Genes

Last updated: 2021 Oct 27
Total hit(s): 79
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Original Article
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A209C mutation in the nsp16 of SARS-CoV-2, in the adenosine binding pocket might influence the RNA cap binding. A distant (25 ) ligand-binding site unique to SARS-CoV-2 was discovered which can be targeted for antiviral development.
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 		32709886
(Nat Commun)
PMID
32709886
Date of Publishing: 2020 Jul 24
Title Structural basis of RNA cap modification by SARS-CoV-2
Author(s) nameViswanathan T, Arya S et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 92
Date of Entry 2021 Oct 27

Korber et al. present evidence that there are now more SARS-CoV-2 viruses circulating in the human population globally that have the G614 form of the Spike protein versus the D614 form that was originally identified from the first human cases in Wuhan, China. Follow-up studies show that patients infected with G614 shed more viral nucleic acid compared with those with D614, and G614-bearing viruses show significantly higher infectious titers in vitro than their D614 counterparts.
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 		32697968
(Cell)
PMID
32697968
Date of Publishing: 2020 Aug 20
Title Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus
Author(s) nameKorber B, Fischer WM et al.
Journal Cell
Impact factor
27.35
Citation count: 1755
Date of Entry 2021 Jul 13

Virus mutagenic capability depends upon several factors, including the fdelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp) According to the observations of the authors, after February 2020, when the first locally transmitted SARS-CoV-2 cases out of Asia were reported, viral genomes presented diferent point mutations, clearly distinguishable within different geographic areas. Over time, it was observed that they were able to identify three recurrent mutations in Europe (in positions 3036, 14408 and 23403) and 3 other different mutations in North America (in positions 17746, 17857 and 18060). So far, these mutations have not been detected in Asia. The number and the occurrence, as well as the median value of virus point mutations registered out of Asia, increase over time. In the preset study, they found that the RdRp mutation, located at position 14408, which is present in European viral genomes starting from February 20th, 2020, is associated with a higher number of point mutations compared to viral genomes from Asia.
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 		32321524
(J Transl Med)
PMID
32321524
Date of Publishing: 2020 Apr 22
Title Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant
Author(s) namePachetti M, Marini B et al.
Journal J Transl Med
Impact factor
4.2
Citation count: 414
Date of Entry 2021 Jul 13

Mutational and Co-mutational analysis of SARS-CoV-2 Sequences from India revealed different Co-mutation patterns and clade-specific mutations across seven Indian states and one union territory during term2 (April 2020 to July 2020) and term3 (August 2020 to December 2020). 70% of sequences from Telangana had 8 and above mutations within a single viral strain. 45% of sequences from Maharashtra possessed 7 co-mutations. West Bengal had a lower number of co-mutations even in ‘Term3’ (nearly 60% of sequences having 2 and 3 co-mutations per viral sequence).
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 		Pre-print (bioRXiv)
Date of Publishing 2021 Mar 25
Title Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India
Author(s) nameNupur Biswas, Priyanka Mallick et al.
Impact factor
N/A
Date of Entry 2021 Jun 14

Indian metadata was analyzed to associate the frequent mutations and co-mutation patterns with COVID-19 patient status (deceased, symptomatic, mild, and asymptomatic groups). Patient status was reported for only 806 sequences where 95 were marked as deceased, and 631, 49, 31 were marked as symptomatic, mild, and asymptomatic, respectively
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 		Pre-print (bioRXiv)
Date of Publishing 2021 Mar 25
Title Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India
Author(s) nameNupur Biswas, Priyanka Mallick et al.
Impact factor
N/A
Date of Entry 2021 Jun 14

The study reports a newly identified SARS-CoV-2 Strain from Israel. The strain included a non-synonymous mutation in the S protein: P681H (C23604A) and additional four synonymous mutations, Nsp3:C7765T, Nsp12b: C13821T, Nsp16:T21111C, and C29545A. Phylogenetic analysis was also performed to find the lineage and transmission patterns of the viral strain.
In vitro-neutralization assays were also assessed to find the effect of mutations on viral infectivity.
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 		Pre-print (medRXiv)
Title A unique SARS-CoV-2 spike protein P681H strain detected in Israel
Author(s) name -
Impact factor
N/A
Date of Entry 2021 Jun 14

