SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity
Many SARS-CoV-2 variants with naturally acquired mutations have emerged. These mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has been investigated, sensitivity to human leukocyt...
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| Published in | Cell host & microbe Vol. 29; no. 7; pp. 1124 - 1136.e11 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
14.07.2021
The Authors. Published by Elsevier Inc |
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| Online Access | Get full text |
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| Abstract | Many SARS-CoV-2 variants with naturally acquired mutations have emerged. These mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has been investigated, sensitivity to human leukocyte antigen (HLA)-restricted cellular immunity remains largely unexplored. Here, we demonstrate that two recently emerging mutations in the receptor-binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429 and B.1.617) and Y453F (in B.1.1.298), confer escape from HLA-A24-restricted cellular immunity. These mutations reinforce affinity toward the host entry receptor ACE2. Notably, the L452R mutation increases spike stability, viral infectivity, viral fusogenicity, and thereby promotes viral replication. These data suggest that HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes and that a further threat of the SARS-CoV-2 pandemic is escape from cellular immunity.
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•L452R and Y453F mutations in the SARS-CoV-2 spike RBM have emerged•L452R and Y453F mutants escape HLA-A24-restricted cellular immunity•L452R increases viral infectivity and fusogenicity and promotes viral replication
Motozono and G2P-Japan Consortium et al. show that the emerging mutations L452R and Y453F in the SARS-CoV-2 spike receptor-binding motif evade HLA-A24-restricted cellular immunity. L452R increases spike stability, viral infectivity, and viral fusogenicity, thereby promoting viral replication. These data suggest that HLA-restricted cellular immunity potentially affects evolution of viral phenotypes. |
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| AbstractList | Many SARS-CoV-2 variants with naturally acquired mutations have emerged. These mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has been investigated, sensitivity to human leukocyte antigen (HLA)-restricted cellular immunity remains largely unexplored. Here, we demonstrate that two recently emerging mutations in the receptor-binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429 and B.1.617) and Y453F (in B.1.1.298), confer escape from HLA-A24-restricted cellular immunity. These mutations reinforce affinity toward the host entry receptor ACE2. Notably, the L452R mutation increases spike stability, viral infectivity, viral fusogenicity, and thereby promotes viral replication. These data suggest that HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes and that a further threat of the SARS-CoV-2 pandemic is escape from cellular immunity.Many SARS-CoV-2 variants with naturally acquired mutations have emerged. These mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has been investigated, sensitivity to human leukocyte antigen (HLA)-restricted cellular immunity remains largely unexplored. Here, we demonstrate that two recently emerging mutations in the receptor-binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429 and B.1.617) and Y453F (in B.1.1.298), confer escape from HLA-A24-restricted cellular immunity. These mutations reinforce affinity toward the host entry receptor ACE2. Notably, the L452R mutation increases spike stability, viral infectivity, viral fusogenicity, and thereby promotes viral replication. These data suggest that HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes and that a further threat of the SARS-CoV-2 pandemic is escape from cellular immunity. Many SARS-CoV-2 variants with naturally acquired mutations have emerged. These mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has been investigated, sensitivity to human leukocyte antigen (HLA)-restricted cellular immunity remains largely unexplored. Here, we demonstrate that two recently emerging mutations in the receptor-binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429 and B.1.617) and Y453F (in B.1.1.298), confer escape from HLA-A24-restricted cellular immunity. These mutations reinforce affinity toward the host entry receptor ACE2. Notably, the L452R mutation increases spike stability, viral infectivity, viral fusogenicity, and thereby promotes viral replication. These data suggest that HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes and that a further threat of the SARS-CoV-2 pandemic is escape from cellular immunity. Motozono and G2P-Japan Consortium et al. show that the emerging mutations L452R and Y453F in the SARS-CoV-2 spike receptor-binding motif evade HLA-A24-restricted cellular immunity. L452R increases spike stability, viral infectivity, and viral fusogenicity, thereby promoting viral replication. These data suggest that HLA-restricted cellular immunity potentially affects evolution of viral phenotypes. Many SARS-CoV-2 variants with naturally acquired mutations have emerged. These mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has been investigated, sensitivity to human leukocyte antigen (HLA)-restricted cellular immunity remains largely unexplored. Here, we demonstrate that two recently emerging mutations in the receptor-binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429 and B.1.617) and Y453F (in B.1.1.298), confer escape from HLA-A24-restricted cellular immunity. These mutations reinforce affinity toward the host entry receptor ACE2. Notably, the L452R mutation increases spike stability, viral infectivity, viral fusogenicity, and thereby promotes viral replication. These data suggest that HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes and that a further threat of the SARS-CoV-2 pandemic is escape from cellular immunity. Many SARS-CoV-2 variants with naturally acquired mutations have emerged. These mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has been investigated, sensitivity to human leukocyte antigen (HLA)-restricted cellular immunity remains largely unexplored. Here, we demonstrate that two recently emerging mutations in the receptor-binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429 and B.1.617) and Y453F (in B.1.1.298), confer escape from HLA-A24-restricted cellular immunity. These mutations reinforce affinity toward the host entry receptor ACE2. Notably, the L452R mutation increases spike stability, viral infectivity, viral fusogenicity, and thereby promotes viral replication. These data suggest that HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes and that a further threat of the SARS-CoV-2 pandemic is escape from cellular immunity. [Display omitted] •L452R and Y453F mutations in the SARS-CoV-2 spike RBM have emerged•L452R and Y453F mutants escape HLA-A24-restricted cellular immunity•L452R increases viral infectivity and fusogenicity and promotes viral replication Motozono and G2P-Japan Consortium et al. show that the emerging mutations L452R and Y453F in the SARS-CoV-2 spike receptor-binding motif evade HLA-A24-restricted cellular immunity. L452R increases spike stability, viral infectivity, and viral fusogenicity, thereby promoting viral replication. These data suggest that HLA-restricted cellular immunity potentially affects evolution of viral phenotypes. |
| Author | Tan, Toong Seng Toya, Takashi Nakagawa, So Kosugi, Yusuke Sato, Kei Shimono, Nobuyuki Yue, Yuan Schreiber, Gideon Kimura, Izumi Shimizu, Ryo Nagasaki, Yoji Matsuura, Yoshiharu Ikeda, Terumasa Nasser, Hesham Saito, Akatsuki Uriu, Keiya Motozono, Chihiro Sekiya, Noritaka Ueno, Takamasa Fukuhara, Takasuke Zahradnik, Jiri Torii, Shiho Yonekawa, Akiko Minami, Rumi Ngare, Isaac Ito, Jumpei Toyoda, Mako |
