{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T09:20:40Z","timestamp":1791451240452,"version":"4.3.3"},"reference-count":41,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2018,10,6]],"date-time":"2018-10-06T00:00:00Z","timestamp":1538784000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003196","name":"Ministero della Salute","doi-asserted-by":"publisher","award":["Ricerca Corrente INMI and IZSLT"],"award-info":[{"award-number":["Ricerca Corrente INMI and IZSLT"]}],"id":[{"id":"10.13039\/501100003196","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020","doi-asserted-by":"publisher","award":["653316"],"award-info":[{"award-number":["653316"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007565","name":"Consumers, Health, Agriculture and Food Executive Agency","doi-asserted-by":"publisher","award":["677066"],"award-info":[{"award-number":["677066"]}],"id":[{"id":"10.13039\/501100007565","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Orthopoxviruses (OPVs) are diffused over the complete Eurasian continent, but previously described strains are mostly from northern Europe, and few infections have been reported from Italy. Here we present the extended genomic characterization of OPV Abatino, a novel OPV isolated in Italy from an infected Tonkean macaque, with zoonotic potential. Phylogenetic analysis based on 102 conserved OPV genes (core gene set) showed that OPV Abatino is most closely related to the Ectromelia virus species (ECTV), although placed on a separate branch of the phylogenetic tree, bringing substantial support to the hypothesis that this strain may be part of a novel OPV clade. Extending the analysis to the entire set of genes (coding sequences, CDS) further substantiated this hypothesis. In fact the genome of OPV Abatino included more CDS than ECTV; most of the extra genes (mainly located in the terminal genome regions), showed the highest similarity with cowpox virus (CPXV); however vaccinia virus (VACV) and monkeypox virus (MPXV) were the closest OPV for certain CDS. These findings suggest that OPV Abatino could be the result of complex evolutionary events, diverging from any other previously described OPV, and may indicate that previously reported cases in Italy could represent the tip of the iceberg yet to be explored.<\/jats:p>","DOI":"10.3390\/v10100546","type":"journal-article","created":{"date-parts":[[2018,10,8]],"date-time":"2018-10-08T10:44:53Z","timestamp":1538995493000},"page":"546","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":28,"title":["Whole Genome Characterization of Orthopoxvirus (OPV) Abatino, a Zoonotic Virus Representing a Putative Novel Clade of Old World Orthopoxviruses"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8831-3380","authenticated-orcid":false,"given":"Cesare E. M.","family":"Gruber","sequence":"first","affiliation":[{"name":"National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2237-9755","authenticated-orcid":false,"given":"Emanuela","family":"Giombini","sequence":"additional","affiliation":[{"name":"National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9131-7502","authenticated-orcid":false,"given":"Marina","family":"Selleri","sequence":"additional","affiliation":[{"name":"National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6874-233X","authenticated-orcid":false,"given":"Simon H.","family":"Tausch","sequence":"additional","affiliation":[{"name":"Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Seestra\u00dfe 10, 13353 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Andrusch","sequence":"additional","affiliation":[{"name":"Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Seestra\u00dfe 10, 13353 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alona","family":"Tyshaieva","sequence":"additional","affiliation":[{"name":"Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Seestra\u00dfe 10, 13353 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3365-9437","authenticated-orcid":false,"given":"Giusy","family":"Cardeti","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, via Appia Nuova 1411, 00178 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raniero","family":"Lorenzetti","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, via Appia Nuova 1411, 00178 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorenzo","family":"De Marco","sequence":"additional","affiliation":[{"name":"Parco Faunistico Piano dell\u2019Abatino, via Capo Farfa 50, 02030 Poggio San Lorenzo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1952-5117","authenticated-orcid":false,"given":"Fabrizio","family":"Carletti","sequence":"additional","affiliation":[{"name":"National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Nitsche","sequence":"additional","affiliation":[{"name":"Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Seestra\u00dfe 10, 13353 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria R.","family":"Capobianchi","sequence":"additional","affiliation":[{"name":"National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1076-2979","authenticated-orcid":false,"given":"Giuseppe","family":"Ippolito","sequence":"additional","affiliation":[{"name":"National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gian Luca","family":"Autorino","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, via Appia Nuova 1411, 00178 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9819-236X","authenticated-orcid":false,"given":"Concetta","family":"Castilletti","sequence":"additional","affiliation":[{"name":"National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2018,10,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nrmicro1099","article-title":"Poxvirus tropism","volume":"3","author":"McFadden","year":"2005","journal-title":"Nat. Rev. Micro."