Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR.
PMID: 34822912
2022
Journal of virological methods
Abstract: RESULTS: Of the 664/934 that were subjected to the multiplex qRT-PCR, 638 (96.1
Result: 638 (96.1 %) samples showed amplification for the genes targeting L452R and K417 and therefore, were considered to be the delta variant.
Result: We also tested 20 samples that were assigned the delta lineage by sequencing and the only genes targeting L452R was amplified.
Discussion: However, in situations where there is a dominant variant with L452R or N501Y, confirmed by whole genomic sequencing, this would be an easy to use, low-cost assay to rapidly identify the prevalence of VOCs such as delta.
Discussion: However, the SNPs resulting in L452R and K417 mutations is not unique to delta alone and is detected in several variants of interest such as Kappa (B.1.617.1), Epsilon (B.1.427/9) and C.36.
Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation.
Introduction: 1d, the L452R and P681R mutations were highly conserved in the B.1.617 lineage and, notably, the P681R mutation (16,650 out of 16,759 sequences, 99.3%) was the most representative mutation in this lineage.
Method: However, the S protein of this viral sequence (GISAID ID: EPI_ISL_2220643) possesses neither L452R nor P681R mutations, both of which are features of the B.1.617 lineage.
Proteolytic activation of SARS-CoV-2 spike protein.
Abstract: Thus, the spike Q677H substitution should be considered as another example of convergent evolution, as it is the case of spike substitutions L18F, E484K, L452R, and N501Y which also independently appeared in various lineages.
Result: Therefore, the spike Q677H substitution should be considered as another example of convergent evolution, in addition to spike amino acid substitutions N501Y, L452R, and L18F which also independently appeared in various lineages.
Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants.
PMID: 34537361
2022
Clinical microbiology and infection
Table: L452R
Discussion: Based on local frequency of these variants, parallel or sequential (P681R when L452R present) evaluation can be performed.
Discussion: Similarly, the Lambda variant might display an aberrant Tm in the L452R-specific assay as it harbors the L452Q mutation, but this was not assessed in the current manuscript.
Discussion: The B.1.617 sublineages harbor both L452R and P681R whereas B.1.427/B.1.429 harbors only L452R.
Discussion: The data obtained by surveillance sequencing during this study showed increasing occurrence of the Delta variant, leading to the incorporation of the P681R and L452R PCR
A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain).
Abstract: But some mutations of concern, such as E484K from B.1.351 and P.1 lineages are currently under monitoring, together with those observed in the receptor-binding domain or N-terminal domain, such as L452R and T478K from B.1.617.2 lineage.
Result: Other mutations of concern such as E484K, usually observed in B.1.351, B.1.525, B.1.621, and P.1 lineages are currently being monitored as well as the gain of changes in the RBD (L452R and T478 K) reported on B.1.617.2 viruses.
Discussion: The L452R mutation was previously observed in the United States due to the higher circulation of lineages B.1.427 and B.1.429 (variant Epsilon) and related to a partial immune evasio
Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021.
PMID: 34848355
2022
Infection, genetics and evolution
Abstract: Meanwhile, the new haplotype 2C_3 bearing the mutations at EFR156-158del, T19R, A222V, L452R, T478K, and D614G in Spike occupied over 54.8% in May 2021 in the low partly vaccinated rate group (India, Malaysia, Taiwan, and Vietnam).
Result: Significantly, haplotype 2C variant (66.8%) was leading in the partly vaccinated rate group, which sub-haplotype 2C_3 contained two unique mutations in spike protein (EFR156-158del, L452R, P681R), one mutation in ORF3a (S26L), and one mutation in N (R203M).
Table:
Highly sensitive and specific detection of the SARS-CoV-2 Delta variant by double-mismatch allele-specific real time reverse transcription PCR.
Abstract: The technique exploits allele-specific primers, targeting two spike gene mu
Introduction: In contrast, the double-mismatch allele-specific real time RT-PCR (DMAS-RT-PCR) method that we describe here does not exhibit such non-specificity because it targets two separate Delta spike gene mutations, L452R and T478K, within the same amplicon.
Method: Some of these individual mutations are shared by other variants but we noted that the combination of spike mutations L452R and T478K (nucleotide positions T22917G and C22995A, respectively) within the receptor binding domain can effectively differentiate Delta from other variants.
In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion.
Result: Anti-RBD IgG ELISA shows that antibodies induced by infection with wild-type Wuhan SARS-CoV-2 fail to recognize the RBD mutants L452R/E484Q (variant B.1.617) and E484K (variants P.1 and B.1.351), while recognition of RBDN440K is unaltered.
Result: Binding kinetics of RBD mutants to ACE2 show increased affinity due L452R/E484Q and E484K mutations.
Result: In contrast to direct binding of immune sera to RBD, inhibition of the RBD-ACE2 interaction was more severely affected and reduced for all mutations, most notably E484K<
A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients.
Introduction: While most of alterations in the receptor binding domain (RBD) reduce infectivity, A475V, L452R, V483A, and F490L variants induce resistance to some neutralizing antibodies.
Table: L452R
Discussion: L452R, T478K, N501Y and S477N have been the most frequently detected mutations in RDB.
SARS_CoV_2 mutation literature information.
PMID: 
2022
Journal of virological methods
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