{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T22:21:46Z","timestamp":1785277306073,"version":"3.55.0"},"reference-count":116,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2021,12,24]],"date-time":"2021-12-24T00:00:00Z","timestamp":1640304000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["17-74-20096"],"award-info":[{"award-number":["17-74-20096"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Discovery and study of viruses carried by migratory birds are tasks of high importance due to the host\u2019s ability to spread infectious diseases over significant distances. With this paper, we present and characterize the first complete genome sequence of atadenovirus from a tern bird (common tern, Sterna hirundo) preliminarily named tern atadenovirus 1 (TeAdV-1). TeAdV-1 genome is a linear double-stranded DNA molecule, 31,334 base pairs which contain 30 methionine-initiated open reading frames with gene structure typical for Atadenovirus genus, and the shortest known inverted terminal repeats (ITRs) within the Atadenovirus genus consisted of 25 bases. The nucleotide composition of the genome is characterized by a low G + C content (33.86%), which is the most AT-rich genome of known avian adenoviruses within Atadenovirus genus. The nucleotide sequence of the TeAdV-1 genome shows high divergence compared to known representatives of the Atadenovirus genus with the highest similarity to the duck atadenovirus 1 (53.7%). Phylogenetic analysis of the protein sequences of core genes confirms the taxonomic affiliation of the new representative to the genus Atadenovirus with the degree of divergence from the known representatives exceeding the interspecies distance within the genus. Thereby we proposed a novel TeAdV-1 to be considered as a separate species.<\/jats:p>","DOI":"10.3390\/microorganisms10010031","type":"journal-article","created":{"date-parts":[[2021,12,27]],"date-time":"2021-12-27T01:06:54Z","timestamp":1640567214000},"page":"31","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus"],"prefix":"10.3390","volume":"10","author":[{"given":"Alina","family":"Matsvay","sequence":"first","affiliation":[{"name":"Federal State Budgetary Institution \u201cCentre for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical Biological Agency, 119121 Moscow, Russia"},{"name":"Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina","family":"Dyachkova","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCentre for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical Biological Agency, 119121 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan","family":"Mikhaylov","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCentre for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical Biological Agency, 119121 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8074-8411","authenticated-orcid":false,"given":"Daniil","family":"Kiselev","sequence":"additional","affiliation":[{"name":"Institute for Neurosciences of Montpellier, University of Montpellier, INSERM, 34091 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2151-9920","authenticated-orcid":false,"given":"Anna","family":"Say","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCentre for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical Biological Agency, 119121 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valentina","family":"Burskaia","sequence":"additional","affiliation":[{"name":"Skolkovo Institute of Science and Technology, 143026 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4911-3677","authenticated-orcid":false,"given":"Ilya","family":"Artyushin","sequence":"additional","affiliation":[{"name":"Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5524-0296","authenticated-orcid":false,"given":"Kamil","family":"Khafizov","sequence":"additional","affiliation":[{"name":"Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"German","family":"Shipulin","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCentre for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical Biological Agency, 119121 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,12,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"3660","DOI":"10.1002\/1873-3468.13687","article-title":"Adenoviruses across the animal kingdom: A walk in the zoo","volume":"593","author":"Harrach","year":"2019","journal-title":"FEBS Lett."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"D708","DOI":"10.1093\/nar\/gkx932","article-title":"Virus taxonomy: The database of the International Committee on Taxonomy of Viruses (ICTV)","volume":"46","author":"Lefkowitz","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Benk\u0151, M., Aoki, K., Arnberg, N., and Davison, A.J. (J. Gen. Virol., 2021). ICTV Virus Taxonomy Profile: Adenoviridae, J. Gen. Virol., in press.","DOI":"10.1099\/jgv.0.001721"},{"key":"ref_4","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_5","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.virol.2005.07.020","article-title":"LH3, a \u201chomologue\u201d of the mastadenoviral E1B 55-kDa protein is a structural protein of atadenoviruses","volume":"342","author":"Gorman","year":"2005","journal-title":"Virology"},{"key":"ref_6","unstructured":"Ritchie, B.W., Harrison, G.J., and Harrison, L.R. (1994). Viruses. Avian Medicine: Principles and Application, Wingers Publishing Inc."