7sbo Citations

Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.

Abstract

The Delta variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has outcompeted previously prevalent variants and become a dominant strain worldwide. We report the structure, function, and antigenicity of its full-length spike (S) trimer as well as those of the Gamma and Kappa variants, and compare their characteristics with the G614, Alpha, and Beta variants. Delta S can fuse membranes more efficiently at low levels of cellular receptor angiotensin converting enzyme 2 (ACE2), and its pseudotyped viruses infect target cells substantially faster than the other five variants, possibly accounting for its heightened transmissibility. Each variant shows different rearrangement of the antigenic surface of the amino-terminal domain of the S protein but only makes produces changes in the receptor binding domain (RBD), making the RBD a better target for therapeutic antibodies.

Reviews - 7sbo mentioned but not cited (1)

  1. The atomic portrait of SARS-CoV-2 as captured by cryo-electron microscopy. Fertig TE, Chitoiu L, Terinte-Balcan G, Peteu VE, Marta D, Gherghiceanu M. J Cell Mol Med 26 25-34 (2022)

Articles - 7sbo mentioned but not cited (4)

  1. Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. Yang H, Liu P, Zhang Y, Du T, Zhou Y, Lu S, Peng X. MedComm (2020) 3 e129 (2022)
  2. Evaluation of Potential Peptide-Based Inhibitors against SARS-CoV-2 and Variants of Concern. Boshah H, Samkari F, Valle-Pérez AU, Alsawaf SM, Aldoukhi AH, Bilalis P, Alshehri SA, Susapto HH, Hauser CAE. Biomed Res Int 2023 3892370 (2023)
  3. research-article Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. Ketaren NE, Mast FD, Fridy PC, Olivier JP, Sanyal T, Sali A, Chait BT, Rout MP, Aitchison JD. bioRxiv 2023.07.14.549041 (2024)
  4. Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. Ketaren NE, Mast FD, Fridy PC, Olivier JP, Sanyal T, Sali A, Chait BT, Rout MP, Aitchison JD. Elife 12 RP89423 (2024)


Reviews citing this publication (35)

  1. The humoral response and antibodies against SARS-CoV-2 infection. Qi H, Liu B, Wang X, Zhang L. Nat Immunol 23 1008-1020 (2022)
  2. COVID-19 vaccinations: The unknowns, challenges, and hopes. Mohamed K, Rzymski P, Islam MS, Makuku R, Mushtaq A, Khan A, Ivanovska M, Makka SA, Hashem F, Marquez L, Cseprekal O, Filgueiras IS, Fonseca DLM, Mickael E, Ling I, Arero AG, Cuschieri S, Minakova K, Rodríguez-Román E, Abarikwu SO, Faten AB, Grancini G, Cabral-Marques O, Rezaei N. J Med Virol 94 1336-1349 (2022)
  3. Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants. Mittal A, Khattri A, Verma V. PLoS Pathog 18 e1010260 (2022)
  4. Mutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity. Mengist HM, Kombe Kombe AJ, Mekonnen D, Abebaw A, Getachew M, Jin T. Semin Immunol 55 101533 (2021)
  5. Evolutionary and Structural Insights about Potential SARS-CoV-2 Evasion of Nirmatrelvir. Yang KS, Leeuwon SZ, Xu S, Liu WR. J Med Chem 65 8686-8698 (2022)
  6. The Emergence of the Spike Furin Cleavage Site in SARS-CoV-2. Chan YA, Zhan SH. Mol Biol Evol 39 msab327 (2022)
  7. Small molecules in the treatment of COVID-19. Lei S, Chen X, Wu J, Duan X, Men K. Signal Transduct Target Ther 7 387 (2022)
  8. Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences. Hoteit R, Yassine HM. Vaccines (Basel) 10 919 (2022)
  9. Challenges and developments in universal vaccine design against SARS-CoV-2 variants. Zhao F, Zai X, Zhang Z, Xu J, Chen W. NPJ Vaccines 7 167 (2022)
  10. Structural Plasticity and Immune Evasion of SARS-CoV-2 Spike Variants. Ghimire D, Han Y, Lu M. Viruses 14 1255 (2022)
  11. Delta variant (B.1.617.2) of SARS-CoV-2: current understanding of infection, transmission, immune escape, and mutational landscape. Bhattacharya M, Chatterjee S, Sharma AR, Lee SS, Chakraborty C. Folia Microbiol (Praha) 68 17-28 (2023)
  12. Defending against SARS-CoV-2: The T cell perspective. Almendro-Vázquez P, Laguna-Goya R, Paz-Artal E. Front Immunol 14 1107803 (2023)
  13. SARS-CoV-2: The Monster Causes COVID-19. Song C, Li Z, Li C, Huang M, Liu J, Fang Q, Cao Z, Zhang L, Gao P, Nie W, Luo X, Kang J, Xie S, Lyu J, Zhu X. Front Cell Infect Microbiol 12 835750 (2022)
  14. Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging More Transmissible and Vaccine-Resistant Strains. de Souza AS, de Freitas Amorim VM, Guardia GDA, Dos Santos FF, Ulrich H, Galante PAF, de Souza RF, Guzzo CR. Viruses 14 827 (2022)
  15. COVID-19 pandemic: the delta variant, T-cell responses, and the efficacy of developing vaccines. Biswas B, Chattopadhyay S, Hazra S, Hansda AK, Goswami R. Inflamm Res 71 377-396 (2022)
  16. SARS-CoV-2 Transmission and Prevention in the Era of the Delta Variant. Meyerowitz EA, Richterman A. Infect Dis Clin North Am 36 267-293 (2022)
  17. COVID-19 Genetic Variants and Their Potential Impact in Vaccine Development. Vo GV, Bagyinszky E, An SSA. Microorganisms 10 598 (2022)
  18. Molecular mechanisms involved in anosmia induced by SARS-CoV-2, with a focus on the transmembrane serine protease TMPRSS2. Karimian A, Behjati M, Karimian M. Arch Virol 167 1931-1946 (2022)
  19. A comprehensive insight into current control of COVID-19: Immunogenicity, vaccination, and treatment. Mohamed Y, El-Maradny YA, Saleh AK, Nayl AA, El-Gendi H, El-Fakharany EM. Biomed Pharmacother 153 113499 (2022)
