat posed by the emerging viruses. Regarding the latter, the main concern lies in monitoring the presence of RNA viruses, but the zoonotic potential of some DNA viruses, on which we have focused in the present study, should also be highlighted. For this purpose, we analyzed 160 fecal samples from 14 species of small terrestrial mammals, 9 of them belonging to the order Rodentia. This allowed us to identify a total of 25 complete or near-complete genomes belonging to the families Papillomaviridae, Polyomaviridae, Adenoviridae, Circoviridae, and Genomoviridae, 18 of which could be considered new species or types. Our results provide a significant increase in the number of complete genomes of DNA viruses of European origin with zoonotic potential in databases, which are at present under-represented compared to RNA viruses. In addition, the characterization of whole genomes is of relevance for the further study of the evolutionary forces governing virus adaptation, such as recombination, which may play an important role in cross-species transmission.<\/jats:p>","DOI":"10.3390\/v16121885","type":"journal-article","created":{"date-parts":[[2024,12,5]],"date-time":"2024-12-05T06:24:44Z","timestamp":1733379884000},"page":"1885","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Complete Genomes of DNA Viruses in Fecal Samples from Small Terrestrial Mammals in Spain"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9016-4628","authenticated-orcid":false,"given":"Jaime","family":"Buigues","sequence":"first","affiliation":[{"name":"Institute for Integrative Systems Biology (I2SysBio), Universitat de Val\u00e8ncia and Consejo Superior de Investigaciones Cient\u00edficas, 46980 Val\u00e8ncia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adri\u00e0","family":"Vi\u00f1als","sequence":"additional","affiliation":[{"name":"Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Val\u00e8ncia, 46980 Val\u00e8ncia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raquel","family":"Mart\u00ednez-Recio","sequence":"additional","affiliation":[{"name":"Institute for Integrative Systems Biology (I2SysBio), Universitat de Val\u00e8ncia and Consejo Superior de Investigaciones Cient\u00edficas, 46980 Val\u00e8ncia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0952-2089","authenticated-orcid":false,"given":"Juan S.","family":"Monr\u00f3s","sequence":"additional","affiliation":[{"name":"Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Val\u00e8ncia, 46980 Val\u00e8ncia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1844-545X","authenticated-orcid":false,"given":"Rafael","family":"Sanju\u00e1n","sequence":"additional","affiliation":[{"name":"Institute for Integrative Systems Biology (I2SysBio), Universitat de Val\u00e8ncia and Consejo Superior de Investigaciones Cient\u00edficas, 46980 Val\u00e8ncia, Spain"},{"name":"Department of Genetics, Universitat de Val\u00e8ncia, 46100 Val\u00e8ncia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2049-3554","authenticated-orcid":false,"given":"Jos\u00e9 M.","family":"Cuevas","sequence":"additional","affiliation":[{"name":"Institute for Integrative Systems Biology (I2SysBio), Universitat de Val\u00e8ncia and Consejo Superior de Investigaciones Cient\u00edficas, 46980 Val\u00e8ncia, Spain"},{"name":"Department of Genetics, Universitat de Val\u00e8ncia, 46100 Val\u00e8ncia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,12,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1038\/nrmicro.2016.177","article-title":"Consensus Statement: Virus Taxonomy in the Age of Metagenomics","volume":"15","author":"Simmonds","year":"2017","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1016\/j.cell.2018.02.043","article-title":"Using Metagenomics to Characterize an Expanding Virosphere","volume":"172","author":"Zhang","year":"2018","journal-title":"Cell"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"499","DOI":"10.20506\/rst.36.2.2669","article-title":"Viral Discovery as a Tool for Pandemic Preparedness","volume":"36","author":"Epstein","year":"2017","journal-title":"Rev. Sci. Tech."