Cele S, Gazy I, Jackson L, Hwa SH, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021;593(7857):142–6.
Planas D, Bruel T, Grzelak L, Guivel-Benhassine F, Staropoli I, Porrot F, et al. Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies. Nat Med. 2021;27(5):917–24.
Uriu K, Kimura I, Shirakawa K, Takaori-Kondo A, Nakada TA, Kaneda A, et al. Neutralization of the SARS-CoV-2 Mu variant by Convalescent and Vaccine serum. N Engl J Med. 2021;385(25):2397–9.
Planas D, Veyer D, Baidaliuk A, Staropoli I, Guivel-Benhassine F, Rajah MM, et al. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature. 2021;596(7871):276–80.
Liu L, Iketani S, Guo Y, Chan JFW, Wang M, Liu L, et al. Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2. Nature. 2022;602(7898):676–81.
Barnes CO, West AP, Huey-Tubman KE, Hoffmann MAG, Sharaf NG, Hoffman PR, et al. Structures of human antibodies bound to SARS-CoV-2 Spike Reveal Common Epitopes and recurrent features of antibodies. Cell. 2020;182(4):828–42e16.
Barnes CO, Jette CA, Abernathy ME, Dam KA, Esswein SR, Gristick HB, et al. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature. 2020;588(7839):682–7.
Piccoli L, Park Y-J, Tortorici MA, Czudnochowski N, Walls AC, Beltramello M, et al. Mapping neutralizing and Immunodominant Sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology. Cell. 2020;183(4):1024–42e21.
Greaney AJ, Loes AN, Crawford KHD, Starr TN, Malone KD, Chu HY, 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. 2021;29(3):463–76e6.
Robbiani DF, Gaebler C, Muecksch F, Lorenzi JCC, Wang Z, Cho A, et al. Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature. 2020;584(7821):437–42.
Hoffmann M, Kleine-Weber H, Schroeder S, Kruger N, Herrler T, Erichsen S et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell. 2020.
Voss WN, Hou YJ, Johnson NV, Delidakis G, Kim JE, Javanmardi K, et al. Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes. Science. 2021;372(6546):1108–12.
McCarthy KR, Rennick LJ, Nambulli S, Robinson-McCarthy LR, Bain WG, Haidar G, et al. Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape. Science. 2021;371(6534):1139–42.
Hou YJ, Chiba S, Halfmann P, Ehre C, Kuroda M, Dinnon KH 3, et al. SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Science. 2020;370(6523):1464–8.
Zhou B, Thao TTN, Hoffmann D, Taddeo A, Ebert N, Labroussaa F, et al. SARS-CoV-2 spike D614G change enhances replication and transmission. Nature. 2021;592(7852):122–7.
Niemeyer D, Stenzel S, Veith T, Schroeder S, Friedmann K, Weege F, et al. SARS-CoV-2 variant alpha has a spike-dependent replication advantage over the ancestral B.1 strain in human cells with low ACE2 expression. PLoS Biol. 2022;20(11):e3001871.
Greaney AJ, Starr TN, Barnes CO, Weisblum Y, Schmidt F, Caskey M, et al. Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies. Nat Commun. 2021;12(1):4196.
Huang KA, Tan TK, Chen TH, Huang CG, Harvey R, Hussain S, et al. Breadth and function of antibody response to acute SARS-CoV-2 infection in humans. PLoS Pathog. 2021;17(2):e1009352.
Hoffmann M, Arora P, Groß R, Seidel A, Hörnich BF, Hahn AS, et al. SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies. Cell. 2021;184(9):2384–93e12.
Lucas C, Vogels CBF, Yildirim I, Rothman JE, Lu P, Monteiro V, et al. Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity. Nature. 2021;600(7889):523–9.
Weisblum Y, Schmidt F, Zhang F, DaSilva J, Poston D, Lorenzi JCC, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. eLife. 2020;9:e61312.
Mykytyn AZ, Rissmann M, Kok A, Rosu ME, Schipper D, Breugem TI et al. Antigenic cartography of SARS-CoV-2 reveals that Omicron BA.1 and BA.2 are antigenically distinct. Sci Immunol.0(0):eabq4450.
Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature. 2022;603(7902):679–86.
Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature. 2021;592(7854):438–43.
Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DdS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021;372(6544):815–21.
Starr TN, Greaney AJ, Hilton SK, Ellis D, Crawford KHD, Dingens AS, et al. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell. 2020;182(5):1295–310e20.
Zahradník J, Marciano S, Shemesh M, Zoler E, Harari D, Chiaravalli J, et al. SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. Nat Microbiol. 2021;6(9):1188–98.
Collier DA, De Marco A, Ferreira I, Meng B, Datir RP, Walls AC, et al. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature. 2021;593(7857):136–41.
Wang P, Nair MS, Liu L, Iketani S, Luo Y, Guo Y, et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature. 2021;593(7857):130–5.
