title: 17thCentury Variola Virus Reveals the Recent History of Smallpox.
abstract: Smallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there have been claims of smallpox in Egypt, India, and China dating back millennia [1-4], the timescale of emergence of the causative agent, variola virus (VARV), and how it evolved in the context of increasingly widespread immunization, have proven controversial [4-9]. In particular, some molecular-clock-based studies have suggested that key events in VARV evolution only occurred during the last two centuries [4-6] and hence in apparent conflict with anecdotal historical reports, although it is difficult to distinguish smallpox from other pustular rashes by description alone. To address these issues, we captured, sequenced, and reconstructed a draft genome of an ancient strain of VARV, sampled from a Lithuanian child mummy dating between 1643 and 1665 and close to the time of several documented European epidemics [1, 2, 10]. When compared to vaccinia virus, this archival strain contained the same pattern of gene degradation as 20thcentury VARVs, indicating that such loss of gene function had occurred before ca. 1650. Strikingly, the mummy sequence fell basal to all currently sequenced strains of VARV on phylogenetic trees. Molecular-clock analyses revealed a strong clock-like structure and that the timescale of smallpox evolution is more recent than often supposed, with the diversification of major viral lineages only occurring within the 18thand 19thcenturies, concomitant with the development of modern vaccination.
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada. Electronic address: duggana@mcmaster.ca.
authors.forename: Ana T
authors.initials: AT
authors.lastname: Duggan
authors.affiliation: Department of Virology, University of Helsinki, Helsinki 00014, Finland.
authors.forename: Maria F
authors.initials: MF
authors.lastname: Perdomo
authors.affiliation: Department of Anatomy, Histology, and Anthropology, Faculty of Medicine, Vilnius University, Vilnius 03101, Lithuania.
authors.forename: Dario
authors.initials: D
authors.lastname: Piombino-Mascali
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Marciniak
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada.
authors.forename: Debi
authors.initials: D
authors.lastname: Poinar
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada.
authors.forename: Matthew V
authors.initials: MV
authors.lastname: Emery
authors.affiliation: 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 2145, Australia.
authors.forename: Jan P
authors.initials: JP
authors.lastname: Buchmann
authors.affiliation: 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 2145, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Duchêne
authors.affiliation: Department of Anatomy, Histology, and Anthropology, Faculty of Medicine, Vilnius University, Vilnius 03101, Lithuania.
authors.forename: Rimantas
authors.initials: R
authors.lastname: Jankauskas
authors.affiliation: Department of History, Duke University, Durham, NC 27708-0719, USA.
authors.forename: Margaret
authors.initials: M
authors.lastname: Humphreys
authors.affiliation: Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada.
authors.forename: G Brian
authors.initials: GB
authors.lastname: Golding
authors.affiliation: Keck Carbon Cycle Accelerator Mass Spectrometer, Earth Systems Science Department, University of California, Irvine, CA 92697-3100, USA.
authors.forename: John
authors.initials: J
authors.lastname: Southon
authors.affiliation: MYcroarray, Ann Arbor, MI 48105, USA.
authors.forename: Alison
authors.initials: A
authors.lastname: Devault
authors.affiliation: MYcroarray, Ann Arbor, MI 48105, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2136, USA.
authors.forename: Jean-Marie
authors.initials: JM
authors.lastname: Rouillard
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
authors.forename: Jason W
authors.initials: JW
authors.lastname: Sahl
authors.affiliation: Laboratoire d'Anthropologie Biologique Paul Broca, Ecole Pratique des Hautes Etudes, PSL Research University, Paris 75014, France; PACEA, CNRS, Université de Bordeaux, Pessac 33615, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Dutour
authors.affiliation: Department of Virology, University of Helsinki, Helsinki 00014, Finland; Helsinki University Hospital, Helsinki 00029, Finland.
authors.forename: Klaus
authors.initials: K
authors.lastname: Hedman
authors.affiliation: Department of Forensic Medicine, University of Helsinki, Helsinki 00014, Finland.
authors.forename: Antti
authors.initials: A
authors.lastname: Sajantila
authors.affiliation: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.
authors.forename: Geoffrey L
authors.initials: GL
authors.lastname: Smith
authors.affiliation: 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 2145, Australia. Electronic address: edward.holmes@sydney.edu.au.
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada. Electronic address: poinarh@mcmaster.ca.
authors.forename: Hendrik N
authors.initials: HN
authors.lastname: Poinar
mesh_terms: D002675:Child, Preschool; D004279:DNA, Viral / Q000235:genetics* / Q000302:isolation & purification; D019143:Evolution, Molecular; D016679:Genome, Viral; D049670:History, 17th Century; D049671:History, 18th Century; D049672:History, 19th Century; D049673:History, 20th Century; D049674:History, 21st Century; D006801:Humans; D009106:Mummies / Q000266:history / Q000821:virology; D010802:Phylogeny; D012899:Smallpox / Q000266:history* / Q000821:virology; D012900:Smallpox Vaccine / Q000266:history; D014611:Vaccination / Q000266:history; D012901:Variola virus / Q000235:genetics*
chemical_list: D004279:DNA, Viral; D012900:Smallpox Vaccine
keywords: Lithuanian Mummy Project; ancient DNA; evolution; molecular clock; phylogeny; smallpox; variola virus