Genetic, Structural, Physicochemical, and Molecular Epidemiological Landscape of Three New Mutations Found in the Spike (S) Protein of Highly Transmissible Sri Lankan Delta Variant Sub-lineage AY.28: A222V, A701S, and A1078S

TL;DR

This paper analyzes three new mutations in the spike protein of the Sri Lankan Delta variant and their potential impact on virus transmission and vaccine effectiveness.

Contribution

The study identifies the A701S mutation as a globally convergent and structurally significant change in the SARS-CoV-2 spike protein.

Findings

The A701S mutation is structurally disruptive and may enhance virus transmission by aiding protease cleavage.

The A701S mutation is found in multiple SARS-CoV-2 strains across different regions, indicating global convergence.

The A222V mutation is deemed conservative and likely not impactful, while A1078S is highly prevalent in SARS-CoV-2.

Abstract

Recently, three new mutations were identified in Sri Lanka in the spike protein of the rapidly spreading delta variant of the SARS-CoV-2 virus identified by the sublineage AY.28. They were A222V, A701S, and A1078S. The primary focus here is on the A701S mutation that is (1) found in the immediate vicinity of the S1/S2 cleavage site (PRRAR∗SV) that separates S1 and S2 subunits of the spike protein; (2) has high structural disorder of the region spanning Serine-701 (Ser-701), which promotes a longer flexible loop forming a better substrate; (3) collapses a loose, short, unstable, tripeptide beta strand (ENS), which is likely to assist the host proteases to cleave the S1-S2 interface easily than when an alanine is present. The same A701S mutation is found in at least 10 other strains of SARS-CoV-2 found in India, USA (East and West Coasts), and China, which classifies this mutation as geographically widespread and convergent in etiology. Conversely, the A1078S mutation is a highly present (>60 strains) mutation in terms of the SARS-CoV-2 coronaviruses, while the highly abundant A222V mutation is inferred by the genetic code, structural and topological features, and placement (in a beta strand) to be an innocuous, conservative mutation. The critical nature of S1/S2-dependent cleavage of S1 and S2 subunits of the spike protein makes the A701S mutation one of significance not just for possible higher virus transmission but also for subsequent fates such as viral load and vaccine effectivity against the delta variant.

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