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.
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
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.
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).
Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model.
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.
The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients.
Result: Twelve signature amino acid mutations (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F) were observed in the S protein as well as other consensus changes, including ORF1a (S1188L and K1795Q), ORF1b (P214L and E1164D), ORF3a (S253P), 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
SARS_CoV_2 mutation literature information.
PMID: 
2021
PloS one
Browser Board
Co-occurred Entities
Filtrator
ViMRT