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e0168323","DOI":"10.1128\/jvi.01683-23","article-title":"\u201cSmart Markets\u201d: Harnessing the Potential of New Technologies for Endemic and Emerging Infectious Disease Surveillance in Traditional Food Markets","volume":"98","author":"Sievers","year":"2024","journal-title":"J. Virol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Yang, S., He, Y., Chen, X., Kalim, U., Wang, Y., Yang, S., Qi, H., Cheng, H., Lu, X., and Wang, X. (2021). Viral Metagenomics Reveals Diverse Viruses in the Feces Samples of Raccoon Dogs. Front. Vet. Sci., 8.","DOI":"10.3389\/fvets.2021.693564"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"A Duarte, M., F Silva, J.M., R Brito, C., S Teixeira, D., L Melo, F., M Ribeiro, B., Nagata, T., and S Campos, F. (2019). Faecal Virome Analysis of Wild Animals from Brazil. Viruses, 11.","DOI":"10.3390\/v11090803"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1007\/s10393-023-01659-2","article-title":"Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies","volume":"20","author":"Okoh","year":"2023","journal-title":"Ecohealth"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1016\/j.coviro.2021.12.008","article-title":"Zoonotic Disease and Virome Diversity in Bats","volume":"52","author":"Holmes","year":"2022","journal-title":"Curr. Opin. Virol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e00373-17","DOI":"10.1128\/mBio.00373-17","article-title":"Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus","volume":"8","author":"Anthony","year":"2017","journal-title":"mBio"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"14040","DOI":"10.1073\/pnas.0506735102","article-title":"Severe Acute Respiratory Syndrome Coronavirus-like Virus in Chinese Horseshoe Bats","volume":"102","author":"Lau","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Field, H., Jordan, D., Edson, D., Morris, S., Melville, D., Parry-Jones, K., Broos, A., Divljan, A., McMichael, L., and Davis, R. (2015). Spatiotemporal Aspects of Hendra Virus Infection in Pteropid Bats (Flying-Foxes) in Eastern Australia. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0144055"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1126\/science.288.5470.1432","article-title":"Nipah Virus: A Recently Emergent Deadly Paramyxovirus","volume":"288","author":"Chua","year":"2000","journal-title":"Science"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Fabre, P.-H., Hautier, L., Dimitrov, D., and Douzery, E.J.P. (2012). A Glimpse on the Pattern of Rodent Diversification: A Phylogenetic Approach. BMC Evol. Biol., 12.","DOI":"10.1186\/1471-2148-12-88"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"7039","DOI":"10.1073\/pnas.1501598112","article-title":"Rodent Reservoirs of Future Zoonotic Diseases","volume":"112","author":"Han","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1128\/CMR.00062-09","article-title":"A Global Perspective on Hantavirus Ecology, Epidemiology, and Disease","volume":"23","author":"Jonsson","year":"2010","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1093\/infdis\/155.3.437","article-title":"A Prospective Study of the Epidemiology and Ecology of Lassa Fever","volume":"155","author":"McCormick","year":"1987","journal-title":"J. Infect. Dis."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1111\/ele.12491","article-title":"Network Analysis of Host-Virus Communities in Bats and Rodents Reveals Determinants of Cross-Species Transmission","volume":"18","author":"Luis","year":"2015","journal-title":"Ecol. Lett."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1093\/ilar\/ilx026","article-title":"Are RNA Viruses Candidate Agents for the Next Global Pandemic? A Review","volume":"58","year":"2017","journal-title":"ILAR J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1038\/nature22975","article-title":"Host and Viral Traits Predict Zoonotic Spillover from Mammals","volume":"546","author":"Olival","year":"2017","journal-title":"Nature"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Munch, M.M., Chambers, L.C., Manhart, L.E., Domogala, D., Lopez, A., Fredricks, D.N., and Srinivasan, S. (2019). Optimizing Bacterial DNA Extraction in Urine. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0222962"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"109735","DOI":"10.1016\/j.foodcont.2023.109735","article-title":"Optimization of an Approach to Detect Low-Concentration MNV-1 and HAV from Soil-Rich or Non-Soil Post-Washing Water Containing Various PCR Inhibitory Substances","volume":"150","author":"Wang","year":"2023","journal-title":"Food Control"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Buigues, J., Vi\u00f1als, A., Mart\u00ednez-Recio, R., Monr\u00f3s, J.S., Sanju\u00e1n, R., and Cuevas, J.M. (2024). Full-Genome Sequencing of Dozens of New DNA Viruses Found in Spanish Bat Feces. Microbiol. Spectr., 12.","DOI":"10.1128\/spectrum.00675-24"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"eabd4942","DOI":"10.1126\/sciadv.abd4942","article-title":"Cooperative Nature of Viral Replication","volume":"6","author":"Bou","year":"2020","journal-title":"Sci. Adv."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e02156-19","DOI":"10.1128\/mBio.02156-19","article-title":"Collective Viral Spread Mediated by Virion Aggregates Promotes the Evolution of Defective Interfering Particles","volume":"11","year":"2020","journal-title":"mBio"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Cebri\u00e1-Mendoza, M., D\u00edaz, W., Sanju\u00e1n, R., and Cuevas, J.M. (2024). Optimized Recovery of Viral DNA and RNA from Blood Plasma for Viral Metagenomics. Viral Metagenomics: Methods and Protocols, Springer.","DOI":"10.1007\/978-1-0716-3515-5_11"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"59","DOI":"10.21775\/cimb.024.059","article-title":"Comparing Viral Metagenomic Extraction Methods","volume":"24","author":"Klenner","year":"2017","journal-title":"Curr. Issues Mol. Biol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"4126","DOI":"10.1093\/bioinformatics\/btaa490","article-title":"Metaviral SPAdes: Assembly of Viruses from Metagenomic Data","volume":"36","author":"Antipov","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An Ultra-Fast Single-Node Solution for Large and Complex Metagenomics Assembly via Succinct de Bruijn Graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-Hit: A Fast Program for Clustering and Comparing Large Sets of Protein or Nucleotide Sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"11257","DOI":"10.1038\/ncomms11257","article-title":"Fast and Sensitive Taxonomic Classification for Metagenomics with Kaiju","volume":"7","author":"Menzel","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Guo, J., Bolduc, B., Zayed, A.A., Varsani, A., Dominguez-Huerta, G., Delmont, T.O., Pratama, A.A., Gazit\u00faa, M.C., Vik, D., and Sullivan, M.B. (2021). VirSorter2: A Multi-Classifier, Expert-Guided Approach to Detect Diverse DNA and RNA Viruses. Microbiome, 9.","DOI":"10.1186\/s40168-020-00990-y"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","article-title":"CheckV Assesses the Quality and Completeness of Metagenome-Assembled Viral Genomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast Gapped-Read Alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic Local Alignment Search Tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and Sensitive Protein Alignment Using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: Genome-Scale Protein Function Classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., and S\u00f6ding, J. (2011). Fast, Scalable Generation of High-quality Protein Multiple Sequence Alignments Using Clustal Omega. Mol. Syst. Biol., 7.","DOI":"10.1038\/msb.2011.75"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: Improving the Ultrafast Bootstrap Approximation","volume":"35","author":"Hoang","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1186\/s12985-024-02456-1","article-title":"Genetic Diversity and Cross-Species Transmissibility of Bat-Associated Picornaviruses from Spain","volume":"21","author":"Buigues","year":"2024","journal-title":"Virol. J."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Bolatti, E.M., Viarengo, G., Zorec, T.M., Cerri, A., Montani, M.E., Hosnjak, L., Casal, P.E., Bortolotto, E., Di Domenica, V., and Chouhy, D. (2022). Viral Metagenomic Data Analyses of Five New World Bat Species from Argentina: Identification of 35 Novel DNA Viruses. Microorganisms, 10.","DOI":"10.3390\/microorganisms10020266"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"e17222","DOI":"10.1016\/j.heliyon.2023.e17222","article-title":"Comparison of Viral Communities in the Blood, Feces and Various Tissues of Wild Brown Rats (Rattus Norvegicus)","volume":"9","author":"Zhuang","year":"2023","journal-title":"Heliyon"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Dugat-Bony, E., Lossouarn, J., De Paepe, M., Sarthou, A.-S., Fedala, Y., Petit, M.