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1007\/s11262-016-1388-9","article-title":"The genomes of three North American orthopoxviruses","volume":"53","author":"Smithson","year":"2017","journal-title":"Virus Genes"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Carroll, D.S., Emerson, G.L., Li, Y., Sammons, S., Olson, V., Frace, M., Nakazawa, Y., Czerny, C.P., and Tryland, M. (2011). Chasing Jenner\u2019s Vaccine: Revisiting Cowpox Virus Classification. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0023086"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.coviro.2017.11.012","article-title":"Understanding orthopoxvirus host range and evolution: from the enigmatic to the usual suspects","volume":"28","author":"Reynolds","year":"2018","journal-title":"Curr. Opin. Virol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Mauldin, M., Antwerpen, M., Emerson, G., Li, Y., Zoeller, G., Carroll, D., and Meyer, H. (2017). Cowpox virus: What\u2019s in a Name?. Viruses, 9.","DOI":"10.3390\/v9050101"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1126\/science.1125134","article-title":"Genome Sequence Diversity and Clues to the Evolution of Variola (Smallpox) Virus","volume":"313","author":"Esposito","year":"2006","journal-title":"Science"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"a010199","DOI":"10.1101\/cshperspect.a010199","article-title":"Poxvirus DNA Replication","volume":"5","author":"Moss","year":"2013","journal-title":"Cold Spr. Harbor Persp. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1933","DOI":"10.3390\/v2091933","article-title":"Orthopoxvirus Genome Evolution: The Role of Gene Loss","volume":"2","author":"Hendrickson","year":"2010","journal-title":"Viruses"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.virusres.2006.01.016","article-title":"Poxviruses: past, present and future","volume":"117","author":"Lefkowitz","year":"2006","journal-title":"Virus Res."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1038\/sj.icb.7100033","article-title":"Immunopathogenesis of poxvirus infections: forecasting the impending storm","volume":"85","author":"Stanford","year":"2007","journal-title":"Immunol. Cell Biol."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Bratke, K.A., and McLysaght, A. (2008). Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach. BMC Evolut. Biol., 8.","DOI":"10.1186\/1471-2148-8-67"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"15655","DOI":"10.1073\/pnas.2136653100","article-title":"Extensive gene gain associated with adaptive evolution of poxviruses","volume":"100","author":"McLysaght","year":"2003","journal-title":"Proc. Nat. Acad. Sci. USA"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1016\/j.meegid.2012.12.002","article-title":"A survey of host range genes in poxvirus genomes","volume":"14","author":"Bratke","year":"2013","journal-title":"Infect. Genet. Evol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1016\/j.meegid.2009.10.001","article-title":"The evolutionary biology of poxviruses","volume":"10","author":"Hughes","year":"2010","journal-title":"Infect. Genet. Evol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1016\/j.virol.2014.06.010","article-title":"The genome sequence of ectromelia virus Naval and Cornell isolates from outbreaks in North America","volume":"462\u2013463","author":"Mavian","year":"2014","journal-title":"Virology"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Franke, A., Ulrich, R., Weber, S., Osterrieder, N., Keller, M., Hoffmann, D., and Beer, M. (2017). Experimental Cowpox Virus (CPXV) Infections of Bank Voles: Exceptional Clinical Resistance and Variable Reservoir Competence. Viruses, 9.","DOI":"10.3390\/v9120391"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Dabrowski, P.W., Radoni\u0107, A., Kurth, A., and Nitsche, A. (2013). Genome-Wide Comparison of Cowpox Viruses Reveals a New Clade Related to Variola Virus. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0079953"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Franke, A., Pfaff, F., Jenckel, M., Hoffmann, B., H\u00f6per, D., Antwerpen, M., Meyer, H., Beer, M., and Hoffmann, D. (2017). Classification of Cowpox Viruses into Several Distinct Clades and Identification of a Novel Lineage. Viruses, 9.","DOI":"10.3390\/v9060142"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"10959","DOI":"10.1128\/JVI.01195-15","article-title":"Out of the Reservoir: Phenotypic and Genotypic Characterization of a Novel Cowpox Virus Isolated from a Common Vole","volume":"89","author":"Hoffmann","year":"2015","journal-title":"J. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"670","DOI":"10.3201\/eid1404.070817","article-title":"Rat-to-Elephant-to-Human Transmission of Cowpox Virus","volume":"14","author":"Kurth","year":"2008","journal-title":"Emer. Infect. Dis."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Stagegaard, J., Kurth, A., Stern, D., Dabrowski, P.W., Pocknell, A., Nitsche, A., and Schrick, L. (2017). Seasonal recurrence of cowpox virus outbreaks in captive cheetahs (Acinonyx jubatus). PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0187089"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Prkno, A., Hoffmann, D., Goerigk, D., Kaiser, M., van Maanen, A., Jeske, K., Jenckel, M., Pfaff, F., Vahlenkamp, T., and Beer, M. (2017). Epidemiological Investigations of Four Cowpox Virus Outbreaks in Alpaca Herds, Germany. Viruses, 9.","DOI":"10.3390\/v9110344"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.1093\/cid\/cix219","article-title":"Novel Orthopoxvirus Infection in an Alaska Resident","volume":"64","author":"Springer","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Gao, J., Gigante, C., Khmaladze, E., Liu, P., Tang, S., Wilkins, K., Zhao, K., Davidson, W., Nakazawa, Y., and Maghlakelidze, G. (2018). Genome Sequences of Akhmeta Virus, an Early Divergent Old World Orthopoxvirus. Viruses, 10.","DOI":"10.3390\/v10050252"},{"key":"ref_25","first-page":"454","article-title":"Feline Poxvirus Infection: A case report","volume":"139","author":"Canese","year":"1997","journal-title":"Schweiz. Arch. Tierheilkd."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1177\/1040638715614604","article-title":"Evidence of zoonotic Poxviridae coinfections in clinically diagnosed papillomas using a newly developed mini-array test","volume":"28","author":"Scagliarini","year":"2016","journal-title":"J. Vet. Diag. Invest."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Cardeti, G., Brozzi, A., Eleni, C., Polici, N., D\u2019Alterio, G., Carletti, F., Scicluna, M.T., Castilletti, C., di Caro, A., and Autorino, G.L. (2011). Cowpox Virus in Llama, Italy. Emer. Infect. Dis.","DOI":"10.3201\/eid1708.101912"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"499","DOI":"10.3201\/eid1503.080813","article-title":"Cat-to-Human Orthopoxvirus Transmission, Northeastern Italy","volume":"15","author":"Carletti","year":"2009","journal-title":"Emer. Infect. Dis."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1941","DOI":"10.3201\/eid2312.162098","article-title":"Fatal Outbreak in Tonkean Macaques Caused by Possibly Novel Orthopoxvirus, Italy, January 20151","volume":"23","author":"Cardeti","year":"2017","journal-title":"Emer. Infect. Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1111\/zph.12459","article-title":"Occupational transmission of an Orthopoxvirus infection during an outbreak in a colony of Macaca. tonkeana in Lazio Region, Italy, 2015","volume":"65","author":"Puro","year":"2018","journal-title":"Zoonoses. Public Health"},{"key":"ref_31","first-page":"1665","article-title":"Novel Orthopoxvirus and Lethal Disease in Cat, Italy","volume":"24","author":"Lanave","year":"2018","journal-title":"EID"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Tausch, S.H., Renard, B.Y., Nitsche, A., and Dabrowski, P.W. (2015). RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0137896"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: Algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Gen. Res."},{"key":"ref_34","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_35","doi-asserted-by":"crossref","unstructured":"Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: architecture and applications. BMC Bioinfor., 10.","DOI":"10.1186\/1471-2105-10-421"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","article-title":"Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data","volume":"28","author":"Kearse","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_37","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_38","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucl. Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","article-title":"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models","volume":"22","author":"Stamatakis","year":"2006","journal-title":"Bioinformatics"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Emerson, G.L., Li, Y., Frace, M.A., Olsen-Rasmussen, M.A., Khristova, M.L., Govil, D., Sammons, S.A., Regnery, R.L., Karem, K.L., and Damon, I.K. (2009). The phylogenetics and ecology of the orthopoxviruses endemic to North America. PLoS ONE, 29.","DOI":"10.1371\/journal.pone.0007666"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/10\/10\/546\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T15:24:14Z","timestamp":1760196254000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/10\/10\/546"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,10,6]]},"references-count":41,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2018,10]]}},"alternative-id":["v10100546"],"URL":"https:\/\/doi.org\/10.3390\/v10100546","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,10,6]]}}}