literature

SARS_CoV_2 mutation literature information.

Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay.

PMID: 35285705 2022 Microbiology spectrum

Abstract: The Alpha reaction targets the D3L substitution in the N gene, and the Delta reaction targets the spike gene 156 to 158 mutations.

In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape.

PMID: 35149224 2022 Infection, genetics and evolution

Discussion: D3L, P80R, S235F, and T205I, generated more potential epitopes in comparison to the REF peptides.

Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India.

PMID: 35000004 2022 Archives of virology

Result: The Indian variants were distinct in this protein as well (Table 3) and did not share the D3L and S236F mutations and the P80R mutation seen in the UK and Brazilian variants, respectively.

SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance.

PMID: 34758391 2022 International journal of infectious diseases

Abstract: These isolates belonged to the B.1.1.7 variant, exhibiting several amino acid substitutions, including D3L, R203K, G204R, and S235F N protein mutations.

Result: These mutations occurred in the N protein (Table 1), including D3L, R203K, G204R, and S235F mutations in Cases 1-5.

RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples.

PMID: 34756912 2022 The Science of the total environment

Method: The N D3L mutation, consisting of a GAT->CTA mutation at position 28280 in B.1.1.7 was chosen due to close proximity to the N1 RT-qPCR assay currently in use for detection of SARS-CoV-2 in wastewater.

Method: To further support the specificity of these SNPs, an investigation of 20,000 Canadian SARS-CoV-2 sequences collected prior to the detection of B.1.1.7, B.1.351, and P.1 in Canada, occurrences of S N501Y, S 69/70 del, and N D3L were found to be 0.019%, 0.028%, and 0.014% respectively, thus making them effective targets for variant detection (G.

Method: Two gene targets were chosen from the S gene: a deletion at 69-70 (Sdel) associated with B.1.1.7, and the N501Y mutation (SN501Y) associated with B.1.1.7, B.1.351, and P.1, al

Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis.

PMID: 34671771 2022 bioRxiv

Result: Interestingly, the mobilities of the alpha variant bands were decreased compared to the KR mt indicating an even higher level of phosphorylation, potentially due to the additional nucleocapsid mutations at D3L and S235F that alpha carries.

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.

PMID: 34541432 2021 Pathogens & immunity

Result: Interestingly, the increased levels of ORF9b may be due to the D3L mutation in the nucleocapsid that we have proposed to have arisen similarly to the R203G/G204R mutations and is associated with increased levels of B.1.1.7 sgRNA encoding ORF9b in clinical samples.

Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia.

PMID: 35095827 2021 Frontiers in microbiology

Result: Table 4 also reports the global percentage frequencies, which showed that D3L, R203_G204delinsKR, and S235F were the most globally frequent ones, among the substitutions found in our dataset.

Result: The III wave saw the introduction of the substitutions D3L and S235F.

Table: p.Asp3Leu

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

Result: D3L, P13L, S183Y, S186Y, S194L, R262H, and D377Y have a deleterious effect on Nucleocapsid protein.

Result: Conversely, 3 missense mutations (D3L, L5F, and S97I) were found to largely increase (DDG value > 0.5) the structural stability of the corresponding proteins.

Discussion: On the contrary, D3L, L5F, and S97I missense mutations were found to largely increase the structural stability of the nucleocapsid, ORF7a, and

Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach.

PMID: 34700382 2021 mBio

Result: When aligning the alpha (B.1.1.7) whole genomes against the prototype, at least 10 conserved amino acid variations within ORF1a (T1001I, A1708D, I2230T), ORF1b (P214L), ORF8 (R52I, Y73C), and N gene (D3L, R203K, G204R, S235F) were observed.

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