Symptomatic reinfection of SARS‐CoV‐2 with spike protein variant N440K associated with immune escape

Rani, Pallavali R.; Imran, Mohamed; Lakshmi, J Vijaya; Jolly, Bani; Jain, Abhinav; Surekha, A.; Senthivel, Vigneshwar; Chandrasekhar, Pulala; Divakar, Mohit Kumar; Srinivasulu, Damam; Bhoyar, Rahul C.; Vanaja, P. R.; Scaria, Vinod; Sivasubbu, Sridhar

doi:10.1002/jmv.26997

Cited by 39 publications

(35 citation statements)

References 18 publications

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“…The Center for Cellular and Molecular Biology found that this variant has enhanced binding to ACE2 receptors, 10 to 1,000 folds more transmissible and resistant to class 3 monoclonal antibodies C135 and REGN10987. There are several documented cases of reinfection with the presence of anti-SARS-CoV-2 antibodies indicating the possibility of loss of neutralizing activity of antibodies elicited by vaccines [ 44 , 45 ].…”

Section: The Covid-19 Variantsmentioning

confidence: 99%

Review of COVID-19 Variants and COVID-19 Vaccine Efficacy: What the Clinician Should Know?

Vasireddy¹,

Vanaparthy

Mohan³

et al. 2021

J Clin Med Res

179

122

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta coronavirus that belongs to the Coronaviridae family. SARS-CoV-2 is an enveloped spherical-shaped virus. The ribonucleic acid (RNA) is oriented in a 5'-3'direction which makes it a positive sense RNA virus, and the RNA can be read directly as a messenger RNA. The nonstructural protein 14 (nsp14) has proofreading activity which allows the rate of mutations to stay low. A change in the genetic sequence is called a mutation. Genomes that differ from each other in genetic sequence are called variants. Variants are the result of mutations but differ from each other by one or more mutations. When a phenotypic difference is demonstrated among the variants, they are called strains. Viruses constantly change in two different ways, antigenic drift and antigenic shift. SARS-CoV-2 genome is also prone to various mutations that led to antigenic drift resulting in escape from immune recognition. The Center of Disease Control and Prevention (CDC) updates the variant strains in the different classes. The classes are variant of interest, variant of concern and variant of high consequence. The current variants included in the variant of interest by the USA are:

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Section: The Covid-19 Variantsmentioning

confidence: 99%

Review of COVID-19 Variants and COVID-19 Vaccine Efficacy: What the Clinician Should Know?

Vasireddy¹,

Vanaparthy

Mohan³

et al. 2021

J Clin Med Res

179

122

View full text Add to dashboard Cite

show abstract

“…These gain-of-function mutations increase the binding interaction of Spike RBD with hACE2 and also escape from important antibody classes (3,74). These immune escape variants could also cause reinfections and reduce vaccine efficacy (75). The increased affinity of the S mutant protein with hACE2 was also identified in the cluster-five variant, initially identified in the farmed minks in Denmark, which have an Y453F residue mutation in the RBD.…”

Section: New Strains and Spike Mutationsmentioning

confidence: 95%

The Spike of SARS-CoV-2: Uniqueness and Applications

et al. 2021

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The Spike (S) protein of the SARS-CoV-2 virus is critical for its ability to attach and fuse into the host cells, leading to infection, and transmission. In this review, we have initially performed a meta-analysis of keywords associated with the S protein to frame the outline of important research findings and directions related to it. Based on this outline, we have reviewed the structure, uniqueness, and origin of the S protein of SARS-CoV-2. Furthermore, the interactions of the Spike protein with host and its implications in COVID-19 pathogenesis, as well as drug and vaccine development, are discussed. We have also summarized the recent advances in detection methods using S protein-based RT-PCR, ELISA, point‐of‐care lateral flow immunoassay, and graphene-based field-effect transistor (FET) biosensors. Finally, we have also discussed the emerging Spike mutants and the efficacy of the Spike-based vaccines against those strains. Overall, we have covered most of the recent advances on the SARS-CoV-2 Spike protein and its possible implications in countering this virus.

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Section: Epidemiologic Trajectory and Patient Overviewmentioning

confidence: 99%

“…The N440K amino acid change in spike protein has recently been of interest because samples with this polymorphism have been reported to cause widespread COVID-19 in some states in India, increase viral titer in vitro, and have been associated with resistance to some candidate monoclonal antibody therapies. 58,59 We identified 18 patients with this N440K replacement, and ten patients had the identical combination of spike amino acid replacements: L18R, T95I, R158S, N440K, D614G, P681H, A688V, S735A, and T1027I. Two additional patients had SARS-CoV-2 of this same spike protein genotype with an additional T376I amino acid replacement.…”

Section: N440k Spike Protein Replacementmentioning

confidence: 99%

Trajectory of Growth of SARS-CoV-2 Variants in Houston, Texas, January through May 2021 Based on 12,476 Genome Sequences

Olsen

Christensen

Long

et al. 2021

Preprint

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Genetic variants of the SARS-CoV-2 virus are of substantial concern because they can detrimentally alter the trajectory of the ongoing pandemic, and disease course in individual patients. Here we report genome sequences from 11,568 COVID-19 patients in the Houston Methodist healthcare system dispersed throughout the metroplex that were diagnosed from January 1, 2021 through April 30, 2021. This sample represents 94% of Houston Methodist cases and 4.6% of all reported cases in the metropolitan area during this period. The SARS-CoV-2 variant designated UK B.1.1.7 increased very rapidly, and now causes 75%-90% of all new cases in the Houston area. Five of the 2,543 B.1.1.7 genomes had an E484K change in spike protein. Compared with non-B.1.1.7 patients, individuals infected with B.1.1.7 had a significantly lower cycle threshold value (considered to be a proxy for higher virus load) and higher rate of hospitalization. Other variants (e.g., B.1.429, B.1.427, P.1, P.2, and R.1) also increased rapidly in frequency, although the magnitude was less than for B.1.1.7. We also identified 42 patients with a recently described R.1 variant that has an E484K amino acid replacement, and seven patients with the B.1.617 "India" variants. In the aggregate, our study shows the occurrence of a diverse array of concerning SARS-CoV-2 variants circulating in a major metropolitan area, documents B.1.1.7 as the major cause of new cases in Houston and heralds the arrival and spread of B.1.617 variants in the metroplex.

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Symptomatic reinfection of SARS‐CoV‐2 with spike protein variant N440K associated with immune escape

Cited by 39 publications

References 18 publications

Review of COVID-19 Variants and COVID-19 Vaccine Efficacy: What the Clinician Should Know?

Review of COVID-19 Variants and COVID-19 Vaccine Efficacy: What the Clinician Should Know?

The Spike of SARS-CoV-2: Uniqueness and Applications

Trajectory of Growth of SARS-CoV-2 Variants in Houston, Texas, January through May 2021 Based on 12,476 Genome Sequences

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