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
Introduction: Particularly in spike, this variant emerged with several other mutations like 69/70 deletion and P681H mutation present in the N-terminal domain (NTD) and near S1/S2 si
Result: Eight prominent mutations were present in the first group with more than 50% frequency; N501Y, P681H, T716I, D1118H, A570D, S982A, HV69/70del, and Y144del.
Result: The linker region consists of variant stretches contributed from three prominent mutations A570D, H655Y, and P681 H/R along with D614G.
The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice.
Method: The B.1.1.7 differs from the B.1 in the spike protein on positions S:N501Y, S:A570D, S:T716I, S:P681H, S:S982A, S:D1118H, S:del69/70, and S:del144/145.
Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India.
Result: The B.1.1.159 variant is characterized by 9 mutations (C203T, C222T, C3140T, C10954T, A11117G, C12789T, C21306T, C22995A, and C23604A), four ORF1a substitutions (P959S, T3255I, I3618V, and T4175I) and three spike substitutions (T478K, P681H, and T732A) (Figure 1C).
Discussion: An in vitro assay with SARS-CoV-2 PMID: 34846283
2021
Microbial genomics
Result: 2(b) further validates the co-occurring mutations of concern mentioned above, particularly between T478K, P681H and T732A, from the dominant clade 20B of variant 20B/478K.V1.
Result: Besides the conserved D614G mutation, sequences from the newly detected and proposed VOI 20B/478 K.V1 and 20B/P.4, share, in different combinations, mutations T478K, E484K, P681H/R with VOC alpha, gamma and delta (20I/B.1.1.7, 20J/P.1 and 21A/B.1.617.2).
Result: For this, we focused on S477N, E484K and D614G as previously identified mutations of concern; and in mutations T478K,
Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants.
Result: Indeed, all of the SARS-CoV-2 B.1.1.7 genomes analyzed in our cohort contained all the so-called signature mutations in the Spike glycoprotein, including p.H69-V70del, p.Y144del, p.N501Y, p.A570D, p.P681H, p.T716I, p.S982A, and p.D1118H.
Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York.
Discussion: P681H/R mutations were both detected more frequently among breakthrough infections in our previous study of breakthrough infections in New York when Alpha and Iota variants were dominant regionally, and in this study during the current Delta wave.
Discussion: A substitution at the same site (P681H) is found in Alpha, which evolved independently of Delta and dominated the global infection landscape between January and June 2021.
Discussion: Efficient spike cleavage (P681H/R) and replicative competence appear to be central checkpoints for SARS-CoV-2's epidemiological success, with Delta being improved compared to Alpha.
SARS_CoV_2 mutation literature information.
PMID: 
2021
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