  20. Breakthrough COVID-19 Infections in the US: Implications for Prolonging the Pandemic. Alcendor DJ, Matthews-Juarez P, Smoot D, Hildreth JEK, Lamar K, Tabatabai M, Wilus D, Juarez PD. Vaccines (Basel) 10 755 (2022)
  21. SARS-CoV-2 Virology. Li Y, Li JZ. Infect Dis Clin North Am 36 251-265 (2022)
  22. SARS-CoV-2 before and after Omicron: two different viruses and two different diseases? Gili R, Burioni R. J Transl Med 21 251 (2023)
  23. The mechanisms of immune response and evasion by the main SARS-CoV-2 variants. Chen Q, Zhang J, Wang P, Zhang Z. iScience 25 105044 (2022)
  24. Potential of Endogenous Oxytocin in Endocrine Treatment and Prevention of COVID-19. Wang SC, Zhang F, Zhu H, Yang H, Liu Y, Wang P, Parpura V, Wang YF. Front Endocrinol (Lausanne) 13 799521 (2022)
  25. Evolutionary dynamics of the severe acute respiratory syndrome coronavirus 2 genomes. Qian Z, Li P, Tang X, Lu J. Med Rev (2021) 2 3-22 (2022)
  26. The Physical Basis for pH Sensitivity in Biomolecular Structure and Function, With Application to the Spike Protein of SARS-CoV-2. Warwicker J. Front Mol Biosci 9 834011 (2022)
  27. The effect of various compounds on the COVID mechanisms, from chemical to molecular aspects. Mahmoudi S, Dehkordi MM, Asgarshamsi MH. Biophys Chem 288 106824 (2022)
  28. Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory. Ching WY, Adhikari P, Jawad B, Podgornik R. Biomedicines 11 517 (2023)
  29. Biology of the SARS-CoV-2 Coronavirus. Mingaleeva RN, Nigmatulina NA, Sharafetdinova LM, Romozanova AM, Gabdoulkhakova AG, Filina YV, Shavaliyev RF, Rizvanov AA, Miftakhova RR. Biochemistry (Mosc) 87 1662-1678 (2022)
  30. Nanostructures for prevention, diagnosis, and treatment of viral respiratory infections: from influenza virus to SARS-CoV-2 variants. Sharifi E, Yousefiasl S, Trovato M, Sartorius R, Esmaeili Y, Goodarzi H, Ghomi M, Bigham A, Moghaddam FD, Heidarifard M, Pourmotabed S, Nazarzadeh Zare E, Paiva-Santos AC, Rabiee N, Wang X, Tay FR. J Nanobiotechnology 21 199 (2023)
  31. Mutations in the SARS-CoV-2 spike receptor binding domain and their delicate balance between ACE2 affinity and antibody evasion. Xue S, Han Y, Wu F, Wang Q. Protein Cell 15 403-418 (2024)
  32. Overview of immunological & virological factors driving the evolution & global spread of SARS-CoV-2 variants. Ramasamy R. Indian J Med Res 158 257-268 (2023)
  33. SARS-CoV-2 Omicron: Viral Evolution, Immune Evasion, and Alternative Durable Therapeutic Strategies. Guo H, Ha S, Botten JW, Xu K, Zhang N, An Z, Strohl WR, Shiver JW, Fu TM. Viruses 16 697 (2024)
  34. Structural understanding of SARS-CoV-2 virus entry to host cells. Le K, Kannappan S, Kim T, Lee JH, Lee HR, Kim KK. Front Mol Biosci 10 1288686 (2023)
  35. Cryo-electron microscopy in the study of virus entry and infection. Dutta M, Acharya P. Front Mol Biosci 11 1429180 (2024)

Articles citing this publication (142)

  1. mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant. Garcia-Beltran WF, St Denis KJ, Hoelzemer A, Lam EC, Nitido AD, Sheehan ML, Berrios C, Ofoman O, Chang CC, Hauser BM, Feldman J, Roederer AL, Gregory DJ, Poznansky MC, Schmidt AG, Iafrate AJ, Naranbhai V, Balazs AB. Cell 185 457-466.e4 (2022)
  2. SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex. Mannar D, Saville JW, Zhu X, Srivastava SS, Berezuk AM, Tuttle KS, Marquez AC, Sekirov I, Subramaniam S. Science 375 760-764 (2022)
  3. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Willett BJ, Grove J, MacLean OA, Wilkie C, De Lorenzo G, Furnon W, Cantoni D, Scott S, Logan N, Ashraf S, Manali M, Szemiel A, Cowton V, Vink E, Harvey WT, Davis C, Asamaphan P, Smollett K, Tong L, Orton R, Hughes J, Holland P, Silva V, Pascall DJ, Puxty K, da Silva Filipe A, Yebra G, Shaaban S, Holden MTG, Pinto RM, Gunson R, Templeton K, Murcia PR, Patel AH, Klenerman P, Dunachie S, PITCH Consortium, COVID-19 Genomics UK (COG-UK) Consortium, Haughney J, Robertson DL, Palmarini M, Ray S, Thomson EC. Nat Microbiol 7 1161-1179 (2022)
  4. Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cui Z, Liu P, Wang N, Wang L, Fan K, Zhu Q, Wang K, Chen R, Feng R, Jia Z, Yang M, Xu G, Zhu B, Fu W, Chu T, Feng L, Wang Y, Pei X, Yang P, Xie XS, Cao L, Cao Y, Wang X. Cell 185 860-871.e13 (2022)
  5. SARS-CoV-2 Omicron variant shows less efficient replication and fusion activity when compared with Delta variant in TMPRSS2-expressed cells. Zhao H, Lu L, Peng Z, Chen LL, Meng X, Zhang C, Ip JD, Chan WM, Chu AW, Chan KH, Jin DY, Chen H, Yuen KY, To KK. Emerg Microbes Infect 11 277-283 (2022)
  6. Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Lubinski B, Fernandes MHV, Frazier L, Tang T, Daniel S, Diel DG, Jaimes JA, Whittaker GR. iScience 25 103589 (2022)
  7. Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. Wang K, Jia Z, Bao L, Wang L, Cao L, Chi H, Hu Y, Li Q, Zhou Y, Jiang Y, Zhu Q, Deng Y, Liu P, Wang N, Wang L, Liu M, Li Y, Zhu B, Fan K, Fu W, Yang P, Pei X, Cui Z, Qin L, Ge P, Wu J, Liu S, Chen Y, Huang W, Wang Q, Qin CF, Wang Y, Qin C, Wang X. Nature 603 919-925 (2022)
  8. Structural diversity of the SARS-CoV-2 Omicron spike. Gobeil SM, Henderson R, Stalls V, Janowska K, Huang X, May A, Speakman M, Beaudoin E, Manne K, Li D, Parks R, Barr M, Deyton M, Martin M, Mansouri K, Edwards RJ, Eaton A, Montefiori DC, Sempowski GD, Saunders KO, Wiehe K, Williams W, Korber B, Haynes BF, Acharya P. Mol Cell 82 2050-2068.e6 (2022)
  9. Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Wang Y, Liu C, Zhang C, Wang Y, Hong Q, Xu S, Li Z, Yang Y, Huang Z, Cong Y. Nat Commun 13 871 (2022)