-A., and Chaillou, S. (2020). Viral Metagenomic Analysis of the Cheese Surface: A Comparative Study of Rapid Procedures for Extracting Viral Particles. Food Microbiol., 85.","DOI":"10.1016\/j.fm.2019.103278"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e01767-15","DOI":"10.1128\/mBio.01767-15","article-title":"Probing the Viromic Frontiers","volume":"6","author":"Rasmussen","year":"2015","journal-title":"mBio"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1099\/jgv.0.001072","article-title":"ICTV Virus Taxonomy Profile: Papillomaviridae","volume":"99","author":"Chen","year":"2018","journal-title":"J. Gen. Virol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1093\/gbe\/evt211","article-title":"Novel Papillomaviruses in Free-Ranging Iberian Bats: No Virus-Host Co-Evolution, No Strict Host Specificity, and Hints for Recombination","volume":"6","author":"Garin","year":"2014","journal-title":"Genome Biol. Evol."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Schulz, E., Gottschling, M., Ulrich, R.G., Richter, D., Stockfleth, E., and Nindl, I. (2012). Isolation of Three Novel Rat and Mouse Papillomaviruses and Their Genomic Characterization. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0047164"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1126\/science.2537532","article-title":"The Human Papilloma Virus-16 E7 Oncoprotein Is Able to Bind to the Retinoblastoma Gene Product","volume":"243","author":"Dyson","year":"1989","journal-title":"Science"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"200213","DOI":"10.1016\/j.tvr.2021.200213","article-title":"Human Papillomavirus E6 and E7: What Remains?","volume":"11","author":"Vats","year":"2021","journal-title":"Tumour Virus Res."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1099\/vir.0.19765-0","article-title":"Lack of the Canonical PRB-Binding Domain in the E7 ORF of Artiodactyl Papillomaviruses Is Associated with the Development of Fibropapillomas","volume":"85","author":"Narechania","year":"2004","journal-title":"J. Gen. Virol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Tse, H., Tsang, A.K.L., Tsoi, H.-W., Leung, A.S.P., Ho, C.-C., Lau, S.K.P., Woo, P.C.Y., and Yuen, K.-Y. (2012). Identification of a Novel Bat Papillomavirus by Metagenomics. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0043986"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Munday, J.S., Gedye, K., Knox, M.A., Ravens, P., and Lin, X. (2022). Genomic Characterisation of Canis Familiaris Papillomavirus Type 24, a Novel Papillomavirus Associated with Extensive Pigmented Plaque Formation in a Pug Dog. Viruses, 14.","DOI":"10.3390\/v14112357"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"e00054-22","DOI":"10.1128\/mbio.00054-22","article-title":"Coevolutionary Analysis Implicates Toll-Like Receptor 9 in Papillomavirus Restriction","volume":"13","author":"King","year":"2022","journal-title":"mBio"},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Buck, C.B., Welch, N., Belford, A.K., Varsani, A., Pastrana, D.V., Tisza, M.J., and Starrett, G.J. (2024). Widespread Horizontal Gene Transfer Among Animal Viruses. bioRxiv.","DOI":"10.7554\/eLife.97647.1"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Gimpelj Domjani\u010d, G., Ho\u0161njak, L., Lunar, M.M., Skubic, L., Zorec, T.M., Ra\u010dnik, J., Cigler, B., and Poljak, M. (2021). First Report of Phodopus sungorus Papillomavirus Type 1 Infection in Roborovski Hamsters (Phodopus roborovskii). Viruses, 13.","DOI":"10.3390\/v13050739"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1099\/jgv.0.000839","article-title":"ICTV Virus Taxonomy Profile: Polyomaviridae","volume":"98","author":"Moens","year":"2017","journal-title":"J. Gen. Virol."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses, Calvignac-Spencer, S., Feltkamp, M.C.W., Daugherty, M.D., Moens, U., Ramqvist, T., Johne, R., and Ehlers, B. (2016). A Taxonomy Update for the Family Polyomaviridae. Arch. Virol., 161, 1739\u20131750.","DOI":"10.1007\/s00705-016-2794-y"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1126\/science.1152586","article-title":"Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma","volume":"319","author":"Feng","year":"2008","journal-title":"Science"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"12744","DOI":"10.1073\/pnas.1303526110","article-title":"Identification of an Overprinting Gene in Merkel Cell Polyomavirus Provides Evolutionary