},{"key":"ref_7","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_8","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/nature02746","article-title":"Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia","volume":"430","author":"Li","year":"2004","journal-title":"Nature"},{"key":"ref_9","unstructured":"(2021, November 30). World Health Organization Pandemic H1N1. Available online: http:\/\/apps.who.int\/iris\/bitstream\/handle\/10665\/78414\/9789241503051_eng.pdf?sequence=1."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1038\/nature08157","article-title":"Emergence and pandemic potential of swine-origin H1N1 influenza virus","volume":"459","author":"Neumann","year":"2009","journal-title":"Nature"},{"key":"ref_11","unstructured":"(2021, November 30). World Health Organization Statement on the second meeting of the International Health Regulations. Available online: https:\/\/www.who.int\/news\/item\/30-01-2020-statement-on-the-second-meeting-of-the-international-health-regulations-(2005)-emergency-committee-regarding-the-outbreak-of-novel-coronavirus-(2019-ncov)."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1038\/s41591-020-0820-9","article-title":"The proximal origin of SARS-CoV-2","volume":"26","author":"Andersen","year":"2020","journal-title":"Nat. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1093\/icb\/icw054","article-title":"Are Migratory Animals Superspreaders of Infection?: An Introduction to the Symposium","volume":"56","author":"Hoye","year":"2016","journal-title":"Integr. Comp. Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2018\/3248285","article-title":"The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels","volume":"2018","author":"Ayginin","year":"2018","journal-title":"Adv. Virol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"W20","DOI":"10.1093\/nar\/gkh435","article-title":"BLAST: At the core of a powerful and diverse set of sequence analysis tools","volume":"32","author":"McGinnis","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","article-title":"The NCBI Taxonomy database","volume":"40","author":"Federhen","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinforma. Oxf. Engl."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinforma. Oxf. Engl."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1093\/bib\/bbs012","article-title":"Using Tablet for visual exploration of second-generation sequencing data","volume":"14","author":"Milne","year":"2013","journal-title":"Brief. Bioinform."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"184","DOI":"10.3389\/fmicb.2019.00184","article-title":"Vgas: A Viral Genome Annotation System","volume":"10","author":"Zhang","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: Phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1089\/cmb.1997.4.311","article-title":"Improved Splice Site Detection in Genie","volume":"4","author":"Reese","year":"1997","journal-title":"J. Comput. Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: Freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinforma. Oxf. Engl."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"D67","DOI":"10.1093\/nar\/gkv1276","article-title":"GenBank","volume":"44","author":"Clark","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and Clustal X version 2.0","volume":"23","author":"Larkin","year":"2007","journal-title":"Bioinforma. Oxf. Engl."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis","volume":"17","author":"Castresana","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"ref_30","first-page":"772","article-title":"PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses","volume":"34","author":"Lanfear","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"4453","DOI":"10.1093\/bioinformatics\/btz305","article-title":"RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference","volume":"35","author":"Kozlov","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_32","unstructured":"Rambaut, A. (2021, November 30). FigTree v. 1.4.3. 2018. Available online: http:\/\/tree.bio.ed.ac.uk\/software\/figtree\/."