  10. Structural and functional impact by SARS-CoV-2 Omicron spike mutations. Zhang J, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Rits-Volloch S, Wang S, Sliz P, Wesemann DR, Yang W, Seaman MS, Lu J, Xiao T, Chen B. Cell Rep 39 110729 (2022)
  11. Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain. Ye G, Liu B, Li F. Nat Commun 13 1214 (2022)
  12. Analysis of memory B cells identifies conserved neutralizing epitopes on the N-terminal domain of variant SARS-Cov-2 spike proteins. Wang Z, Muecksch F, Cho A, Gaebler C, Hoffmann HH, Ramos V, Zong S, Cipolla M, Johnson B, Schmidt F, DaSilva J, Bednarski E, Ben Tanfous T, Raspe R, Yao K, Lee YE, Chen T, Turroja M, Milard KG, Dizon J, Kaczynska A, Gazumyan A, Oliveira TY, Rice CM, Caskey M, Bieniasz PD, Hatziioannou T, Barnes CO, Nussenzweig MC. Immunity 55 998-1012.e8 (2022)
  13. Cryo-EM structure of the SARS-CoV-2 Omicron spike. Cerutti G, Guo Y, Liu L, Liu L, Zhang Z, Luo Y, Huang Y, Wang HH, Ho DD, Sheng Z, Shapiro L. Cell Rep 38 110428 (2022)
  14. Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape. Zhao Z, Zhou J, Tian M, Huang M, Liu S, Xie Y, Han P, Bai C, Han P, Zheng A, Fu L, Gao Y, Peng Q, Li Y, Chai Y, Zhang Z, Zhao X, Song H, Qi J, Wang Q, Wang P, Gao GF. Nat Commun 13 4958 (2022)
  15. Insights on the mutational landscape of the SARS-CoV-2 Omicron variant receptor-binding domain. Miller NL, Clark T, Raman R, Sasisekharan R. Cell Rep Med 3 100527 (2022)
  16. Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Saville JW, Mannar D, Zhu X, Srivastava SS, Berezuk AM, Demers JP, Zhou S, Tuttle KS, Sekirov I, Kim A, Li W, Dimitrov DS, Subramaniam S. Nat Commun 13 742 (2022)
  17. Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM. Wang Y, Xu C, Wang Y, Hong Q, Zhang C, Li Z, Xu S, Zuo Q, Liu C, Huang Z, Cong Y. Nat Commun 12 7345 (2021)
  18. Neuropilin-1 Mediates SARS-CoV-2 Infection of Astrocytes in Brain Organoids, Inducing Inflammation Leading to Dysfunction and Death of Neurons. Kong W, Montano M, Corley MJ, Helmy E, Kobayashi H, Kinisu M, Suryawanshi R, Luo X, Royer LA, Roan NR, Ott M, Ndhlovu LC, Greene WC. mBio 13 e0230822 (2022)
  19. Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization. Shan S, Luo S, Yang Z, Hong J, Su Y, Ding F, Fu L, Li C, Chen P, Ma J, Shi X, Zhang Q, Berger B, Zhang L, Peng J. Proc Natl Acad Sci U S A 119 e2122954119 (2022)
  20. Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. Ma C, Chen X, Mei F, Xiong Q, Liu Q, Dong L, Liu C, Zou W, Zhan F, Hu B, Liu Y, Liu F, Zhou L, Xu J, Jiang Y, Xu K, Cai K, Chen Y, Yan H, Lan K. Emerg Microbes Infect 11 567-572 (2022)
  21. The challenges of COVID-19 Delta variant: Prevention and vaccine development. He X, He C, Hong W, Zhang K, Wei X. MedComm (2020) 2 846-854 (2021)
  22. Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle. Yang K, Wang C, White KI, Pfuetzner RA, Esquivies L, Brunger AT. Proc Natl Acad Sci U S A 119 e2119467119 (2022)
  23. Improved Binding Affinity of Omicron's Spike Protein for the Human Angiotensin-Converting Enzyme 2 Receptor Is the Key behind Its Increased Virulence. Kumar R, Murugan NA, Srivastava V. Int J Mol Sci 23 3409 (2022)
  24. Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions. Cheng MH, Krieger JM, Banerjee A, Xiang Y, Kaynak B, Shi Y, Arditi M, Bahar I. iScience 25 103939 (2022)
  25. An antibody from single human VH-rearranging mouse neutralizes all SARS-CoV-2 variants through BA.5 by inhibiting membrane fusion. Luo S, Zhang J, Kreutzberger AJB, Eaton A, Edwards RJ, Jing C, Dai HQ, Sempowski GD, Cronin K, Parks R, Ye AY, Mansouri K, Barr M, Pishesha N, Williams AC, Vieira Francisco L, Saminathan A, Peng H, Batra H, Bellusci L, Khurana S, Alam SM, Montefiori DC, Saunders KO, Tian M, Ploegh H, Kirchhausen T, Chen B, Haynes BF, Alt FW. Sci Immunol 7 eadd5446 (2022)
  26. A modified vaccinia Ankara vaccine expressing spike and nucleocapsid protects rhesus macaques against SARS-CoV-2 Delta infection. Routhu NK, Gangadhara S, Lai L, Davis-Gardner ME, Floyd K, Shiferaw A, Bartsch YC, Fischinger S, Khoury G, Rahman SA, Stampfer SD, Schäfer A, Jean SM, Wallace C, Stammen RL, Wood J, Joyce C, Nagy T, Parsons MS, Gralinski L, Kozlowski PA, Alter G, Suthar MS, Amara RR. Sci Immunol 7 eabo0226 (2022)
  27. Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses. Li M, Ren Y, Aw ZQ, Chen B, Yang Z, Lei Y, Cheng L, Liang Q, Hong J, Yang Y, Chen J, Wong YH, Wei J, Shan S, Zhang S, Ge J, Wang R, Dong JZ, Chen Y, Shi X, Zhang Q, Zhang Z, Chu JJH, Wang X, Zhang L. Nat Commun 13 7957 (2022)
  28. Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core. Pak AJ, Yu A, Ke Z, Briggs JAG, Voth GA. Nat Commun 13 1002 (2022)
  29. SARS-CoV-2 spike N-terminal domain modulates TMPRSS2-dependent viral entry and fusogenicity. Meng B, Datir R, Choi J, CITIID-NIHR Bioresource COVID-19 Collaboration, Bradley JR, Smith KGC, Lee JH, Gupta RK. Cell Rep 40 111220 (2022)
  30. Letter Peptide-based pan-CoV fusion inhibitors maintain high potency against SARS-CoV-2 Omicron variant. Xia S, Chan JF, Wang L, Jiao F, Chik KK, Chu H, Lan Q, Xu W, Wang Q, Wang C, Yuen KY, Lu L, Jiang S. Cell Res 32 404-406 (2022)
  31. SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Neerukonda SN, Vassell R, Lusvarghi S, Wang R, Echegaray F, Bentley L, Eakin AE, Erlandson KJ, Katzelnick LC, Weiss CD, Wang W. Viruses 13 2485 (2021)
