Abstract: Recombinant genomes were also found to contain substitutions of concern for elevated transmissibility and lower vaccine efficacy, including D614G, N501Y, E484K, and L452R.
Result: Notably, two N501Y recombinant genotypes appear to be spreading, having been sampled multiple times in South Africa and in multiple provinces in Belgium.
Result: These putative recombinants include 847 genomes that harbor the D614G substitution, 8 with N501Y, and 5 with E484K.
Discussion: Similarly, recent waves of infection driven by three clade 20 N501Y bearing lineages have further reduced our ability to detect recombinant genomes.
The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD.
Result: Interestingly, almost all sera bound better to N501Y RBD (B.1.1.7) than to wild type (average 129% compared to wild type).
Result: Specifically, N501Y and Y453F combined with N439K increased affinity for human ACE2 by 5-fold (Figure 4, Suppl.
Result: Using biolayer interferometry (BLI), we measured rates of association and dissociation of the N501Y RBD mutant (B.1.1.7 carries that mutation as its sole RBD mutation), Y453F as found in mink isolates, N439K which is found in some European clades, a combination of Y453F and N439K, PMID: 33758892
2021
medRxiv
Method: A 250-nucleotide region around the N501Y (A23063T) position in the reference strain (GenBank accession number MN908947) was selected and used to identify the corresponding regions in the GISAID dataset using BLAST.
Method: An 89 bp region surrounding the 23063 posit
Discussion: In designing this assay, we took advantage of the fact that the N501Y mutation is common to the three major SARS-CoV-2 variants of concern.
Discussion: Thus, this assay has the potential for relatively inexpensive high throughput testing for rapid identification of N501Y variants.
Discussion: Thus, we expect that our assay should continue to be able to identify N501Y variants even if additional mutations develop near this primary mutation once the specific Tm signatures of each new genotype are characterized.
Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation.
Abstract: Our analyses revealed 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation found in the B.1.1.7, B.1.351, and P.1 variants.
Introduction: The B.1.1.7 variant, originally detected in the United Kingdom (UK), has accumulated 17 lineage-defining mutations, including the spike protein N501Y mutation that confers increased transmissibility over other circulating viruses.
Introduction: The other two VOCs, B.1.351 detected in South Africa and P.1 first detected in Brazil, carry E484K and K417N/K417T in addition to N501Y mutations.
Discussion:
Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein.
PMID: 33774075
2021
Journal of virological methods
Abstract: N501Y was fou
Abstract: In order to discriminate N501Y variants quickly, a single nucleotide polymorphism (SNP) discrimination assay was designed and validated.
Method: A total of 64 SARS-CoV-2 positive nasopharyngeal swabs collected in UTM media (Copan, Italy) between December 2020-January 2021 and previously characterized by sequencing (35 of which had the N501Y mutation) were used to validate the method.
Method: Next, the novel N501Y VD RT-PCR method was used on 757 nasopharyngeal swabs collected prospectively between January 20 and 27 2021, under the same conditions as previous samples.
Method: Three positive controls were also tested in each run: a confirmed N501 N variant sequence, a confirmed N501Y variant sequence and a mixture of the two.
Mutational analysis of structural proteins of SARS-CoV-2.
Method: Three separate structures of RBD with a point mutation, each namely S477N, V483A, and N501Y were created.
Result: Another was in the case of the docked structure of N501Y-RBD: ACE-2 interaction, T500 of S protein failed to form H bond with Y41 of ACE-2 and showed only hydrophobic interaction.
Result: Further, Q498 (S) generated an additional hydrophobic interaction with L45 (ACE-2) in the docked structure of N501Y-RBD: ACE
Discussion: Both the variants carry N501Y mutation lying in the RBD region of S protein.
SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera.
Introduction: Additional mutations in spike, three amino acid deletions and seven missense mutations, including N501Y in RBD, make B.1.1.7 more infectious than the wild-type or the D614G strain.
Introduction: Both wild-type and the UK-N501Y pseudoviruses were efficiently neutralized by tested sera.
Introduction: Early reports have indicated that while the N501Y
Table: N501Y
Figure: Pseudoviruses displaying wild-type or mutant SARS-CoV-2 spike from UK-N50Y or SA-N501Y/K417N/E484K variants were used in neutralization assays.
Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2.
Introduction: The spike mutations observed in current variants can be broadly divided into three categories based on their locations: N-terminal domain (NTD) mutations including deletions found in both B.1.1.7 and B.1.351; receptor binding domain (RBD) mutations including N501Y (B.1.1.7, B.1.351 and P.1) and E484K (B.1.351 and P.1); and stalk/S2 mutations including P681H proximal to the polybasic S1/S2 cleavage site (B.1.1.7).
Discussion: Thus far, studies have focussed on the contribution made by RBD mutations, and with good reason; N501Y and E484K have been implicated in increased ACE2 affinity and escape from anti- PMID: 33791722
2021
medRxiv
Result: Three of the analyzed sequences showed the aminoacid changes T183I, A890D, I1412T, P323L, L493F, N501Y, T553I, A570D, D614G, P681H, T716I, S982A, D1118H, Q27, R52I, Y73C, D3L, R203K, G204R and S235F placing them in the B.1.1.7 lineage.
Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant.
Introduction: The B.1.351 RBD contains three mutations (K417N, E484K and N501Y) which reduces antibody binding.
Introduction: The B.1.351 viral variant contains the following amino acid mutations within the viral spike protein: L18F, D80A, D215G, deletion at positions 242-244 (L242del, A243del, and L244del), K417N, E484K, N501Y, and D614G.
Introduction: The emerging B.1.351 SARS-CoV-2 variant includes three mutations within the receptor-binding domain (
SARS_CoV_2 mutation literature information.
PMID: 
2021
bioRxiv
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