Rapid Increase in SARS-CoV-2 P.1 Lineage Leading to Codominance with B.1.1.7 Lineage, British Columbia, Canada, January–April 2021

Abstract

C haracterizing mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome has led to the identifi cation of variants of concern (VOCs) on the basis of such criteria as increased transmissibility, clinical severity, effect on diagnostic testing, and reduced vaccine effi cacy (1-5). Globally, the B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma) lineages represented the 3 main actively circulating VOCs in late 2020 and early 2021 (6). B.1.1.7 was fi rst detected in England in September 2020 and progressed to become the dominant lineage in this setting within months (4,7). By early January 2021, >40 countries had documented B.1.1.7 cases, demonstrating rapid international spread (8). This lineage has been associated with an estimated 40%-90% increase in transmissibility (4,7), variable effects on clinical severity and mortality rates (5,9,10), and limited effect on vaccine effectiveness (11). In contrast, whereas B.1.351 and P.1 also emerged in fall 2020 and spread rapidly locally, initial evidence of international transmission beyond South Africa and Brazil was limited (8,12,13). The P.1 lineage poses concern given its associations with an estimated 70%-240% increase in transmissibility ( 12), decreased neutralization capacity by monoclonal and serum-derived polyclonal antibodies ( 14), and increased risk for reinfection (12). Limited evidence from Italy, where B.1.1.7 and P.1 lineages have cocirculated, has shown the potential for B.1.1.7 to surpass P.1 for dominant VOC status in a short timeframe (15; P. Stefanelli et al., unpub. data, https://www.medrxiv.org/content/10.1101/ 2021.04.06.21254923v1). However, recent evidence from the United States suggests that infection after vaccination might be attributed to variants characterized by such mutations as E484K, T95I, del142-144, and D614G (16). The SARS-CoV-2 spike E484K mutation, which is present in the P. 1 and B.1.351 lineages,

Competitive Endogenous RNA Network Activates Host Immune Response in SARS-CoV-2-, panH1N1 (A/California/07/2009)-, and H7N9 (A/Shanghai/1/2013)-Infected Cells

“…The receptorbinding domain (RBD) of SARS-CoV-2 spike (S) protein mediates receptor binding and fusion of the viral and cellular membrane via angiotensin-converting enzyme 2 (ACE2) [17]. There were so many variants of SARS-CoV-2 encoding mutations in the RBD of spike protein that have been identified, including B.1.1.7 (Alpha) [35], B.1.351 (Beta) [36], B.1.617.2 (Delta) [37], P.1 (Gamma) [38], and B.1.1.529 (Omicron) [39], which have been proved with the more efficient transmission. The effectiveness of vaccines and neutralizing antibody drugs has been observed to decline as mutants of SARS-CoV-2 continue to appear [40].…”

Comparative single-dose mRNA and ChAdOx1 vaccine effectiveness against SARS-CoV-2, including early variants of concern: a test-negative design, British Columbia, Canada

“…In variant-specific analyses, cases were categorized as due to VOC (Alpha, Beta, Gamma, Delta) or non-VOC, the latter also including variants of interest (VOI) in primary analysis but excluding them in sensitivity analyses. Detailed methods for genetic characterization are provided in Supplementary Material 1, predicated foremost on whole genome sequencing but also RT-PCR single-nucleotide polymorphism screen for Alpha and Gamma variants [10,15,16].…”

“…Community vaccination in British Columbia (BC), Canada followed a sequential age-based strategy, prioritizing mRNA vaccines for the eldest citizens beginning around week 10. The spring 2021 pandemic wave in BC was comprised of unique co-dominance by Alpha and Gamma variants of concern (VOC), with lesser Delta contribution [8][9][10]. Using a test-negative design (TND) we previously reported single-dose mRNA (foremost BNT162b2) vaccine effectiveness All rights reserved.…”

Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering

“…The emergence of variants of concern (VOC's) with the enhanced transmissibility and infectivity profile including D614G variant [54][55][56][57], B.1.1.7 (alpha) [58][59][60][61], B. 1.351 (beta) [62,63], B.1.1.28/P.1 (gamma) [64], and B.1.1.427/B.1.429 (epsilon) variants [65,66] revealed complex mechanisms underlying function and dynamics of the S proteins in different biological environments. Structural and biophysical studies characterized a diversity of S functional states for B.1.1.7 (B.1.1.7), B.1.351 (beta), P1 (gamma), and B.1.1.427/B.1.429 (epsilon) variants and showed that conformational plasticity of S proteins is modulated by mutations and determines the ability to evade host immunity and incur resistance to antibodies [67][68][69].…”