  32. Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein. Calvaresi V, Wrobel AG, Toporowska J, Hammerschmid D, Doores KJ, Bradshaw RT, Parsons RB, Benton DJ, Roustan C, Reading E, Malim MH, Gamblin SJ, Politis A. Nat Commun 14 1421 (2023)
  33. Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the prehairpin intermediate of the spike protein. Yang K, Wang C, Kreutzberger AJB, Ojha R, Kuivanen S, Couoh-Cardel S, Muratcioglu S, Eisen TJ, White KI, Held RG, Subramanian S, Marcus K, Pfuetzner RA, Esquivies L, Doyle CA, Kuriyan J, Vapalahti O, Balistreri G, Kirchhausen T, Brunger AT. Proc Natl Acad Sci U S A 119 e2210990119 (2022)
  34. Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants. Bendall EE, Callear AP, Getz A, Goforth K, Edwards D, Monto AS, Martin ET, Lauring AS. Nat Commun 14 272 (2023)
  35. Clinical Features of Adult COVID-19 Patients without Risk Factors before and after the Nationwide SARS-CoV-2 B.1.617.2 (Delta)-variant Outbreak in Korea: Experience from Gyeongsangnam-do. Ryu BH, Hong SI, Lim SJ, Cho Y, Hwang C, Kang H, Kim SH, Wi YM, Hong KW, Bae IG, Cho OH. J Korean Med Sci 36 e341 (2021)
  36. Structural Analysis of the SARS-CoV-2 Omicron Variant Proteins. Yang Q, Syed AAS, Fahira A, Shi Y. Research (Wash D C) 2021 9769586 (2021)
  37. Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics. Newby ML, Fogarty CA, Allen JD, Butler J, Fadda E, Crispin M. J Mol Biol 435 167928 (2023)
  38. In SARS-CoV-2 delta variants, Spike-P681R and D950N promote membrane fusion, Spike-P681R enhances spike cleavage, but neither substitution affects pathogenicity in hamsters. Furusawa Y, Kiso M, Iida S, Uraki R, Hirata Y, Imai M, Suzuki T, Yamayoshi S, Kawaoka Y. EBioMedicine 91 104561 (2023)
  39. The SARS-CoV-2 S1 Spike Protein Promotes MAPK and NF-kB Activation in Human Lung Cells and Inflammatory Cytokine Production in Human Lung and Intestinal Epithelial Cells. Forsyth CB, Zhang L, Bhushan A, Swanson B, Zhang L, Mamede JI, Voigt RM, Shaikh M, Engen PA, Keshavarzian A. Microorganisms 10 1996 (2022)
  40. Differential proinflammatory activities of Spike proteins of SARS-CoV-2 variants of concern. Tyrkalska SD, Martínez-López A, Arroyo AB, Martínez-Morcillo FJ, Candel S, García-Moreno D, Mesa-Del-Castillo P, Cayuela ML, Mulero V. Sci Adv 8 eabo0732 (2022)
  41. Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. Zhu R, Canena D, Sikora M, Klausberger M, Seferovic H, Mehdipour AR, Hain L, Laurent E, Monteil V, Wirnsberger G, Wieneke R, Tampé R, Kienzl NF, Mach L, Mirazimi A, Oh YJ, Penninger JM, Hummer G, Hinterdorfer P. Nat Commun 13 7926 (2022)
  42. Structural insights into the binding of SARS-CoV-2, SARS-CoV, and hCoV-NL63 spike receptor-binding domain to horse ACE2. Lan J, Chen P, Liu W, Ren W, Zhang L, Ding Q, Zhang Q, Wang X, Ge J. Structure 30 1432-1442.e4 (2022)
  43. Alpha variant SARS-CoV-2 infection: How it all starts. Domingo P, de Benito N. EBioMedicine 74 103703 (2021)
  44. An intranasal influenza virus-vectored vaccine prevents SARS-CoV-2 replication in respiratory tissues of mice and hamsters. Deng S, Liu Y, Tam RC, Chen P, Zhang AJ, Mok BW, Long T, Kukic A, Zhou R, Xu H, Song W, Chan JF, To KK, Chen Z, Yuen KY, Wang P, Chen H. Nat Commun 14 2081 (2023)
  45. Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. Verkhivker G, Agajanian S, Kassab R, Krishnan K. Int J Mol Sci 23 4376 (2022)
  46. Imaging Severity COVID-19 Assessment in Vaccinated and Unvaccinated Patients: Comparison of the Different Variants in a High Volume Italian Reference Center. Granata V, Fusco R, Villanacci A, Magliocchetti S, Urraro F, Tetaj N, Marchioni L, Albarello F, Campioni P, Cristofaro M, Di Stefano F, Fusco N, Petrone A, Schininà V, Grassi F, Girardi E, Ianniello S. J Pers Med 12 955 (2022)
  47. Rapid Hypermutation B Cell Trajectory Recruits Previously Primed B Cells Upon Third SARS-Cov-2 mRNA Vaccination. Paschold L, Klee B, Gottschick C, Willscher E, Diexer S, Schultheiß C, Simnica D, Sedding D, Girndt M, Gekle M, Mikolajczyk R, Binder M. Front Immunol 13 876306 (2022)
  48. Structural Dynamics of the SARS-CoV-2 Spike Protein: A 2-Year Retrospective Analysis of SARS-CoV-2 Variants (from Alpha to Omicron) Reveals an Early Divergence between Conserved and Variable Epitopes. Guérin P, Yahi N, Azzaz F, Chahinian H, Sabatier JM, Fantini J. Molecules 27 3851 (2022)
  49. Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein. Zhang J, Tang W, Gao H, Lavine CL, Shi W, Peng H, Zhu H, Anand K, Kosikova M, Kwon HJ, Tong P, Gautam A, Rits-Volloch S, Wang S, Mayer ML, Wesemann DR, Seaman MS, Lu J, Xiao T, Xie H, Chen B. Nat Struct Mol Biol 30 980-990 (2023)
  50. When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy. Coderc de Lacam EG, Blazhynska M, Chen H, Gumbart JC, Chipot C. J Chem Theory Comput 18 5890-5900 (2022)
  51. In silico analysis of mutations near S1/S2 cleavage site in SARS-CoV-2 spike protein reveals increased propensity of glycosylation in Omicron strain. Beaudoin CA, Pandurangan AP, Kim SY, Hamaia SW, Huang CL, Blundell TL, Vedithi SC, Jackson AP. J Med Virol 94 4181-4192 (2022)
  52. Neutralizing Response Against SARS-CoV-2 Variants 8 Months After BNT162b2 Vaccination in Naive and COVID-19-Convalescent Individuals. Luczkowiak J, Labiod N, Rivas G, Rolo M, Lasala F, Lora-Tamayo J, Mancheno-Losa M, Rial-Crestelo D, Pérez-Rivilla A, Folgueira MD, Delgado R. J Infect Dis 225 1905-1908 (2022)
