{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T11:22:44Z","timestamp":1785410564088,"version":"3.56.0"},"posted":{"date-parts":[[2026,7,22]]},"group-title":"Evolutionary Biology","reference-count":64,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T00:00:00Z","timestamp":1784678400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["Freeman Hrabowski Scholars Program"],"award-info":[{"award-number":["Freeman Hrabowski Scholars Program"]}],"id":[{"id":"https:\/\/ror.org\/006w34k90","id-type":"ROR","asserted-by":"publisher"}]},{"award":["UM1AI64565"],"award-info":[{"award-number":["UM1AI64565"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}]},{"award":["U01AI169385"],"award-info":[{"award-number":["U01AI169385"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000875","name":"Pew Charitable Trusts","doi-asserted-by":"crossref","award":["Pew Research Scholars Program"],"award-info":[{"award-number":["Pew Research Scholars Program"]}],"id":[{"id":"10.13039\/100000875","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Many urgent medical and agricultural challenges are driven by resistance evolution via soft selective sweeps of multiple simultaneous mutations. Standard approaches to detect these mutations involve genome scans for regions with reduced diversity and increased haplotype lengths. However, it is unknown the extent to which those signatures persist as the number of mutations driving resistance grows. Here, we analyzed longitudinal linkage-resolved data from 10 intra-host HIV populations treated with broadly neutralizing antibody 10-1074. We found that HIV escapes 10-1074 with minimal perturbations to diversity and haplotype homozygosity in the region surrounding the sweep in the majority (8\/10) of treated individuals. We matched these\n                  <jats:italic>in vivo<\/jats:italic>\n                  escape trajectories to forward simulations and found that adaptive mutations conferring escape must have been present on 20 or more genetic backgrounds to generate these signatures. These \u201cultra-soft\u201d sweep signatures more closely resemble genetic patterns in a treatment non-responder without an adaptive response to 10-1074 than those of two other trial participants where adaptation occurred via harder selective sweeps. Our results demonstrate that HIV can adapt to a broadly neutralizing antibody treatment while retaining nearly all of its standing genetic diversity and that selection scans dependent on regional diversity and haplotype homozygosity signatures fail in this \u201cultra-soft\u201d regime.\n                <\/jats:p>","DOI":"10.64898\/2026.07.21.739925","type":"posted-content","created":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T03:40:16Z","timestamp":1784778016000},"source":"Crossref","is-referenced-by-count":0,"title":["Haplotype and diversity signatures of ultra-soft selective sweeps in HIV-1"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2631-3289","authenticated-orcid":false,"given":"Elena V.","family":"Romero","sequence":"first","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, WA, USA"},{"name":"Howard Hughes Medical Institute, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-5127-6234","authenticated-orcid":false,"given":"Dylan A.","family":"Clark","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3485-8692","authenticated-orcid":false,"given":"Lillian B.","family":"Cohn","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA 98109"},{"name":"Department of Global Health, University of Washington, Seattle, WA 98105"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2915-089X","authenticated-orcid":false,"given":"Alison F.","family":"Feder","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, WA, USA"},{"name":"Howard Hughes Medical Institute, Seattle, WA, USA"},{"name":"Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026072701400479000_2026.07.21.739925v1.1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.0020186"},{"key":"2026072701400479000_2026.07.21.739925v1.2","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.104.036947"},{"issue":"6","key":"2026072701400479000_2026.07.21.739925v1.3","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1111\/2041-210X.12808","article-title":"Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation","volume":"8","year":"2017","journal-title":"Methods in Ecology and 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