Elsevier

Indian Journal of Medical Microbiology

Volume 40, Issue 3, July–September 2022, Pages 413-419
Indian Journal of Medical Microbiology

Original Research Article
Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach

https://doi.org/10.1016/j.ijmmb.2022.03.009Get rights and content

Highlights

  • The speedy evolution of new variants of SARS-CoV-2 is of high concern for Covid-19 Pandemic.

  • New B.1.617 variant (L452R & E484Q) caused a surge in the number of infections as well as re-infections in India.

  • In silico analysis showing RBD variants affecting the ability of CR3022 and ACE2 to bind with the SARS-CoV-2 RBD.

  • Docking results of RBD variants revealed lowest binding affinity of double mutant for antibody over other variants.

  • MD simulation of RBD variants showed that stability and flexibility of structure has been hampered.

  • The B.1.617 variant could lessen the impact of the current vaccine & causes chance of reinfections.

Abstract

Purpose

The existing panels of COVID-19 vaccines are based on the spike protein of an earlier SARS-CoV-2 strain that emerged in Wuhan, China. However, the evolving nature of SARS-CoV-2 has resulted in the emergence of new variants, thereby posing a greater challenge in the management of the disease. India faced a deadlier second wave of infections very recently, and genomic surveillance revealed that the B.1.617 variant and its sublineages are responsible for the majority of the cases. Hence, it's crucial to determine if the current vaccines available can be effective against these variants.

Methods

To address this, we performed molecular dynamics (MD) simulation on B.1.617 along with K417G variants and other RBD variants. We studied structural alteration of the spike protein and factors affecting antibody neutralization and immune escape via In silico docking.

Results

We found that in seven of the 12 variants studied, there was a structural alteration in the RBD region, further affecting its stability and function. Docking analysis of RBD variants and wild-type strains revealed that these variants have a higher affinity for the ACE2 (angiotensin 2 altered enzymes) receptor. Molecular interaction with CR3022 antibody revealed that binding affinity was less in comparison to wild type, with B.1.617 showing the least binding affinity.

Conclusions

The results of the extensive simulations provide novel mechanistic insights into the conformational dynamics and improve our understanding of the enhanced properties of these variants in terms of infectivity, transmissibility, neutralization potential, virulence, and host-viral replication fitness.

Keywords

SARS-CoV-2
B.1.617
MD Simulation
In silico
Vaccine efficacy

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