{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T14:36:09Z","timestamp":1786545369960,"version":"build-2736575974"},"reference-count":72,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T00:00:00Z","timestamp":1784505600000},"content-version":"vor","delay-in-days":19,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"},{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100011094","name":"Public Health Agency of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011094","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Influenza Resp Viruses"],"published-print":{"date-parts":[[2026,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>With increased transmission but reduced disease severity, the Omicron SARS\u2010CoV\u20102 variants have contributed to the multifaceted transition of COVID\u201019 from a global pandemic to an endemic disease. Nonetheless, the persistence of hypermutable viral variants and their ability to infect both vaccinated and previously infected individuals raise concerns about continued viral evolution and immune evasion.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>This study employs comprehensive in silico analyses to compare the five former variants of concern (VOCs) to elucidate their T cell antigenic variations in relation to human leukocyte antigen (HLA) recognition and binding.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Our major histocompatibility complex (MHC) class I and II epitope predictions suggest that the Omicron BA.1 variant harbors more putative epitopes than other VOCs (2.0\u201311.0 times more). Moreover, the distribution of predicted MHC\u2010II epitopes across HLA alleles differs substantially, with Omicron displaying significant differences from at least three VOCs in all analyses. Investigation of HLA\u2010epitope binding affinities indicates that Omicron epitopes often exhibit enhanced HLA binding compared with the Wuhan Reference (57.8%, 81.8%, and 60.0% of MHC\u2010I, MHC\u2010II regular, and MHC\u2010II promiscuous pairs, respectively), which could influence immune responses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>These findings reveal marked differences in the putative epitope profiles of Omicron BA.1 and the Wuhan Reference, as well as other pre\u2010Omicron VOCs, highlighting its altered HLA recognition status. Given the continued transmission and emergence of new SARS\u2010CoV\u20102 lineages, this study highlights the importance of ongoing research to understand the evolutionary dynamics of high\u2010risk SARS\u2010CoV\u20102 variants, their host immune system interactions, and the downstream implications in vaccine and therapeutic development.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1111\/irv.70286","type":"journal-article","created":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T04:19:00Z","timestamp":1784607540000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Antigenic Variation and Immune Recognition Inference From the COVID\u201019 Pandemic: An In Silico Comparative Analysis of Spike T Cell Epitopes From the SARS\u2010CoV\u20102 Variants of Concern"],"prefix":"10.1111","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9473-9612","authenticated-orcid":false,"given":"Katherine L.","family":"Li","sequence":"first","affiliation":[{"name":"National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre Public Health Agency of Canada  Winnipeg Manitoba Canada"},{"name":"Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine University of Manitoba  Winnipeg Manitoba Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Sandstrom","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre Public Health Agency of Canada  Winnipeg Manitoba Canada"},{"name":"Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine University of Manitoba  Winnipeg Manitoba Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5451-6294","authenticated-orcid":false,"given":"Hezhao","family":"Ji","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre Public Health Agency of Canada  Winnipeg Manitoba Canada"},{"name":"Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine University of Manitoba  Winnipeg Manitoba Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,20]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1002\/rmv.2381"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.3349\/YMJ.2021.62.11.961"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abg3055"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41401\u2010020\u20100485\u20104"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1222301"},{"key":"e_1_2_10_7_1","unstructured":"E. 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