{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T20:52:09Z","timestamp":1792443129282,"version":"4.5.0"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,12,10]],"date-time":"2025-12-10T00:00:00Z","timestamp":1765324800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["313694\/Z\/24\/Z"],"award-info":[{"award-number":["313694\/Z\/24\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["206298\/Z\/17\/Z"],"award-info":[{"award-number":["206298\/Z\/17\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>High numbers of reported mpox cases and recent identification of multiple sustained human outbreaks of mpox virus (MPXV) have highlighted the need for robust, best-practice genomic surveillance tools. In light of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, many labs across the globe developed the capacity to do virus genome sequencing; however, MPXV presents additional analytical challenges due to its large genome size, tracts of low-complexity or repeat regions, genetically distinct clades, and the need to perform bespoke apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3)-mutation reconstruction. We present squirrel (Some Quick Reconstruction to Resolve Evolutionary Links), an open source bioinformatic tool that can perform clade-aware alignment, mutation quality assessment, phylogenetic inference, and automated APOBEC3-mutation classification on branches of the phylogeny. Squirrel can be run on the command line or launched through the EPI2ME graphical user interface through the squirrel-nf workflow, enabling robust analysis without need for the command line. With the interactive output report produced and publication-ready APOBEC3-reconstruction visualization, squirrel enables researchers to distinguish between zoonotic and sustained human outbreaks and help accurately inform public health responses.<\/jats:p>","DOI":"10.1093\/ve\/veaf095","type":"journal-article","created":{"date-parts":[[2025,12,10]],"date-time":"2025-12-10T13:16:17Z","timestamp":1765372577000},"source":"Crossref","is-referenced-by-count":8,"title":["Human outbreak detection and best practice MPXV analysis and interpretation with squirrel"],"prefix":"10.1093","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8083-474X","authenticated-orcid":false,"given":"\u00c1ine","family":"O\u2019Toole","sequence":"first","affiliation":[{"name":"Institute of Ecology & Evolution, University of Edinburgh , Edinburgh, EH93FL ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eddy","family":"Kinganda-Lusamaki","sequence":"additional","affiliation":[{"name":"Institut National de Recherche Biom\u00e9dicale , Kinshasa, P.O. 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Box 127,","place":["Democratic Republic of the Congo"]},{"name":"TransVIHMI, Universit\u00e9 de Montpellier, INSERM, IRD , Montpellier 34394 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Colquhoun","sequence":"additional","affiliation":[{"name":"Institute of Ecology & Evolution, University of Edinburgh , Edinburgh, EH93FL ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Connor","family":"Chato","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada , Winnipeg, MB R3E 3M4 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"Scher","sequence":"additional","affiliation":[{"name":"Institute of Ecology & Evolution, University of Edinburgh , Edinburgh, EH93FL ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4269-0153","authenticated-orcid":false,"given":"Chris","family":"Kent","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Infection, University of Birmingham , B15 2TT ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sam","family":"Wilkinson","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Infection, University of Birmingham , B15 2TT ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"Quick","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Infection, University of Birmingham , B15 2TT ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"Loman","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Infection, University of Birmingham , B15 2TT ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2582-2954","authenticated-orcid":false,"given":"Ana T","family":"Duggan","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada , Winnipeg, MB R3E 3M4 ,","place":["Canada"]},{"name":"McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University , Hamilton , L8S 4L9,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Placide","family":"Mbala","sequence":"additional","affiliation":[{"name":"Institut National de Recherche Biom\u00e9dicale , Kinshasa, P.O. 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