Of 3080 SARS-CoV-2 genomes analyzed, ~1.5% genome had a rare missense mutation in three accessory proteins ORF6, ORF7b, and ORF10. The mutation caused several changes in the R-group properties of amino acids. Of 3080 genomes analyzed, 2126 genomes were from the USA, 306 genomes were from Asia, 281 genomes were from Europe, 365 genomes were from Oceania, and one genome from Africa. Mutations in putative diacidic motif- may affect the suppression of the expression of co-transfected myc-nsp8.
Mutated ORF7b(F(19)L)-Retention in Golgi complex is affected.
Mutated ORF7b (L(20)STOP)-Non-functional protein.
Nonsense mutation in ORF10- Non-functional protein.
Mutated ORF10 (V(6)I)-synonymous change of R-group property (Functions not affected).
Mutation may have potential role in viral rapid replications, virulence and pathogenicity.
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 		33619452
(Meta Gene)
PMID
33619452
Date of Publishing: 2021 Jun
Title Rare mutations in the accessory proteins ORF6, ORF7b, and ORF10 of the SARS-CoV-2 genomes
Author(s) name Hassan SS, Choudhury PP, Roy B.
Journal Meta Gene
Impact factor
0.88
Citation count: 3

Both the clusters (C1, C2) identified in the Amazon basin showed 4 mutations in the ORF1ab region and 1 mutation in the Spike gene but at different positions within the region for each cluster.
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 		33857136
(PLoS Negl Trop Dis)
PMID
33857136
Date of Publishing: 2021 Apr
Title Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin
Author(s) nameBallesteros N, Muñoz M et al.
Journal PLoS Negl Trop Dis
Impact factor
4.4
Citation count: 6

Mutation analysis of 2213 complete genomes from six geographical regions worldwide revealed 3178 polymorphic sites. Of these polymorphic sites, 58.5% (1861 sites) were non-synonymous, compared with the reference genome, Wuhan-Hu-1. Seven frequent non-synonymous mutations were observed in the global population of SARS-CoV-2. SARS-CoV-2 from six regions around the world (United States of America (US), Latin America (LA), Europe (EU), Africa (AF), Asia (AS), and Oceania (OC)) were taken randomly from NCBI and GISAID databases up to November 13, 2020, for the analysis.
DnaSP v5.1 software was used to determine the number of polymorphisms.
The difference between synonymous and non-synonymous substitutions (dN/dS) was evaluated using the software MEGA v6.0.
dN frequencies were obtained using Jalview v2.11 software.
P323L substitution in nsp12 (replication/transcription of the SARS-CoV-2 genome) provides structural stability, S447N substitution is located in the RBM (S protein) increases the affinity for the ACE-2 receptor, G614 substitution makes the virus 2.4 times more infectious.
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 		33572190
(Pathogens)
PMID
33572190
Date of Publishing: 2021 Feb 9
Title Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging
Author(s) nameFlores-Alanis A, Cruz-Rangel A et al.
Journal Pathogens
Impact factor
3.31
Citation count: 15

SARS-CoV-2 immunosuppressed patients had recurrent deletions in the spike glycoprotein. The deletions altered immunodominant epitope positions within the NTD of S glycoprotein and caused resistance to a neutralizing antibody. 3 RDR2 deletions and one RDR4 deleteion and double RDR1/2 deletion completely abolished binding of antibodies thereby concluding that the deletion mutants confer resistance to a neutralizing antibody.
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 		33536258
(Science)
PMID
33536258
Date of Publishing: 2021 Feb 3
Title Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Author(s) nameMcCarthy KR, Rennick LJ et al.
Journal Science
Impact factor
20.57
Citation count: 220

Complete Coding Sequence of surface glycoprotein (S) gene, reported from an immunocompromised cancer patient infected with long-term SARS-CoV-2 infection (Pittsburgh long-term infection 1). The patient was named Pittsburgh long-term infection 1 (PLTI1) because the infection persisted 74 days after the COVID-19 diagnosis.
Two variants with deletions in the NTD of S glycoprotein, were identified.
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 		33536258
(Science)
PMID
33536258
Date of Publishing: 2021 Feb 3
Title Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Author(s) nameMcCarthy KR, Rennick LJ et al.
Journal Science
Impact factor
20.57
Citation count: 220

62 mutations identified, including 30 mis-sense mutations, in 22 Moroccan patient isolates showed that Spike_D614G and NSP12_P323L mutations were present in all the analyzed sequences, whereas N_G204R and N_R203K were present in 9 sequences. Link to Clock Diagram depicting Mutation Evolution Rate in Morrocan Isolates,
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 		33558859
(Biosaf Health)
PMID
33558859
Date of Publishing: 2021 Feb 3
Title Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco
Author(s) nameBadaoui B, Sadki K et al.
Journal Biosaf Health
Impact factor
- n/a -
Citation count: 7