Insight into the Birth of Viral Genes","volume":"110","author":"Carter","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"e2403133121","DOI":"10.1073\/pnas.2403133121","article-title":"Polyomavirus ALTOs, but Not MTs, Downregulate Viral Early Gene Expression by Activating the NF-\u039aB Pathway","volume":"121","author":"Salisbury","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"e00888-15","DOI":"10.1128\/genomeA.00888-15","article-title":"Genome Sequence of a Central Chimpanzee-Associated Polyomavirus Related to BK and JC Polyomaviruses, Pan Troglodytes Troglodytes Polyomavirus 1","volume":"3","author":"Madinda","year":"2015","journal-title":"Genome Announc."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"e01406-15","DOI":"10.1128\/genomeA.01406-15","article-title":"Complete Genome Sequence of a Novel Chimpanzee Polyomavirus from a Western Common Chimpanzee","volume":"4","author":"Buitendijk","year":"2016","journal-title":"Genome Announc."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"e01101-16","DOI":"10.1128\/genomeA.01101-16","article-title":"Genome Sequences of Polyomaviruses from the Wild-Living Red Colobus (Piliocolobus badius) and Western Chimpanzee (Pan troglodytes verus)","volume":"4","author":"Leendertz","year":"2016","journal-title":"Genome Announc."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"TrimAl: A Tool for Automated Alignment Trimming in Large-Scale Phylogenetic Analyses","volume":"25","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_68","first-page":"001721","article-title":"ICTV Virus Taxonomy Profile: Adenoviridae 2022","volume":"103","author":"Aoki","year":"2022","journal-title":"J. Gen. Virol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"2895","DOI":"10.1099\/vir.0.19497-0","article-title":"Genetic Content and Evolution of Adenoviruses","volume":"84","author":"Davison","year":"2003","journal-title":"J. Gen. Virol."},{"key":"ref_70","first-page":"12","article-title":"CD200\/CD200R Paired Potent Inhibitory Molecules Regulating Immune and Inflammatory Responses; Part I: CD200\/CD200R Structure, Activation, and Function","volume":"55","author":"Kunes","year":"2012","journal-title":"Acta Medica"},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Wu, Z., Lu, L., Du, J., Yang, L., Ren, X., Liu, B., Jiang, J., Yang, J., Dong, J., and Sun, L. (2018). Comparative Analysis of Rodent and Small Mammal Viromes to Better Understand the Wildlife Origin of Emerging Infectious Diseases. Microbiome, 6.","DOI":"10.1186\/s40168-018-0554-9"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Geldenhuys, M., Mortlock, M., Weyer, J., Bezuidt, O., Seamark, E.C.J., Kearney, T., Gleasner, C., Erkkila, T.H., Cui, H., and Markotter, W. (2018). A Metagenomic Viral Discovery Approach Identifies Potential Zoonotic and Novel Mammalian Viruses in Neoromicia Bats within South Africa. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0194527"},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Hardmeier, I., Aeberhard, N., Qi, W., Schoenbaechler, K., Kraettli, H., Hatt, J.-M., Fraefel, C., and Kubacki, J. (2021). Metagenomic Analysis of Fecal and Tissue Samples from 18 Endemic Bat Species in Switzerland Revealed a Diverse Virus Composition Including Potentially Zoonotic Viruses. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0252534"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1679","DOI":"10.1080\/22221751.2019.1690953","article-title":"Are Adenoviruses Zoonotic? A Systematic Review of the Evidence","volume":"8","author":"Borkenhagen","year":"2019","journal-title":"Emerg. Microbes Infect."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"2072","DOI":"10.1093\/molbev\/msv090","article-title":"Multiple Cross-Species Transmission Events of Human Adenoviruses (HAdV) during Hominine Evolution","volume":"32","author":"Hoppe","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/j.virol.2013.05.014","article-title":"Computational Analysis of Four Human Adenovirus Type 4 Genomes Reveals Molecular Evolution through Two Interspecies Recombination Events","volume":"443","author":"Dehghan","year":"2013","journal-title":"Virology"},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Medkour, H., Amona, I., Akiana, J., Davoust, B., Bitam, I., Levasseur, A., Tall, M.L., Diatta, G., Sokhna, C., and Hernandez-Aguilar, R.A. (2020). Adenovirus Infections in