{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T14:58:44Z","timestamp":1790521124235,"version":"4.1.0"},"reference-count":14,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2017,9,28]],"date-time":"2017-09-28T00:00:00Z","timestamp":1506556800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Health and Medical Research Council Australia","award":["GNT1065106"],"award-info":[{"award-number":["GNT1065106"]}]},{"name":"National Health and Medical Research Council Australia","award":["GNT1037231"],"award-info":[{"award-number":["GNT1037231"]}]},{"name":"National Sciences and Engineering Research Council of Canada","award":["Canada Research Chair"],"award-info":[{"award-number":["Canada Research Chair"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The complete genome sequences of two strains of variola virus (VARV) sampled from human smallpox specimens present in the Czech National Museum, Prague, were recently determined, with one of the sequences estimated to date to the mid-19th century. Using molecular clock methods, the authors of this study go on to infer that the currently available strains of VARV share an older common ancestor, at around 1350 AD, than some recent estimates based on other archival human samples. Herein, we show that the two Czech strains exhibit anomalous branch lengths given their proposed age, and by assuming a constant rate of evolutionary change across the rest of the VARV phylogeny estimate that their true age in fact lies between 1918 and 1937. We therefore suggest that the age of the common ancestor of currently available VARV genomes most likely dates to late 16th and early 17th centuries and not ~1350 AD.<\/jats:p>","DOI":"10.3390\/v9100276","type":"journal-article","created":{"date-parts":[[2017,9,28]],"date-time":"2017-09-28T11:22:44Z","timestamp":1506597764000},"page":"276","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum"],"prefix":"10.3390","volume":"9","author":[{"given":"Ashleigh","family":"Porter","sequence":"first","affiliation":[{"name":"Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Duggan","sequence":"additional","affiliation":[{"name":"McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0314-4160","authenticated-orcid":false,"given":"Hendrik","family":"Poinar","sequence":"additional","affiliation":[{"name":"McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada"},{"name":"Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry, McMaster University, Hamilton, ON L8S 4L8, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9596-3552","authenticated-orcid":false,"given":"Edward","family":"Holmes","sequence":"additional","affiliation":[{"name":"Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2017,9,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Pajer, P., Dresler, J., Kab\u00edckova, H., P\u00edsa, L., Aganov, P., Fucik, K., Elleder, D., Hron, T., Kuzelka, V., and Velem\u00ednsky, P. (2017). Characterization of Two Historic Smallpox Specimens from a Czech Museum. Viruses, 9.","DOI":"10.3390\/v9080200"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.cub.2016.10.061","article-title":"17th Century Variola Virus Reveals the Recent History of Smallpox","volume":"26","author":"Duggan","year":"2016","journal-title":"Curr. Biol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Smithson, C., Imbery, J., and Upton, C. (2017). Re-Assembly and Analysis of an Ancient Variola Virus Genome. Viruses, 9.","DOI":"10.3390\/v9090253"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1146\/annurev.ea.13.050185.001325","article-title":"Amino-acid racemization dating of fossil bones","volume":"13","author":"Bada","year":"1985","journal-title":"Annu. Rev. Earth Planet. Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1021\/jo00395a001","article-title":"Factors affecting the rate of racemization of amino acids and their significance to geochronology","volume":"43","author":"Smith","year":"1978","journal-title":"J. Org. Chem."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.3390\/v7031100","article-title":"The origin of the variola virus","volume":"7","author":"Babkin","year":"2015","journal-title":"Viruses"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"15787","DOI":"10.1073\/pnas.0609268104","article-title":"On the origin of smallpox: Correlating variola phylogenics with historical smallpox records","volume":"104","author":"Li","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1093\/molbev\/mss075","article-title":"Bayesian Phylogenetics with BEAUti and the BEAST 1.7","volume":"29","author":"Drummond","year":"2012","journal-title":"Mol. Biol. Evolut."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"12129","DOI":"10.1128\/JVI.01523-09","article-title":"The Origin and Phylodynamics of Rabbit Hemorrhagic Disease virus","volume":"83","author":"Kerr","year":"2009","journal-title":"J. Virol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Wertheim, J.O. (2010). The re-emergence of H1N1 influenza virus in 1977: A cautionary tale for estimating divergence times using biologically unrealistic sampling dates. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0011184"},{"key":"ref_11","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_12","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1080\/10635150701472164","article-title":"Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments","volume":"56","author":"Talavera","year":"2007","journal-title":"Syst. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evolut."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/9\/10\/276\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T18:46:09Z","timestamp":1760208369000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/9\/10\/276"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,9,28]]},"references-count":14,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2017,10]]}},"alternative-id":["v9100276"],"URL":"https:\/\/doi.org\/10.3390\/v9100276","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,9,28]]}}}