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

Saathvik R. Kannan, Austin N. Spratt, Kalicharan Sharma, Ramesh Goyal, Anders Sönnerborg, Subbu Apparsundaram, Christian L. Lorson, Siddappa N. Byrareddy, Kamal Singh

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


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.

Original languageEnglish (US)
Article number5534
JournalInternational journal of molecular sciences
Issue number10
StatePublished - May 1 2022


  • BA.2
  • COVID-19
  • Delta
  • Omicron BA.1
  • SARS-CoV-2
  • viruses

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry


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