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1038\/s41467-019-08822-w","article-title":"Model selection may not be a mandatory step for phylogeny reconstruction","volume":"10","author":"Abadi","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2110","DOI":"10.1093\/molbev\/msaa075","article-title":"Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics","volume":"37","author":"Spielman","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2869","DOI":"10.1093\/bioinformatics\/btt499","article-title":"A general species delimitation method with applications to phylogenetic placements","volume":"29","author":"Zhang","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1093\/sysbio\/syt033","article-title":"Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets","volume":"62","author":"Fujisawa","year":"2013","journal-title":"Syst. Biol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1080\/10635150600852011","article-title":"Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects","volume":"55","author":"Pons","year":"2006","journal-title":"Syst. Biol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Fontaneto, D., Herniou, E.A., Boschetti, C., Caprioli, M., Melone, G., Ricci, C., and Barraclough, T.G. (2007). Independently Evolving Species in Asexual Bdelloid Rotifers. PLoS Biol., 5.","DOI":"10.1371\/journal.pbio.0050087"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1111\/j.1096-3642.2010.00674.x","article-title":"Integrating DNA and morphological taxonomy to describe diversity in poorly studied microscopic animals: New species of the genus Abrochtha Bryce, 1910 (Rotifera: Bdelloidea: Philodinavidae): NEW CRYPTIC ROTIFER SPECIES","volume":"161","author":"Birky","year":"2011","journal-title":"Zool. J. Linn. Soc."},{"key":"ref_42","first-page":"21","article-title":"II.\u2014A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F.R.S","volume":"213","author":"Yule","year":"1925","journal-title":"Philos. Trans. R. Soc. Lond. Ser. B Contain. Pap. Biol. Character"},{"key":"ref_43","first-page":"1","article-title":"Gene genealogies and the coalescent process","volume":"7","author":"Hudson","year":"1990","journal-title":"Oxf. Surv. Evol. Biol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"19333","DOI":"10.1073\/pnas.1213199109","article-title":"Estimating divergence times in large molecular phylogenies","volume":"109","author":"Tamura","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1770","DOI":"10.1093\/molbev\/msy044","article-title":"Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates","volume":"35","author":"Tamura","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1046\/j.1365-2540.2001.0923a.x","article-title":"Molecular Evolution and Phylogenetics","volume":"86","author":"Thomas","year":"2001","journal-title":"Heredity"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1111\/1755-0998.13281","article-title":"ASAP: Assemble species by automatic partitioning","volume":"21","author":"Puillandre","year":"2021","journal-title":"Mol. Ecol. Resour."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"W573","DOI":"10.1093\/nar\/gks485","article-title":"T-REX: A web server for inferring, validating and visualizing phylogenetic trees and networks","volume":"40","author":"Boc","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Birky, C.W., Adams, J., Gemmel, M., and Perry, J. (2010). Using Population Genetic Theory and DNA Sequences for Species Detection and Identification in Asexual Organisms. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0010609"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"3096","DOI":"10.1093\/bioinformatics\/btl474","article-title":"GARD: A genetic algorithm for recombination detection","volume":"22","author":"Posada","year":"2006","journal-title":"Bioinformatics"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Pond, S.L.K., and Muse, S.V. (2005). HyPhy: Hypothesis Testing Using Phylogenies. Statistical Methods in Molecular Evolution, Springer.","DOI":"10.1093\/bioinformatics\/bti079"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: Phylogenetic Analysis by Maximum Likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol. Biol. Evol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1093\/molbev\/msi105","article-title":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection","volume":"22","author":"Frost","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2472","DOI":"10.1093\/molbev\/msi237","article-title":"Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level","volume":"22","author":"Zhang","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera?A visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"eabe6008","DOI":"10.1126\/sciadv.abe6008","article-title":"Near-atomic structure of an atadenovirus reveals a conserved capsid-binding motif and intergenera variations in cementing proteins","volume":"7","author":"Marabini","year":"2021","journal-title":"Sci. Adv."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"4132","DOI":"10.1016\/j.jmb.2018.08.011","article-title":"Revised Crystal Structure of Human Adenovirus Reveals the Limits on Protein IX Quasi-Equivalence and on Analyzing Large Macromolecular Complexes","volume":"430","author":"Venkataraman","year":"2018","journal-title":"J. Mol. Biol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"To, K.K.W., Tse, H., Chan, W.