| Author_xml | – sequence: 1 givenname: Chihiro surname: Motozono fullname: Motozono, Chihiro organization: Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan – sequence: 2 givenname: Mako surname: Toyoda fullname: Toyoda, Mako organization: Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan – sequence: 3 givenname: Jiri surname: Zahradnik fullname: Zahradnik, Jiri organization: Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel – sequence: 4 givenname: Akatsuki surname: Saito fullname: Saito, Akatsuki organization: Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan – sequence: 5 givenname: Hesham surname: Nasser fullname: Nasser, Hesham organization: Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan – sequence: 6 givenname: Toong Seng surname: Tan fullname: Tan, Toong Seng organization: Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan – sequence: 7 givenname: Isaac surname: Ngare fullname: Ngare, Isaac organization: Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan – sequence: 8 givenname: Izumi surname: Kimura fullname: Kimura, Izumi organization: Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan – sequence: 9 givenname: Keiya surname: Uriu fullname: Uriu, Keiya organization: Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan – sequence: 10 givenname: Yusuke surname: Kosugi fullname: Kosugi, Yusuke organization: Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan – sequence: 11 givenname: Yuan surname: Yue fullname: Yue, Yuan organization: Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan – sequence: 12 givenname: Ryo surname: Shimizu fullname: Shimizu, Ryo organization: Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan – sequence: 13 givenname: Jumpei surname: Ito fullname: Ito, Jumpei organization: Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan – sequence: 14 givenname: Shiho surname: Torii fullname: Torii, Shiho organization: Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan – sequence: 15 givenname: Akiko surname: Yonekawa fullname: Yonekawa, Akiko organization: Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 8128582, Japan – sequence: 16 givenname: Nobuyuki surname: Shimono fullname: Shimono, Nobuyuki organization: Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 8128582, Japan – sequence: 17 givenname: Yoji surname: Nagasaki fullname: Nagasaki, Yoji organization: Division of Infectious Diseases, Clinical Research Institute, National Hospitalization Organization, Kyushu Medical Center, Fukuoka 8108563, Japan – sequence: 18 givenname: Rumi surname: Minami fullname: Minami, Rumi organization: Internal Medicine, Clinical Research Institute, National Hospital Organization, Kyushu Medical Center, Fukuoka 8108563, Japan – sequence: 19 givenname: Takashi surname: Toya fullname: Toya, Takashi organization: Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo 1138677, Japan – sequence: 20 givenname: Noritaka surname: Sekiya fullname: Sekiya, Noritaka organization: Department of Infection Prevention and Control, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo 1138677, Japan – sequence: 21 givenname: Takasuke surname: Fukuhara fullname: Fukuhara, Takasuke organization: Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Hokkaido 0608638, Japan – sequence: 22 givenname: Yoshiharu surname: Matsuura fullname: Matsuura, Yoshiharu organization: Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan – sequence: 23 givenname: Gideon surname: Schreiber fullname: Schreiber, Gideon organization: Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel – sequence: 24 givenname: Terumasa surname: Ikeda fullname: Ikeda, Terumasa email: ikedat@kumamoto-u.ac.jp organization: Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan – sequence: 25 givenname: So surname: Nakagawa fullname: Nakagawa, So email: so@tokai.ac.jp organization: Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan – sequence: 26 givenname: Takamasa surname: Ueno fullname: Ueno, Takamasa email: uenotaka@kumamoto-u.ac.jp organization: Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan – sequence: 27 givenname: Kei surname: Sato fullname: Sato, Kei email: keisato@g.ecc.u-tokyo.ac.jp organization: Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/34171266$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1128/JVI.00940-20 10.1038/s10038-020-0771-5 10.1093/bioinformatics/btz305 10.1016/j.cell.2021.02.033 10.1016/j.cell.2021.03.036 10.1016/j.chom.2020.03.023 10.1016/S1473-3099(20)30912-9 10.1038/s41590-020-00808-x 10.1073/pnas.2002589117 10.1016/j.cell.2021.02.042 10.1016/j.xcrm.2021.100221 10.1126/science.abb2762 10.1016/j.chom.2021.01.004 10.1016/j.celrep.2021.109017 10.1016/j.pecon.2020.09.008 10.1016/j.abb.2012.04.022 10.1038/s41586-021-03361-1 10.1038/s41586-020-2895-3 10.1128/mSphere.00658-20 10.1128/JVI.07020-11 10.1172/JCI145476 10.1016/j.cell.2020.11.020 10.1001/jama.2021.1612 10.1038/s41586-021-03398-2 10.1038/s41586-020-2324-7 10.1038/s41564-020-0770-5 10.1186/s12864-020-6635-8 10.1371/journal.ppat.1007010 10.1016/j.cell.2021.03.013 10.1038/s41586-020-2008-3 10.1016/j.cell.2020.03.045 10.1038/76744 10.1110/ps.0239403 10.1093/bioinformatics/btv639 10.1007/s00251-011-0579-8 10.1016/j.humimm.2018.09.008 10.2807/1560-7917.ES.2021.26.11.2100256 10.1016/j.jbc.2021.100536 10.1038/nrg2323 10.1126/science.abc6284 10.1016/j.chom.2021.01.014 10.1186/s12977-018-0459-5 10.1002/0471143030.cb2609s50 10.1038/s41591-021-01294-w 10.1073/pnas.2010146117 10.1038/s41586-020-2012-7 10.1093/nar/gkaa379 10.1126/science.272.5259.263 10.1128/JVI.01143-07 10.1056/NEJMc2013400 10.1016/j.cell.2020.07.012 10.1093/molbev/mst010 10.1074/jbc.RA120.013887 10.1084/jem.20202617 10.1182/blood-2006-11-056168 10.1038/nm992 10.1136/bmj.n579 10.1093/molbev/msz189 10.1016/0378-1119(91)90434-D 10.1099/jgv.0.001276 10.1038/s41591-020-01143-2 10.1089/crispr.2018.0014 10.1126/science.abf6950 10.1002/jcc.20084 10.1126/science.abe5901 10.1186/1742-4690-6-53 10.1016/j.celrep.2021.109014 10.1038/s41586-020-2180-5 10.1093/bioinformatics/btp348 10.1016/j.isci.2021.102311 10.1016/j.cell.2020.06.043 10.1128/MMBR.00004-08 10.1016/j.cell.2020.09.032 10.1038/s41586-021-03412-7 10.1093/nar/gkn202 10.1007/BF00216838 10.1126/science.abc4776 10.1038/s41467-021-21118-2 10.1016/j.chom.2021.03.002 10.1038/s41586-021-03426-1 10.7554/eLife.61312.sa2 10.1126/science.abd0831 10.1126/science.abb7015 10.1016/j.chom.2021.02.020 10.1126/science.abe8499 10.1056/NEJMc2102017 10.1093/bioinformatics/btp137 10.1038/s41577-018-0007-5 10.1007/978-1-62703-764-8_6 10.1038/s41590-021-00902-8 |
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| References | Zhao, Chen, Szabla, Zheng, Li, Du, Zheng, Li, Song, Li (bib100) 2020 Schulien, Kemming, Oberhardt, Wild, Seidel, Killmer, Sagar, Daul, Salvat Lago, Decker (bib75) 2021; 27 Liu, Hu, Wang, Ren, Zhao, Ji, Zhu, Feng, Gong, Ju (bib48) 2021; 118 Anderson, Ikeda, Moghadasi, Martin, Brown, Harris (bib1) 2018; 15 Niwa, Yamamura, Miyazaki (bib61) 1991; 108 Challen, Brooks-Pollock, Read, Dyson, Tsaneva-Atanasova, Danon (bib9) 2021; 372 Katoh, Standley (bib34) 2013; 30 Reynisson, Alvarez, Paul, Peters, Nielsen (bib73) 2020; 48 Karosiene, Lundegaard, Lund, Nielsen (bib33) 2012; 64 Zhou, Yang, Wang, Hu, Zhang, Zhang, Si, Zhu, Li, Huang (bib101) 2020; 579 Zahradník, Marciano, Shemesh, Zoler, Chiaravalli, Meyer, Rudich, Dym, Elad, Schreiber (bib97) 2021 Yan, Zhang, Li, Xia, Guo, Zhou (bib93) 2020; 367 (bib7) 2019 Capella-Gutiérrez, Silla-Martínez, Gabaldón (bib6) 2009; 25 Zhang, Lund, Nielsen (bib98) 2009; 25 Pettersen, Goddard, Huang, Couch, Greenblatt, Meng, Ferrin (bib68) 2004; 25 Davies, Jarvis, Edmunds, Jewell, Diaz-Ordaz, Keogh (bib15) 2021; 593 Hoffmann, Zhang, Krüger, Graichen, Kleine-Weber, Hofmann-Winkler, Kempf, Nessler, Riggert, Winkler (bib26) 2021; 35 Matsuyama, Nao, Shirato, Kawase, Saito, Takayama, Nagata, Sekizuka, Katoh, Kato (bib53) 2020; 117 Ikeda, Symeonides, Albin, Li, Thali, Harris (bib29) 2018; 14 Wang, Zhang, Wu, Niu, Song, Zhang, Lu, Qiao, Hu, Yuen (bib84) 2020; 181 Leslie, Pfafferott, Chetty, Draenert, Addo, Feeney, Tang, Holmes, Allen, Prado (bib45) 2004; 10 Peleg, Unger (bib67) 2014; 1116 Liu, Liu, Xia, Zhang, Fontes-Garfias, Swanson, Cai, Sarkar, Chen, Cutler (bib49) 2021; 384 Kozlov, Darriba, Flouri, Morel, Stamatakis (bib41) 2019; 35 Bayarri-Olmos, Rosbjerg, Johnsen, Helgstrand, Bak-Thomsen, Garred, Skjoedt (bib5) 2021; 296 Torii, Ono, Suzuki, Morioka, Anzai, Fauzyah, Maeda, Kamitani, Fukuhara, Matsuura (bib81) 2021; 35 Ozono, Zhang, Ode, Sano, Tan, Imai, Miyoshi, Kishigami, Ueno, Iwatani (bib65) 2021; 12 Shen, Tang, McDanal, Wagh, Fischer, Theiler, Yoon, Li, Haynes, Sanders (bib78) 2021; 29 (bib89) 2020 Volz, Hill, McCrone, Price, Jorgensen, O’Toole, Southgate, Johnson, Jackson, Nascimento (bib83) 2021; 184 Wang, Nair, Liu, Iketani, Luo, Guo, Wang, Yu, Zhang, Kwong (bib86) 2021; 593 Montagutelli, Prot, Levillayer, Salazar, Jouvion, Conquet, Donati, Albert, Gambaro, Behillil (bib55) 2021 