Sequence alignment of 22164 SARS-CoV-2 genomes from the GISAID database with the reference genome revealed 9210 single nucleotide changes (C>U being the most abundant), resulting in CpG loss. APOBEC protein catalyze cytosine to uracil (C>U) deamination in ssDNA and ssRNA and ZAP selectively binds to viral CpG regions. High amount of APOBEC and ZAP was found in COVID-19 patients.Selective pressure driving the adaptation of SARS-CoV-2 to its host. Absence of APOBEC enhances zinc-finger antiviral protein (ZAP) activity leading to viral degradation.
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 		33630074
(J Mol Cell Biol)
PMID
33630074
Date of Publishing: 2021 Feb 25
Title Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction
Author(s) nameSadykov M, Mourier T et al.
Journal J Mol Cell Biol
Impact factor
4.4
Citation count: 9

Isolate UF-8 (GenBank accession No. MW221275.1) had 12-nucleotide in-frame deletion within ORF3a that encodes viroporin 3a protein. Viroporins are hydrophobic proteins that are considered virulence factors, not essential for virus replication.
No clear evidence of decreased clinical virulence caused by SARS-CoV-2 UF-8 was observed.
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 		33632859
(Microbiol Resour Announc)
PMID
33632859
Date of Publishing: 2021 Feb 25
Title In-Frame 12-Nucleotide Deletion within Open Reading Frame 3a in a SARS-CoV-2 Strain Isolated from a Patient Hospitalized with COVID-19
Author(s) nameLednicky JA, Cherabuddi K et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 3

Mutation analysis of 59MDW SARS-CoV-2 genomes (n=37, collected from JBSA/Lackland military members and beneficiaries from May 14, 2020, to July 28, 2020) revealed 109 nucleotide changes in the coding region of the SARS-CoV-2 genome (which caused 63 unique, non-synonymous amino acid mutations), one mutation in the 5-UTR, and two mutations in the 3UTR. The biochemical properties of mutations in the SARS-CoV-2 structural proteins (S, E, and N) were studied. The effect of the mutation in viral spike protein is predicted.
✍
 		33609027
(Mil Med)
PMID
33609027
Date of Publishing: 2021 Feb 20
Title Whole-genome Sequencing of SARS-CoV-2: Using Phylogeny and Structural Modeling to Contextualize Local Viral Evolution
Author(s) name Nazario-Toole AE, Xia H, Gibbons TF.
Journal Mil Med
Impact factor
1.6
Citation count: 3

Mutation analysis of 59MDW SARS-CoV-2 genomes (n=37, collected from JBSA/Lackland military members and beneficiaries from May 14, 2020, to July 28, 2020) revealed 14 non-synonymous mutations in the structural proteins. The effect and the biochemical properties of all mutations were studied. Visualization of the mutations on the viral spike protein was done using pymol, the visualization clearly defines the mutation sites and can help in vaccine design and predicting potential spread
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 		33609027
(Mil Med)
PMID
33609027
Date of Publishing: 2021 Feb 20
Title Whole-genome Sequencing of SARS-CoV-2: Using Phylogeny and Structural Modeling to Contextualize Local Viral Evolution
Author(s) name Nazario-Toole AE, Xia H, Gibbons TF.
Journal Mil Med
Impact factor
1.6
Citation count: 3

Mutation analysis of 469 complete Indian SARS-CoV-2 nucleotide sequences from GenBank revealed that five proteins ORF1ab, ORF3a, S, N, and M had multiple mutations in different variants. While six proteins ORF6, ORF7a, ORF7b, ORF8, ORF10, and E had a single mutation in each variant. The study focuses on constituent proteins of 469 Indian SARS-CoV-2 genome samples, collected from NCBI (as reported till August 28, 2020). Sample detail provided in Supplementary-1 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893251/#ec0005)
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 		33623833
(Gene Rep)
PMID
33623833
Date of Publishing: 2021 Feb 19
Title Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates
Author(s) nameDas JK, Sengupta A et al.
Journal Gene Rep
Impact factor
0.61
Citation count: 11

Mutation analysis of 469 complete Indian SARS-CoV-2 nucleotide sequences from GenBank revealed 536 mutated positions within the coding regions of SARS-CoV-2 proteins. The study focuses on constituent proteins of 469 Indian SARS-CoV-2 genome samples, collected from NCBI (as reported till August 28, 2020). Sample detail provided in Supplementary-1 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893251/#ec0005)
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 		33623833
(Gene Rep)
PMID
33623833
Date of Publishing: 2021 Feb 19
Title Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates
Author(s) nameDas JK, Sengupta A et al.
Journal Gene Rep
Impact factor
0.61
Citation count: 11

