{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,12]],"date-time":"2026-11-12T03:35:13Z","timestamp":1794454513592,"version":"4.9.1"},"reference-count":211,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2023,1,18]],"date-time":"2023-01-18T00:00:00Z","timestamp":1674000000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,1,18]],"date-time":"2023-01-18T00:00:00Z","timestamp":1674000000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Rev Microbiol"],"DOI":"10.1038\/s41579-022-00841-7","type":"journal-article","created":{"date-parts":[[2023,1,18]],"date-time":"2023-01-18T07:03:04Z","timestamp":1674025384000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":611,"title":["SARS-CoV-2 variant biology: immune escape, transmission and fitness"],"prefix":"10.1038","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3625-4021","authenticated-orcid":false,"given":"Alessandro M.","family":"Carabelli","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas P.","family":"Peacock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucy G.","family":"Thorne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9529-1127","authenticated-orcid":false,"given":"William T.","family":"Harvey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2556-2563","authenticated-orcid":false,"given":"Joseph","family":"Hughes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"COVID-19 Genomics UK Consortium","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thushan I.","family":"de Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1718-2782","authenticated-orcid":false,"given":"Sharon J.","family":"Peacock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wendy S.","family":"Barclay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thushan I.","family":"de Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Greg J.","family":"Towers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6338-0221","authenticated-orcid":false,"given":"David L.","family":"Robertson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,1,18]]},"reference":[{"key":"841_CR1","unstructured":"World Health Organization. https:\/\/www.who.int\/news\/item\/05-05-2022-14.9-million-excess-deaths-were-associated-with-the-covid-19-pandemic-in-2020-and-2021WHO (2022)."},{"key":"841_CR2","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1038\/s41564-020-0695-z","volume":"5","author":"AE Gorbalenya","year":"2020","unstructured":"Gorbalenya, A. E. et al. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 5, 536\u2013544 (2020).","journal-title":"Nat. Microbiol."},{"key":"841_CR3","doi-asserted-by":"publisher","DOI":"10.1099\/jgv.0.001584","author":"TP Peacock","year":"2021","unstructured":"Peacock, T. P., Penrice-Randal, R., Hiscox, J. A. & Barclay, W. S. SARS-CoV-2 one year on: evidence for ongoing viral adaptation. J. Gen. Virol. https:\/\/doi.org\/10.1099\/jgv.0.001584 (2021).","journal-title":"J. Gen. Virol."},{"key":"841_CR4","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-27096-9","volume":"12","author":"L Lu","year":"2021","unstructured":"Lu, L. et al. Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands. Nat. Commun. 12, 6802 (2021).","journal-title":"Nat. Commun."},{"key":"841_CR5","doi-asserted-by":"publisher","first-page":"e02101-22","DOI":"10.1128\/mbio.02101-22","volume":"13","author":"AD Marques","year":"2022","unstructured":"Marques, A. D. et al. Multiple introductions of SARS-CoV-2 Alpha and Delta variants into white-tailed deer in Pennsylvania. mBio 13, e02101-22 (2022).","journal-title":"mBio"},{"key":"841_CR6","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1038\/s41586-021-04353-x","volume":"602","author":"VL Hale","year":"2022","unstructured":"Hale, V. L. et al. SARS-CoV-2 infection in free-ranging white-tailed deer. Nature 602, 481\u2013486 (2022).","journal-title":"Nature"},{"key":"841_CR7","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2105253118","volume":"118","author":"L Bashor","year":"2021","unstructured":"Bashor, L. et al. SARS-CoV-2 evolution in animals suggests mechanisms for rapid variant selection. Proc. Natl Acad. Sci. USA 118, e2105253118 (2021).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"841_CR8","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veaa034","author":"OA MacLean","year":"2020","unstructured":"MacLean, O. A., Orton, R. J., Singer, J. B. & Robertson, D. L. No evidence for distinct types in the evolution of SARS-CoV-2. Virus Evolut. https:\/\/doi.org\/10.1093\/ve\/veaa034 (2020).","journal-title":"Virus Evolut."},{"key":"841_CR9","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1016\/j.cell.2020.11.020","volume":"184","author":"E Volz","year":"2021","unstructured":"Volz, E. et al. Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity. Cell 184, 64\u201375.e11 (2021).","journal-title":"Cell"},{"key":"841_CR10","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1186\/s12864-022-08358-2","volume":"23","author":"\u00c1 O\u2019Toole","year":"2022","unstructured":"O\u2019Toole, \u00c1., Pybus, O. G., Abram, M. E., Kelly, E. J. & Rambaut, A. Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences. BMC Genom. 23, 121\u2013121 (2022).","journal-title":"BMC Genom."},{"key":"841_CR11","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1038\/s41579-021-00573-0","volume":"19","author":"WT Harvey","year":"2021","unstructured":"Harvey, W. T. et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat. Rev. Microbiol. 19, 409\u2013424 (2021).","journal-title":"Nat. Rev. Microbiol."},{"key":"841_CR12","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1126\/science.1059026","volume":"292","author":"ME Woolhouse","year":"2001","unstructured":"Woolhouse, M. E., Taylor, L. H. & Haydon, D. T. Population biology of multihost pathogens. Science 292, 1109\u20131112 (2001).","journal-title":"Science"},{"key":"841_CR13","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1128\/MMBR.00004-08","volume":"72","author":"CR Parrish","year":"2008","unstructured":"Parrish, C. R. et al. Cross-species virus transmission and the emergence of new epidemic diseases. Microbiol. Mol. Biol. Rev. 72, 457\u2013470 (2008).","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"841_CR14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3001115","volume":"19","author":"OA MacLean","year":"2021","unstructured":"MacLean, O. A. et al. Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen. PLoS Biol. 19, e3001115 (2021).","journal-title":"PLoS Biol."},{"key":"841_CR15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3001016","volume":"18","author":"C Conceicao","year":"2020","unstructured":"Conceicao, C. et al. The SARS-CoV-2 spike protein has a broad tropism for mammalian ACE2 proteins. PLoS Biol. 18, e3001016 (2020).","journal-title":"PLoS Biol."},{"key":"841_CR16","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-26809-4","volume":"12","author":"D Delaune","year":"2021","unstructured":"Delaune, D. et al. A novel SARS-CoV-2 related coronavirus in bats from Cambodia. Nat. Commun. 12, 6563 (2021).","journal-title":"Nat. Commun."},{"key":"841_CR17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.virol.2017.03.019","volume":"507","author":"XD Lin","year":"2017","unstructured":"Lin, X. D. et al. Extensive diversity of coronaviruses in bats from China. Virology 507, 1\u201310 (2017).","journal-title":"Virology"},{"key":"841_CR18","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1038\/s41586-022-04464-z","volume":"603","author":"TN Starr","year":"2022","unstructured":"Starr, T. N. et al. ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. Nature 603, 913\u2013918 (2022).","journal-title":"Nature"},{"key":"841_CR19","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1038\/s41564-021-00908-w","volume":"6","author":"TP Peacock","year":"2021","unstructured":"Peacock, T. P. et al. The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets. Nat. Microbiol. 6, 899\u2013909 (2021).","journal-title":"Nat. Microbiol."},{"key":"841_CR20","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1016\/j.cell.2020.02.052","volume":"181","author":"M Hoffmann","year":"2020","unstructured":"Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271\u2013280.e8 (2020).","journal-title":"Cell"},{"key":"841_CR21","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21213-4","volume":"12","author":"Y Zhu","year":"2021","unstructured":"Zhu, Y. et al. A genome-wide CRISPR screen identifies host factors that regulate SARS-CoV-2 entry. Nat. Commun. 12, 961 (2021).","journal-title":"Nat. Commun."},{"key":"841_CR22","doi-asserted-by":"publisher","unstructured":"Peacock, T. P. et al. The SARS-CoV-2 variants associated with infections in India, B.1.617, show enhanced spike cleavage by furin. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2021.05.28.446163 (2021).","DOI":"10.1101\/2021.05.28.446163"},{"key":"841_CR23","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1038\/s41586-021-03944-y","volume":"599","author":"P Mlcochova","year":"2021","unstructured":"Mlcochova, P. et al. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 599, 114\u2013119 (2021).","journal-title":"Nature"},{"key":"841_CR24","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01514-22","volume":"10","author":"B Lubinski","year":"2022","unstructured":"Lubinski, B. et al. Spike protein cleavage-activation in the context of the SARS-CoV-2 P681R mutation: an analysis from its first appearance in lineage A.23.1 identified in Uganda. Microbiol. Spectr. 10, e0151422 (2022).","journal-title":"Microbiol. Spectr."},{"key":"841_CR25","doi-asserted-by":"publisher","unstructured":"Brown, J. C. et al. Increased transmission of SARS-CoV-2 lineage B.1.1.7 (VOC 2020212\/01) is not accounted for by a replicative advantage in primary airway cells or antibody escape. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2021.02.24.432576 (2021).","DOI":"10.1101\/2021.02.24.432576"},{"key":"841_CR26","doi-asserted-by":"publisher","first-page":"1295","DOI":"10.1016\/j.cell.2020.08.012","volume":"182","author":"TN Starr","year":"2020","unstructured":"Starr, T. N. et al. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell 182, 1295\u20131310.e20 (2020).","journal-title":"Cell"},{"key":"841_CR27","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1038\/s41586-021-04245-0","volume":"602","author":"Y Liu","year":"2022","unstructured":"Liu, Y. et al. The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. Nature 602, 294\u2013299 (2022).","journal-title":"Nature"},{"key":"841_CR28","doi-asserted-by":"publisher","first-page":"2100509","DOI":"10.2807\/1560-7917.ES.2021.26.24.2100509","volume":"26","author":"F Campbell","year":"2021","unstructured":"Campbell, F. et al. Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021. Eurosurveillance 26, 2100509 (2021).","journal-title":"Eurosurveillance"},{"key":"841_CR29","doi-asserted-by":"publisher","first-page":"eabg3055","DOI":"10.1126\/science.abg3055","volume":"372","author":"NG Davies","year":"2021","unstructured":"Davies, N. G. et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science 372, eabg3055 (2021).","journal-title":"Science"},{"key":"841_CR30","doi-asserted-by":"publisher","first-page":"110829","DOI":"10.1016\/j.celrep.2022.110829","volume":"39","author":"Y Liu","year":"2022","unstructured":"Liu, Y. et al. Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Cell Rep. 39, 110829 (2022).","journal-title":"Cell Rep."},{"key":"841_CR31","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-022-01143-7","author":"BJ Willett","year":"2022","unstructured":"Willett, B. J. et al. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nat. Microbiol. https:\/\/doi.org\/10.1038\/s41564-022-01143-7 (2022).","journal-title":"Nat. Microbiol."},{"key":"841_CR32","doi-asserted-by":"publisher","unstructured":"Peacock, T. P. et al. The altered entry pathway and antigenic distance of the SARS-CoV-2 Omicron variant map to separate domains of spike protein. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2021.12.31.474653 (2022).","DOI":"10.1101\/2021.12.31.474653"},{"key":"841_CR33","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1038\/s41586-021-04385-3","volume":"602","author":"Y Cao","year":"2022","unstructured":"Cao, Y. et al. Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature 602, 657\u2013663 (2022).","journal-title":"Nature"},{"key":"841_CR34","doi-asserted-by":"publisher","unstructured":"Zhou, J. et al. Omicron breakthrough infections in vaccinated or previously infected hamsters. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.05.20.492779 (2022).","DOI":"10.1101\/2022.05.20.492779"},{"key":"841_CR35","doi-asserted-by":"publisher","first-page":"1171","DOI":"10.1016\/j.cell.2021.01.037","volume":"184","author":"EC Thomson","year":"2021","unstructured":"Thomson, E. C. et al. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell 184, 1171\u20131187.e20 (2021).","journal-title":"Cell"},{"key":"841_CR36","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1126\/science.abd0826","volume":"369","author":"C-L Hsieh","year":"2020","unstructured":"Hsieh, C.-L. et al. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 369, 1501\u20131505 (2020).","journal-title":"Science"},{"key":"841_CR37","doi-asserted-by":"publisher","first-page":"2372","DOI":"10.1016\/j.cell.2021.03.013","volume":"184","author":"WF Garcia-Beltran","year":"2021","unstructured":"Garcia-Beltran, W. F. et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell 184, 2372\u20132383.e9 (2021).","journal-title":"Cell"},{"key":"841_CR38","doi-asserted-by":"publisher","first-page":"1180","DOI":"10.1038\/s41564-022-01163-3","volume":"7","author":"J Newman","year":"2022","unstructured":"Newman, J. et al. Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2. Nat. Microbiol. 7, 1180\u20131188 (2022).","journal-title":"Nat. Microbiol."},{"key":"841_CR39","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010022","volume":"17","author":"C Davis","year":"2021","unstructured":"Davis, C. et al. Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. PLoS Pathog. 17, e1010022 (2021).","journal-title":"PLoS Pathog."},{"key":"841_CR40","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1056\/NEJMoa2108891","volume":"385","author":"J Lopez Bernal","year":"2021","unstructured":"Lopez Bernal, J. et al. Effectiveness of Covid-19 vaccines against the B.1.617.2 (Delta) variant. N. Engl. J. Med. 385, 585\u2013594 (2021).","journal-title":"N. Engl. J. Med."},{"key":"841_CR41","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2119451","author":"N Andrews","year":"2022","unstructured":"Andrews, N. et al. Covid-19 Vaccine Effectiveness against the Omicron (B.1.1.529) Variant. N. Engl. J. Med. https:\/\/doi.org\/10.1056\/NEJMoa2119451 (2022).","journal-title":"N. Engl. J. Med."},{"key":"841_CR42","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1056\/NEJMc2104974","volume":"385","author":"LJ Abu-Raddad","year":"2021","unstructured":"Abu-Raddad, L. J., Chemaitelly, H. & Butt, A. A. Effectiveness of the BNT162b2 Covid-19 vaccine against the B.1.1.7 and B.1.351 variants. N. Engl. J. Med. 385, 187\u2013189 (2021).","journal-title":"N. Engl. J. Med."},{"key":"841_CR43","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-022-01911-2","author":"H Tegally","year":"2022","unstructured":"Tegally, H. et al. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat. Med. https:\/\/doi.org\/10.1038\/s41591-022-01911-2 (2022).","journal-title":"Nat. Med."},{"key":"841_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04411-y","author":"R Viana","year":"2022","unstructured":"Viana, R. et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature https:\/\/doi.org\/10.1038\/s41586-022-04411-y (2022).","journal-title":"Nature"},{"key":"841_CR45","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1038\/s41586-021-04387-1","volume":"602","author":"S Cele","year":"2022","unstructured":"Cele, S. et al. Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization. Nature 602, 654\u2013656 (2022).","journal-title":"Nature"},{"key":"841_CR46","doi-asserted-by":"publisher","unstructured":"Willett, B. J. et al. Distinct antigenic properties of the SARS-CoV-2 Omicron lineages BA.4 and BA.5. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.05.25.493397 (2022).","DOI":"10.1101\/2022.05.25.493397"},{"key":"841_CR47","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.06.005","author":"A Tuekprakhon","year":"2022","unstructured":"Tuekprakhon, A. et al. Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum. Cell https:\/\/doi.org\/10.1016\/j.cell.2022.06.005 (2022).","journal-title":"Cell"},{"key":"841_CR48","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04980-y","author":"Y Cao","year":"2022","unstructured":"Cao, Y. et al. BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature https:\/\/doi.org\/10.1038\/s41586-022-04980-y (2022).","journal-title":"Nature"},{"key":"841_CR49","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-32396-9","volume":"13","author":"K Khan","year":"2022","unstructured":"Khan, K. et al. Omicron BA.4\/BA.5 escape neutralizing immunity elicited by BA.1 infection. Nat. Commun. 13, 4686 (2022).","journal-title":"Nat. Commun."},{"key":"841_CR50","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04474-x","author":"B Meng","year":"2022","unstructured":"Meng, B. et al. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity. Nature https:\/\/doi.org\/10.1038\/s41586-022-04474-x (2022).","journal-title":"Nature"},{"key":"841_CR51","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1038\/s41579-022-00708-x","volume":"20","author":"E Simon-Loriere","year":"2022","unstructured":"Simon-Loriere, E. & Schwartz, O. Towards SARS-CoV-2 serotypes? Nat. Rev. Microbiol. 20, 187\u2013188 (2022).","journal-title":"Nat. Rev. Microbiol."},{"key":"841_CR52","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2022.07.018","author":"K van der Straten","year":"2022","unstructured":"van der Straten, K. et al. Antigenic cartography using sera from sequence-confirmed SARS-CoV-2 variants of concern infections reveals antigenic divergence of Omicron. Immunity https:\/\/doi.org\/10.1016\/j.immuni.2022.07.018 (2022).","journal-title":"Immunity"},{"key":"841_CR53","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1001\/jama.2022.0470","volume":"327","author":"EK Accorsi","year":"2022","unstructured":"Accorsi, E. K. et al. Association between 3 doses of mRNA COVID-19 vaccine and symptomatic infection caused by the SARS-CoV-2 Omicron and Delta variants. JAMA 327, 639\u2013651 (2022).","journal-title":"JAMA"},{"key":"841_CR54","doi-asserted-by":"publisher","first-page":"2086","DOI":"10.3390\/v14102086","volume":"14","author":"Y Kherabi","year":"2022","unstructured":"Kherabi, Y., Launay, O. & Luong Nguyen, L. B. COVID-19 vaccines against Omicron variant: real-world data on effectiveness. Viruses 14, 2086 (2022).","journal-title":"Viruses"},{"key":"841_CR55","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(22)00309-7","author":"FCM Kirsebom","year":"2022","unstructured":"Kirsebom, F. C. M. et al. COVID-19 vaccine effectiveness against the omicron (BA.2) variant in England. Lancet Infect. Dis. https:\/\/doi.org\/10.1016\/S1473-3099(22)00309-7 (2022).","journal-title":"Lancet Infect. Dis."},{"key":"841_CR56","unstructured":"Ferdinands, J. M. et al. Waning 2-dose and 3-dose effectiveness of mRNA vaccines against COVID-19-associated emergency department and urgent care encounters and hospitalizations among adults during periods of Delta and Omicron variant predominance - VISION Network, 10 states, August 2021-January 2022. MMWR Morb. Mortal. Wkly Rep. 71, 255\u2013263 (2022)."},{"key":"841_CR57","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1056\/NEJMc2119270","volume":"386","author":"S Collie","year":"2021","unstructured":"Collie, S., Champion, J., Moultrie, H., Bekker, L.-G. & Gray, G. Effectiveness of BNT162b2 vaccine against Omicron variant in South Africa. N. Engl. J. Med. 386, 494\u2013496 (2021).","journal-title":"N. Engl. J. Med."},{"key":"841_CR58","doi-asserted-by":"publisher","first-page":"1114","DOI":"10.1016\/S1473-3099(22)00409-1","volume":"22","author":"MM Higdon","year":"2022","unstructured":"Higdon, M. M. et al. Duration of effectiveness of vaccination against COVID-19 caused by the omicron variant. Lancet Infect. Dis. 22, 1114\u20131116 (2022).","journal-title":"Lancet Infect. Dis."},{"key":"841_CR59","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-30878-4","volume":"13","author":"Z Fang","year":"2022","unstructured":"Fang, Z. et al. Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2. Nat. Commun. 13, 3250 (2022).","journal-title":"Nat. Commun."},{"key":"841_CR60","doi-asserted-by":"publisher","first-page":"103841","DOI":"10.1016\/j.ebiom.2022.103841","volume":"76","author":"A Alu","year":"2022","unstructured":"Alu, A. et al. Intranasal COVID-19 vaccines: from bench to bed. eBioMedicine 76, 103841 (2022).","journal-title":"eBioMedicine"},{"key":"841_CR61","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1038\/d41573-022-00074-6","volume":"21","author":"E Dolgin","year":"2022","unstructured":"Dolgin, E. Pan-coronavirus vaccine pipeline takes form. Nat. Rev. Drug Discov. 21, 324\u2013326 (2022).","journal-title":"Nat. Rev. Drug Discov."},{"key":"841_CR62","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1009453","volume":"17","author":"RT Eguia","year":"2021","unstructured":"Eguia, R. T. et al. A human coronavirus evolves antigenically to escape antibody immunity. PLoS Pathog. 17, e1009453 (2021).","journal-title":"PLoS Pathog."},{"key":"841_CR63","doi-asserted-by":"publisher","first-page":"1691","DOI":"10.1038\/s41591-020-1083-1","volume":"26","author":"AWD Edridge","year":"2020","unstructured":"Edridge, A. W. D. et al. Seasonal coronavirus protective immunity is short-lasting. Nat. Med. 26, 1691\u20131693 (2020).","journal-title":"Nat. Med."},{"key":"841_CR64","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1016\/j.molcel.2020.04.022","volume":"78","author":"M Hoffmann","year":"2020","unstructured":"Hoffmann, M., Kleine-Weber, H. & P\u00f6hlmann, S. A multibasic cleavage site in the spike protein of SARS-CoV-2 is essential for infection of human lung cells. Mol. Cell 78, 779\u2013784.e5 (2020).","journal-title":"Mol. Cell"},{"key":"841_CR65","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1038\/s41586-021-03237-4","volume":"591","author":"BA Johnson","year":"2021","unstructured":"Johnson, B. A. et al. Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis. Nature 591, 293\u2013299 (2021).","journal-title":"Nature"},{"key":"841_CR66","doi-asserted-by":"publisher","first-page":"16954","DOI":"10.1016\/S0021-9258(18)55396-5","volume":"266","author":"Y Misumi","year":"1991","unstructured":"Misumi, Y. et al. Functional expression of furin demonstrating its intracellular localization and endoprotease activity for processing of proalbumin and complement pro-C3. J. Biol. Chem. 266, 16954\u201316959 (1991).","journal-title":"J. Biol. Chem."},{"key":"841_CR67","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veac080","author":"V Hill","year":"2022","unstructured":"Hill, V. et al. The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evol. https:\/\/doi.org\/10.1093\/ve\/veac080 (2022).","journal-title":"Virus Evol."},{"key":"841_CR68","doi-asserted-by":"publisher","first-page":"105038","DOI":"10.1016\/j.meegid.2021.105038","volume":"95","author":"K Laiton-Donato","year":"2021","unstructured":"Laiton-Donato, K. et al. Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. Infect. Genet. Evol. 95, 105038 (2021).","journal-title":"Infect. Genet. Evol."},{"key":"841_CR69","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1038\/s41586-021-04266-9","volume":"602","author":"A Saito","year":"2022","unstructured":"Saito, A. et al. Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Nature 602, 300\u2013306 (2022).","journal-title":"Nature"},{"key":"841_CR70","doi-asserted-by":"publisher","unstructured":"Lubinski, B., Jaimes, J. A. & Whittaker, G. R. Intrinsic furin-mediated cleavability of the spike S1\/S2 site from SARS-CoV-2 variant B.1.1.529 (Omicron). Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.04.20.488969 (2022).","DOI":"10.1101\/2022.04.20.488969"},{"key":"841_CR71","doi-asserted-by":"publisher","first-page":"103589","DOI":"10.1016\/j.isci.2021.103589","volume":"25","author":"B Lubinski","year":"2022","unstructured":"Lubinski, B. et al. Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. iScience 25, 103589 (2022).","journal-title":"iScience"},{"key":"841_CR72","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2109905118","volume":"118","author":"L Zhang","year":"2021","unstructured":"Zhang, L. et al. Furin cleavage of the SARS-CoV-2 spike is modulated by O-glycosylation. Proc. Natl Acad. Sci. USA 118, e2109905118 (2021).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"841_CR73","doi-asserted-by":"publisher","first-page":"2003","DOI":"10.1021\/acs.analchem.0c03173","volume":"93","author":"M Sanda","year":"2021","unstructured":"Sanda, M., Morrison, L. & Goldman, R. N- and O-glycosylation of the SARS-CoV-2 spike protein. Anal. Chem. 93, 2003\u20132009 (2021).","journal-title":"Anal. Chem."},{"key":"841_CR74","doi-asserted-by":"publisher","unstructured":"Gonzalez-Rodriguez, E. et al. O-linked sialoglycans modulate the proteolysis of SARS-CoV-2 spike and contribute to the mutational trajectory in variants of concern. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.09.15.508093 (2022).","DOI":"10.1101\/2022.09.15.508093"},{"key":"841_CR75","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04462-1","author":"R Suzuki","year":"2022","unstructured":"Suzuki, R. et al. Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant. Nature https:\/\/doi.org\/10.1038\/s41586-022-04462-1 (2022).","journal-title":"Nature"},{"key":"841_CR76","doi-asserted-by":"publisher","unstructured":"Mesner, D. et al. SARS-CoV-2 Spike evolution influences GBP and IFITM sensitivity. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.03.07.481785 (2022).","DOI":"10.1101\/2022.03.07.481785"},{"key":"841_CR77","doi-asserted-by":"publisher","unstructured":"Reuschl, A.-K. et al. Enhanced innate immune suppression by SARS-CoV-2 Omicron subvariants BA.4 and BA.5. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.07.12.499603 (2022).","DOI":"10.1101\/2022.07.12.499603"},{"key":"841_CR78","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04479-6","author":"KPY Hui","year":"2022","unstructured":"Hui, K. P. Y. et al. SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo. Nature https:\/\/doi.org\/10.1038\/s41586-022-04479-6 (2022).","journal-title":"Nature"},{"key":"841_CR79","doi-asserted-by":"publisher","first-page":"896","DOI":"10.1038\/s41564-022-01135-7","volume":"7","author":"A Aggarwal","year":"2022","unstructured":"Aggarwal, A. et al. Platform for isolation and characterization of SARS-CoV-2 variants enables rapid characterization of Omicron in Australia. Nat. Microbiol. 7, 896\u2013908 (2022).","journal-title":"Nat. Microbiol."},{"key":"841_CR80","doi-asserted-by":"publisher","unstructured":"Barut, T. et al. The spike gene is a major determinant for the SARS-CoV-2 Omicron-BA.1 phenotype. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.04.28.489537 (2022).","DOI":"10.1101\/2022.04.28.489537"},{"key":"841_CR81","doi-asserted-by":"publisher","unstructured":"Bentley, E. G. et al. SARS-CoV-2 Omicron-B.1.1.529 Variant leads to less severe disease than Pango B and Delta variants strains in a mouse model of severe COVID-19. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2021.12.26.474085 (2021).","DOI":"10.1101\/2021.12.26.474085"},{"key":"841_CR82","doi-asserted-by":"publisher","unstructured":"Kimura, I. et al. SARS-CoV-2 spike S375F mutation characterizes the Omicron BA.1 variant. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.04.03.486864 (2022).","DOI":"10.1101\/2022.04.03.486864"},{"key":"841_CR83","doi-asserted-by":"publisher","unstructured":"Yamamoto, M. et al. SARS-CoV-2 Omicron spike H655Y mutation is responsible for enhancement of the endosomal entry pathway and reduction of cell surface entry pathways. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.03.21.485084 (2022).","DOI":"10.1101\/2022.03.21.485084"},{"key":"841_CR84","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.09.018","author":"I Kimura","year":"2022","unstructured":"Kimura, I. et al. Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants including BA.4 and BA.5. Cell https:\/\/doi.org\/10.1016\/j.cell.2022.09.018 (2022).","journal-title":"Cell"},{"key":"841_CR85","doi-asserted-by":"publisher","unstructured":"Allen, H. et al. Comparative transmission of SARS-CoV-2 Omicron (B.1.1.529) and Delta (B.1.617.2) variants and the impact of vaccination: national cohort study, England. Preprint at medRxiv https:\/\/doi.org\/10.1101\/2022.02.15.22271001 (2022).","DOI":"10.1101\/2022.02.15.22271001"},{"key":"841_CR86","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-33328-3","volume":"13","author":"FP Lyngse","year":"2022","unstructured":"Lyngse, F. P. et al. Household transmission of the SARS-CoV-2 Omicron variant in Denmark. Nat. Commun. 13, 5573 (2022).","journal-title":"Nat. Commun."},{"key":"841_CR87","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2111199119","volume":"119","author":"S Yu","year":"2022","unstructured":"Yu, S. et al. SARS-CoV-2 spike engagement of ACE2 primes S2\u2032 site cleavage and fusion initiation. Proc. Natl Acad. Sci. USA 119, e2111199119 (2022).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"841_CR88","doi-asserted-by":"publisher","first-page":"15214","DOI":"10.1073\/pnas.1407087111","volume":"111","author":"JK Millet","year":"2014","unstructured":"Millet, J. K. & Whittaker, G. R. Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein. Proc. Natl Acad. Sci. USA 111, 15214\u201315219 (2014).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"841_CR89","doi-asserted-by":"publisher","first-page":"5871","DOI":"10.1073\/pnas.0809524106","volume":"106","author":"S Belouzard","year":"2009","unstructured":"Belouzard, S., Chu, V. C. & Whittaker, G. R. Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites. Proc. Natl Acad. Sci. USA 106, 5871\u20135876 (2009).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"841_CR90","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1038\/s41586-020-2772-0","volume":"588","author":"DJ Benton","year":"2020","unstructured":"Benton, D. J. et al. Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion. Nature 588, 327\u2013330 (2020).","journal-title":"Nature"},{"key":"841_CR91","doi-asserted-by":"publisher","DOI":"10.26508\/lsa.202000786","volume":"3","author":"D Bestle","year":"2020","unstructured":"Bestle, D. et al. TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells. Life Sci. Alliance 3, e202000786 (2020).","journal-title":"Life Sci. Alliance"},{"key":"841_CR92","doi-asserted-by":"publisher","first-page":"110786","DOI":"10.1016\/j.celrep.2022.110786","volume":"39","author":"E Qing","year":"2022","unstructured":"Qing, E. et al. Inter-domain communication in SARS-CoV-2 spike proteins controls protease-triggered cell entry. Cell Rep. 39, 110786 (2022).","journal-title":"Cell Rep."},{"key":"841_CR93","doi-asserted-by":"publisher","first-page":"111220","DOI":"10.1016\/j.celrep.2022.111220","volume":"40","author":"B Meng","year":"2022","unstructured":"Meng, B. et al. SARS-CoV-2 spike N-terminal domain modulates TMPRSS2-dependent viral entry and fusogenicity. Cell Rep. 40, 111220 (2022).","journal-title":"Cell Rep."},{"key":"841_CR94","doi-asserted-by":"publisher","DOI":"10.15252\/embr.202154322","volume":"23","author":"D Cantoni","year":"2022","unstructured":"Cantoni, D. et al. Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike. EMBO Rep. 23, e54322 (2022).","journal-title":"EMBO Rep."},{"key":"841_CR95","doi-asserted-by":"publisher","first-page":"1626","DOI":"10.1126\/science.abl6184","volume":"374","author":"AM Syed","year":"2021","unstructured":"Syed, A. M. et al. Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles. Science 374, 1626\u20131632 (2021).","journal-title":"Science"},{"key":"841_CR96","doi-asserted-by":"publisher","first-page":"1788","DOI":"10.1016\/j.chom.2021.11.005","volume":"29","author":"H Wu","year":"2021","unstructured":"Wu, H. et al. Nucleocapsid mutations R203K\/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Cell Host Microbe 29, 1788\u20131801.e6 (2021).","journal-title":"Cell Host Microbe"},{"key":"841_CR97","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010627","volume":"18","author":"BA Johnson","year":"2022","unstructured":"Johnson, B. A. et al. Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. PLoS Pathog. 18, e1010627 (2022).","journal-title":"PLoS Pathog."},{"key":"841_CR98","doi-asserted-by":"publisher","unstructured":"Mears, H. V. et al. Emergence of new subgenomic mRNAs in SARS-CoV-2. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.04.20.488895 (2022).","DOI":"10.1101\/2022.04.20.488895"},{"key":"841_CR99","doi-asserted-by":"publisher","first-page":"27","DOI":"10.20411\/pai.v6i2.460","volume":"6","author":"S Leary","year":"2021","unstructured":"Leary, S. et al. Generation of a novel SARS-CoV-2 sub-genomic RNA due to the R203K\/G204R variant in nucleocapsid: homologous recombination has potential to change SARS-CoV-2 at both protein and RNA level. Pathog. Immun. 6, 27\u201349 (2021).","journal-title":"Pathog. Immun."},{"key":"841_CR100","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2200592119","volume":"119","author":"AM Syed","year":"2022","unstructured":"Syed, A. M. et al. Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles. Proc. Natl Acad. Sci. USA 119, e2200592119 (2022).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"841_CR101","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1186\/s12985-019-1182-0","volume":"16","author":"D Schoeman","year":"2019","unstructured":"Schoeman, D. & Fielding, B. C. Coronavirus envelope protein: current knowledge. Virol. J. 16, 69 (2019).","journal-title":"Virol. J."},{"key":"841_CR102","doi-asserted-by":"publisher","unstructured":"Xia, B. et al. Why SARS-CoV-2 Omicron variant is milder? A single high-frequency mutation of structural envelope protein matters. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.02.01.478647 (2022).","DOI":"10.1101\/2022.02.01.478647"},{"key":"841_CR103","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04835-6","author":"S Ricciardi","year":"2022","unstructured":"Ricciardi, S. et al. The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle. Nature https:\/\/doi.org\/10.1038\/s41586-022-04835-6 (2022).","journal-title":"Nature"},{"key":"841_CR104","doi-asserted-by":"publisher","first-page":"1336","DOI":"10.1038\/s41590-020-0782-6","volume":"21","author":"Y Peng","year":"2020","unstructured":"Peng, Y. et al. Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nat. Immunol. 21, 1336\u20131345 (2020).","journal-title":"Nat. Immunol."},{"key":"841_CR105","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1038\/s41590-021-01122-w","volume":"23","author":"P Moss","year":"2022","unstructured":"Moss, P. The T cell immune response against SARS-CoV-2. Nat. Immunol. 23, 186\u2013193 (2022).","journal-title":"Nat. Immunol."},{"key":"841_CR106","doi-asserted-by":"publisher","first-page":"2032","DOI":"10.1038\/s41591-021-01540-1","volume":"27","author":"S Feng","year":"2021","unstructured":"Feng, S. et al. Correlates of protection against symptomatic and asymptomatic SARS-CoV-2 infection. Nat. Med. 27, 2032\u20132040 (2021).","journal-title":"Nat. Med."},{"key":"841_CR107","doi-asserted-by":"publisher","first-page":"108728","DOI":"10.1016\/j.celrep.2021.108728","volume":"34","author":"AT Tan","year":"2021","unstructured":"Tan, A. T. et al. Early induction of functional SARS-CoV-2-specific T cells associates with rapid viral clearance and mild disease in COVID-19 patients. Cell Rep. 34, 108728 (2021).","journal-title":"Cell Rep."},{"key":"841_CR108","doi-asserted-by":"publisher","first-page":"1280","DOI":"10.1038\/s41591-021-01386-7","volume":"27","author":"EM Bange","year":"2021","unstructured":"Bange, E. M. et al. CD8+ T cells contribute to survival in patients with COVID-19 and hematologic cancer. Nat. Med. 27, 1280\u20131289 (2021).","journal-title":"Nat. Med."},{"key":"841_CR109","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1038\/s41586-021-03841-4","volume":"597","author":"V Oberhardt","year":"2021","unstructured":"Oberhardt, V. et al. Rapid and stable mobilization of CD8+ T cells by SARS-CoV-2 mRNA vaccine. Nature 597, 268\u2013273 (2021).","journal-title":"Nature"},{"key":"841_CR110","doi-asserted-by":"publisher","first-page":"100204","DOI":"10.1016\/j.xcrm.2021.100204","volume":"2","author":"A Tarke","year":"2021","unstructured":"Tarke, A. et al. Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. Cell Rep. Med. 2, 100204 (2021).","journal-title":"Cell Rep. Med."},{"key":"841_CR111","doi-asserted-by":"publisher","first-page":"eabg6461","DOI":"10.1126\/sciimmunol.abg6461","volume":"6","author":"B Agerer","year":"2021","unstructured":"Agerer, B. et al. SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8+ T cell responses. Sci. Immunol. 6, eabg6461 (2021).","journal-title":"Sci. Immunol."},{"key":"841_CR112","doi-asserted-by":"publisher","first-page":"1253","DOI":"10.1084\/jem.20090365","volume":"206","author":"N Goonetilleke","year":"2009","unstructured":"Goonetilleke, N. et al. The first T cell response to transmitted\/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med. 206, 1253\u20131272 (2009).","journal-title":"J. Exp. Med."},{"key":"841_CR113","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veac050","author":"SAJ Wilkinson","year":"2022","unstructured":"Wilkinson, S. A. J. et al. Recurrent SARS-CoV-2 mutations in immunodeficient patients. Virus Evol. https:\/\/doi.org\/10.1093\/ve\/veac050 (2022).","journal-title":"Virus Evol."},{"key":"841_CR114","doi-asserted-by":"publisher","unstructured":"Stanevich, O. et al. SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19. Preprint at Res. Sq. https:\/\/doi.org\/10.21203\/rs.3.rs-750741\/v1 (2021).","DOI":"10.21203\/rs.3.rs-750741\/v1"},{"key":"841_CR115","doi-asserted-by":"publisher","first-page":"103353","DOI":"10.1016\/j.isci.2021.103353","volume":"24","author":"TI de Silva","year":"2021","unstructured":"de Silva, T. I. et al. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. iScience 24, 103353 (2021).","journal-title":"iScience"},{"key":"841_CR116","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1016\/j.chom.2021.06.006","volume":"29","author":"C Motozono","year":"2021","unstructured":"Motozono, C. et al. SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Cell Host Microbe 29, 1124\u20131136.e11 (2021).","journal-title":"Cell Host Microbe"},{"key":"841_CR117","doi-asserted-by":"publisher","first-page":"2936","DOI":"10.1016\/j.cell.2022.07.002","volume":"185","author":"G Dolton","year":"2022","unstructured":"Dolton, G. et al. Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell 185, 2936\u20132951.e19 (2022).","journal-title":"Cell"},{"key":"841_CR118","doi-asserted-by":"publisher","first-page":"eabj6824","DOI":"10.1126\/scitranslmed.abj6824","volume":"14","author":"C Riou","year":"2022","unstructured":"Riou, C. et al. Escape from recognition of SARS-CoV-2 variant spike epitopes but overall preservation of T cell immunity. Sci. Transl Med. 14, eabj6824 (2022).","journal-title":"Sci. Transl Med."},{"key":"841_CR119","doi-asserted-by":"publisher","first-page":"1418","DOI":"10.1126\/science.abh1282","volume":"372","author":"CJ Reynolds","year":"2021","unstructured":"Reynolds, C. J. et al. Prior SARS-CoV-2 infection rescues B and T cell responses to variants after first vaccine dose. Science 372, 1418\u20131423 (2021).","journal-title":"Science"},{"key":"841_CR120","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1016\/j.cell.2022.01.015","volume":"185","author":"A Tarke","year":"2022","unstructured":"Tarke, A. et al. SARS-CoV-2 vaccination induces immunological T cell memory able to cross-recognize variants from Alpha to Omicron. Cell 185, 847\u2013859.e11 (2022).","journal-title":"Cell"},{"key":"841_CR121","unstructured":"UKHSA. COVID-19 Vaccine Surveillance Report (UKHSA, 2022)."},{"key":"841_CR122","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.1016\/j.cell.2022.01.029","volume":"185","author":"V Naranbhai","year":"2022","unstructured":"Naranbhai, V. et al. T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals. Cell 185, 1041\u20131051.e6 (2022).","journal-title":"Cell"},{"key":"841_CR123","doi-asserted-by":"publisher","unstructured":"Wellington, D. et al. SARS-CoV-2 mutations affect proteasome processing to alter CD8+ T cell responses. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.04.08.487623 (2022).","DOI":"10.1101\/2022.04.08.487623"},{"key":"841_CR124","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1016\/j.immuni.2012.11.021","volume":"38","author":"K Ladell","year":"2013","unstructured":"Ladell, K. et al. A molecular basis for the control of preimmune escape variants by HIV-specific CD8+ T cells. Immunity 38, 425\u2013436 (2013).","journal-title":"Immunity"},{"key":"841_CR125","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2024202118","volume":"118","author":"Y Zhang","year":"2021","unstructured":"Zhang, Y. et al. The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating MHC-I. Proc. Natl Acad. Sci. USA 118, e2024202118 (2021).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"841_CR126","doi-asserted-by":"publisher","unstructured":"Moriyama, M., Lucas, C., Monteiro, V. S., Yale SARS-CoV-2 Genomic Surveillance Initiative & Iwasaki, A. SARS-CoV-2 Omicron subvariants evolved to promote further escape from MHC-I recognition. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.05.04.490614 (2022).","DOI":"10.1101\/2022.05.04.490614"},{"key":"841_CR127","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-26910-8","volume":"12","author":"J-S Yoo","year":"2021","unstructured":"Yoo, J.-S. et al. SARS-CoV-2 inhibits induction of the MHC class I pathway by targeting the STAT1-IRF1-NLRC5 axis. Nat. Commun. 12, 6602 (2021).","journal-title":"Nat. Commun."},{"key":"841_CR128","doi-asserted-by":"publisher","unstructured":"Arshad, N. et al. SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to downregulate MHC-I surface expression. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.05.17.492198 (2022).","DOI":"10.1101\/2022.05.17.492198"},{"key":"841_CR129","doi-asserted-by":"publisher","unstructured":"Zhang, F. et al. Inhibition of major histocompatibility complex-I antigen presentation by sarbecovirus ORF7a proteins. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.05.25.493467 (2022).","DOI":"10.1101\/2022.05.25.493467"},{"key":"841_CR130","doi-asserted-by":"publisher","unstructured":"Stewart, H. et al. Tetherin antagonism by SARS-CoV-2 enhances virus release: multiple mechanisms including ORF3a-mediated defective retrograde traffic. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2021.01.06.425396 (2021).","DOI":"10.1101\/2021.01.06.425396"},{"key":"841_CR131","unstructured":"Rambaut, A. et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological.org https:\/\/virological.org\/t\/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations\/563 (2020)."},{"key":"841_CR132","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/j.cell.2014.12.003","volume":"160","author":"JN Mandl","year":"2015","unstructured":"Mandl, J. N. et al. Reservoir host immune responses to emerging zoonotic viruses. Cell 160, 20\u201335 (2015).","journal-title":"Cell"},{"key":"841_CR133","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1038\/s41586-021-04352-y","volume":"602","author":"LG Thorne","year":"2022","unstructured":"Thorne, L. G. et al. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature 602, 487\u2013495 (2022).","journal-title":"Nature"},{"key":"841_CR134","doi-asserted-by":"publisher","unstructured":"Lista, M. J. et al. The P681H mutation in the spike glycoprotein confers type I interferon resistance in the SARS-CoV-2 alpha (B.1.1.7) variant. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2021.11.09.467693 (2021).","DOI":"10.1101\/2021.11.09.467693"},{"key":"841_CR135","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2203760119","volume":"119","author":"K Guo","year":"2022","unstructured":"Guo, K. et al. Interferon resistance of emerging SARS-CoV-2 variants. Proc. Natl Acad. Sci. USA 119, e2203760119 (2022).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"841_CR136","doi-asserted-by":"publisher","unstructured":"Bouhaddoum, M. et al. Global landscape of the host response to SARS-CoV-2 variants reveals viral evolutionary trajectories. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.10.19.512927 (2022).","DOI":"10.1101\/2022.10.19.512927"},{"key":"841_CR137","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010349","volume":"18","author":"R Hall","year":"2022","unstructured":"Hall, R. et al. SARS-CoV-2 ORF6 disrupts innate immune signalling by inhibiting cellular mRNA export. PLoS Pathog. 18, e1010349 (2022).","journal-title":"PLoS Pathog."},{"key":"841_CR138","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1038\/s41423-020-0514-8","volume":"17","author":"H-w Jiang","year":"2020","unstructured":"Jiang, H.-w et al. SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70. Cell. Mol. Immunol. 17, 998\u20131000 (2020).","journal-title":"Cell. Mol. Immunol."},{"key":"841_CR139","doi-asserted-by":"publisher","first-page":"167265","DOI":"10.1016\/j.jmb.2021.167265","volume":"434","author":"DK Beyer","year":"2022","unstructured":"Beyer, D. K. & Forero, A. Mechanisms of antiviral immune evasion of SARS-CoV-2. J. Mol. Biol. 434, 167265 (2022).","journal-title":"J. Mol. Biol."},{"key":"841_CR140","doi-asserted-by":"publisher","first-page":"100013","DOI":"10.1016\/j.crviro.2021.100013","volume":"2","author":"D Xu","year":"2021","unstructured":"Xu, D., Biswal, M., Neal, A. & Hai, R. Devil\u2019s tools: SARS-CoV-2 antagonists against innate immunity. Curr. Res. Virol. Sci. 2, 100013 (2021).","journal-title":"Curr. Res. Virol. Sci."},{"key":"841_CR141","doi-asserted-by":"publisher","DOI":"10.1093\/pnasnexus\/pgac067","author":"L Shalamova","year":"2022","unstructured":"Shalamova, L. et al. Omicron variant of SARS-CoV-2 exhibits an increased resilience to the antiviral type I interferon response. PNAS Nexus https:\/\/doi.org\/10.1093\/pnasnexus\/pgac067 (2022).","journal-title":"PNAS Nexus"},{"key":"841_CR142","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.02422-20","author":"H Winstone","year":"2021","unstructured":"Winstone, H. et al. The polybasic cleavage site in SARS-CoV-2 spike modulates viral sensitivity to type I interferon and IFITM2. J. Virol. https:\/\/doi.org\/10.1128\/jvi.02422-20 (2021).","journal-title":"J. Virol."},{"key":"841_CR143","doi-asserted-by":"publisher","first-page":"6756","DOI":"10.1073\/pnas.1320856111","volume":"111","author":"X Zhao","year":"2014","unstructured":"Zhao, X. et al. Interferon induction of IFITM proteins promotes infection by human coronavirus OC43. Proc. Natl Acad. Sci. USA 111, 6756\u20136761 (2014).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"841_CR144","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24817-y","volume":"12","author":"C Prelli Bozzo","year":"2021","unstructured":"Prelli Bozzo, C. et al. IFITM proteins promote SARS-CoV-2 infection and are targets for virus inhibition in vitro. Nat. Commun. 12, 4584 (2021).","journal-title":"Nat. Commun."},{"key":"841_CR145","doi-asserted-by":"publisher","first-page":"e00594-22","DOI":"10.1128\/jvi.00594-22","volume":"96","author":"R Nchioua","year":"2022","unstructured":"Nchioua, R. et al. SARS-CoV-2 variants of concern hijack IFITM2 for efficient replication in human lung cells. J. Virol. 96, e00594-22 (2022).","journal-title":"J. Virol."},{"key":"841_CR146","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1038\/nri3344","volume":"13","author":"MS Diamond","year":"2013","unstructured":"Diamond, M. S. & Farzan, M. The broad-spectrum antiviral functions of IFIT and IFITM proteins. Nat. Rev. Immunol. 13, 46\u201357 (2013).","journal-title":"Nat. Rev. Immunol."},{"key":"841_CR147","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003124","volume":"9","author":"K Li","year":"2013","unstructured":"Li, K. et al. IFITM proteins restrict viral membrane hemifusion. PLoS Pathog. 9, e1003124 (2013).","journal-title":"PLoS Pathog."},{"key":"841_CR148","doi-asserted-by":"publisher","unstructured":"Klein, S. et al. IFITM3 blocks viral entry by sorting lipids and stabilizing hemifusion. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.09.01.506185 (2022).","DOI":"10.1101\/2022.09.01.506185"},{"key":"841_CR149","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1038\/nrmicro2848","volume":"10","author":"NG Sandler","year":"2012","unstructured":"Sandler, N. G. & Douek, D. C. Microbial translocation in HIV infection: causes, consequences and treatment opportunities. Nat. Rev. Microbiol. 10, 655\u2013666 (2012).","journal-title":"Nat. Rev. Microbiol."},{"key":"841_CR150","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1038\/s41586-021-03696-9","volume":"595","author":"Z Wang","year":"2021","unstructured":"Wang, Z. et al. Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection. Nature 595, 426\u2013431 (2021).","journal-title":"Nature"},{"key":"841_CR151","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2114583","volume":"385","author":"EG Levin","year":"2021","unstructured":"Levin, E. G. et al. Waning immune humoral response to BNT162b2 Covid-19 vaccine over 6 months. N. Engl. J. Med. 385, e84 (2021).","journal-title":"N. Engl. J. Med."},{"key":"841_CR152","doi-asserted-by":"publisher","first-page":"eabo5395","DOI":"10.1126\/scitranslmed.abo5395","volume":"14","author":"RS Paton","year":"2022","unstructured":"Paton, R. S., Overton, C. E. & Ward, T. The rapid replacement of the Delta variant by Omicron (B.1.1.529) in England. Sci. Transl Med. 14, eabo5395 (2022).","journal-title":"Sci. Transl Med."},{"key":"841_CR153","doi-asserted-by":"publisher","first-page":"100583","DOI":"10.1016\/j.xcrm.2022.100583","volume":"3","author":"R Earnest","year":"2022","unstructured":"Earnest, R. et al. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. Cell Rep. Med. 3, 100583 (2022).","journal-title":"Cell Rep. Med."},{"key":"841_CR154","doi-asserted-by":"publisher","first-page":"2136","DOI":"10.1038\/s41591-021-01583-4","volume":"27","author":"P Tang","year":"2021","unstructured":"Tang, P. et al. BNT162b2 and mRNA-1273 COVID-19 vaccine effectiveness against the SARS-CoV-2 Delta variant in Qatar. Nat. Med. 27, 2136\u20132143 (2021).","journal-title":"Nat. Med."},{"key":"841_CR155","doi-asserted-by":"publisher","DOI":"10.1136\/bmj-2021-068848","volume":"375","author":"KJ Bruxvoort","year":"2021","unstructured":"Bruxvoort, K. J. et al. Effectiveness of mRNA-1273 against delta, mu, and other emerging variants of SARS-CoV-2: test negative case-control study. BMJ 375, e068848 (2021).","journal-title":"BMJ"},{"key":"841_CR156","doi-asserted-by":"publisher","unstructured":"Lyngse, F. P. et al. Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: evidence from Danish households. Preprint at medRxiv https:\/\/doi.org\/10.1101\/2022.01.28.22270044 (2022).","DOI":"10.1101\/2022.01.28.22270044"},{"key":"841_CR157","doi-asserted-by":"publisher","unstructured":"Cao, Y. et al. Imprinted SARS-CoV-2 humoral immunity induces converging Omicron RBD evolution. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.09.15.507787 (2022).","DOI":"10.1101\/2022.09.15.507787"},{"key":"841_CR158","doi-asserted-by":"publisher","unstructured":"Sheward, D. J. et al. Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.09.16.508299 (2022).","DOI":"10.1101\/2022.09.16.508299"},{"key":"841_CR159","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(22)00524-2","author":"DJ Sheward","year":"2022","unstructured":"Sheward, D. J. et al. Evasion of neutralising antibodies by omicron sublineage BA.2.75. Lancet Infect. Dis. https:\/\/doi.org\/10.1016\/S1473-3099(22)00524-2 (2022).","journal-title":"Lancet Infect. Dis."},{"key":"841_CR160","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1038\/s41586-022-05053-w","volume":"608","author":"Q Wang","year":"2022","unstructured":"Wang, Q. et al. Antibody evasion by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4 and BA.5. Nature 608, 603\u2013608 (2022).","journal-title":"Nature"},{"key":"841_CR161","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1017\/S0031182000055360","volume":"85","author":"RM Anderson","year":"1982","unstructured":"Anderson, R. M. & May, R. M. Coevolution of hosts and parasites. Parasitology 85, 411\u2013426 (1982).","journal-title":"Parasitology"},{"key":"841_CR162","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1111\/j.1420-9101.2008.01658.x","volume":"22","author":"S Alizon","year":"2009","unstructured":"Alizon, S., Hurford, A., Mideo, N. & Van Baalen, M. Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future. J. Evol. Biol. 22, 245\u2013259 (2009).","journal-title":"J. Evol. Biol."},{"key":"841_CR163","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1038\/s41559-021-01603-z","volume":"6","author":"A Sasaki","year":"2022","unstructured":"Sasaki, A., Lion, S. & Boots, M. Antigenic escape selects for the evolution of higher pathogen transmission and virulence. Nat. Ecol. Evol. 6, 51\u201362 (2022).","journal-title":"Nat. Ecol. Evol."},{"key":"841_CR164","doi-asserted-by":"publisher","unstructured":"Pascall, D. J. et al. Inconsistent directions of change in case severity across successive SARS-CoV-2 variant waves suggests an unpredictable future. Preprint at medRxiv https:\/\/doi.org\/10.1101\/2022.03.24.22272915 (2022).","DOI":"10.1101\/2022.03.24.22272915"},{"key":"841_CR165","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1016\/S0140-6736(22)00017-4","volume":"399","author":"N Wolter","year":"2022","unstructured":"Wolter, N. et al. Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study. Lancet 399, 437\u2013446 (2022).","journal-title":"Lancet"},{"key":"841_CR166","doi-asserted-by":"publisher","DOI":"10.1016\/s1473-3099(22)00154-2","author":"P Bager","year":"2022","unstructured":"Bager, P. et al. Risk of hospitalisation associated with infection with SARS-CoV-2 omicron variant versus delta variant in Denmark: an observational cohort study. Lancet Infect. Dis. https:\/\/doi.org\/10.1016\/s1473-3099(22)00154-2 (2022).","journal-title":"Lancet Infect. Dis."},{"key":"841_CR167","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(22)00462-7","author":"T Nyberg","year":"2022","unstructured":"Nyberg, T. et al. Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 omicron (B.1.1.529) and delta (B.1.617.2) variants in England: a cohort study. Lancet https:\/\/doi.org\/10.1016\/S0140-6736(22)00462-7 (2022).","journal-title":"Lancet"},{"key":"841_CR168","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-022-01887-z","author":"JA Lewnard","year":"2022","unstructured":"Lewnard, J. A. et al. Clinical outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) variant and BA.1\/BA.1.1 or BA.2 subvariant infection in southern California. Nat. Med. https:\/\/doi.org\/10.1038\/s41591-022-01887-z (2022).","journal-title":"Nat. Med."},{"key":"841_CR169","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1038\/s41579-022-00713-0","volume":"20","author":"MM Lamers","year":"2022","unstructured":"Lamers, M. M. & Haagmans, B. L. SARS-CoV-2 pathogenesis. Nat. Rev. Microbiol. 20, 270\u2013284 (2022).","journal-title":"Nat. Rev. Microbiol."},{"key":"841_CR170","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00964-21","volume":"96","author":"W Dong","year":"2022","unstructured":"Dong, W. et al. The K18-human ACE2 transgenic mouse model recapitulates non-severe and severe COVID-19 in response to an infectious dose of the SARS-CoV-2 virus. J. Virol. 96, e0096421 (2022).","journal-title":"J. Virol."},{"key":"841_CR171","doi-asserted-by":"publisher","DOI":"10.1099\/jgv.0.001735","author":"N Thakur","year":"2022","unstructured":"Thakur, N. et al. SARS-CoV-2 variants of concern alpha, beta, gamma and delta have extended ACE2 receptor host ranges. J. Gen. Virol. https:\/\/doi.org\/10.1099\/jgv.0.001735 (2022).","journal-title":"J. Gen. Virol."},{"key":"841_CR172","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0131451","volume":"10","author":"VD Menachery","year":"2015","unstructured":"Menachery, V. D., Gralinski, L. E., Baric, R. S. & Ferris, M. T. New metrics for evaluating viral respiratory pathogenesis. PLoS ONE 10, e0131451 (2015).","journal-title":"PLoS ONE"},{"key":"841_CR173","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04856-1","author":"R Uraki","year":"2022","unstructured":"Uraki, R. et al. Characterization and antiviral susceptibility of SARS-CoV-2 Omicron\/BA.2. Nature https:\/\/doi.org\/10.1038\/s41586-022-04856-1 (2022).","journal-title":"Nature"},{"key":"841_CR174","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1038\/s41586-022-04441-6","volume":"603","author":"PJ Halfmann","year":"2022","unstructured":"Halfmann, P. J. et al. SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters. Nature 603, 687\u2013692 (2022).","journal-title":"Nature"},{"key":"841_CR175","doi-asserted-by":"publisher","unstructured":"Mefsin, Y. et al. Epidemiology of infections with SARS-CoV-2 Omicron BA.2 variant in Hong Kong, January-March 2022. Preprint at medRxiv https:\/\/doi.org\/10.1101\/2022.04.07.22273595 (2022).","DOI":"10.1101\/2022.04.07.22273595"},{"key":"841_CR176","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1038\/s41586-022-04442-5","volume":"603","author":"H Shuai","year":"2022","unstructured":"Shuai, H. et al. Attenuated replication and pathogenicity of SARS-CoV-2 B.1.1.529 Omicron. Nature 603, 693\u2013699 (2022).","journal-title":"Nature"},{"key":"841_CR177","doi-asserted-by":"publisher","unstructured":"van Doremalen, N. et al. SARS-CoV-2 Omicron BA.1 and BA.2 are attenuated in rhesus macaques as compared to Delta. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.08.01.502390 (2022).","DOI":"10.1101\/2022.08.01.502390"},{"key":"841_CR178","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiac276","author":"W Su","year":"2022","unstructured":"Su, W. et al. Omicron BA.1 and BA.2 sub-lineages show reduced pathogenicity and transmission potential than the early SARS-CoV-2 D614G variant in Syrian hamsters. J. Infect. Dis. https:\/\/doi.org\/10.1093\/infdis\/jiac276 (2022).","journal-title":"J. Infect. Dis."},{"key":"841_CR179","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/s41579-020-00459-7","volume":"19","author":"B Hu","year":"2021","unstructured":"Hu, B., Guo, H., Zhou, P. & Shi, Z.-L. Characteristics of SARS-CoV-2 and COVID-19. Nat. Rev. Microbiol. 19, 141\u2013154 (2021).","journal-title":"Nat. Rev. Microbiol."},{"key":"841_CR180","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-022-00478-5","author":"MEK Niemi","year":"2022","unstructured":"Niemi, M. E. K., Daly, M. J. & Ganna, A. The human genetic epidemiology of COVID-19. Nat. Rev. Genet. https:\/\/doi.org\/10.1038\/s41576-022-00478-5 (2022).","journal-title":"Nat. Rev. Genet."},{"key":"841_CR181","doi-asserted-by":"publisher","unstructured":"Whitaker, M. et al. Variant-specific symptoms of COVID-19 among 1,542,510 people in England. Preprint at medRxiv https:\/\/doi.org\/10.1101\/2022.05.21.22275368 (2022).","DOI":"10.1101\/2022.05.21.22275368"},{"key":"841_CR182","doi-asserted-by":"publisher","unstructured":"Gonzalez-Reiche, A. S. et al. SARS-CoV-2 variants in the making: Sequential intrahost evolution and forward transmissions in the context of persistent infections. Preprint at medRxiv https:\/\/doi.org\/10.1101\/2022.05.25.22275533 (2022).","DOI":"10.1101\/2022.05.25.22275533"},{"key":"841_CR183","doi-asserted-by":"publisher","DOI":"10.3389\/fviro.2022.942555","author":"M Ghafari","year":"2022","unstructured":"Ghafari, M., Liu, Q., Dhillon, A., Katzourakis, A. & Weissman, D. B. Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern. Front. Virol. https:\/\/doi.org\/10.3389\/fviro.2022.942555 (2022).","journal-title":"Front. Virol."},{"key":"841_CR184","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-022-01882-4","author":"S Harari","year":"2022","unstructured":"Harari, S. et al. Drivers of adaptive evolution during chronic SARS-CoV-2 infections. Nat. Med. https:\/\/doi.org\/10.1038\/s41591-022-01882-4 (2022).","journal-title":"Nat. Med."