Case JB, Rothlauf PW, Chen RE, Liu Z, Zhao H, Kim AS, Bloyet LM, Zeng Q, Tahan S, Droit L, Ilagan MXG, Tartell MA, Amarasinghe G, Henderson JP, Miersch S, Ustav M, Sidhu S, Virgin HW, Wang D, Ding S, Corti D, Theel ES, Fremont DH, Diamond MS, Whelan SPJ. Neutralizing antibody and Soluble ACE2 Inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2. Cell Host Microbe. 2020;28(3):475–485e5. Epub 2020 Jul 3. PMID: 32735849; PMCID: PMC7332453.
Khare S, Gurry C, Freitas L, Schultz MB, Bach G, Diallo A, et al. GISAID’s role in Pandemic Response. China CDC Wkly. 2021;3(49):1049–51.
SARS-CoV-2 NETWORKA. V4.1 update for Omicron variant 2021 [Available from: https://community.artic.network/t/sars-cov-2-v4-1-update-for-omicron-variant/342.
Okoh OS, Nii-Trebi NI, Jakkari A, Olaniran TT, Senbadejo TY, Kafintu-kwashie AA, et al. Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa. iScience. 2022;25(3):103880.
Cherian S, Potdar V, Jadhav S, Yadav P, Gupta N, Das M et al. SARS-CoV-2 spike mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Microorganisms. 2021;9(7).
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 24 UK Health Security Agency. 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1030146/technical-briefing-24.pdf.
SARS-CoV-2. variants of concern and variants under investigation in England Technical briefing 25: UK Health Security Agency 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1025827/Technical_Briefing_25.pdf.
Koch J, Uckeley ZM, Doldan P, Stanifer M, Boulant S, Lozach PY. TMPRSS2 expression dictates the entry route used by SARS-CoV-2 to infect host cells. Embo j. 2021;40(16):e107821.
Schroeder S, Pott F, Niemeyer D, Veith T, Richter A, Muth D, et al. Interferon antagonism by SARS-CoV-2: a functional study using reverse genetics. The Lancet Microbe. 2021;2(5):e210–e8.
Han P, Li L, Liu S, Wang Q, Zhang D, Xu Z, et al. Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2. Cell. 2022;185(4):630–40e10.
Starr TN, Greaney AJ, Stewart CM, Walls AC, Hannon WW, Veesler D, et al. Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains. PLoS Pathog. 2022;18(11):e1010951. https://doi.org/10.1371/journal.ppat.1010951.
Mannar D, Saville JW, Zhu X, Srivastava SS, Berezuk AM, Zhou S, et al. Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Cell Rep. 2021;37(12):110156.
Starr Tyler N, Greaney Allison J, Addetia A, Hannon William W, Choudhary Manish C, Dingens Adam S, et al. Prospective mapping of viral mutations that escape antibodies used to treat COVID-19. Science. 2021;371(6531):850–4.
Nelson G, Buzko O, Spilman P, Niazi K, Rabizadeh S, Soon-Shiong P. Molecular dynamic simulation reveals E484K mutation enhances spike RBD-ACE2 affinity and the combination of E484K, K417N and N501Y mutations (501Y.V2 variant) induces conformational change greater than N501Y mutant alone, potentially resulting in an escape mutant. bioRxiv. 2021:2021.01.13.426558.
Ulrich L, Halwe NJ, Taddeo A, Ebert N, Schön J, Devisme C, et al. Enhanced fitness of SARS-CoV-2 variant of concern alpha but not Beta. Nature. 2022;602(7896):307–13.
Motozono C, Toyoda M, Zahradnik J, Saito A, Nasser H, Tan TS, et al. SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Cell Host Microbe. 2021;29(7):1124–36e11.
Liu Y, Liu J, Johnson BA, Xia H, Ku Z, Schindewolf C, et al. Delta spike P681R mutation enhances SARS-CoV-2 fitness over alpha variant. Cell Rep. 2022;39(7):110829.
Schlickeiser S, Schwarz T, Steiner S, Wittke K, Al Besher N, Meyer O et al. Disease Severity, Fever, Age, and sex correlate with SARS-CoV-2 neutralizing antibody responses. Front Immunol. 2021;11.
Wang Q, Zhang Y, Wu L, Niu S, Song C, Zhang Z, et al. Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell. 2020;181(4):894–904e9.
Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 2018;27(1):112–28.
Thi Nhu Thao T, Labroussaa F, Ebert N, V’kovski P, Stalder H, Portmann J, et al. Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform. Nature. 2020;582(7813):561–5.
Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DKW, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25(3):2000045.
Schroeder S, Mache C, Kleine-Weber H, Corman VM, Muth D, Richter A, et al. Functional comparison of MERS-coronavirus lineages reveals increased replicative fitness of the recombinant lineage 5. Nat Commun. 2021;12(1):5324.
Website. Python Software Foundation, https://www.python.org/.
Reback J et al. pandas-dev/pandas: pandas 1.2.2. (2021), doi:https://doi.org/10.5281/zenodo.4524629.
Hunter JD, Matplotlib. A 2D Graphics Environment. Comput Sci Eng. 2007;9:90–5.
Waskom M. Seaborn: statistical data visualization. J Open Source Softw. 2021;6:3021.
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