In this study, Indian SARS-CoV-2 genomes were analyzed to find out genomic variants of SARS-CoV-2 proteins. It was found that ORF1ab, S, N, and ORF3a proteins had higher variants than other SARS-CoV-2 proteins. The study focuses on constituent proteins of 469 Indian SARS-CoV-2 genome samples, collected from NCBI (as reported till August 28, 2020). Sample detail provided in Supplementary-1 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893251/#ec0005)
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 		33623833
(Gene Rep)
PMID
33623833
Date of Publishing: 2021 Feb 19
Title Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates
Author(s) nameDas JK, Sengupta A et al.
Journal Gene Rep
Impact factor
0.61
Citation count: 11

Of 333 non-synonymous mutations (obtained from the Mutation analysis of 469 complete Indian SARS-CoV-2 nucleotide sequences from GenBank), 57 possible deleterious amino acid substitutions are predicted, which may impact the protein stability. Tool : PROVEAN is used to predict mutation type whether deleterious or neutral.
G values are used for predicting the stability variations (increase or decrease or neutral).
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 		33623833
(Gene Rep)
PMID
33623833
Date of Publishing: 2021 Feb 19
Title Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates
Author(s) nameDas JK, Sengupta A et al.
Journal Gene Rep
Impact factor
0.61
Citation count: 11

Six mutations were reported in the study, which separates recent ancestors of Group 1 and 2 belonging to B.1.1 lineage from Group 3 belonging to B.1.5 lineage.
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 		33510171
(Nat Commun)
PMID
33510171
Date of Publishing: 2021 Jan 28
Title Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia
Author(s) nameKomissarov AB, Safina KR et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 23

Compared to the reference Wuhan Hu-1 genome, the sequenced genome (GenBank accession no. MW079418- MW079427) from Malta/Sliema had 15 nucleotide variations.
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 		33509993
(Microbiol Resour Announc)
PMID
33509993
Date of Publishing: 2021 Jan 28
Title Genome Sequences of 10 SARS-CoV-2 Viral Strains Obtained by Nanopore Sequencing of Nasopharyngeal Swabs in Malta
Author(s) nameBiazzo M, Madeddu S et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 1

In silico analysis of whole-genome sequences from India revealed the deletions of E protein. Patient data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7645280/table/tbl0005/?report=objectonly Of the 34 sequences with E gene deletions, 15 belonged to 19A, one belonged to 19B, 4 belonged to 20A and 20B each and remaining sequences could not be categorised into any of the clades defined by Nextstrain. C-terminal deletion in the E-gene of SARS-CoV-2 was loacated in different lineages and geographical locations (none of them had a travel history to COVID-19 infected countries)
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 		33166565
(Virus Res)
PMID
33166565
Date of Publishing: 2021 Jan 2
Title Deletion in the C-terminal region of the envelope glycoprotein in some of the Indian SARS-CoV-2 genome
Author(s) nameKumar BK, Rohit A et al.
Journal Virus Res
Impact factor
2.6
Citation count: 7

The in vitro mutation analysis showed that the D614G mutation changes the spike protein sorting, enhances the trafficking of spike protein to the lysosome, and thus accelerates the entry of SARS-CoV-2 in uninfected cells.
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 		33330866
(bioRxiv)
PMID
33330866
Date of Publishing: 2020 Dec 9
Title The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike
Author(s) nameGuo C, Tsai SJ et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 3

Most frequent and prevalent mutation reported, with reference to Wuhan sequence (hCoV-19/Wuhan/WIV04/2019), was P323L in the non-structural protein 12 (94.7%) whereas the second frequent mutation was D614G in the Spike glycoprotein region (92.6%), followed by G71S in the non-structural protein 5 (70%). SARS-CoV-2 Genome sequences generated in the study (Refer Supplementary Table 1 and 2)
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 		33359061
(Int J Infect Dis)
PMID
33359061
Date of Publishing: 2020 Dec 21
Title Molecular epidemiology of COVID-19 in Oman: A molecular andsurveillance study for the early transmission of COVID-19 in thecountry
Author(s) nameAl-Mahruqi S, Al-Wahaibi A et al.
Journal Int J Infect Dis
Impact factor
3.42
Citation count: 6