-M., Choi, G.K.Y., Zhang, A.J.X., Sridhar, S., Wong, S.C.Y., Chan, J.F.W., Chan, A.S.F., and Woo, P.C.Y. (2014). A Novel Psittacine Adenovirus Identified During an Outbreak of Avian Chlamydiosis and Human Psittacosis: Zoonosis Associated with Virus-Bacterium Coinfection in Birds. PLoS Negl. Trop. Dis., 8.","DOI":"10.1371\/journal.pntd.0003318"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Harrach, B. (2014). Adenoviruses: General Features. Reference Module in Biomedical Sciences, Elsevier.","DOI":"10.1016\/B978-0-12-801238-3.02523-X"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/0042-6822(83)90402-6","article-title":"Analysis of Ad5 Hexon and 100K is mutants using conformation-specific monoclonal antibodies","volume":"129","author":"Cepko","year":"1983","journal-title":"Virology"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1099\/vir.0.003087-0","article-title":"Adenoviruses: Update on structure and function","volume":"90","author":"Russell","year":"2009","journal-title":"J. Gen. Virol."},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Kulanayake, S., and Tikoo, S.K. (2021). Adenovirus Core Proteins: Structure and Function. Viruses, 13.","DOI":"10.3390\/v13030388"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"1240","DOI":"10.1093\/nar\/26.5.1240","article-title":"Adenovirus DNA polymerase: Domain organisation and interaction with preterminal protein","volume":"26","author":"Parker","year":"1998","journal-title":"Nucleic Acids Res."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1581","DOI":"10.1099\/vir.0.80877-0","article-title":"The adenovirus capsid: Major progress in minor proteins","volume":"86","author":"Vellinga","year":"2005","journal-title":"J. Gen. Virol."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Duarte, M.A., Silva, J.M.F., Brito, C.R., Teixeira, D.S., Melo, F.L., Ribeiro, B.M., Nagata, T., and Campos, F.S. (2019). Faecal Virome Analysis of Wild Animals from Brazil. Viruses, 11.","DOI":"10.3390\/v11090803"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1017\/S0016672303006128","article-title":"Potential impact of recombination on sitewise approaches for detecting positive natural selection","volume":"81","author":"Shriner","year":"2003","journal-title":"Genet. Res."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1006\/viro.1996.0299","article-title":"Unique Genome Arrangement of an Ovine Adenovirus: Identification of New Proteins and Proteinase Cleavage Sites","volume":"220","author":"Vrati","year":"1996","journal-title":"Virology"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"104321","DOI":"10.1016\/j.meegid.2020.104321","article-title":"The complete genome sequence of bearded dragon adenovirus 1 harbors three genes encoding proteins of the C-type lectin-like domain superfamily","volume":"83","author":"Szirovicza","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Athukorala, A., Forwood, J.K., Phalen, D.N., and Sarker, S. (2020). Molecular Characterisation of a Novel and Highly Divergent Passerine Adenovirus 1. Viruses, 12.","DOI":"10.3390\/v12091036"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1007\/s007050050335","article-title":"A proposal for a new (third) genus within the family Adenoviridae","volume":"143","author":"Harrach","year":"1998","journal-title":"Arch. Virol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"646300","DOI":"10.3389\/fmicb.2021.646300","article-title":"Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts","volume":"12","author":"Cristina","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"347","DOI":"10.3201\/eid1402.070932","article-title":"Isolation of Novel Adenovirus from Fruit Bat (Pteropus dasymallus yayeyamae)","volume":"14","author":"Maeda","year":"2008","journal-title":"Emerg. Infect. Dis."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"e5521","DOI":"10.7717\/peerj.5521","article-title":"Detection and phylogenetic analysis of adenoviruses occurring in a single anole species","volume":"6","author":"Geneva","year":"2018","journal-title":"PeerJ"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1080\/03079450903183660","article-title":"Siadenovirus infection in two psittacine bird species","volume":"38","author":"Wellehan","year":"2009","journal-title":"Avian Pathol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"258","DOI":"10.4269\/ajtmh.13-0664","article-title":"Molecular Detection of Adenoviruses, Rhabdoviruses, and Paramyxoviruses in Bats from Kenya","volume":"91","author":"Conrardy","year":"2014","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"4222","DOI":"10.1128\/JVI.02407-10","article-title":"Recombinant Adenovirus Serotype 26 (Ad26) and Ad35 Vaccine Vectors Bypass Immunity to Ad5 and Protect Nonhuman Primates against Ebolavirus Challenge","volume":"85","author":"Geisbert","year":"2011","journal-title":"J. Virol."