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: Besides D416G, F106F, P314L, and 5' UTR:C241T, our large scale analysis also identify C22227T;L93L (membrane protein), G29645T;A222V (spike protein), G21255C;A199A (NSP16), C28932T;V30L (ORF10), and T445C;A220V (nucleocapsid protein) mutations which are in top 10 mutations found in our investigation and should get importance in evaluating their
Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2.
5Result: The decrease of R203K/G204R in D and the increase in I2 are associated with the increase of
Method: To further understand the confounding effects of A222V (LG_4) and N501Y (LG_5) on 203K/204R, we evaluated the IF changes of the 8 combinations of these polymorphisms and identified four dominant lineages, ANR, VNR, ANK and AYK (Figure 3A).
Method: We first created 7-bp sequences by combining the nucleotide sequences of different strains at seven mutation sites (R203K/G204R (LG_3), N501Y (LG_5), A222V (LG_4), C313T, S477N, S194L and I120F).
Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure.
Method: Single mutations Ala222Val, Tyr265Cys, and Asp614Gly were introduced to the spike glycoprotein structure via Visual Molecular Dynamics (VMD) software with a Mutator Plugin.
Method: Single mutations Ala222Val, Tyr265Cys, and Asp614Gly, were introduced to the structure using the CHARMM-GUI Solution Builder module.
Result: All the spike mutations were found to be in medium proximity to the human ACE2 receptor binding motif (RBM), with the exception of Ala222Val.
Result: The mutation Ala222Val was located in a region with the highest variability score.
Figure: (B) RMSD of alpha carbon atoms of the reference SARS-C
Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021.
Introduction: The A222V mutation occurred in SARS-CoV-2 variants that emerged in June 2020, but has been shown not to contribute to increased transmissibility or immune escape in those variants.
Introduction: The Delta sub-lineage AY.4.2 bears the same spike mutations as the Delta lineage AY.4 with the addition of Y145H and A222V in the N-terminal domain (Figure 1).
Result: Some important hotspot mutations like H69-, V70-, Y144-, A222V, N501Y, A570D, P681H, and P681R identified in this study are associated with the different SARS-CoV-2 variants of concern like Alpha, Beta, Gamma, and Delta.
Table: A222V
Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing.
Introduction: For instance, the European lineage B.1.177 (clade 20E(EU1)) differs from ancestral sequences at 6 or more positions, including a A222V mutation in the spike protein.
Result: The missing mutations were not located in the same region as previously, but rather over the amplicon NC_045512.2:21743-21961 (T95I, V130F, G142D, E156G, F157del, and R158del, A222V).
Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study.
Discussion: This lineage, initially named 20E-EU1 variant and characterized by the spike substitution A222V, was identified in Spain in early summer 2020 and rapidly became the dominant lineage in several European countries.
Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Informatics in medicine unlocked
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