Damas, Hughes, Keough, Painter, Persky, Corbo, Hiller, Koepfli, Pfenning, Zhao (bib13) 2020; 117 Naldini, Blömer, Gallay, Ory, Mulligan, Gage, Verma, Trono (bib58) 1996; 272 Wang, Nair, Liu, Iketani, Luo, Guo, Wang, Yu, Zhang, Kwong (bib85) 2021; 593 Darriba, Posada, Kozlov, Stamatakis, Morel, Flouri (bib14) 2020; 37 La Gruta, Gras, Daley, Thomas, Rossjohn (bib42) 2018; 18 Wu, Zhao, Yu, Chen, Wang, Song, Hu, Tao, Tian, Pei (bib92) 2020; 579 Plante, Mitchell, Plante, Debbink, Weaver, Menachery (bib70) 2021; 29 Nelde, Bilich, Heitmann, Maringer, Salih, Roerden, Lübke, Bauer, Rieth, Wacker (bib59) 2021; 22 Plante, Liu, Liu, Xia, Johnson, Lokugamage, Zhang, Muruato, Zou, Fontes-Garfias (bib69) 2021; 592 Martínez-Hernández, Isaak-Delgado, Alfonso-Toledo, Muñoz-García, Villalobos, Aréchiga-Ceballos, Rendón-Franco (bib52) 2020; 18 (bib88) 2020 Le Bert, Clapham, Tan, Chia, Tham, Lim, Kunasegaran, Tan, Dutertre, Shankar (bib44) 2021; 218 Wolfl, Kuball, Ho, Nguyen, Manley, Bleakley, Greenberg (bib91) 2007; 110 Li, Nie, Wu, Zhang, Ding, Wang, Zhang, Li, Liu, Zhang (bib47) 2021; 184 Oude Munnink, Sikkema, Nieuwenhuijse, Molenaar, Munger, Molenkamp, van der Spek, Tolsma, Rietveld, Brouwer (bib63) 2021; 371 Moore, Grifoni, Weiskopf, Schulten, Arlehamn, Angelo, Pham, Leary, Sidney, Broide (bib56) 2018; 79 Collier, De Marco, Ferreira, Meng, Datir, Walls, Kemp, Bassi, Pinto, Silacci-Fregni (bib12) 2021; 593 Kim, Kim, Kim, Kim, Park, Yu, Chang, Kim, Lee, Casel (bib35) 2020; 27 Li, Wu, Nie, Zhang, Hao, Liu, Zhao, Zhang, Liu, Nie (bib46) 2020; 182 Nielsen, Lundegaard, Worning, Lauemøller, Lamberth, Buus, Brunak, Lund (bib60) 2003; 12 Fryer, Frater, Duda, Palmer, Phillips, McLean (bib18) 2012; 86 Supasa, Zhou, Dejnirattisai, Liu, Mentzer, Ginn, Zhao, Duyvesteyn, Nutalai, Tuekprakhon (bib80) 2021; 184 Chandrashekar, Liu, Martinot, McMahan, Mercado, Peter, Tostanoski, Yu, Maliga, Nekorchuk (bib10) 2020; 369 Sato, Yamamoto, Misawa, Yoshida, Miyazawa, Koyanagi (bib74) 2009; 6 Banerjee, Mossman, Baker (bib3) 2021; 29 Lan, Ge, Yu, Shan, Zhou, Fan, Zhang, Shi, Wang, Zhang, Wang (bib43) 2020; 581 Hu, Shen, Han, Chen, Li, Chen, Zhang, Gao, Wang, Wang (bib28) 2020 Rambaut, Holmes, O’Toole, Hill, McCrone, Ruis, du Plessis, Pybus (bib71) 2020; 5 Halfmann, Hatta, Chiba, Maemura, Fan, Takeda, Kinoshita, Hattori, Sakai-Tagawa, Iwatsuki-Horimoto (bib24) 2020; 383 Wilson, Hirneise, Singharoy, Anderson (bib90) 2021; 2 Rausch, Fritz, Untergasser, Benes (bib72) 2020; 21 Yu, Tostanoski, Peter, Mercado, McMahan, Mahrokhian, Nkolola, Liu, Li, Chandrashekar (bib94) 2020; 369 Deng, Garcia-Knight, Khalid, Servellita, Wang, Morris, Sotomayor-González, Glasner, Reyes, Gliwa (bib16) 2021 Koopmans (bib39) 2021; 21 Hou, Chiba, Halfmann, Ehre, Kuroda, Dinnon, Leist, Schäfer, Nakajima, Takahashi (bib27) 2020; 370 Zahradník, Dey, Marciano, Schreiber (bib96) 2021 Kluesner, Nedveck, Lahr, Garbe, Abrahante, Webber, Moriarity (bib37) 2018; 1 Selzer, Albeck, Schreiber (bib76) 2000; 7 Zhou, Thao, Hoffmann, Taddeo, Ebert, Labroussaa, Pohlmann, King, Steiner, Kelly (bib102) 2021; 592 Chen, Zhang, Case, Winkler, Liu, VanBlargan, Liu, Errico, Xie, Suryadevara (bib11) 2021; 27 Parrish, Holmes, Morens, Park, Burke, Calisher, Laughlin, Saif, Daszak (bib66) 2008; 72 Duffy, Shackelton, Holmes (bib17) 2008; 9 Zhang, Davis, Chen, Sincuir Martinez, Plummer, Vail (bib99) 2021; 325 Traxlmayr, Obinger (bib82) 2012; 526 Hoffmann, Arora, Groß, Seidel, Hörnich, Hahn, Krüger, Graichen, Hofmann-Winkler, Kempf (bib25) 2021; 184 Gonzalez-Galarza, McCabe, Santos, Jones, Takeshita, Ortega-Rivera, Cid-Pavon, Ramsbottom, Ghattaoraya, Alfirevic (bib22) 2020; 48 Kiyotani, Toyoshima, Nemoto, Nakamura (bib36) 2020; 65 McCarthy, Rennick, Nambulli, Robinson-McCarthy, Bain, Haidar, Duprex (bib54) 2021; 371 Ozono, Zhang, Tobiume, Kishigami, Tokunaga (bib64) 2020; 295 Andreatta, Nielsen (bib2) 2016; 32 Fukushi, Mizutani, Sakai, Saijo, Taguchi, Yokoyama, Kurane, Morikawa (bib19) 2007; 81 Kondo, Miyauchi, Matsuda (bib38) 2011 (bib62) 2021 Grint, Wing, Williamson, McDonald, Bhaskaran, Evans, Evans, Walker, Hickman, Nightingale (bib23) 2021; 26 Ikeda, Molan, Jarvis, Carpenter, Salamango, Brown, Harris (bib30) 2019; 100 (bib8) 2020 Gao, Chen, Amitai, Doelger, Mallajosyula, Sundquist, Segal, Carrington, Davis, Streeck (bib20) 2021; 24 Weisblum, Schmidt, Zhang, DaSilva, Poston, Lorenzi, Muecksch, Rutkowska, Hoffmann, Michailidis (bib87) 2020 Munster, Feldmann, Williamson, van Doremalen, Pérez-Pérez, Schulz, Meade-White, Okumura, Callison, Brumbaugh (bib57) 2020; 585 Lundegaard, Lamberth, Harndahl, Buus, Lund, Nielsen (bib51) 2008; 36 Yurkovetskiy, Wang, Pascal, Tomkins-Tinch, Nyalile, Wang, Baum, Diehl, Dauphin, Carbone (bib95) 2020; 183 Shi, Wen, Zhong, Yang, Wang, Huang, Liu, He, Shuai, Sun (bib79) 2020; 368 Karaki, Kariyone, Kato, Kano, Iwakura, Takiguchi (bib31) 1993; 37 Liu, VanBlargan, Bloyet, Rothlauf, Chen, Stumpf, Zhao, Errico, Theel, Liebeskind (bib50) 2021; 29 Garcia-Beltran, Lam, St Denis, Nitido, Garcia, Hauser, Feldman, Pavlovic, Gregory, Poznansky (bib21) 2021; 184 Korber, Fischer, Gnanakaran, Yoon, Theiler, Abfalterer, Hengartner, Giorgi, Bhattacharya, Foley (bib40) 2020; 182 Kared, Redd, Bloch, Bonny, Sumatoh, Kairi, Carbajo, Abel, Newell, Bettinotti (bib32) 2021; 131 Zuo, Dowell, Pearce, Verma, Long, Begum, Aiano, Amin-Chowdhury, Hoschler, Brooks (bib103) 2021; 22 Shema Mugisha, Vuong, Puray-Chavez, Bailey, Fox, Chen, Wessel, Scott, Harastani, Boon (bib77) 2020; 5 Baum, Fulton, Wloga, Copin, Pascal, Russo, Giordano, Lanza, Negron, Ni (bib4) 2020; 369 Kondo (10.1016/j.chom.2021.06.006_bib38) 2011 Ozono (10.1016/j.chom.2021.06.006_bib65) 2021; 12 Wang (10.1016/j.chom.2021.06.006_bib86) 2021; 593 Capella-Gutiérrez (10.1016/j.chom.2021.06.006_bib6) 2009; 25 Naldini (10.1016/j.chom.2021.06.006_bib58) 1996; 272 Yan (10.1016/j.chom.2021.06.006_bib93) 2020; 367 Banerjee (10.1016/j.chom.2021.06.006_bib3) 2021; 29 Lundegaard (10.1016/j.chom.2021.06.006_bib51) 2008; 36 Grint (10.1016/j.chom.2021.06.006_bib23) 2021; 26 Zhou (10.1016/j.chom.2021.06.006_bib101) 2020; 579 Liu (10.1016/j.chom.2021.06.006_bib50) 2021; 29 Torii (10.1016/j.chom.2021.06.006_bib81) 2021; 35 Martínez-Hernández (10.1016/j.chom.2021.06.006_bib52) 2020; 18 Montagutelli (10.1016/j.chom.2021.06.006_bib55) 2021 Wolfl (10.1016/j.chom.2021.06.006_bib91) 2007; 110 Hoffmann (10.1016/j.chom.2021.06.006_bib25) 2021; 184 Hu (10.1016/j.chom.2021.06.006_bib28) 2020 McCarthy (10.1016/j.chom.2021.06.006_bib54) 2021; 371 Weisblum (10.1016/j.chom.2021.06.006_bib87) 2020 Wu (10.1016/j.chom.2021.06.006_bib92) 2020; 579 Li (10.1016/j.chom.2021.06.006_bib47) 2021; 184 Zahradník (10.1016/j.chom.2021.06.006_bib97) 2021 Moore (10.1016/j.chom.2021.06.006_bib56) 2018; 79 Zhou (10.1016/j.chom.2021.06.006_bib102) 2021; 592 Kiyotani (10.1016/j.chom.2021.06.006_bib36) 2020; 65 Shen (10.1016/j.chom.2021.06.006_bib78) 2021; 29 Deng (10.1016/j.chom.2021.06.006_bib16) 2021 Shema Mugisha (10.1016/j.chom.2021.06.006_bib77) 2020; 5 La Gruta (10.1016/j.chom.2021.06.006_bib42) 2018; 18 Bayarri-Olmos (10.1016/j.chom.2021.06.006_bib5) 2021; 296 Traxlmayr (10.1016/j.chom.2021.06.006_bib82) 2012; 526 Selzer (10.1016/j.chom.2021.06.006_bib76) 2000; 7 Challen (10.1016/j.chom.2021.06.006_bib9) 2021; 372 Reynisson (10.1016/j.chom.2021.06.006_bib73) 2020; 48 Karaki (10.1016/j.chom.2021.06.006_bib31) 1993; 37 Fryer (10.1016/j.chom.2021.06.006_bib18) 2012; 86 Matsuyama (10.1016/j.chom.2021.06.006_bib53) 2020; 117 Wang (10.1016/j.chom.2021.06.006_bib85) 2021; 593 Kluesner (10.1016/j.chom.2021.06.006_bib37) 2018; 1 Yurkovetskiy (10.1016/j.chom.2021.06.006_bib95) 2020; 183 Plante (10.1016/j.chom.2021.06.006_bib70) 2021; 29 Parrish (10.1016/j.chom.2021.06.006_bib66) 2008; 72 Koopmans (10.1016/j.chom.2021.06.006_bib39) 2021; 21 Rausch (10.1016/j.chom.2021.06.006_bib72) 2020; 21 Katoh (10.1016/j.chom.2021.06.006_bib34) 2013; 30 Ozono (10.1016/j.chom.2021.06.006_bib64) 2020; 295 Gonzalez-Galarza (10.1016/j.chom.2021.06.006_bib22) 2020; 48 Nielsen (10.1016/j.chom.2021.06.006_bib60) 2003; 12 Anderson (10.1016/j.chom.2021.06.006_bib1) 2018; 15 Darriba (10.1016/j.chom.2021.06.006_bib14) 2020; 37 Korber (10.1016/j.chom.2021.06.006_bib40) 2020; 182 Gao (10.1016/j.chom.2021.06.006_bib20) 2021; 24 Liu (10.1016/j.chom.2021.06.006_bib49) 2021; 384 Plante (10.1016/j.chom.2021.06.006_bib69) 2021; 592 Zhao (10.1016/j.chom.2021.06.006_bib100) 2020 Hou (10.1016/j.chom.2021.06.006_bib27) 2020; 370 Yu (10.1016/j.chom.2021.06.006_bib94) 2020; 