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We sequenced 699 isolates, primarily\n                    <jats:italic>C. neoformans<\/jats:italic>\n                    from HIV-infected patients, from 5 countries in Asia and Africa. The phylogeny of\n                    <jats:italic>C. neoformans<\/jats:italic>\n                    reveals a recent exponential population expansion, consistent with the increase in the number of susceptible hosts. In our study population, this expansion has been driven by three sub-clades of the\n                    <jats:italic>C. neoformans<\/jats:italic>\n                    VNIa lineage; VNIa-4, VNIa-5 and VNIa-93. These three sub-clades account for 91% of clinical isolates sequenced in our study. Combining the genome data with clinical information, we find that the VNIa-93 sub-clade, the most common sub-clade in Uganda and Malawi, was associated with better outcomes than VNIa-4 and VNIa-5, which predominate in Southeast\u00a0Asia. This study lays the foundation for further work investigating the dominance of VNIa-4, VNIa-5 and VNIa-93 and the association between lineage and clinical phenotype.\n                  <\/jats:p>","DOI":"10.1038\/s41467-019-10092-5","type":"journal-article","created":{"date-parts":[[2019,5,2]],"date-time":"2019-05-02T06:04:37Z","timestamp":1556777077000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":63,"title":["Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans"],"prefix":"10.1038","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1545-9661","authenticated-orcid":false,"given":"P. M.","family":"Ashton","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L. T.","family":"Thanh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P. 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