},{"key":"ref_78","unstructured":"(2012). Adenoviridae. Virus Taxonomy, Elsevier."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1007\/BF00985210","article-title":"New classification of liverworts based on molecular and morphological data","volume":"207","author":"Capesius","year":"1997","journal-title":"Plant Syst. Evol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"12390","DOI":"10.1073\/pnas.95.21.12390","article-title":"The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small","volume":"95","author":"Nei","year":"1998","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1038\/18592","article-title":"Taxon sampling revisited","volume":"398","author":"Poe","year":"1999","journal-title":"Nature"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"1885","DOI":"10.1093\/oxfordjournals.molbev.a026290","article-title":"Multigene Phylogeny of Land Plants with Special Reference to Bryophytes and the Earliest Land Plants","volume":"17","author":"Nickrent","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1078\/S1434-4610(04)70029-2","article-title":"Opinion: Long Branch Attraction and Protist Phylogeny","volume":"151","year":"2000","journal-title":"Protist"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1007\/s00239-002-2313-5","article-title":"Nuclear and Nucleomorph SSU rDNA Phylogeny in the Cryptophyta and the Evolution of Cryptophyte Diversity","volume":"55","author":"Marin","year":"2002","journal-title":"J. Mol. Evol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"4693","DOI":"10.1128\/JVI.06969-11","article-title":"Overreliance on the Hexon Gene, Leading to Misclassification of Human Adenoviruses: Fig 1","volume":"86","author":"Singh","year":"2012","journal-title":"J. Virol."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1038\/383130a0","article-title":"Inferring complex phytogenies","volume":"383","author":"Hillis","year":"1996","journal-title":"Nature"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1093\/molbev\/msh052","article-title":"Are Combined Analyses Better Than Single Gene Phylogenies? A Case Study Using SSU rDNA and rbcL Sequence Comparisons in the Zygnematophyceae (Streptophyta)","volume":"21","author":"Gontcharov","year":"2003","journal-title":"Mol. Biol. Evol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1111\/syen.12406","article-title":"Phylogenomics\u2014Principles, opportunities and pitfalls of big-data phylogenetics","volume":"45","author":"Young","year":"2020","journal-title":"Syst. Entomol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.3389\/fmicb.2016.01137","article-title":"Phylogenomic Analyses and Reclassification of Species within the Genus Tsukamurella: Insights to Species Definition in the Post-genomic Era","volume":"7","author":"Teng","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"301","DOI":"10.6026\/97320630012301","article-title":"An Analysis of Adenovirus Genomes Using Whole Genome Software Tools","volume":"12","author":"Mahadevan","year":"2016","journal-title":"Bioinformation"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"2567","DOI":"10.1073\/pnas.0409727102","article-title":"Genomic insights that advance the species definition for prokaryotes","volume":"102","author":"Konstantinidis","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.ympev.2016.08.023","article-title":"Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species","volume":"105","author":"Arrigoni","year":"2016","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.ympev.2016.12.018","article-title":"By how much do we underestimate species diversity of liverworts using morphological evidence? An example from Australasian Plagiochila (Plagiochilaceae: Jungermanniopsida)","volume":"107","author":"Renner","year":"2017","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.ympev.2016.09.001","article-title":"Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity","volume":"106","author":"Barley","year":"2017","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1111\/2041-210X.12246","article-title":"Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data","volume":"5","author":"Tang","year":"2014","journal-title":"Methods Ecol. Evol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"2282","DOI":"10.1093\/bioinformatics\/btz911","article-title":"LIMES: A tool for comparing species partition","volume":"36","author":"Ducasse","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_97","unstructured":"(2021, November 30). International Committee on Taxonomy of Viruses Virus Taxonomy: The ICTV Report on Virus Classification and Taxon Nomenclature. Available online: https:\/\/talk.ictvonline.org\/ictv-reports\/ictv_online_report\/."