369 Collier (10.1016/j.chom.2021.06.006_bib12) 2021; 593 Munster (10.1016/j.chom.2021.06.006_bib57) 2020; 585 Oude Munnink (10.1016/j.chom.2021.06.006_bib63) 2021; 371 Chandrashekar (10.1016/j.chom.2021.06.006_bib10) 2020; 369 Duffy (10.1016/j.chom.2021.06.006_bib17) 2008; 9 Baum (10.1016/j.chom.2021.06.006_bib4) 2020; 369 Liu (10.1016/j.chom.2021.06.006_bib48) 2021; 118 Chen (10.1016/j.chom.2021.06.006_bib11) 2021; 27 Ikeda (10.1016/j.chom.2021.06.006_bib29) 2018; 14 Zuo (10.1016/j.chom.2021.06.006_bib103) 2021; 22 Li (10.1016/j.chom.2021.06.006_bib46) 2020; 182 Wang (10.1016/j.chom.2021.06.006_bib84) 2020; 181 Wilson (10.1016/j.chom.2021.06.006_bib90) 2021; 2 Schulien (10.1016/j.chom.2021.06.006_bib75) 2021; 27 Halfmann (10.1016/j.chom.2021.06.006_bib24) 2020; 383 Kozlov (10.1016/j.chom.2021.06.006_bib41) 2019; 35 Shi (10.1016/j.chom.2021.06.006_bib79) 2020; 368 Niwa (10.1016/j.chom.2021.06.006_bib61) 1991; 108 Sato (10.1016/j.chom.2021.06.006_bib74) 2009; 6 Karosiene (10.1016/j.chom.2021.06.006_bib33) 2012; 64 Lan (10.1016/j.chom.2021.06.006_bib43) 2020; 581 Ikeda (10.1016/j.chom.2021.06.006_bib30) 2019; 100 Damas (10.1016/j.chom.2021.06.006_bib13) 2020; 117 Fukushi (10.1016/j.chom.2021.06.006_bib19) 2007; 81 Zahradník (10.1016/j.chom.2021.06.006_bib96) 2021 Hoffmann (10.1016/j.chom.2021.06.006_bib26) 2021; 35 Pettersen (10.1016/j.chom.2021.06.006_bib68) 2004; 25 Nelde (10.1016/j.chom.2021.06.006_bib59) 2021; 22 Volz (10.1016/j.chom.2021.06.006_bib83) 2021; 184 Kim (10.1016/j.chom.2021.06.006_bib35) 2020; 27 Davies (10.1016/j.chom.2021.06.006_bib15) 2021; 593 Leslie (10.1016/j.chom.2021.06.006_bib45) 2004; 10 Andreatta (10.1016/j.chom.2021.06.006_bib2) 2016; 32 Garcia-Beltran (10.1016/j.chom.2021.06.006_bib21) 2021; 184 Zhang (10.1016/j.chom.2021.06.006_bib99) 2021; 325 Kared (10.1016/j.chom.2021.06.006_bib32) 2021; 131 Le Bert (10.1016/j.chom.2021.06.006_bib44) 2021; 218 Rambaut (10.1016/j.chom.2021.06.006_bib71) 2020; 5 Supasa (10.1016/j.chom.2021.06.006_bib80) 2021; 184 Peleg (10.1016/j.chom.2021.06.006_bib67) 2014; 1116 Zhang (10.1016/j.chom.2021.06.006_bib98) 2009; 25 |
| References_xml | – volume: 369 start-page: 812 year: 2020 end-page: 817 ident: bib10 article-title: SARS-CoV-2 infection protects against rechallenge in rhesus macaques publication-title: Science – year: 2020 ident: bib28 article-title: Identification of cross-reactive CD8 publication-title: bioRxiv – volume: 79 start-page: 821 year: 2018 end-page: 822 ident: bib56 article-title: Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 496 adults from San Diego, California, USA publication-title: Hum. Immunol. – volume: 29 start-page: 508 year: 2021 end-page: 515 ident: bib70 article-title: The variant gambit: COVID-19's next move publication-title: Cell Host Microbe – volume: 6 start-page: 53 year: 2009 ident: bib74 article-title: Comparative study on the effect of human BST-2/Tetherin on HIV-1 release in cells of various species publication-title: Retrovirology – volume: 25 start-page: 1972 year: 2009 end-page: 1973 ident: bib6 article-title: trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses publication-title: Bioinformatics – volume: 372 start-page: n579 year: 2021 ident: bib9 article-title: Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study publication-title: BMJ – volume: 184 start-page: 2384 year: 2021 end-page: 2393.e12 ident: bib25 article-title: SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies publication-title: Cell – volume: 48 start-page: W449 year: 2020 end-page: W454 ident: bib73 article-title: NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data publication-title: Nucleic Acids Res. – volume: 5 year: 2020 ident: bib77 article-title: A simplified quantitative real-time PCR assay for monitoring SARS-CoV-2 growth in cell culture publication-title: MSphere – volume: 9 start-page: 267 year: 2008 end-page: 276 ident: bib17 article-title: Rates of evolutionary change in viruses: patterns and determinants publication-title: Nat. Rev. Genet. – volume: 25 start-page: 1605 year: 2004 end-page: 1612 ident: bib68 article-title: UCSF Chimera--a visualization system for exploratory research and analysis publication-title: J. Comput. Chem. – volume: 21 start-page: 18 year: 2021 end-page: 19 ident: bib39 article-title: SARS-CoV-2 and the human-animal interface: outbreaks on mink farms publication-title: Lancet Infect. Dis. – volume: 2 start-page: 100221 year: 2021 ident: bib90 article-title: Total predicted MHC-I epitope load is inversely associated with population mortality from SARS-CoV-2 publication-title: Cell Rep. Med. – volume: 117 start-page: 22311 year: 2020 end-page: 22322 ident: bib13 article-title: Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates publication-title: Proc. Natl. Acad. Sci. USA – volume: 37 start-page: 291 year: 2020 end-page: 294 ident: bib14 article-title: ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models publication-title: Mol. Biol. Evol. – volume: 183 start-page: 739 year: 2020 end-page: 751.e8 ident: bib95 article-title: Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant publication-title: Cell – volume: 371 start-page: 1139 year: 2021 end-page: 1142 ident: bib54 article-title: Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape publication-title: Science – volume: 131 start-page: e145476 year: 2021 ident: bib32 article-title: SARS-CoV-2-specific CD8 publication-title: J. Clin. Invest. – start-page: 436013 year: 2021 ident: bib55 article-title: The B1.351 and P.1 variants extend SARS-CoV-2 host range to mice publication-title: bioRxiv – year: 2020 ident: bib100 article-title: Broad and differential animal angiotensin-converting enzyme 2 receptor usage by SARS-CoV-2 publication-title: J. Virol. – volume: 370 start-page: 1464 year: 2020 end-page: 1468 ident: bib27 article-title: SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo publication-title: Science – volume: 35 start-page: 4453 year: 2019 end-page: 4455 ident: bib41 article-title: RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference publication-title: Bioinformatics – volume: 585 start-page: 268 year: 2020 end-page: 272 ident: bib57 article-title: Respiratory disease in rhesus macaques inoculated with SARS-CoV-2 publication-title: Nature – volume: 1116 start-page: 73 year: 2014 end-page: 87 ident: bib67 article-title: Application of the Restriction-Free (RF) cloning for multicomponents assembly publication-title: Methods Mol. Biol. – volume: 184 start-page: 64 year: 2021 end-page: 75.e11 ident: bib83 article-title: Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity publication-title: Cell – volume: 15 start-page: 78 year: 2018 ident: bib1 article-title: Natural APOBEC3C variants can elicit differential HIV-1 restriction activity publication-title: Retrovirology – volume: 12 start-page: 1007 year: 2003 end-page: 1017 ident: bib60 article-title: Reliable prediction of T-cell epitopes using neural networks with novel sequence representations publication-title: Protein Sci. – volume: 5 start-page: 1403 year: 2020 end-page: 1407 ident: bib71 article-title: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology publication-title: Nat. Microbiol. – volume: 65 start-page: 569 year: 2020 end-page: 575 ident: bib36 article-title: Bioinformatic prediction of potential T cell epitopes for SARS-Cov-2 publication-title: J. Hum. Genet. – volume: 593 start-page: 130 year: 2021 end-page: 135 ident: bib86 article-title: Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 publication-title: Nature – volume: 581 start-page: 215 year: 2020 end-page: 220 ident: bib43 article-title: Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor publication-title: Nature – year: 2020 ident: bib89 article-title: SARS-CoV-2 mink-associated variant strain – Denmark (November 6, 2020) – volume: 295 start-page: 13023 year: 2020 end-page: 13030 ident: bib64 article-title: Super-rapid quantitation of the production of HIV-1 harboring a luminescent peptide tag publication-title: J. Biol. Chem. – volume: 21 start-page: 230 year: 2020 ident: bib72 article-title: Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files publication-title: BMC Genomics – volume: 35 start-page: 109014 year: 2021 ident: bib81 article-title: Establishment of a reverse genetics system for SARS-CoV-2 using circular polymerase extension reaction publication-title: Cell Rep. – volume: 182 start-page: 812 year: 2020 end-page: 827.e19 ident: bib40 