  53. Potent inhibition of diverse Omicron sublineages by SARS-CoV-2 fusion-inhibitory lipopeptides. Zhu Y, Hu Y, Liu N, Chong H, He Y. Antiviral Res 208 105445 (2022)
  54. Probing Mechanisms of Binding and Allostery in the SARS-CoV-2 Spike Omicron Variant Complexes with the Host Receptor: Revealing Functional Roles of the Binding Hotspots in Mediating Epistatic Effects and Communication with Allosteric Pockets. Verkhivker G, Agajanian S, Kassab R, Krishnan K. Int J Mol Sci 23 11542 (2022)
  55. SARS-CoV-2 variant Alpha has a spike-dependent replication advantage over the ancestral B.1 strain in human cells with low ACE2 expression. Niemeyer D, Stenzel S, Veith T, Schroeder S, Friedmann K, Weege F, Trimpert J, Heinze J, Richter A, Jansen J, Emanuel J, Kazmierski J, Pott F, Jeworowski LM, Olmer R, Jaboreck MC, Tenner B, Papies J, Walper F, Schmidt ML, Heinemann N, Möncke-Buchner E, Baumgardt M, Hoffmann K, Widera M, Thao TTN, Balázs A, Schulze J, Mache C, Jones TC, Morkel M, Ciesek S, Hanitsch LG, Mall MA, Hocke AC, Thiel V, Osterrieder K, Wolff T, Martin U, Corman VM, Müller MA, Goffinet C, Drosten C. PLoS Biol 20 e3001871 (2022)
  56. Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York. Duerr R, Dimartino D, Marier C, Zappile P, Levine S, Francois F, Iturrate E, Wang G, Dittmann M, Lighter J, Elbel B, Troxel AB, Goldfeld KS, Heguy A. EBioMedicine 82 104141 (2022)
  57. Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity. Sergeeva AP, Katsamba PS, Liao J, Sampson JM, Bahna F, Mannepalli S, Morano NC, Shapiro L, Friesner RA, Honig B. J Mol Biol 435 168187 (2023)
  58. Investigating SARS-CoV-2 breakthrough infections per variant and vaccine type. Dingemans J, van der Veer BMJW, Gorgels KMF, Hackert V, den Heijer CDJ, Hoebe CJPA, Savelkoul PHM, van Alphen LB. Front Microbiol 13 1027271 (2022)
  59. SARS-CoV-2 Delta spike protein enhances the viral fusogenicity and inflammatory cytokine production. Ao Z, Ouyang MJ, Olukitibi TA, Yao X. iScience 25 104759 (2022)
  60. SARS-CoV-2 fusion-inhibitory lipopeptides maintain high potency against divergent variants of concern including Omicron. Zhu Y, Dong X, Liu N, Wu T, Chong H, Lei X, Ren L, Wang J, He Y. Emerg Microbes Infect 11 1819-1827 (2022)
  61. Cold atmospheric plasma for preventing infection of viruses that use ACE2 for entry. Wang P, Zhou R, Zhou R, Li W, Weerasinghe J, Chen S, Rehm BHA, Zhao L, Frentiu FD, Zhang Z, Yan K, Lor M, Suhrbier A, Richard DJ, Thompson EW, Ostrikov KK, Dai X. Theranostics 12 2811-2832 (2022)
  62. Development of SARS-CoV-2 variant protein microarray for profiling humoral immunity in vaccinated subjects. Ho TS, Du PX, Su WY, Santos HM, Lin YL, Chou YY, Keskin BB, Pau CH, Syu GD. Biosens Bioelectron 204 114067 (2022)
  63. Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex. Ching WY, Adhikari P, Jawad B, Podgornik R. Int J Mol Sci 23 10091 (2022)
  64. Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. Saunders N, Planas D, Bolland WH, Rodriguez C, Fourati S, Buchrieser J, Planchais C, Prot M, Staropoli I, Guivel-Benhassine F, Porrot F, Veyer D, Péré H, Robillard N, Saliba M, Baidaliuk A, Seve A, Hocqueloux L, Prazuck T, Rey FA, Mouquet H, Simon-Lorière E, Bruel T, Pawlotsky JM, Schwartz O. EBioMedicine 77 103934 (2022)
  65. Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein. Saville JW, Mannar D, Zhu X, Berezuk AM, Cholak S, Tuttle KS, Vahdatihassani F, Subramaniam S. Cell Rep 42 111964 (2023)
  66. The Runaway Evolution of SARS-CoV-2 Leading to the Highly Evolved Delta Strain. Ruan Y, Hou M, Tang X, He X, Lu X, Lu J, Wu CI, Wen H. Mol Biol Evol 39 msac046 (2022)
  67. Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes. Verkhivker G, Alshahrani M, Gupta G. Viruses 15 1143 (2023)
  68. Enhanced virulence and waning vaccine-elicited antibodies account for breakthrough infections caused by SARS-CoV-2 delta and beyond. Kwon HJ, Kosikova M, Tang W, Ortega-Rodriguez U, Radvak P, Xiang R, Mercer KE, Muskhelishvili L, Davis K, Ward JM, Kosik I, Holly J, Kang I, Yewdell JW, Plant EP, Chen WH, Shriver MC, Barnes RS, Pasetti MF, Zhou B, Wentworth DE, Xie H. iScience 25 105507 (2022)
  69. Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. Tang H, Gao L, Wu Z, Meng F, Zhao X, Shao Y, Hou G, Du X, Qin FX. Front Immunol 13 836232 (2022)
  70. Targeted escape of SARS-CoV-2 in vitro from monoclonal antibody S309, the precursor of sotrovimab. Magnus CL, Hiergeist A, Schuster P, Rohrhofer A, Medenbach J, Gessner A, Peterhoff D, Schmidt B. Front Immunol 13 966236 (2022)
  71. A Potent Neutralizing Nanobody Targeting the Spike Receptor-Binding Domain of SARS-CoV-2 and the Structural Basis of Its Intimate Binding. Yang J, Lin S, Sun H, Chen Z, Yang F, Lin X, Guo L, Wang L, Wen A, Zhang X, Dai Y, He B, Cao Y, Dong H, Liu X, Chen B, Li J, Zhao Q, Lu G. Front Immunol 13 820336 (2022)
  72. Differences in airborne stability of SARS-CoV-2 variants of concern is impacted by alkalinity of surrogates of respiratory aerosol. Haddrell A, Otero-Fernandez M, Oswin H, Cogan T, Bazire J, Tian J, Alexander R, Mann JFS, Hill D, Finn A, Davidson AD, Reid JP. J R Soc Interface 20 20230062 (2023)
  73. Differential avidity determination of IgG directed towards the receptor-binding domain (RBD) of SARS-CoV-2 wild-type and its variants in one assay: Rational tool for the assessment of protective immunity. Bauer G, Struck F, Staschik E, Maile J, Wochinz-Richter K, Motz M, Soutschek E. J Med Virol 94 5294-5303 (2022)
