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
Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2.
Figure: (D) IFs of 203K/204R (orange) and R203K/G204 (gray) among continents.
Figure: (G-I) show that the R203K/G204R substitutions enhance SARS-CoV-2 replication in primary human airway tissues.
Figure: Changes in the IF of 8 lineages including A222V (LG_4), N510Y (LG_5), and R203K/G204R (LG_3) and the distribution of lineages in the phylogenetic tree of all strains (H).
Figure: Effects of R203K/G204R on the severity of disease.
Figure: Evidence showing the adaptation of R203K/G204R.
Figure: Graphical overview of virology experiments to evaluate the impact of
SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity.
Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms.
Result: Overall, we found that most of the genomic variants (SNVs+indels) occur in low frequencies, except for a few point variants, such as P323L in the RdRp protein, E484K, D614G and V1176F spanning the spike protein region, and R203K and S194L in the nucleocapsid region.
Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals.
Result: Other commonly found mutations were Y453F (50.3%), S194L (49.4%), R203K (49.1%), and G204R (47.6%) in N protein of mink (Fig 13).
Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning.
PMID: 34812411
2021
Informatics in medicine unlocked
Discussion: Along with the previously found GGG > AAC mutation, our mutational type analysis identify some another multi-nucleotide mutations CC > TT, TG > CA, and AT > TA which are in the top 20 mutational type and should be monitored for the future as the GGG > AAC (R203K and G204R) reported to be associated with the insertion of a lysine in SR domain of N protein which might affect the phosphorylation.
SARS_CoV_2 mutation literature information.
PMID: 
2021
bioRxiv
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