article-title: Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus publication-title: Cell – volume: 10 start-page: 282 year: 2004 end-page: 289 ident: bib45 article-title: HIV evolution: CTL escape mutation and reversion after transmission publication-title: Nat. Med. – volume: 7 start-page: 537 year: 2000 end-page: 541 ident: bib76 article-title: Rational design of faster associating and tighter binding protein complexes publication-title: Nat. Struct. Biol. – volume: 368 start-page: 1016 year: 2020 end-page: 1020 ident: bib79 article-title: Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 publication-title: Science – volume: 184 start-page: 2372 year: 2021 end-page: 2383.e9 ident: bib21 article-title: Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity publication-title: Cell – volume: 272 start-page: 263 year: 1996 end-page: 267 ident: bib58 article-title: In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector publication-title: Science – volume: 383 start-page: 592 year: 2020 end-page: 594 ident: bib24 article-title: Transmission of SARS-CoV-2 in domestic cats publication-title: N. Engl. J. Med. – volume: 24 start-page: 102311 year: 2021 ident: bib20 article-title: Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-COV-2 publication-title: iScience – year: 2021 ident: bib96 article-title: An enhanced yeast display platform demonstrates the binding plasticity under various selection pressures publication-title: bioRxiv – volume: 296 start-page: 100536 year: 2021 ident: bib5 article-title: The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization publication-title: J. Biol. Chem. – year: 2021 ident: bib16 article-title: Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation publication-title: medRxiv – volume: 592 start-page: 122 year: 2021 end-page: 127 ident: bib102 article-title: SARS-CoV-2 spike D614G change enhances replication and transmission publication-title: Nature – year: 2020 ident: bib87 article-title: Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants publication-title: eLife – volume: 118 year: 2021 ident: bib48 article-title: Functional and genetic analysis of viral receptor ACE2 orthologs reveals a broad potential host range of SARS-CoV-2 publication-title: Proc. Natl. Acad. Sci. USA – volume: 12 start-page: 848 year: 2021 ident: bib65 article-title: SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity publication-title: Nat. Commun. – volume: 81 start-page: 10831 year: 2007 end-page: 10834 ident: bib19 article-title: Amino acid substitutions in the s2 region enhance severe acute respiratory syndrome coronavirus infectivity in rat angiotensin-converting enzyme 2-expressing cells publication-title: J. Virol. – volume: 26 start-page: 2100256 year: 2021 ident: bib23 article-title: Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England, 16 November to 5 February publication-title: Euro Surveill. – volume: 184 start-page: 2201 year: 2021 end-page: 2211.e7 ident: bib80 article-title: Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera publication-title: Cell – year: 2020 ident: bib88 article-title: Coronavirus disease 2019 – volume: 369 start-page: 1014 year: 2020 end-page: 1018 ident: bib4 article-title: Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies publication-title: Science – volume: 526 start-page: 174 year: 2012 end-page: 180 ident: bib82 article-title: Directed evolution of proteins for increased stability and expression using yeast display publication-title: Arch. Biochem. Biophys. – volume: 593 start-page: 130 year: 2021 end-page: 135 ident: bib85 article-title: Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 publication-title: Nature – volume: 25 start-page: 1293 year: 2009 end-page: 1299 ident: bib98 article-title: The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding publication-title: Bioinformatics – volume: 593 start-page: 136 year: 2021 end-page: 141 ident: bib12 article-title: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies publication-title: Nature – volume: 27 start-page: 717 year: 2021 end-page: 726 ident: bib11 article-title: Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies publication-title: Nat. Med. – volume: 29 start-page: 477 year: 2021 end-page: 488.e44 ident: bib50 article-title: Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization publication-title: Cell Host Microbe – volume: 182 start-page: 1284 year: 2020 end-page: 1294.e9 ident: bib46 article-title: The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity publication-title: Cell – volume: 72 start-page: 457 year: 2008 end-page: 470 ident: bib66 article-title: Cross-species virus transmission and the emergence of new epidemic diseases publication-title: Microbiol. Mol. Biol. Rev. – volume: 64 start-page: 177 year: 2012 end-page: 186 ident: bib33 article-title: NetMHCcons: a consensus method for the major histocompatibility complex class I predictions publication-title: Immunogenetics – volume: 22 start-page: 74 year: 2021 end-page: 85 ident: bib59 article-title: SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition publication-title: Nat. Immunol. – volume: 32 start-page: 511 year: 2016 end-page: 517 ident: bib2 article-title: Gapped sequence alignment using artificial neural networks: application to the MHC class I system publication-title: Bioinformatics – volume: 579 start-page: 265 year: 2020 end-page: 269 ident: bib92 article-title: A new coronavirus associated with human respiratory disease in China publication-title: Nature – year: 2011 ident: bib38 article-title: Monitoring viral-mediated membrane fusion using fluorescent reporter methods publication-title: Curr Protoc Cell Biol – volume: 22 start-page: 620 year: 2021 end-page: 626 ident: bib103 article-title: Robust SARS-CoV-2-specific T cell immunity is maintained at 6 months following primary infection publication-title: Nat. Immunol. – volume: 579 start-page: 270 year: 2020 end-page: 273 ident: bib101 article-title: A pneumonia outbreak associated with a new coronavirus of probable bat origin publication-title: Nature – volume: 218 start-page: e20202617 year: 2021 ident: bib44 article-title: Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection publication-title: J. Exp. Med. – volume: 325 start-page: 1324 year: 2021 end-page: 1326 ident: bib99 article-title: Emergence of a novel SARS-CoV-2 variant in Southern California publication-title: JAMA – volume: 36 year: 2008 ident: bib51 article-title: NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11 publication-title: Nucleic Acids Res. – volume: 367 start-page: 1444 year: 2020 end-page: 1448 ident: bib93 article-title: Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 publication-title: Science – volume: 371 start-page: 172 year: 2021 end-page: 177 ident: bib63 article-title: Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans publication-title: Science – year: 2021 ident: bib62 article-title: Infection with SARS-CoV-2 in animals (January 2021) – volume: 117 start-page: 7001 year: 2020 end-page: 7003 ident: bib53 article-title: Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells publication-title: Proc. Natl. Acad. Sci. USA – volume: 18 start-page: 467 year: 2018 end-page: 478 ident: bib42 article-title: Understanding the drivers of MHC restriction of T cell receptors publication-title: Nat. Rev. Immunol. – volume: 184 start-page: 2362 year: 2021 end-page: 2371.e9 ident: bib47 article-title: SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape publication-title: Cell – year: 2019 ident: bib7 article-title: Birth: final data for 2018 – volume: 384 start-page: 1466 year: 2021 end-page: 1468 ident: bib49 article-title: Neutralizing activity of BNT162b2-elicited serum publication-title: N. Engl. J. Med. – volume: 27 start-page: 78 year: 2021 end-page: 85 ident: bib75 article-title: Characterization of pre-existing and induced SARS-CoV-2-specific CD8 publication-title: Nat. Med. – volume: 48 start-page: D783 year: 2020 end-page: D788 ident: bib22 article-title: Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools publication-title: Nucleic Acids Res. – volume: 592 start-page: 116 year: 2021 end-page: 121 ident: bib69 article-title: Spike mutation D614G alters SARS-CoV-2 fitness publication-title: Nature – volume: 29 start-page: 529 year: 2021 end-page: 539.e3 ident: bib78 article-title: SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines publication-title: Cell Host Microbe – volume: 18 start-page: 223 year: 2020 end-page: 234 ident: bib52 article-title: Assessing the SARS-CoV-2 threat to wildlife: Potential risk to a broad range of mammals publication-title: Perspectives in Ecology and Conservation – volume: 108 start-page: 193 year: 1991 end-page: 199 ident: bib61 article-title: Efficient selection for high-expression transfectants with a novel eukaryotic vector publication-title: Gene – volume: 369 start-page: 806 year: 2020 end-page: 811 ident: bib94 article-title: DNA vaccine protection against SARS-CoV-2 in rhesus macaques publication-title: Science – year: 2020 ident: bib8 article-title: Emerging SARS-CoV-2 variants (updated January 28, 2021) – volume: 100 start-page: 1140 year: 2019 end-page: 1152 ident: bib30 article-title: HIV-1 restriction by endogenous APOBEC3G in the myeloid cell line THP-1 publication-title: J. Gen. Virol. – volume: 37 start-page: 139 year: 1993 end-page: 142 ident: bib31 article-title: HLA-B51 transgenic mice as recipients for production of polymorphic HLA-A, B-specific antibodies publication-title: Immunogenetics – volume: 29 start-page: 160 year: 2021 end-page: 164 ident: bib3 article-title: Zooanthroponotic potential of SARS-CoV-2 and implications of reintroduction into human populations publication-title: Cell Host Microbe – volume: 86 start-page: 8568 year: 2012 end-page: 8580 ident: bib18 article-title: Cytotoxic T-lymphocyte escape mutations identified by HLA association favor those which escape and revert rapidly publication-title: J. Virol. – volume: 14 start-page: e1007010 year: 2018 ident: bib29 article-title: HIV-1 adaptation studies reveal a novel Env-mediated homeostasis mechanism for evading lethal hypermutation by APOBEC3G publication-title: PLoS Pathog. – volume: 27 start-page: 704 year: 2020 end-page: 709.e2 ident: bib35 article-title: Infection and rapid transmission of SARS-CoV-2 in ferrets publication-title: Cell Host Microbe – volume: 110 start-page: 201 year: 2007 end-page: 210 ident: bib91 article-title: Activation-induced expression of CD137 permits detection, isolation, and expansion of the full repertoire of CD8 publication-title: Blood – volume: 593 start-page: 270 year: 2021 end-page: 274 ident: bib15 article-title: Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 publication-title: Nature – volume: 35 start-page: 109017 year: 2021 ident: bib26 article-title: SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization publication-title: Cell Rep. – volume: 30 start-page: 772 year: 2013 end-page: 780 ident: bib34 article-title: MAFFT multiple sequence alignment software version 7: improvements in performance and usability publication-title: Mol. Biol. Evol. – volume: 181 start-page: 894 year: 2020 end-page: 904.e9 ident: bib84 article-title: Structural and functional basis of SARS-CoV-2 entry by using human ACE2 publication-title: Cell – volume: 1 start-page: 239 year: 2018 end-page: 250 ident: bib37 article-title: EditR: a method to quantify base editing from Sanger sequencing publication-title: The CRISPR Journal – year: 2021 ident: bib97 article-title: SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread yet generates an able infection inhibitor publication-title: bioRxiv – year: 2020 ident: 10.1016/j.chom.2021.06.006_bib100 article-title: Broad and differential animal angiotensin-converting enzyme 2 receptor usage by SARS-CoV-2 publication-title: J. Virol. doi: 10.1128/JVI.00940-20 – volume: 65 start-page: 569 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib36 article-title: Bioinformatic prediction of potential T cell epitopes for SARS-Cov-2 publication-title: J. Hum. Genet. doi: 10.1038/s10038-020-0771-5 – volume: 35 start-page: 4453 year: 2019 ident: 10.1016/j.chom.2021.06.006_bib41 article-title: RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz305 – volume: 184 start-page: 2201 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib80 article-title: Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera publication-title: Cell doi: 10.1016/j.cell.2021.02.033 – volume: 184 start-page: 2384 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib25 article-title: SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies publication-title: Cell doi: 10.1016/j.cell.2021.03.036 – volume: 27 start-page: 704 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib35 article-title: Infection and rapid transmission of SARS-CoV-2 in ferrets publication-title: Cell Host Microbe doi: 10.1016/j.chom.2020.03.023 – year: 2021 ident: 10.1016/j.chom.2021.06.006_bib96 article-title: An enhanced yeast display platform demonstrates the binding plasticity under various selection pressures publication-title: bioRxiv – volume: 21 start-page: 18 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib39 article-title: SARS-CoV-2 and the human-animal interface: outbreaks on mink farms publication-title: Lancet Infect. Dis. doi: 10.1016/S1473-3099(20)30912-9 – volume: 22 start-page: 74 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib59 article-title: SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition publication-title: Nat. Immunol. doi: 10.1038/s41590-020-00808-x – volume: 117 start-page: 7001 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib53 article-title: Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.2002589117 – volume: 184 start-page: 2362 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib47 article-title: SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape publication-title: Cell doi: 10.1016/j.cell.2021.02.042 – volume: 2 start-page: 100221 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib90 article-title: Total predicted MHC-I epitope load is inversely associated with population mortality from SARS-CoV-2 publication-title: Cell Rep. Med. doi: 10.1016/j.xcrm.2021.100221 – volume: 367 start-page: 1444 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib93 article-title: Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 publication-title: Science doi: 10.1126/science.abb2762 – volume: 29 start-page: 160 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib3 article-title: Zooanthroponotic potential of SARS-CoV-2 and implications of reintroduction into human populations publication-title: Cell Host Microbe doi: 10.1016/j.chom.2021.01.004 – volume: 35 start-page: 109017 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib26 article-title: SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization publication-title: Cell Rep. doi: 10.1016/j.celrep.2021.109017 – volume: 18 start-page: 223 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib52 article-title: Assessing the SARS-CoV-2 threat to wildlife: Potential risk to a broad range of mammals publication-title: Perspectives in Ecology and Conservation doi: 10.1016/j.pecon.2020.09.008 – volume: 526 start-page: 174 year: 2012 ident: 10.1016/j.chom.2021.06.006_bib82 article-title: Directed evolution of proteins for increased stability and expression using yeast display publication-title: Arch. Biochem. Biophys. doi: 10.1016/j.abb.2012.04.022 – volume: 592 start-page: 122 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib102 article-title: SARS-CoV-2 spike D614G change enhances replication and transmission publication-title: Nature doi: 10.1038/s41586-021-03361-1 – volume: 592 start-page: 116 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib69 article-title: Spike mutation D614G alters SARS-CoV-2 fitness publication-title: Nature doi: 10.1038/s41586-020-2895-3 – volume: 5 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib77 article-title: A simplified quantitative real-time PCR assay for monitoring SARS-CoV-2 growth in cell culture publication-title: MSphere doi: 10.1128/mSphere.00658-20 – volume: 86 start-page: 8568 year: 2012 ident: 10.1016/j.chom.2021.06.006_bib18 article-title: Cytotoxic T-lymphocyte escape mutations identified by HLA association favor those which escape and revert rapidly publication-title: J. Virol. doi: 10.1128/JVI.07020-11 – volume: 131 start-page: e145476 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib32 article-title: SARS-CoV-2-specific CD8+ T cell responses in convalescent COVID-19 individuals publication-title: J. Clin. Invest. doi: 10.1172/JCI145476 – volume: 184 start-page: 64 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib83 article-title: Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity publication-title: Cell doi: 10.1016/j.cell.2020.11.020 – volume: 325 start-page: 1324 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib99 