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1007\/978-1-4939-9074-0_14","article-title":"Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces","volume":"Volume 1910","author":"Anisimova","year":"2019","journal-title":"Evolutionary Genomics"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1007\/BF01796554","article-title":"Molecular evolution as predicted by natural selection","volume":"3","year":"1974","journal-title":"J. Mol. Evol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"870","DOI":"10.2307\/2408397","article-title":"Coevolution in Ecosystems: Red Queen Evolution or Stasis?","volume":"38","author":"Stenseth","year":"1984","journal-title":"Evolution"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1086\/285643","article-title":"Evolutionary Genetics of the Major Histocompatibility Complex","volume":"143","author":"Hedrick","year":"1994","journal-title":"Am. Nat."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1016\/j.cub.2006.01.065","article-title":"Natural Selection Drives Extremely Rapid Evolution in Antiviral RNAi Genes","volume":"16","author":"Obbard","year":"2006","journal-title":"Curr. Biol."},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"(2007). Drosophila 12 Genomes Consortium Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450, 203\u2013218.","DOI":"10.1038\/nature06341"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"2073","DOI":"10.1093\/molbev\/msi199","article-title":"Molecular Evolution of Rickettsia Surface Antigens: Evidence of Positive Selection","volume":"22","author":"Blanc","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1038\/ng1924","article-title":"Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome","volume":"39","author":"Mu","year":"2007","journal-title":"Nat. Genet."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"2499","DOI":"10.1093\/molbev\/msp166","article-title":"Diversity and Evolution of Effector Loci in Natural Populations of the Plant Pathogen Melampsora lini","volume":"26","author":"Barrett","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"19715","DOI":"10.1073\/pnas.1203456109","article-title":"Variable evolutionary routes to host establishment across repeated rabies virus host shifts among bats","volume":"109","author":"Streicker","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"20141382","DOI":"10.1098\/rspb.2014.1382","article-title":"Running with the Red Queen: The role of biotic conflicts in evolution","volume":"281","author":"Brockhurst","year":"2014","journal-title":"Proc. R. Soc. B Biol. Sci."},{"key":"ref_109","doi-asserted-by":"crossref","unstructured":"Frank, H.K., Enard, D., and Boyd, S.D. (2020). Exceptional diversity and selection pressure on SARS-CoV and SARS-CoV-2 host receptor in bats compared to other mammals. bioRxiv.","DOI":"10.1101\/2020.04.20.051656"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"6283","DOI":"10.1073\/pnas.0701396104","article-title":"Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution","volume":"104","author":"Shih","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"2443","DOI":"10.1093\/molbev\/msr044","article-title":"The Genomic Rate of Molecular Adaptation of the Human Influenza A Virus","volume":"28","author":"Bhatt","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1534\/genetics.112.143396","article-title":"Clonal Interference in the Evolution of Influenza","volume":"192","author":"Strelkowa","year":"2012","journal-title":"Genetics"},{"key":"ref_113","doi-asserted-by":"crossref","unstructured":"Illingworth, C.J.R., and Mustonen, V. (2012). Components of Selection in the Evolution of the Influenza Virus: Linkage Effects Beat Inherent Selection. PLoS Pathog., 8.","DOI":"10.1371\/journal.ppat.1003091"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"20120334","DOI":"10.1098\/rstb.2012.0334","article-title":"Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin","volume":"368","author":"Meyer","year":"2013","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"6700","DOI":"10.1073\/pnas.0901855106","article-title":"Reliabilities of identifying positive selection by the branch-site and the site-prediction methods","volume":"106","author":"Nozawa","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_116","doi-asserted-by":"crossref","unstructured":"Longdon, B., Day, J.P., Alves, J.M., Smith, S.C.L., Houslay, T.M., McGonigle, J.E., Tagliaferri, L., and Jiggins, F.M. (2018). Host shifts result in parallel genetic changes when viruses evolve in closely related species. PLoS Pathog., 14.","DOI":"10.1371\/journal.ppat.1006951"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/1\/31\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:53:02Z","timestamp":1760169182000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/1\/31"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12,24]]},"references-count":116,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,1]]}},"alternative-id":["microorganisms10010031"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms10010031","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,12,24]]}}}