Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York

Abstract

Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. We develop the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detect an emerging lineage of SARS-CoV-2 in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage was first sequenced in late November 2020. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage. In concert with other variants, like B.1.1.7, the rise of B.1.526 appears to have extended the duration of the second wave of COVID-19 cases in NYC in early 2021. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, supporting the public health relevance of this lineage.

Exploring the Binding Mechanism of PF-07321332 SARS-CoV-2 Protease Inhibitor through Molecular Dynamics and Binding Free Energy Simulations

“…Several mutations have been reported in the viral genome so far; 106 major amino acid substitutions were found to be responsible for increased virulence and transmissibility of the virus [26]. Most of these missense mutations occurred in structural proteins of SARS-CoV-2, such as spike (S) [27] and nucleocapsid (N) proteins. Only one point mutation, G15S, has been predicted using in silico studies in 3CL pro , but this residue is far from the active site and has a destabilizing effect on the protein structure [26].…”

D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity

“…It replaces aspartic acid residue in the 614th position, and it has a significant impact on vaccine efficacy and therapeutics. As a consequence, it is known to be very detrimental to public health (West et al 2021 ). On June 22, 2021, the WHO declared it as the “VOI” due to its potential to decrease neutralization efficiency, enhanced transmission efficiency, and virulence (Aleem et al 2021 ).…”

Real Concerns over COVID-19 Variants of Concern

“…These changes are associated with immune evasion and diagnostic failures, prominent characteristics of variants of concern (2). Variants of concern (VOC) appeared to be overrepresented in numerous breakthrough infections of fully vaccinated people in the United States and (1,(3)(4)(5)(6), and Israel (7). These findings confirm concerns about the relation of SARS-CoV-2 variants with vaccine breakthrough, and urged us to attempt clarifying the likely link between vaccination with the currently used vaccines and VOC emergence.…”