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Article

Complex Mutation Pattern of Omicron BA.2: Evading Antibodies without Losing Receptor Interactions

1
Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
2
Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India
3
Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, 14186 Stockholm, Sweden
4
Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
5
Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
6
Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
7
Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Giovanni Maga
Int. J. Mol. Sci. 2022, 23(10), 5534; https://doi.org/10.3390/ijms23105534
Received: 25 March 2022 / Revised: 4 May 2022 / Accepted: 10 May 2022 / Published: 16 May 2022
(This article belongs to the Special Issue Antiviral Drugs and Virus Infection)
BA.2, a sublineage of Omicron BA.1, is now prominent in many parts of the world. Early reports have indicated that BA.2 is more infectious than BA.1. To gain insight into BA.2 mutation profile and the resulting impact of mutations on interactions with receptor and/or monoclonal antibodies, we analyzed available sequences, structures of Spike/receptor and Spike/antibody complexes, and conducted molecular dynamics simulations. The results showed that BA.2 had 50 high-prevalent mutations, compared to 48 in BA.1. Additionally, 17 BA.1 mutations were not present in BA.2. Instead, BA.2 had 19 unique mutations and a signature Delta variant mutation (G142D). The BA.2 had 28 signature mutations in Spike, compared to 30 in BA.1. This was due to two revertant mutations, S446G and S496G, in the receptor-binding domain (RBD), making BA.2 somewhat similar to Wuhan-Hu-1 (WT), which had G446 and G496. The molecular dynamics simulations showed that the RBD consisting of G446/G496 was more stable than S446/S496 containing RBD. Thus, our analyses suggested that BA.2 evolved with novel mutations (i) to maintain receptor binding similar to WT, (ii) evade the antibody binding greater than BA.1, and (iii) acquire mutation of the Delta variant that may be associated with the high infectivity. View Full-Text
Keywords: COVID-19; SARS-CoV-2; viruses; Omicron BA.1; BA.2; Delta COVID-19; SARS-CoV-2; viruses; Omicron BA.1; BA.2; Delta
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MDPI and ACS Style

Kannan, S.R.; Spratt, A.N.; Sharma, K.; Goyal, R.; Sönnerborg, A.; Apparsundaram, S.; Lorson, C.L.; Byrareddy, S.N.; Singh, K. Complex Mutation Pattern of Omicron BA.2: Evading Antibodies without Losing Receptor Interactions. Int. J. Mol. Sci. 2022, 23, 5534. https://doi.org/10.3390/ijms23105534

AMA Style

Kannan SR, Spratt AN, Sharma K, Goyal R, Sönnerborg A, Apparsundaram S, Lorson CL, Byrareddy SN, Singh K. Complex Mutation Pattern of Omicron BA.2: Evading Antibodies without Losing Receptor Interactions. International Journal of Molecular Sciences. 2022; 23(10):5534. https://doi.org/10.3390/ijms23105534

Chicago/Turabian Style

Kannan, Saathvik R., Austin N. Spratt, Kalicharan Sharma, Ramesh Goyal, Anders Sönnerborg, Subbu Apparsundaram, Christian L. Lorson, Siddappa N. Byrareddy, and Kamal Singh. 2022. "Complex Mutation Pattern of Omicron BA.2: Evading Antibodies without Losing Receptor Interactions" International Journal of Molecular Sciences 23, no. 10: 5534. https://doi.org/10.3390/ijms23105534

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