  74. Mechanosensing view of SARS-CoV-2 infection by a DNA nano-assembly. Zhang J, Huang Y, Sun M, Song T, Wan S, Yang C, Song Y. Cell Rep Phys Sci 3 101048 (2022)
  75. Progressive membrane-binding mechanism of SARS-CoV-2 variant spike proteins. Overduin M, Kervin TA, Tran A. iScience 25 104722 (2022)
  76. SARS-CoV-2 Spike Protein Is Capable of Inducing Cell-Cell Fusions Independent from Its Receptor ACE2 and This Activity Can Be Impaired by Furin Inhibitors or a Subset of Monoclonal Antibodies. Reuter N, Chen X, Kropff B, Peter AS, Britt WJ, Mach M, Überla K, Thomas M. Viruses 15 1500 (2023)
  77. The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2. Wassenaar TM, Wanchai V, Buzard G, Ussery DW. FEMS Microbiol Rev 46 fuac003 (2022)
  78. Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants. Neamtu A, Mocci F, Laaksonen A, Barroso da Silva FL. Colloids Surf B Biointerfaces 221 112986 (2023)
  79. Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Zhang L, Li Q, Wu J, Yu Y, Zhang Y, Nie J, Liang Z, Cui Z, Liu S, Wang H, Ding R, Jiang F, Li T, Nie L, Lu Q, Li J, Qin L, Jiang Y, Shi Y, Xu W, Huang W, Wang Y. Emerg Microbes Infect 11 1024-1036 (2022)
  80. SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding. Dudouet P, Colson P, Aherfi S, Levasseur A, Beye M, Delerce J, Burel E, Lavrard P, Bader W, Lagier JC, Fournier PE, La Scola B, Raoult D. Sci Rep 12 18721 (2022)
  81. Structural effects of spike protein D614G mutation in SARS-CoV-2. Dokainish HM, Sugita Y. Biophys J 122 2910-2920 (2023)
  82. Temporal changes in the accessory protein mutations of SARS-CoV-2 variants and their predicted structural and functional effects. Cruz CAK, Medina PMB. J Med Virol 94 5189-5200 (2022)
  83. Conformational stability of SARS-CoV-2 glycoprotein spike variants. Arruda HRS, Lima TM, Alvim RGF, Victorio FBA, Abreu DPB, Marsili FF, Cruz KD, Marques MA, Sosa-Acosta P, Quinones-Vega M, de S Guedes J, Nogueira FCS, Silva JL, Castilho LR, de Oliveira GAP. iScience 26 105696 (2023)
  84. Detecting Potentially Adaptive Mutations from the Parallel and Fixed Patterns in SARS-CoV-2 Evolution. Ji CY, Han N, Cheng YX, Shang J, Weng S, Yang R, Zhou HY, Wu A. Viruses 14 1087 (2022)
  85. Evolutionary Pattern Comparisons of the SARS-CoV-2 Delta Variant in Countries/Regions with High and Low Vaccine Coverage. Zhang J, Fan L, Xu H, Fu Y, Peng X, Zheng Y, Yu J, He J. Viruses 14 2296 (2022)
  86. Fusion assays for screening of fusion inhibitors targeting SARS-CoV-2 entry and syncytia formation. Chan SW. Front Pharmacol 13 1007527 (2022)
  87. Host heparan sulfate promotes ACE2 super-cluster assembly and enhances SARS-CoV-2-associated syncytium formation. Zhang Q, Tang W, Stancanelli E, Jung E, Syed Z, Pagadala V, Saidi L, Chen CZ, Gao P, Xu M, Pavlinov I, Li B, Huang W, Chen L, Liu J, Xie H, Zheng W, Ye Y. Nat Commun 14 5777 (2023)
  88. In situ architecture and membrane fusion of SARS-CoV-2 Delta variant. Song Y, Yao H, Wu N, Xu J, Zhang Z, Peng C, Li S, Kong W, Chen Y, Zhu M, Wang J, Shi D, Zhao C, Lu X, Echavarría Galindo M, Li S. Proc Natl Acad Sci U S A 120 e2213332120 (2023)
  89. Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru. Justo Arevalo S, Uribe Calampa CS, Jimenez Silva C, Quiñones Aguilar M, Bouckaert R, Rebello Pinho JR. Nat Commun 14 3557 (2023)
  90. Rational Development of Hypervalent Glycan Shield-Binding Nanoparticles with Broad-Spectrum Inhibition against Fatal Viruses Including SARS-CoV-2 Variants. Li Y, Xu S, Ye Q, Chi H, Guo Z, Chen J, Wu M, Fan B, Li B, Qin CF, Liu Z. Adv Sci (Weinh) 10 e2202689 (2023)
  91. Spike Mutation Profiles Associated With SARS-CoV-2 Breakthrough Infections in Delta Emerging and Predominant Time Periods in British Columbia, Canada. Fibke CD, Joffres Y, Tyson JR, Colijn C, Janjua NZ, Fjell C, Prystajecky N, Jassem A, Sbihi H. Front Public Health 10 915363 (2022)
  92. The impact of SARS-CoV-2 3CL protease mutations on nirmatrelvir inhibitory efficiency. Computational insights into potential resistance mechanisms. Ramos-Guzmán CA, Andjelkovic M, Zinovjev K, Ruiz-Pernía JJ, Tuñón I. Chem Sci 14 2686-2697 (2023)
  93. Biochemical Characterization of Emerging SARS-CoV-2 Nsp15 Endoribonuclease Variants. Wilson IM, Frazier MN, Li JL, Randall TA, Stanley RE. J Mol Biol 434 167796 (2022)
  94. Detection of the Omicron SARS-CoV-2 Lineage and Its BA.1 Variant with Multiplex RT-qPCR. Yolshin ND, Komissarov AB, Varchenko KV, Musaeva TD, Fadeev AV, Lioznov DA. Int J Mol Sci 23 16153 (2022)
  95. Development of highly effective LCB1-based lipopeptides targeting the spike receptor-binding motif of SARS-CoV-2. Zhu Y, Li M, Liu N, Wu T, Han X, Zhao G, He Y. Antiviral Res 211 105541 (2023)
  96. Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA.1 and BA.2 Trimers: Mutation-Induced Modulation of Protein Dynamics and Network-Guided Prediction of Variant-Specific Allosteric Binding Sites. Verkhivker G, Alshahrani M, Gupta G. Viruses 15 2009 (2023)
  97. Global "flu-ization" of COVID-19: A perspective from Vietnam. Nguyen KQ, Nguyen LMA, Taylor-Robinson AW. Front Public Health 10 987467 (2022)
  98. Increased pathogenicity and aerosol transmission for one SARS-CoV-2 B.1.617.2 Delta variant over the wild-type strain in hamsters. Zhang X, Chen S, Cao Z, Yao Y, Yu J, Zhou J, Gao G, He P, Dong Z, Zhong J, Luo J, Wei H, Zhang H. Virol Sin 37 796-803 (2022)
