Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern.
Introduction: Since there are multiple mutations in variants, the current ARMS-PCR methods for screening SARS-CoV-2 variants depend on the combination of multiple hot spot mutations, such as D614G and R203K.
Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India.
Result: The remaining Indian sequences continued to harbour the R203K and G204R mutations, which were present since May 2020.
Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals.
PMID: 35035981
2022
New microbes and new infections
Introduction: In the first patient, we found substitution at position N:S255A and S:N501Y on the first swab and revert back to its original sequence on the second swab and additional substitution at N:R203K and N:S235F.
Introduction: Last patient, we found substitutions at N:D3Q and ORF1b:P314L on the first swab and reversion of both substitutions with addition substitution at N:R203K on the second swab.
Introduction: Second patient, we found substitution at position N:R20
Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach.
Discussion: In particular, single high-frequency SNPs in SARS-CoV-2 were found on the spike glycoprotein (D614G, 23364 A > G), as well as in the protein encoding for the nucleocapsid (R203K, R202R, and G204R).
Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk.
Discussion: Among these six SNVs, four nucleotides (c28854, g28881
Discussion: The mutations R203S and G204R are non-conservative and even the R203K mutation is often observed to function as a non-conservative substitution in many cases, due to the different size of the R versus K residues and the notably different chemical features of the side-chain guanidinium group (arginine) versus the primary amine (lysine).
Discussion: The non-synonymous mutations R203K, R203S and G204R in the nucleocapsid protein all occur in the flexible linker region between the N-terminal RNA-binding domain and the C-terminal dimerization domain, and this linker segment is not resolved in any reported cryo-EM or x-ray structures.
Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India.
Figure: Higher viral loads in samples with R203K/G204R SNPs.
Figure: On both plots, lines show the fraction of samples having the R203K/G204R SNPs (red line), having both the R203K/G204R SNPs and the Spike
Figure: a A schematic diagram showing the SARS-CoV-2 N protein different domains (Upper: control, Lower: mutant) and highlighting the mutation site (R203K and G204R) and the linker region (LKR) containing a serine-arginine rich motif (SR-motif).
Figure: b Overview of the three SNPs underlying the N protein R203K/G204R changes.
Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil.
Result: Sequences from this study also share four nonsynonymous mutations, P314L (Nsp12), D614G (Spike), R203K and G204R (Nucleocapsid), with these placenta sequences, in addition to two synonymous mutations (214C>T, 3037 C>T).
Discussion: A critical polymorphic region of this protein is the serine-arginine region located in amino acids 183-206, exactly where the R203K and G204R aa changes locate.
Discussion: Mutations R203K/G204R in the Nucleocapsid gene, were found in both sequences.
Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations?
Discussion: Moreover, the mutation R203K/G204R was found to display a different protein structure morphology from the control and an enhanced intraviral interaction of R203K/G204R in the N and E proteins in molecular docking and protein structure prediction analysis.
Unusual N Gene Dropout and Ct Value Shift in Commercial Multiplex PCR Assays Caused by Mutated SARS-CoV-2 Strain.
Discussion: According to the same tool, the frequency of the four amino acid substitutions, R203K, G204R, A208G and M234I, in 9.525.430 sequences available from the GISAID database (as of 29 March 2022, with collection days 2020-1-29, 2020-1-29, 2020-3-3, 2020-1-26 to 2022-3-29) was 44%, 43%, <0.5% and 2%, respectively.
Discussion: Sequencing analysis revealed four amino acid mutations (R203K, G204R, A208G, M234I) in the N protein sequence of all our B.1.1.318 isolates.
Discussion: The R203K and G204R amino acid changes have been found in several variants beside B.1.1.318 and are considered to contr
SARS_CoV_2 mutation literature information.
PMID: 
2022
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