African Humans and Wild Non-Human Primates: Great Diversity and Cross-Species Transmission. Viruses, 12.","DOI":"10.3390\/v12060657"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1007\/s10393-020-01497-6","article-title":"Molecular Detection of Human Adenovirus and Rotavirus in Feces of White-Eared Opossums","volume":"17","author":"Menezes","year":"2020","journal-title":"Ecohealth"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1177\/03009858231189722","article-title":"Detection of Skunk Adenovirus-1 in Domestic Ferrets (Mustela putorius)","volume":"61","author":"Nilsen","year":"2024","journal-title":"Vet. Pathol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"e00582-20","DOI":"10.1128\/JVI.00582-20","article-title":"Cressdnaviricota: A Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes","volume":"94","author":"Krupovic","year":"2020","journal-title":"J. Virol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1111\/avj.12388","article-title":"Review of Psittacine Beak and Feather Disease and Its Effect on Australian Endangered Species","volume":"93","author":"Raidal","year":"2015","journal-title":"Aust. Vet. J."},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Niu, G., Chen, S., Li, X., Zhang, L., and Ren, L. (2022). Advances in Crosstalk between Porcine Circoviruses and Host. Viruses, 14.","DOI":"10.3390\/v14071419"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"2911","DOI":"10.1007\/s00705-021-05183-y","article-title":"Family Genomoviridae: 2021 Taxonomy Update","volume":"166","author":"Varsani","year":"2021","journal-title":"Arch. Virol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1007\/s00705-024-06107-2","article-title":"2024 Taxonomy Update for the Family Circoviridae","volume":"169","author":"Varsani","year":"2024","journal-title":"Arch. Virol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"4786","DOI":"10.1002\/jmv.27080","article-title":"Cyclovirus Detection in Chilean Adults with and without Community-acquired Pneumonia","volume":"93","author":"Prades","year":"2021","journal-title":"J. Med. Virol."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"e00231-13","DOI":"10.1128\/mBio.00231-13","article-title":"Identification of a New Cyclovirus in Cerebrospinal Fluid of Patients with Acute Central Nervous System Infections","volume":"4","author":"Tan","year":"2013","journal-title":"mBio"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1038\/s41467-017-00923-8","article-title":"Global Hotspots and Correlates of Emerging Zoonotic Diseases","volume":"8","author":"Allen","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"e00219-24","DOI":"10.1128\/msphere.00219-24","article-title":"Gemykibivirus Detection in Acute Encephalitis Patients from Nepal","volume":"9","author":"Tuladhar","year":"2024","journal-title":"mSphere"},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Couto, R.d.S., Abreu, W.U., Rodrigues, L.R.R., Marinho, L.F., Morais, V.D.S., Villanova, F., Pandey, R.P., Deng, X., Delwart, E., and da Costa, A.C. (2024). Genomoviruses in Liver Samples of Molossus Molossus Bats. Microorganisms, 12.","DOI":"10.3390\/microorganisms12040688"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"3425","DOI":"10.1038\/s41467-019-11433-0","article-title":"Multiple Origins of Prokaryotic and Eukaryotic Single-Stranded DNA Viruses from Bacterial and Archaeal Plasmids","volume":"10","author":"Kazlauskas","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_91","doi-asserted-by":"crossref","unstructured":"Kremer, E.J. (2021). What Is the Risk of a Deadly Adenovirus Pandemic?. PLoS Pathog., 17.","DOI":"10.1371\/journal.ppat.1009814"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"10171","DOI":"10.1073\/pnas.0900604106","article-title":"Systematic Identification of Cell Cycle-dependent Yeast Nucleocytoplasmic Shuttling Proteins by Prediction of Composite Motifs","volume":"106","author":"Kosugi","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/12\/1885\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:47:44Z","timestamp":1760114864000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/12\/1885"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,5]]},"references-count":92,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["v16121885"],"URL":"https:\/\/doi.org\/10.3390\/v16121885","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,5]]}}}