},{"key":"841_CR185","unstructured":"Roemer, C. Variant report 2022-08-31. https:\/\/github.com\/neherlab\/SARS-CoV-2_variant-reports\/tree\/main\/reports (2022)."},{"key":"841_CR186","doi-asserted-by":"publisher","unstructured":"Pickering, B. et al. Highly divergent white-tailed deer SARS-CoV-2 with potential deer-to-human transmission. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.02.22.481551 (2022).","DOI":"10.1101\/2022.02.22.481551"},{"key":"841_CR187","doi-asserted-by":"publisher","first-page":"2332","DOI":"10.1016\/j.cell.2021.03.028","volume":"184","author":"M McCallum","year":"2021","unstructured":"McCallum, M. et al. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell 184, 2332\u20132347.e16 (2021).","journal-title":"Cell"},{"key":"841_CR188","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1038\/s41586-020-2852-1","volume":"588","author":"CO Barnes","year":"2020","unstructured":"Barnes, C. O. et al. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature 588, 682\u2013687 (2020).","journal-title":"Nature"},{"key":"841_CR189","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1016\/j.chom.2021.02.003","volume":"29","author":"AJ Greaney","year":"2021","unstructured":"Greaney, A. J. et al. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe 29, 463\u2013476.e6 (2021).","journal-title":"Cell Host Microbe"},{"key":"841_CR190","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/s41586-020-2180-5","volume":"581","author":"J Lan","year":"2020","unstructured":"Lan, J. et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581, 215\u2013220 (2020).","journal-title":"Nature"},{"key":"841_CR191","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1038\/s41591-022-01700-x","volume":"28","author":"Y Gao","year":"2022","unstructured":"Gao, Y. et al. Ancestral SARS-CoV-2-specific T cells cross-recognize the Omicron variant. Nat. Med. 28, 472\u2013476 (2022).","journal-title":"Nat. Med."},{"key":"841_CR192","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veac023","author":"DW Wright","year":"2022","unstructured":"Wright, D. W. et al. Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer. Virus Evol. https:\/\/doi.org\/10.1093\/ve\/veac023 (2022).","journal-title":"Virus Evol."},{"key":"841_CR193","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1126\/science.abh2644","volume":"372","author":"NR Faria","year":"2021","unstructured":"Faria, N. R. et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science 372, 815\u2013821 (2021).","journal-title":"Science"},{"key":"841_CR194","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1038\/s41586-021-03402-9","volume":"592","author":"H Tegally","year":"2021","unstructured":"Tegally, H. et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature 592, 438\u2013443 (2021).","journal-title":"Nature"},{"key":"841_CR195","doi-asserted-by":"publisher","first-page":"995","DOI":"10.1126\/science.abj9932","volume":"374","author":"MS Dhar","year":"2021","unstructured":"Dhar, M. S. et al. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science 374, 995\u2013999 (2021).","journal-title":"Science"},{"key":"841_CR196","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-05200-3","author":"JT McCrone","year":"2022","unstructured":"McCrone, J. T. et al. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature https:\/\/doi.org\/10.1038\/s41586-022-05200-3 (2022).","journal-title":"Nature"},{"key":"841_CR197","unstructured":"UKHSA. SARS-CoV-2 Variants of Concern and Variants Under Investigation in England: Technical Briefing 25 (UKHSA, 2021)."},{"key":"841_CR198","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1038\/d41586-022-00215-2","volume":"602","author":"S Mallapaty","year":"2022","unstructured":"Mallapaty, S. Where did Omicron come from? Three key theories. Nature 602, 26\u201328 (2022).","journal-title":"Nature"},{"key":"841_CR199","doi-asserted-by":"publisher","first-page":"2291","DOI":"10.1056\/NEJMc2031364","volume":"383","author":"B Choi","year":"2020","unstructured":"Choi, B. et al. Persistence and evolution of SARS-CoV-2 in an immunocompromised host. N. Engl. J. Med. 383, 2291\u20132293 (2020).","journal-title":"N. Engl. J. Med."},{"key":"841_CR200","doi-asserted-by":"publisher","unstructured":"Chaguza, C. et al. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Preprint at medRxiv https:\/\/doi.org\/10.1101\/2022.06.29.22276868 (2022).","DOI":"10.1101\/2022.06.29.22276868"},{"key":"841_CR201","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1038\/s41586-021-03291-y","volume":"592","author":"SA Kemp","year":"2021","unstructured":"Kemp, S. A. et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature 592, 277\u2013282 (2021).","journal-title":"Nature"},{"key":"841_CR202","doi-asserted-by":"publisher","first-page":"5179","DOI":"10.1016\/j.cell.2021.08.014","volume":"184","author":"B Jackson","year":"2021","unstructured":"Jackson, B. et al. Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell 184, 5179\u20135188.e8 (2021).","journal-title":"Cell"},{"key":"841_CR203","doi-asserted-by":"publisher","DOI":"10.7883\/yoken.JJID.2021.844","author":"T Sekizuka","year":"2022","unstructured":"Sekizuka, T. et al. Genome recombination between Delta and Alpha variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Jpn J. Infect. Dis. https:\/\/doi.org\/10.7883\/yoken.JJID.2021.844 (2022).","journal-title":"Jpn J. Infect. Dis."},{"key":"841_CR204","doi-asserted-by":"publisher","unstructured":"Simon-Loriere, E. et al. Rapid characterization of a Delta-Omicron SARS-CoV-2 recombinant detected in Europe. Preprint at Res. Sq. https:\/\/doi.org\/10.21203\/rs.3.rs-1502293\/v1 (2022).","DOI":"10.21203\/rs.3.rs-1502293\/v1"},{"key":"841_CR205","unstructured":"UKHSA. SARS-CoV-2 Variants of Concern and Variants Under Investigation in England: Technical Briefing 40 (UKHSA, 2022)."},{"key":"841_CR206","unstructured":"Network for Surveillance-South Africa (NGS-SA). SARS-CoV-2 Sequencing Update 15 July 2022 (NGS-SA, 2022)."},{"key":"841_CR207","doi-asserted-by":"publisher","unstructured":"Cao, Y. et al. Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.09.15.507787 (2022).","DOI":"10.1101\/2022.09.15.507787"},{"key":"841_CR208","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evac018","author":"S Lytras","year":"2022","unstructured":"Lytras, S. et al. Exploring the natural origins of SARS-CoV-2 in the light of recombination. Genome Biol. Evol. https:\/\/doi.org\/10.1093\/gbe\/evac018 (2022).","journal-title":"Genome Biol. Evol."},{"key":"841_CR209","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1016\/j.tpb.2007.05.004","volume":"72","author":"L Demetrius","year":"2007","unstructured":"Demetrius, L. & Ziehe, M. Darwinian fitness. Theor. Popul. Biol. 72, 323\u2013345 (2007).","journal-title":"Theor. Popul. Biol."},{"key":"841_CR210","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1146\/annurev.micro.51.1.151","volume":"51","author":"E Domingo","year":"1997","unstructured":"Domingo, E. & Holland, J. J. RNA virus mutations and fitness for survival. Annu. Rev. Microbiol. 51, 151\u2013178 (1997).","journal-title":"Annu. Rev. Microbiol."},{"key":"841_CR211","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1016\/j.coviro.2012.07.007","volume":"2","author":"AR Wargo","year":"2012","unstructured":"Wargo, A. R. & Kurath, G. Viral fitness: definitions, measurement, and current insights. Curr. Opin. Virol. 2, 538\u2013545 (2012).","journal-title":"Curr. Opin. Virol."}],"container-title":["Nature Reviews Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41579-022-00841-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41579-022-00841-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41579-022-00841-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,18]],"date-time":"2023-01-18T12:10:53Z","timestamp":1674043853000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41579-022-00841-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,18]]},"references-count":211,"alternative-id":["841"],"URL":"https:\/\/doi.org\/10.1038\/s41579-022-00841-7","relation":{},"ISSN":["1740-1526","1740-1534"],"issn-type":[{"value":"1740-1526","type":"print"},{"value":"1740-1534","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,1,18]]},"assertion":[{"value":"7 December 2022","order":1,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 January 2023","order":2,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"This content has been made available to all.","name":"free","label":"Free to read"}]}}