  99. Infectivity of Coronavirus Disease 2019: A Prospective Cohort Study in the Korean Metropolitan Area. Seok H, Lim S, Kim JY, Park CH, Kim JH, Woo ML, Won H, Kang YM, Oh HS, Song KH, Jung YJ, Kim T, Jo S, Choi WS. J Korean Med Sci 37 e106 (2022)
  100. Kaempferol inhibits SARS-CoV-2 invasion by impairing heptad repeats-mediated viral fusion. Gao J, Cao C, Shi M, Hong S, Guo S, Li J, Liang T, Song P, Xu R, Li N. Phytomedicine 118 154942 (2023)
  101. Non-covalent cyclic peptides simultaneously targeting Mpro and NRP1 are highly effective against Omicron BA.2.75. Yin S, Mei S, Li Z, Xu Z, Wu Y, Chen X, Liu D, Niu MM, Li J. Front Pharmacol 13 1037993 (2022)
  102. Profiling Humoral Immunity After Mixing and Matching COVID-19 Vaccines Using SARS-CoV-2 Variant Protein Microarrays. Kuo HC, Kuo KC, Du PX, Keskin BB, Su WY, Ho TS, Tsai PS, Pau CH, Shih HC, Huang YH, Weng KP, Syu GD. Mol Cell Proteomics 22 100507 (2023)
  103. The Delta variant wave in Tunisia: Genetic diversity, spatio-temporal distribution and evidence of the spread of a divergent AY.122 sub-lineage. Haddad-Boubaker S, Arbi M, Souiai O, Chouikha A, Fares W, Edington K, Sims S, Camma C, Lorusso A, Diagne MM, Diallo A, Boubaker IBB, Ferjani S, Mastouri M, Mhalla S, Karray H, Gargouri S, Bahri O, Trabelsi A, Kallala O, Hannachi N, Chaabouni Y, Smaoui H, Meftah K, Bouhalila SB, Foughali S, Zribi M, Lamari A, Touzi H, Safer M, Alaya NB, Kahla AB, Gdoura M, Triki H. Front Public Health 10 990832 (2022)
  104. The role of N-glycosylation in spike antigenicity for the SARS-CoV-2 gamma variant. Pegg CL, Modhiran N, Parry RH, Liang B, Amarilla AA, Khromykh AA, Burr L, Young PR, Chappell K, Schulz BL, Watterson D. Glycobiology 34 cwad097 (2024)
  105. Vaccination reduces viral load and accelerates viral clearance in SARS-CoV-2 Delta variant-infected patients. Li H, Li Y, Liu J, Liu J, Han J, Yang L. Ann Med 55 419-427 (2023)
  106. Changes within the P681 residue of spike dictate cell fusion and syncytia formation of Delta and Omicron variants of SARS-CoV-2 with no effects on neutralization or infectivity. Kuzmina A, Korovin D, Cohen Lass I, Atari N, Ottolenghi A, Hu P, Mandelboim M, Rosental B, Rosenberg E, Diaz-Griffero F, Taube R. Heliyon 9 e16750 (2023)
  107. Characterization of a Vesicular Stomatitis Virus-Vectored Recombinant Virus Bearing Spike Protein of SARS-CoV-2 Delta Variant. He W, Cui H, Wang S, Liang B, Zhang C, Wang W, Wang Q, Li W, Zhao Y, Wang T, Liu Z, Liu B, Yan F, Yang S, Xia X. Microorganisms 11 431 (2023)
  108. Research Support, Non-U.S. Gov't Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1). de Souza AS, de Souza RF, Guzzo CR. J Comput Aided Mol Des 37 585-606 (2023)
  109. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Cell Rep 42 113478 (2023)
  110. Dual mechanism: Epigenetic inhibitor apabetalone reduces SARS-CoV-2 Delta and Omicron variant spike binding and attenuates SARS-CoV-2 RNA induced inflammation. Fu L, Gilham D, Stotz SC, Sarsons CD, Rakai BD, Tsujikawa LM, Wasiak S, Johansson JO, Sweeney M, Wong NCW, Kulikowski E. Int Immunopharmacol 117 109929 (2023)
  111. Duplex One-Step RT-qPCR Assays for Simultaneous Detection of Genomic and Subgenomic RNAs of SARS-CoV-2 Variants. Bhosle SM, Tran JP, Yu S, Geiger J, Jackson JD, Crozier I, Crane A, Wada J, Warren TK, Kuhn JH, Worwa G. Viruses 14 1066 (2022)
  112. Homology Modeling and Molecular Dynamics-Driven Search for Natural Inhibitors That Universally Target Receptor-Binding Domain of Spike Glycoprotein in SARS-CoV-2 Variants. Ovchynnykova O, Kapusta K, Sizochenko N, Sukhyy KM, Kolodziejczyk W, Hill GA, Saloni J. Molecules 27 7336 (2022)
  113. Inhibitors of Activin Receptor-like Kinase 5 Interfere with SARS-CoV-2 S-Protein Processing and Spike-Mediated Cell Fusion via Attenuation of Furin Expression. Mezger MC, Conzelmann C, Weil T, von Maltitz P, Albers DPJ, Münch J, Stamminger T, Schilling EM. Viruses 14 1308 (2022)
  114. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. J Chem Inf Model 63 5272-5296 (2023)
  115. Spike Protein Mutation-Induced Changes in the Kinetic and Thermodynamic Behavior of Its Receptor Binding Domains Explain Their Higher Propensity to Attain Open States in SARS-CoV-2 Variants of Concern. Singh J, Vashishtha S, Kundu B. ACS Cent Sci 9 1894-1904 (2023)
  116. Structural characterization of SARS-CoV-2 dimeric ORF9b reveals potential fold-switching trigger mechanism. Jin X, Sun X, Chai Y, Bai Y, Li Y, Hao T, Qi J, Song H, Wong CCL, Gao GF. Sci China Life Sci 66 152-164 (2023)
  117. The Chimeric Adenovirus (Ad5/35) Expressing Engineered Spike Protein Confers Immunity against SARS-CoV-2 in Mice and Non-Human Primates. Shin SP, Shin KS, Lee JM, Jung IK, Koo J, Lee SW, Park S, Shin J, Park M, Park B, Oh H, Koo BS, Hong J, Ryu CM, Kim JO, Oh T, Kang CY. Vaccines (Basel) 10 712 (2022)
  118. Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein. Ghoula M, Deyawe Kongmeneck A, Eid R, Camproux AC, Moroy G. J Phys Chem B 127 8586-8602 (2023)
  119. Conformational Behavior of SARS-Cov-2 Spike Protein Variants: Evolutionary Jumps in Sequence Reverberate in Structural Dynamic Differences. Triveri A, Casali E, Frasnetti E, Doria F, Frigerio F, Cinquini F, Pavoni S, Moroni E, Marchetti F, Serapian SA, Colombo G. J Chem Theory Comput 19 2120-2134 (2023)
  120. Dual Effects of 3-epi-betulin from Daphniphyllum glaucescens in Suppressing SARS-CoV-2-Induced Inflammation and Inhibiting Virus Entry. Yeh YJ, Chao TL, Chang YJ, Chang SY, Lu CH, Chao CH, Su WC, Tseng CP, Lai MMC, Cheng JC. Int J Mol Sci 24 17040 (2023)
