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While often discussed in an ecological context, this notion is also highly relevant in our clinical understanding of viral infection, in which the novel habitat is a new host. Thus, quantifying the factors determining levels of variation is of considerable importance for the design of improved treatment strategies. Here, we focus on such a quantification of human cytomegalovirus (<jats:styled-content style=\"fixed-case\">HCMV<\/jats:styled-content>) \u2013 a virus which can be transmitted across the placenta, resulting in foetal infection that can potentially cause severe disease in multiple organs. Recent studies using genomewide sequencing data have demonstrated that viral populations in some congenitally infected infants diverge rapidly over time and between tissue compartments within individuals, while in other infants, the populations remain highly stable. Here, we investigate the underlying causes of these extreme differences in observed intrahost levels of variation by estimating the underlying demographic histories of infection. Importantly, reinfection (<jats:italic>i.e<\/jats:italic>. population admixture) appears to be an important, and previously unappreciated, player. We highlight illustrative examples likely to represent a single\u2010population transmission from a mother during pregnancy and multiple\u2010population transmissions during pregnancy and after birth.<\/jats:p>","DOI":"10.1111\/mec.13953","type":"journal-article","created":{"date-parts":[[2016,12,18]],"date-time":"2016-12-18T07:42:57Z","timestamp":1482046977000},"page":"1980-1990","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Characterizing human cytomegalovirus reinfection in congenitally infected infants: an evolutionary perspective"],"prefix":"10.1111","volume":"26","author":[{"given":"Cornelia","family":"Pokalyuk","sequence":"first","affiliation":[{"name":"Institute for Mathematics Goethe Universit\u00e4t Frankfurt Frankfurt am Main Germany"},{"name":"Faculty for Mathematics Otto\u2010von\u2010Guericke University Magdeburg Magdeburg Germany"},{"name":"School of Life Sciences \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) Lausanne Switzerland"},{"name":"Swiss Institute of Bioinformatics (SIB) Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"Renzette","sequence":"additional","affiliation":[{"name":"Swiss Institute of Bioinformatics (SIB) Lausanne Switzerland"},{"name":"Department of Microbiology and Physiological Systems University of Massachusetts Medical School Worcester MA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristen K.","family":"Irwin","sequence":"additional","affiliation":[{"name":"School of Life Sciences \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) Lausanne Switzerland"},{"name":"Swiss Institute of Bioinformatics (SIB) Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanne P.","family":"Pfeifer","sequence":"additional","affiliation":[{"name":"School of Life Sciences \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) Lausanne Switzerland"},{"name":"Swiss Institute of Bioinformatics (SIB) Lausanne Switzerland"},{"name":"School of Life Sciences Arizona State University Tempe AZ USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Gibson","sequence":"additional","affiliation":[{"name":"Departments of Medicine and Pediatrics Divisions of Infectious Diseases and Immunology University of Massachusetts Medical School Worcester MA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William J.","family":"Britt","sequence":"additional","affiliation":[{"name":"Department of Pediatrics University of Alabama Birmingham School of Medicine Birmingham AL USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aparecida Y.","family":"Yamamoto","sequence":"additional","affiliation":[{"name":"Department of Pediatrics Ribeir\u00e3o Preto Medical School University of S\u00e3o Paulo S\u00e3o Paulo 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