article-title: Emergence of a novel SARS-CoV-2 variant in Southern California publication-title: JAMA doi: 10.1001/jama.2021.1612 – volume: 593 start-page: 130 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib86 article-title: Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 publication-title: Nature doi: 10.1038/s41586-021-03398-2 – volume: 585 start-page: 268 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib57 article-title: Respiratory disease in rhesus macaques inoculated with SARS-CoV-2 publication-title: Nature doi: 10.1038/s41586-020-2324-7 – volume: 5 start-page: 1403 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib71 article-title: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology publication-title: Nat. Microbiol. doi: 10.1038/s41564-020-0770-5 – volume: 21 start-page: 230 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib72 article-title: Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files publication-title: BMC Genomics doi: 10.1186/s12864-020-6635-8 – volume: 14 start-page: e1007010 year: 2018 ident: 10.1016/j.chom.2021.06.006_bib29 article-title: HIV-1 adaptation studies reveal a novel Env-mediated homeostasis mechanism for evading lethal hypermutation by APOBEC3G publication-title: PLoS Pathog. doi: 10.1371/journal.ppat.1007010 – volume: 184 start-page: 2372 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib21 article-title: Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity publication-title: Cell doi: 10.1016/j.cell.2021.03.013 – volume: 579 start-page: 265 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib92 article-title: A new coronavirus associated with human respiratory disease in China publication-title: Nature doi: 10.1038/s41586-020-2008-3 – volume: 181 start-page: 894 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib84 article-title: Structural and functional basis of SARS-CoV-2 entry by using human ACE2 publication-title: Cell doi: 10.1016/j.cell.2020.03.045 – volume: 7 start-page: 537 year: 2000 ident: 10.1016/j.chom.2021.06.006_bib76 article-title: Rational design of faster associating and tighter binding protein complexes publication-title: Nat. Struct. Biol. doi: 10.1038/76744 – volume: 12 start-page: 1007 year: 2003 ident: 10.1016/j.chom.2021.06.006_bib60 article-title: Reliable prediction of T-cell epitopes using neural networks with novel sequence representations publication-title: Protein Sci. doi: 10.1110/ps.0239403 – volume: 32 start-page: 511 year: 2016 ident: 10.1016/j.chom.2021.06.006_bib2 article-title: Gapped sequence alignment using artificial neural networks: application to the MHC class I system publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv639 – volume: 64 start-page: 177 year: 2012 ident: 10.1016/j.chom.2021.06.006_bib33 article-title: NetMHCcons: a consensus method for the major histocompatibility complex class I predictions publication-title: Immunogenetics doi: 10.1007/s00251-011-0579-8 – volume: 79 start-page: 821 year: 2018 ident: 10.1016/j.chom.2021.06.006_bib56 article-title: Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 496 adults from San Diego, California, USA publication-title: Hum. Immunol. doi: 10.1016/j.humimm.2018.09.008 – volume: 26 start-page: 2100256 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib23 article-title: Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England, 16 November to 5 February publication-title: Euro Surveill. doi: 10.2807/1560-7917.ES.2021.26.11.2100256 – volume: 296 start-page: 100536 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib5 article-title: The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization publication-title: J. Biol. Chem. doi: 10.1016/j.jbc.2021.100536 – start-page: 436013 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib55 article-title: The B1.351 and P.1 variants extend SARS-CoV-2 host range to mice publication-title: bioRxiv – volume: 9 start-page: 267 year: 2008 ident: 10.1016/j.chom.2021.06.006_bib17 article-title: Rates of evolutionary change in viruses: patterns and determinants publication-title: Nat. Rev. Genet. doi: 10.1038/nrg2323 – volume: 369 start-page: 806 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib94 article-title: DNA vaccine protection against SARS-CoV-2 in rhesus macaques publication-title: Science doi: 10.1126/science.abc6284 – volume: 29 start-page: 477 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib50 article-title: Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization publication-title: Cell Host Microbe doi: 10.1016/j.chom.2021.01.014 – volume: 15 start-page: 78 year: 2018 ident: 10.1016/j.chom.2021.06.006_bib1 article-title: Natural APOBEC3C variants can elicit differential HIV-1 restriction activity publication-title: Retrovirology doi: 10.1186/s12977-018-0459-5 – year: 2011 ident: 10.1016/j.chom.2021.06.006_bib38 article-title: Monitoring viral-mediated membrane fusion using fluorescent reporter methods publication-title: Curr Protoc Cell Biol doi: 10.1002/0471143030.cb2609s50 – volume: 27 start-page: 717 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib11 article-title: Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies publication-title: Nat. Med. doi: 10.1038/s41591-021-01294-w – volume: 117 start-page: 22311 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib13 article-title: Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.2010146117 – volume: 579 start-page: 270 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib101 article-title: A pneumonia outbreak associated with a new coronavirus of probable bat origin publication-title: Nature doi: 10.1038/s41586-020-2012-7 – volume: 48 start-page: W449 issue: W1 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib73 article-title: NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkaa379 – volume: 272 start-page: 263 year: 1996 ident: 10.1016/j.chom.2021.06.006_bib58 article-title: In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector publication-title: Science doi: 10.1126/science.272.5259.263 – volume: 81 start-page: 10831 year: 2007 ident: 10.1016/j.chom.2021.06.006_bib19 article-title: Amino acid substitutions in the s2 region enhance severe acute respiratory syndrome coronavirus infectivity in rat angiotensin-converting enzyme 2-expressing cells publication-title: J. Virol. doi: 10.1128/JVI.01143-07 – volume: 48 start-page: D783 issue: D1 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib22 article-title: Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools publication-title: Nucleic Acids Res. – volume: 118 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib48 article-title: Functional and genetic analysis of viral receptor ACE2 orthologs reveals a broad potential host range of SARS-CoV-2 publication-title: Proc. Natl. Acad. Sci. USA – volume: 383 start-page: 592 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib24 article-title: Transmission of SARS-CoV-2 in domestic cats publication-title: N. Engl. J. Med. doi: 10.1056/NEJMc2013400 – volume: 182 start-page: 1284 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib46 article-title: The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity publication-title: Cell doi: 10.1016/j.cell.2020.07.012 – volume: 30 start-page: 772 year: 2013 ident: 10.1016/j.chom.2021.06.006_bib34 article-title: MAFFT multiple sequence alignment software version 7: improvements in performance and usability publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/mst010 – volume: 295 start-page: 13023 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib64 article-title: Super-rapid quantitation of the production of HIV-1 harboring a luminescent peptide tag publication-title: J. Biol. Chem. doi: 10.1074/jbc.RA120.013887 – volume: 218 start-page: e20202617 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib44 article-title: Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection publication-title: J. Exp. Med. doi: 10.1084/jem.20202617 – volume: 110 start-page: 201 year: 2007 ident: 10.1016/j.chom.2021.06.006_bib91 article-title: Activation-induced expression of CD137 permits detection, isolation, and expansion of the full repertoire of CD8+ T cells responding to antigen without requiring knowledge of epitope specificities publication-title: Blood doi: 10.1182/blood-2006-11-056168 – volume: 10 start-page: 282 year: 2004 ident: 10.1016/j.chom.2021.06.006_bib45 article-title: HIV evolution: CTL escape mutation and reversion after