{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T22:25:13Z","timestamp":1790029513270,"version":"4.0.1"},"reference-count":71,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,2,4]],"date-time":"2026-02-04T00:00:00Z","timestamp":1770163200000},"content-version":"vor","delay-in-days":34,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Fred Hutch REACH (Research Equity Advancement for Cancer with HBCUs) program"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 AI146028"],"award-info":[{"award-number":["R01 AI146028"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016958","name":"ORIP","doi-asserted-by":"publisher","award":["S10OD028685"],"award-info":[{"award-number":["S10OD028685"]}],"id":[{"id":"10.13039\/100016958","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>SARS-CoV-2 has evolved increased resistance to human polyclonal antibody responses. But, how it escaped individual monoclonal antibodies from these responses has not been thoroughly explored. Cao et\u00a0al. used deep mutational scanning to identify mutations that allow SARS-CoV-2 to escape individual antibodies, doing so for hundreds of different antibodies. Here, we use these data to reconstruct how the virus escaped each antibody in nature. For each antibody, we predict how levels of escape changed in the global SARS-CoV-2 population over time. For many antibodies, these levels dramatically fluctuated due to escape mutations being displaced by clade-turnover events. We validate predicted patterns using pseudovirus neutralization data. Fitness effects estimated from natural sequences suggest that mutations are displaced due to clonal interference between clades and that the order in which mutations arose is shaped by changing selective pressures. Overall, this work suggests that SARS-CoV-2 evaded polyclonal responses via complex evolutionary dynamics.<\/jats:p>","DOI":"10.1093\/ve\/veaf104","type":"journal-article","created":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T12:41:22Z","timestamp":1767876082000},"source":"Crossref","is-referenced-by-count":2,"title":["Clonal interference and changing selective pressures shape the escape of SARS-CoV-2 from hundreds of antibodies"],"prefix":"10.1093","volume":"12","author":[{"given":"Hugh K","family":"Haddox","sequence":"first","affiliation":[{"name":"Computational Biology Program, Fred Hutchinson Cancer Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Omar","family":"Abdel Aziz","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Fred Hutchinson Cancer Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jared G","family":"Galloway","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Fred Hutchinson Cancer Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Javen","family":"Kent","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Fred Hutchinson Cancer Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]},{"name":"Morehouse College , 830 Westview Dr SW, Atlanta, GA 30314 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cameron R","family":"Cooper","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Fred Hutchinson Cancer Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]},{"name":"Morehouse College , 830 Westview Dr SW, Atlanta, GA 30314 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chris","family":"Jennings-Shaffer","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Fred Hutchinson Cancer Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Will","family":"Dumm","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Fred Hutchinson Cancer Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seth D","family":"Temple","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Fred Hutchinson Cancer Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]},{"name":"Department of Statistics, University of Washington , 1410 NE Campus Pkwy, Seattle, WA 98195 ,","place":["United States"]},{"name":"Department of Statistics, University of Michigan , 1085 S University Ave, Ann Arbor, MI 48109 ,","place":["United States"]},{"name":"Michigan Institute for Data & AI in Society, University of Michigan , 500 Church Street, Ann Arbor, MI 48109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jesse D","family":"Bloom","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Fred Hutchinson Cancer Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]},{"name":"Basic Sciences Division, Fred Hutchinson Cancer Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]},{"name":"Howard Hughes Medical Institute , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"IV","given":"Frederick A","family":"Matsen","sequence":"additional","affiliation":[{"name":"Computational Biology Program, Fred Hutchinson Cancer Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]},{"name":"Department of Statistics, University of Washington , 1410 NE Campus Pkwy, Seattle, WA 98195 ,","place":["United States"]},{"name":"Howard Hughes Medical Institute , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["United States"]},{"name":"Department of Genome Sciences, University of Washington , 3720 15th Ave NE, Seattle, WA 98195 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,2,4]]},"reference":[{"key":"2026081406565980900_ref1","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1038\/s41586-023-06487-6","article-title":"Neutralization, effector function and immune imprinting of omicron variants","volume":"621","author":"Addetia","year":"2023","journal-title":"Nature"},{"key":"2026081406565980900_ref2","doi-asserted-by":"crossref","article-title":"Deep mutational scanning of rabies glycoprotein defines 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