Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection.
PMID: 34464903
2021
Diagnostic microbiology and infectious disease
Result: Mutations detected in the N protein of all samples analyzed were M1X, D3L, R203K, G204R and S235F.
Discussion: Other mutations detected in all samples analyzed, such as M1X, R203K and G204R, could affect the amplification efficiency of the N-gene target.
Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants.
Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures.
Method: For instance, if 1 week presented 30% of genomes with the mutation R203K, and the number of cases on Monday of that week was 100.
Method: In the case of MF mutation R203K, R203, and N501, we multiply the relative frequencies of the genomes with the state of interest (R203K, R203 or N501) in a determined week by the number of cases in the day.
Result: This explains why this mutation did not increases its frequency steadily and can be an evidence of constant competition between MFR203K and not-MFR203K.
Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level.
Result: Notably, SARS-CoV-2 R203K/G204R polymorphisms modify the predicted binding of putative HLA-restricted T-cell epitopes containing these residues (Supplemental Table 2).
Result: Of the 455,774 circulating variants there were 29 amino acid polymorphisms present in >5% of the deposited sequences (of a total of 9413 sites; Supplemental Table 1) including the spike D614G variant (B.1 lineage) that emerged early in the pandemic and the adjacent R203K/G204R variants (B.1.1 lineage) in the nucleocapsid protein that formed one of the main variants emerging from Europe in early 2020.
Result: The adaptive potential of differential expression of sgRNAs is supported by a recent study by Thorne and colleagues that demonstrates that the B.1.1.7
Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure.
Result: Clade 20A defined by C14408T (Nsp12/RdRp) and A23403G (S: D614G) was seen in 58% of the samples, clade 19A defined by positions 8782C (Nsp3) and 14408C (Nsp12/RdRp) was seen in 38% and 20B denoted by positions C3037T (Nsp3: 106F); A23403G (S: D614G); C14408T (Nsp12/RdRp: P4715L) and G28881A and
Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome.
PMID: 34606987
2021
Infection, genetics and evolution
Result: In addition, very high rate recurrent mutations exist at the following locations: spike protein; D614G, nucleocapsid phosphoprotein; S194L, R203K and G204R, ORF3a; Q57H and G251V, and ORF8; L84S.
Result: The 78% viral samples bearing the D614G and P4715L mutations also bears either the concurrent N protein R203K and G204R or the ORF3a Q57H muta
The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil.
Method: Next, in the set of genomes found, we verified all mutations, excluding those that define the B.1.1.28 lineage (C241T, F924F, P4715L, D614G, V1176F, R203K, R203R and G204R).
The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients.
Introduction: The GR clade or lineage B.1.1.* is classified with additional trinucleotide mutations at 28 881-28 883 (GGG>AAC), creating two consecutive amino acid (aa) changes, R203K and G204R, in N protein.
SARS_CoV_2 mutation literature information.
PMID: 
2021
bioRxiv
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