{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T19:58:20Z","timestamp":1772135900091,"version":"3.50.1"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,9,19]],"date-time":"2017-09-19T00:00:00Z","timestamp":1505779200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2017,9,19]],"date-time":"2017-09-19T00:00:00Z","timestamp":1505779200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Recent history has provided us with one pandemic (Influenza A\/H1N1) and two severe viral outbreaks (Ebola and Zika). In all three cases, post-hoc analyses have given us deep insights into what triggered these outbreaks, their timing, evolutionary dynamics, and phylogeography, but the genomic characteristics of outbreak viruses are still unclear. To address this outstanding question, we searched for a common denominator between these recent outbreaks, positing that the genome of outbreak viruses is in an unstable evolutionary state, while that of non-outbreak viruses is stabilized by a network of correlated substitutions. Here, we show that during regular epidemics, viral genomes are indeed stabilized by a dense network of weakly correlated sites, and that these networks disappear during pandemics and outbreaks when rates of evolution increase transiently. Post-pandemic, these evolutionary networks are progressively re-established. We finally show that destabilization is not caused by substitutions targeting epitopes, but more likely by changes in the environment\n                    <jats:italic>sensu lato<\/jats:italic>\n                    . Our results prompt for a new interpretation of pandemics as being associated with evolutionary destabilized viruses.\n                  <\/jats:p>","DOI":"10.1038\/s41598-017-12268-9","type":"journal-article","created":{"date-parts":[[2017,9,13]],"date-time":"2017-09-13T07:44:23Z","timestamp":1505288663000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Viral outbreaks involve destabilized evolutionary networks: evidence from Ebola, Influenza and Zika"],"prefix":"10.1038","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4987-0296","authenticated-orcid":false,"given":"St\u00e9phane","family":"Aris-Brosou","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Neke","family":"Ibeh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica","family":"No\u00ebl","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,9,19]]},"reference":[{"key":"12268_CR1","doi-asserted-by":"publisher","first-page":"1122","DOI":"10.1038\/nature08182","volume":"459","author":"GJD Smith","year":"2009","unstructured":"Smith, G. J. D. et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature \n                           459, 1122\u20135 (2009).","journal-title":"Nature"},{"key":"12268_CR2","doi-asserted-by":"publisher","first-page":"1369","DOI":"10.1126\/science.1259657","volume":"345","author":"SK Gire","year":"2014","unstructured":"Gire, S. K. et al. Genomic surveillance elucidates Ebola virus origin and transmission during the outbreak. Science \n                           345, 1369\u201372 (2014).","journal-title":"Science"},{"key":"12268_CR3","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1126\/science.aaf5036","volume":"352","author":"NR Faria","year":"2016","unstructured":"Faria, N. R. et al. Zika virus in the Americas: Early epidemiological and genetic findings. 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N. & Grenfell, B. T. Measles metapopulation dynamics: a gravity model for epidemiological coupling and dynamics. Am Nat \n                           164, 267\u201381 (2004).","journal-title":"Am Nat"},{"key":"12268_CR7","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1038\/nature22040","volume":"544","author":"G Dudas","year":"2017","unstructured":"Dudas, G. et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature \n                           544, 309\u2013315 (2017).","journal-title":"Nature"},{"key":"12268_CR8","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1534\/genetics.116.193979","volume":"205","author":"JC Nshogozabahizi","year":"2017","unstructured":"Nshogozabahizi, J. C., Dench, J. & Aris-Brosou, S. Widespread historical contingency in influenza viruses. Genetics \n                           205, 409\u2013420 (2017).","journal-title":"Genetics"},{"key":"12268_CR9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0030231","volume":"3","author":"AFY Poon","year":"2007","unstructured":"Poon, A. F. Y., Lewis, F. I., Pond, S. L. K. & Frost, S. D. W. An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput Biol \n                           3, e231 (2007).","journal-title":"PLoS Comput Biol"},{"key":"12268_CR10","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.00631","volume":"2","author":"LI Gong","year":"2013","unstructured":"Gong, L. I., Suchard, M. A. & Bloom, J. D. Stability-mediated epistasis constrains the evolution of an influenza protein. 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Bioinformatics btu393 (2014).","DOI":"10.1093\/bioinformatics\/btu393"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-12268-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-12268-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-12268-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T06:08:03Z","timestamp":1671775683000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-12268-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,9,19]]},"references-count":38,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,12]]}},"alternative-id":["12268"],"URL":"https:\/\/doi.org\/10.1038\/s41598-017-12268-9","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/070102","asserted-by":"object"}]},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,9,19]]},"assertion":[{"value":"12 June 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 September 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 September 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"11881"}}