{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:42:24Z","timestamp":1791333744437,"version":"4.3.1"},"reference-count":128,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2022,2,17]],"date-time":"2022-02-17T00:00:00Z","timestamp":1645056000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus is continuously evolving, and this poses a major threat to antibody therapies and currently authorized Coronavirus Disease 2019 (COVID-19) vaccines. It is therefore of utmost importance to investigate and predict the putative mutations on the spike protein that confer immune evasion. Antibodies are key components of the human immune system\u2019s response to SARS-CoV-2, and the spike protein is a prime target of neutralizing antibodies (nAbs) as it plays critical roles in host cell recognition, fusion, and virus entry. The potency of therapeutic antibodies and vaccines partly depends on how readily the virus can escape neutralization. Recent structural and functional studies have mapped the epitope landscape of nAbs on the spike protein, which illustrates the footprints of several nAbs and the site of escape mutations. In this review, we discuss (1) the emerging SARS-CoV-2 variants; (2) the structural basis for antibody-mediated neutralization of SARS-CoV-2 and nAb classification; and (3) identification of the RBD escape mutations for several antibodies that resist antibody binding and neutralization. These escape maps are a valuable tool to predict SARS-CoV-2 fitness, and in conjunction with the structures of the spike-nAb complex, they can be utilized to facilitate the rational design of escape-resistant antibody therapeutics and vaccines.<\/jats:p>","DOI":"10.1371\/journal.ppat.1010260","type":"journal-article","created":{"date-parts":[[2022,2,17]],"date-time":"2022-02-17T18:25:56Z","timestamp":1645122356000},"page":"e1010260","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":129,"title":["Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0478-2682","authenticated-orcid":true,"given":"Anshumali","family":"Mittal","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9264-9549","authenticated-orcid":true,"given":"Arun","family":"Khattri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2371-4164","authenticated-orcid":true,"given":"Vikash","family":"Verma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,2,17]]},"reference":[{"issue":"5","key":"ppat.1010260.ref001","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1038\/s41564-019-0392-y","article-title":"Antibody responses to viral infections: a structural perspective across three different enveloped viruses.","volume":"4","author":"CD Murin","year":"2019","journal-title":"Nat Microbiol"},{"issue":"3","key":"ppat.1010260.ref002","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1038\/nrmicro2090","article-title":"The spike protein of SARS-CoV\u2014a target for vaccine and therapeutic development","volume":"7","author":"L Du","year":"2009","journal-title":"Nat Rev Microbiol"},{"issue":"3","key":"ppat.1010260.ref003","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.3390\/v6031294","article-title":"Playing hide and seek: how glycosylation of the influenza virus hemagglutinin can modulate the immune response to infection","volume":"6","author":"MD Tate","year":"2014","journal-title":"Viruses"},{"issue":"10","key":"ppat.1010260.ref004","doi-asserted-by":"crossref","first-page":"6369","DOI":"10.4049\/jimmunol.0804287","article-title":"Proximal glycans outside of the epitopes regulate the presentation of HIV-1 envelope gp120 helper epitopes","volume":"182","author":"H Li","year":"2009","journal-title":"J Immunol"},{"issue":"12","key":"ppat.1010260.ref005","doi-asserted-by":"crossref","first-page":"e1003065","DOI":"10.1371\/journal.ppat.1003065","article-title":"Antigenic subversion: a novel mechanism of host immune evasion by Ebola virus","volume":"8","author":"GS Mohan","year":"2012","journal-title":"PLoS Pathog"},{"issue":"9","key":"ppat.1010260.ref006","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1016\/S0966-842X(00)01830-8","article-title":"Viral mechanisms of immune evasion","volume":"8","author":"A Alcami","year":"2000","journal-title":"Trends Microbiol"},{"key":"ppat.1010260.ref007","article-title":"Antibody and B cell responses to SARS-CoV-2 infection and vaccination","author":"K Roltgen","year":"2021","journal-title":"Cell Host Microbe"},{"issue":"4","key":"ppat.1010260.ref008","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1038\/s41577-019-0244-2","article-title":"B cell memory: building two walls of protection against pathogens","volume":"20","author":"M Akkaya","year":"2020","journal-title":"Nat Rev Immunol"},{"issue":"4","key":"ppat.1010260.ref009","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/j.cell.2021.01.007","article-title":"Adaptive immunity to SARS-CoV-2 and COVID-19","volume":"184","author":"A Sette","year":"2021","journal-title":"Cell"},{"issue":"8","key":"ppat.1010260.ref010","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1056\/NEJMoa2001017","article-title":"A Novel Coronavirus from Patients with Pneumonia in China, 2019","volume":"382","author":"N Zhu","year":"2020","journal-title":"N Engl J Med"},{"key":"ppat.1010260.ref011","article-title":"Coronavirus Disease (COVID-19).","author":"WHO","year":"2020","journal-title":"Dashboard"},{"key":"ppat.1010260.ref012","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1038\/d41586-021-02039-y","article-title":"How the coronavirus infects cells\u2014and why Delta is so dangerous","volume":"595","author":"M. 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