Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation.
PMID: 34763050
2021
Infection, genetics and evolution
Result: The Gamma sequences generated herein presented the classical mutational signatures in spike glycoprotein L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I and V1176F, with some exceptions, as in the sample hCoV-19/Brazil/LMM53965 and hCoV-19/Brazil/LMM54004 that change a guanine for an adenine in 614 position (D614G D614A) and the hCoV-19/Brazil/LMM54029 that change a histidine for a glutamic acid in 655
Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak.
Introduction: For example, the P.1 lineage detected first in Brazil is characterized by several amino acid (AA) substitutions mostly located either in RBD or in NTD: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, and T1027I, which are shown to reduce neutralization by some antibodies.
Table: H655Y
A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features.
PMID: 34806033
2021
Current research in structural biology
Result: The linker region consists of variant stretches contributed from three prominent mutations A570D, H655Y, and P681 H/R along with D614G.
Result: The linker region with P681R and H655Y along with D614G were the main amino acid co-occurring substitutions.
Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal.
Introduction: Likewise, the other lineage defining mutations for variants of concern were absent in the A.27 genomes, with the exception of L18F and H655Y, which are both present in the gamma lineage.
Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants.
Abstract: Here, we developed five SARS-CoV-2 spike gene primer pairs (5-SSG primer assay; 69S, 144S, 417S, 484S, and 570S) and verified their ability to detect nine key spike mutations (DeltaH69/V70, T95I, G142D, DeltaY144, K417T/N, L452R, E484K/Q, N501Y, and H655Y) using a Sanger sequencing-based assay.
SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection.
Method: P2 stock was sequenced and confirmed Omicron with the following substitutions: E:T9I,M:D3G,M:Q19E,M:A63T,N:P13L,N:R203K,N:G204R,ORF1a:K856R,ORF1a:L2084I,ORF1a:A2710T,ORF1a:T3255I,ORF1a:P3395H, PMID: 34925381
2021
Frontiers in immunology
Introduction: The Gamma P.1 variant encodes an S protein with 12 mutations (L18F, T20N, P26S, D138Y, R190S, K417N/T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F), two of which are in the RBD (E484K, and N501Y).
SARS_CoV_2 mutation literature information.
PMID: 
2021
Infection, genetics and evolution
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