{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T13:33:43Z","timestamp":1768484023414,"version":"3.49.0"},"posted":{"date-parts":[[2019,9,11]]},"group-title":"Genomics","reference-count":11,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2019,9,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Despite the Zika virus\u2019 rapid spread throughout the Americas in 2015, its phylogenetic classification is limited to either an \u2018African\u2019 or \u2018Asian\u2019 genotype. This classification no longer reflects the present genetic diversity of circulating strains and their geographic reach. Using 414 publicly available Zika virus genomes from 40 different countries, we created alignments of different genomic fragments with high phylogenetic signal and used these to construct multiple maximum likelihood trees (IQTree). We observed groups of strains from three major geographic regions that consistently cluster into monophyletic clades: African (AF), Asian (AS) and American (AM), the latter of which cluster into four further sub-clades: Caribbean (C), South American (SA1 and SA2) and Central American (CA). The inter-genetic distances of these clades are all significantly greater than their intra-genetic distances (p=0.05). A decision demonstrates that only five nucleotide positions are needed to correctly classify 90% of our dataset into the newly described genotypes.<\/jats:p>","DOI":"10.1101\/760066","type":"posted-content","created":{"date-parts":[[2019,9,11]],"date-time":"2019-09-11T17:05:50Z","timestamp":1568221550000},"source":"Crossref","is-referenced-by-count":0,"title":["An updated genotype classification system for Zika viruses"],"prefix":"10.64898","author":[{"given":"Hanna","family":"Nebenzahl-Guimaraes","sequence":"first","affiliation":[]},{"given":"Pieter","family":"Libin","sequence":"additional","affiliation":[]},{"given":"Victor","family":"Pimentel","sequence":"additional","affiliation":[]},{"given":"Marta","family":"Pingarilho","sequence":"additional","affiliation":[]},{"given":"Kristof","family":"Theys","sequence":"additional","affiliation":[]},{"given":"Ana B.","family":"Abecasis","sequence":"additional","affiliation":[]}],"member":"54368","reference":[{"key":"2019091303545208000_760066v1.1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMp1600297"},{"key":"2019091303545208000_760066v1.2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00496"},{"key":"2019091303545208000_760066v1.3","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.01640"},{"key":"2019091303545208000_760066v1.4","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1111\/2041-210X.12299","article-title":"Split diversity in constrained conservation prioritization using integer linear programming","volume":"6","year":"2015","journal-title":"Methods Ecol. Evol."},{"key":"2019091303545208000_760066v1.5","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a025664"},{"issue":"10","key":"2019091303545208000_760066v1.6","doi-asserted-by":"crossref","first-page":"1763","DOI":"10.1093\/bioinformatics\/bty851","article-title":"VIRULIGN: fast codon-correct alignment and annotation of viral genomes","volume":"35","year":"2019","journal-title":"Bioinformatics"},{"key":"2019091303545208000_760066v1.7","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msu300"},{"key":"2019091303545208000_760066v1.8","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx281"},{"key":"2019091303545208000_760066v1.9","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msy096"},{"issue":"9","key":"2019091303545208000_760066v1.10","doi-asserted-by":"crossref","first-page":"e1006528","DOI":"10.1371\/journal.ppat.1006528","article-title":"Zika genomics urgently need standardized and curated reference sequences","volume":"13","year":"2017","journal-title":"PLoS Pathog"},{"key":"2019091303545208000_760066v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/nature07390"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/760066","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T23:31:56Z","timestamp":1768433516000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/760066"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9,11]]},"references-count":11,"URL":"https:\/\/doi.org\/10.1101\/760066","relation":{},"subject":[],"published":{"date-parts":[[2019,9,11]]},"subtype":"preprint"}}