transmission publication-title: Nat. Med. doi: 10.1038/nm992 – volume: 372 start-page: n579 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib9 article-title: Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study publication-title: BMJ doi: 10.1136/bmj.n579 – volume: 37 start-page: 291 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib14 article-title: ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msz189 – volume: 108 start-page: 193 year: 1991 ident: 10.1016/j.chom.2021.06.006_bib61 article-title: Efficient selection for high-expression transfectants with a novel eukaryotic vector publication-title: Gene doi: 10.1016/0378-1119(91)90434-D – volume: 593 start-page: 130 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib85 article-title: Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 publication-title: Nature doi: 10.1038/s41586-021-03398-2 – volume: 100 start-page: 1140 year: 2019 ident: 10.1016/j.chom.2021.06.006_bib30 article-title: HIV-1 restriction by endogenous APOBEC3G in the myeloid cell line THP-1 publication-title: J. Gen. Virol. doi: 10.1099/jgv.0.001276 – volume: 27 start-page: 78 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib75 article-title: Characterization of pre-existing and induced SARS-CoV-2-specific CD8+ T cells publication-title: Nat. Med. doi: 10.1038/s41591-020-01143-2 – volume: 1 start-page: 239 year: 2018 ident: 10.1016/j.chom.2021.06.006_bib37 article-title: EditR: a method to quantify base editing from Sanger sequencing publication-title: The CRISPR Journal doi: 10.1089/crispr.2018.0014 – volume: 371 start-page: 1139 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib54 article-title: Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape publication-title: Science doi: 10.1126/science.abf6950 – volume: 25 start-page: 1605 year: 2004 ident: 10.1016/j.chom.2021.06.006_bib68 article-title: UCSF Chimera--a visualization system for exploratory research and analysis publication-title: J. Comput. Chem. doi: 10.1002/jcc.20084 – volume: 371 start-page: 172 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib63 article-title: Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans publication-title: Science doi: 10.1126/science.abe5901 – volume: 6 start-page: 53 year: 2009 ident: 10.1016/j.chom.2021.06.006_bib74 article-title: Comparative study on the effect of human BST-2/Tetherin on HIV-1 release in cells of various species publication-title: Retrovirology doi: 10.1186/1742-4690-6-53 – volume: 35 start-page: 109014 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib81 article-title: Establishment of a reverse genetics system for SARS-CoV-2 using circular polymerase extension reaction publication-title: Cell Rep. doi: 10.1016/j.celrep.2021.109014 – volume: 581 start-page: 215 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib43 article-title: Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor publication-title: Nature doi: 10.1038/s41586-020-2180-5 – volume: 25 start-page: 1972 year: 2009 ident: 10.1016/j.chom.2021.06.006_bib6 article-title: trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp348 – year: 2021 ident: 10.1016/j.chom.2021.06.006_bib16 article-title: Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation publication-title: medRxiv – volume: 24 start-page: 102311 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib20 article-title: Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-COV-2 publication-title: iScience doi: 10.1016/j.isci.2021.102311 – volume: 182 start-page: 812 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib40 article-title: Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus publication-title: Cell doi: 10.1016/j.cell.2020.06.043 – volume: 72 start-page: 457 year: 2008 ident: 10.1016/j.chom.2021.06.006_bib66 article-title: Cross-species virus transmission and the emergence of new epidemic diseases publication-title: Microbiol. Mol. Biol. Rev. doi: 10.1128/MMBR.00004-08 – volume: 183 start-page: 739 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib95 article-title: Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant publication-title: Cell doi: 10.1016/j.cell.2020.09.032 – year: 2020 ident: 10.1016/j.chom.2021.06.006_bib28 article-title: Identification of cross-reactive CD8+ T cell receptors with high functional avidity to a SARS-CoV-2 immunodominant epitope and its natural mutant variants publication-title: bioRxiv – volume: 593 start-page: 136 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib12 article-title: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies publication-title: Nature doi: 10.1038/s41586-021-03412-7 – volume: 36 year: 2008 ident: 10.1016/j.chom.2021.06.006_bib51 article-title: NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11 publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkn202 – volume: 37 start-page: 139 year: 1993 ident: 10.1016/j.chom.2021.06.006_bib31 article-title: HLA-B51 transgenic mice as recipients for production of polymorphic HLA-A, B-specific antibodies publication-title: Immunogenetics doi: 10.1007/BF00216838 – volume: 369 start-page: 812 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib10 article-title: SARS-CoV-2 infection protects against rechallenge in rhesus macaques publication-title: Science doi: 10.1126/science.abc4776 – volume: 12 start-page: 848 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib65 article-title: SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity publication-title: Nat. Commun. doi: 10.1038/s41467-021-21118-2 – volume: 29 start-page: 529 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib78 article-title: SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines publication-title: Cell Host Microbe doi: 10.1016/j.chom.2021.03.002 – year: 2021 ident: 10.1016/j.chom.2021.06.006_bib97 article-title: SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread yet generates an able infection inhibitor publication-title: bioRxiv – volume: 593 start-page: 270 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib15 article-title: Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 publication-title: Nature doi: 10.1038/s41586-021-03426-1 – year: 2020 ident: 10.1016/j.chom.2021.06.006_bib87 article-title: Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants publication-title: eLife doi: 10.7554/eLife.61312.sa2 – volume: 369 start-page: 1014 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib4 article-title: Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies publication-title: Science doi: 10.1126/science.abd0831 – volume: 368 start-page: 1016 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib79 article-title: Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 publication-title: Science doi: 10.1126/science.abb7015 – volume: 29 start-page: 508 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib70 article-title: The variant gambit: COVID-19's next move publication-title: Cell Host Microbe doi: 10.1016/j.chom.2021.02.020 – volume: 370 start-page: 1464 year: 2020 ident: 10.1016/j.chom.2021.06.006_bib27 article-title: SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo publication-title: Science doi: 10.1126/science.abe8499 – volume: 384 start-page: 1466 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib49 article-title: Neutralizing activity of BNT162b2-elicited serum publication-title: N. Engl. J. Med. doi: 10.1056/NEJMc2102017 – volume: 25 start-page: 1293 year: 2009 ident: 10.1016/j.chom.2021.06.006_bib98 article-title: The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp137 – volume: 18 start-page: 467 year: 2018 ident: 10.1016/j.chom.2021.06.006_bib42 article-title: Understanding the drivers of MHC restriction of T cell receptors publication-title: Nat. Rev. Immunol. doi: 10.1038/s41577-018-0007-5 – volume: 1116 start-page: 73 year: 2014 ident: 10.1016/j.chom.2021.06.006_bib67 article-title: Application of the Restriction-Free (RF) cloning for multicomponents assembly publication-title: Methods Mol. Biol. doi: 10.1007/978-1-62703-764-8_6 – volume: 22 start-page: 620 year: 2021 ident: 10.1016/j.chom.2021.06.006_bib103 article-title: Robust SARS-CoV-2-specific T cell immunity is maintained at 6 months following primary infection publication-title: Nat. Immunol. doi: 10.1038/s41590-021-00902-8 |
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| Title | SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity |
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