  121. Licorice-saponin A3 is a broad-spectrum inhibitor for COVID-19 by targeting viral spike and anti-inflammation. Yi Y, Li W, Liu K, Xue H, Yu R, Zhang M, Bao YO, Lai X, Fan J, Huang Y, Wang J, Shi X, Li J, Wei H, Xiang K, Li L, Zhang R, Zhao X, Qiao X, Yang H, Ye M. J Pharm Anal (2023)
  122. Mechanistic study of the transmission pattern of the SARS-CoV-2 omicron variant. An K, Yang X, Luo M, Yan J, Xu P, Zhang H, Li Y, Wu S, Warshel A, Bai C. Proteins 92 705-719 (2024)
  123. Predictive Factors of Mortality in Patients with Severe COVID-19 Treated in the Intensive Care Unit: A Single-Center Study in Vietnam. Duong-Quy S, Huynh-Truong-Anh D, Nguyen-Thi-Kim T, Nguyen-Quang T, Tran-Ngoc-Anh T, Nguyen-Van-Hoai N, Do-Thi-Thu M, Nguyen-Chi T, Nguyen-Van T, Tang-Thi-Thao T, Nguyen-Tuan A, Nguyen-Hoang Q, Hoang-Phi-Tuyet P, Vu-Van G, Nguyen-Lan H, Nguyen-Hong C, Dinh-Ngoc S, Truong-Viet D, Nguyen-Nhu V, Nguyen-Duy T. Pulm Ther 9 377-394 (2023)
  124. Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships. Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Phys Chem Chem Phys 25 21245-21266 (2023)
  125. The Relationship between the Transmission of Different SARS-CoV-2 Strains and Air Quality: A Case Study in China. Ma R, Zhang Y, Zhang Y, Li X, Ji Z. Int J Environ Res Public Health 20 1943 (2023)
  126. The anti-SARS-CoV-2 effect and mechanism of Chiehyuan herbal oral protection solution. Wu CY, Yang YH, Lin YS, Shu LH, Cheng YC, Liu HT, Lin YY, Lee IY, Shih WT, Yang PR, Tsai YY, Chang GH, Hsu CM, Yeh RA, Wu YH, Wu YH, Shen RC, Tsai MS. Heliyon 9 e17701 (2023)
  127. Unique Aggregation of Retroviral Particles Pseudotyped with the Delta Variant SARS-CoV-2 Spike Protein. Petersen JD, Lu J, Fitzgerald W, Zhou F, Blank PS, Matthies D, Zimmerberg J. Viruses 14 1024 (2022)
  128. A comparison of the protective effect of vaccination and clinical features between the SARS-CoV-2 wild-type strain and Delta (B.1.617.2) variant. Li Y, Wang Z, Liu J, Han J, Yang L. Arch Med Sci 18 1678-1682 (2022)
  129. Antibody-mediated spike activation promotes cell-cell transmission of SARS-CoV-2. Yu S, Zheng X, Zhou Y, Gao Y, Zhou B, Zhao Y, Li T, Li Y, Mou J, Cui X, Yang Y, Li D, Chen M, Lavillette D, Meng G. PLoS Pathog 19 e1011789 (2023)
  130. Development of potent pan-coronavirus fusion inhibitors with a new design strategy. Zhu Y, Gao Z, Feng X, Cheng L, Liu N, Liu C, Han S, Yang Q, Zou Q, Chong H, Zhang Z, Li M, Song G, He Y. MedComm (2020) 5 e666 (2024)
  131. Differential Outcomes of Infection by Wild-Type SARS-CoV-2 and the B.1.617.2 and B.1.1.529 Variants of Concern in K18-hACE2 Transgenic Mice. He Y, Henley J, Sell P, Comai L. Viruses 16 60 (2023)
  132. Discordant Antigenic Properties of Soluble and Virion SARS-CoV-2 Spike Proteins. Kumar S, Dasgupta S, Sajadi MM, Snyder GA, DeVico AL, Ray K. Viruses 16 407 (2024)
  133. Distinct in vitro and in vivo neutralization profiles of monoclonal antibodies elicited by the receptor binding domain of the ancestral SARS-CoV-2. Kwon HJ, Zhang J, Kosikova M, Tang W, Ortega-Rodriguez U, Peng H, Meseda CA, Pedro CL, Schmeisser F, Lu J, Kang I, Zhou B, Davis CT, Wentworth DE, Chen WH, Shriver MC, Barnes RS, Pasetti MF, Weir JP, Chen B, Xie H. J Med Virol 95 e28673 (2023)
  134. Drug Cocktail Formulation via Circuit Design. Beahm DR, Deng Y, DeAngelo TM, Sarpeshkar R. IEEE Trans Mol Biol Multiscale Commun 9 28-48 (2023)
  135. Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape. Raisinghani N, Alshahrani M, Gupta G, Verkhivker G. Int J Mol Sci 25 4281 (2024)
  136. Factors related to lung function outcomes in critically ill COVID-19 patients in South Korea. Kim TH, Song MJ, Lim SY, Lee YJ, Cho YJ. Acute Crit Care 39 100-107 (2024)
  137. Fitness of B-Cell Responses to SARS-CoV-2 WT and Variants Up to One Year After Mild COVID-19 - A Comprehensive Analysis. Meyer B, Martinez-Murillo PA, Lemaitre B, Blanchard-Rohner G, Didierlaurent AM, Fontannaz P, Eugercios Manzanas C, Lambert PH, Loevy N, Kaiser L, Sartoretti J, Tougne C, Villard J, Huttner A, Siegrist CA, Eberhardt CS. Front Immunol 13 841009 (2022)
  138. Harringtonine: A more effective antagonist for Omicron variant. Hu S, Wang N, Chen S, Zhang H, Wang C, Ma W, Zhang X, Wu Y, Lv Y, Xue Z, Bai H, Ge S, He H, Lu W, Zhang T, Ding Y, Liu R, Han S, Zhan Y, Zhan G, Guo Z, Zhang Y, Lu J, Gao J, Jia Q, Wang Y, Wang H, Lu S, Jin T, Chiu S, He L. Biochem Pharmacol 213 115617 (2023)
  139. Machine learning-based approach KEVOLVE efficiently identifies SARS-CoV-2 variant-specific genomic signatures. Lebatteux D, Soudeyns H, Boucoiran I, Gantt S, Diallo AB. PLoS One 19 e0296627 (2024)
  140. Neutralization against SARS-CoV-2 Delta/Omicron variants and B cell response after inactivated vaccination among COVID-19 convalescents. Wang H, Yuan Y, Wu B, Xiao M, Wang Z, Diao T, Zeng R, Chen L, Lei Y, Long P, Guo Y, Lai X, Wen Y, Li W, Cai H, Song L, Ni W, Zhao Y, Ouyang K, Wang J, Wang Q, Liu L, Wang C, Pan A, Li X, Gong R, Wu T. Front Med 17 747-757 (2023)
  141. Structural and pKa Estimation of the Amphipathic HR1 in SARS-CoV-2: Insights from Constant pH MD, Linear vs. Nonlinear Normal Mode Analysis. Yánez Arcos DL, Thirumuruganandham SP. Int J Mol Sci 24 16190 (2023)
  142. The importance of effect sizes when comparing cycle threshold values of SARS-CoV-2 variants. Brinkmann C, Gohl P, Mack D, Pfeifer J, Palmada Fenés M, Harzer O, Zöllner B. PLoS One 17 e0271808 (2022)