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Most enteroviruses are easy to isolate in cell culture, and many non\u2010polio enterovirus strains were archived worldwide as a byproduct of the WHO poliovirus surveillance system. Common outbreaks and epidemics, most prominently the epidemic of hand\u2010foot\u2010and\u2010mouth disease with severe neurological complications in East and South\u2010East Asia, justify practical interest of non\u2010polio enteroviruses. As a result, there are over 50\u00a0000 enterovirus nucleotide sequences available in GenBank. Technical possibilities have been also improving, as Bayesian phylogenetic methods with an integrated molecular clock were introduced a decade ago and provided unprecedented opportunities for phylogenetic analysis. As a result, hundreds of papers were published on the molecular epidemiology of enteroviruses. This review covers the modern methodology, structure, and biases of the sequence dataset available in GenBank. The relevance of the subtype classification, findings of co\u2010circulation of multiple genetic variants, previously unappreciated complexity of viral populations, and global evolutionary patterns are addressed. The most relevant conclusions and prospects for further studies on outbreak emergence mechanisms are discussed.<\/jats:p>","DOI":"10.1002\/rmv.2002","type":"journal-article","created":{"date-parts":[[2018,8,3]],"date-time":"2018-08-03T14:09:59Z","timestamp":1533305399000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":40,"title":["Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees?"],"prefix":"10.1002","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7365-0352","authenticated-orcid":false,"given":"Alexander N.","family":"Lukashev","sequence":"first","affiliation":[{"name":"Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases Sechenov University  Moscow Russia"},{"name":"Chumakov Federal Scientific Center for Research and Development of Immune\u2010and\u2010Biological Preparations  Moscow Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yulia A.","family":"Vakulenko","sequence":"additional","affiliation":[{"name":"Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases Sechenov University  Moscow Russia"},{"name":"Virology Department, Biological Faculty Lomonosov Moscow State University  Moscow Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia A.","family":"Turbabina","sequence":"additional","affiliation":[{"name":"Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases Sechenov University  Moscow Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrei A.","family":"Deviatkin","sequence":"additional","affiliation":[{"name":"Institute of Molecular Medicine Sechenov University  Moscow Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan Felix","family":"Drexler","sequence":"additional","affiliation":[{"name":"Charit\u00e9\u2010Universit\u00e4tsmedizin Berlin, Corporate Member of Freie Universit\u00e4t Berlin, Humboldt\u2010Universit\u00e4t zu Berlin, and Berlin Institute of Health Institute of Virology  Berlin Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2018,8]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2012.10.016"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00653-06"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0181234"},{"issue":"8","key":"e_1_2_6_5_1","doi-asserted-by":"crossref","first-page":"2873","DOI":"10.1128\/JCM.38.8.2873-2877.2000","article-title":"Enteric virus infections and diarrhea in healthy and human immunodeficiency virus\u2010infected children","volume":"38","author":"Liste MB","year":"2000","journal-title":"J Clin Microbiol"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.23284"},{"key":"e_1_2_6_7_1","first-page":"1988","volume-title":"41st World Health Assembly","author":"WHA"},{"key":"e_1_2_6_8_1","first-page":"692","article-title":"Status of the global laboratory network for poliomyelitis eradication, 1994\u20101996","volume":"46","author":"Centers for Disease C, Prevention","year":"1997","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1099\/jgv.0.000911"},{"key":"e_1_2_6_10_1","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.008540-0"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1007\/s705-002-8307-2"},{"key":"e_1_2_6_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.coviro.2012.02.009"},{"key":"e_1_2_6_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2008.04.009"},{"key":"e_1_2_6_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0168-1702(02)00291-5"},{"key":"e_1_2_6_15_1","first-page":"855","volume-title":"Virus Taxonomy. 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