Variants : Orf6

Total row(s): 2
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Original Article
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Out of 229 samples analysed, 2 different frameshift deletions were detected giving rise to 2 new variants. 6 sequences had a 34 nucleotide deletion (D34) at position 27267-27300 and 1 sequence had a 26 nucleotide deletion (D26) at position 27267- 27292. Both these deletions are in the open reading frame 6 (ORF6) of SARS CoV-2. These deletions have not been updated on the CoV-GLUE resource
33399033
(Emerg Microbes Infect)
PMID
33399033
Date of Publishing: 2021 Jan 5
Title Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster 1 during routine genomic surveillance, Lyon, France
Author(s) nameQuéromès G, Destras G et al.
Journal Emerg Microbes Infect
Impact factor
5.84
Citation count: 15
Date of Entry 2021 Aug 6


The in vitro studies on primate endothelial kidney cells (BGM) and human lung adenocarcinoma cells (Calu-3) indicated comparable replication kinetics with the wild-type but a significant difference was observed between cell lines for each strain. After infection with WT and ORF6 variants, Interferon-stimulated genes were upregulated, the latter inducing overexpression of 9 genes coding for inflammatory cytokines in the NF-kB pathway, including CCL2/MCP1, PTX3, and TNF, for which high plasma levels is associated with severe COVID-19.
33399033
(Emerg Microbes Infect)
PMID
33399033
Date of Publishing: 2021 Jan 5
Title Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster 1 during routine genomic surveillance, Lyon, France
Author(s) nameQuéromès G, Destras G et al.
Journal Emerg Microbes Infect
Impact factor
5.84
Citation count: 15
Date of Entry 2021 Aug 6



Sequence : Orf6

Total row(s): 7
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Key Findings
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Original Article
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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)
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: 6


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)
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: 6


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)
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: 6


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.
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: 1


Mutation analysis of 212 SARS-CoV-2 sequences from Israel revealed 224 unique single nucleotide variants (141 non-synonymous variants, 72 synonymous variants, 11 variants in non-coding regions) and five genomic deletions at different locations. Deletions 2,3, and 4, being a three independent deletions( i.e present in different samples) were found in the same clade which also included 18 samples. This clade is defined by a non-synonymous mutation S2430R (('A20755C', 'A23403G', 'C1059T', 'C14408T', 'C3037T', 'G25563T') in ORF1b, which affects the non-structural protein NSP16.
33139704
(Nat Commun)
PMID
33139704
Date of Publishing: 2020 Nov 2
Title Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel
Author(s) nameMiller D, Martin MA et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 41


Mutation analysis of 2492 SARS-CoV-2 genomes (belonging to 58 different countries representing six continents and five different climatic zones) revealed 1516 nucleotide variations, 744 amino acid substitutions, and 12 deletion sites. The pattern of mutations was different among the six different continents (Europe, Asia, North America, South America, Africa, and Australia) and five different climatic zones (temperate, tropical, diverse, dry, and continental). Sequences under analysis were retrieved from GISAID database (up to 30 March 2020). NCBI reference strain, Wuhan-Hu-1 (Accession NC_045512) was used as a reference genome for the analysis. Mutation analysis reveals diverse mutation pattern. Importantly, four mutations (Q57H, D614G, L3606F, P4714L) were common to all geographical and climatic conditions.
32814791
(Sci Rep)
PMID
32814791
Date of Publishing: 2020 Aug 19
Title Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity
Author(s) nameIslam MR, Hoque MN et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 98


Comparative genomic analysis of 15 SARS-CoV-2 genomes (representing ten countries) revealed several mutations in different genomic regions. Eight mutations in ORF1ab protein, four mutations in ORF3a protein, one mutation in ORF8, one mutation in E and N protein, and four mutations in S protein were observed. No mutations in the ORF6, ORF7a, and ORF10 regions of the genomes were found. Sequences under analysis were retrieved from GenBank: (MN 908947 (China, C1); MN985325 (United States: WA, UW); MN996527 (China, C2); MT007544 (Australia: Victoria, A1); MT027064 (United States: CA, UC); MT039890 (South Korea, K1); MT066175 (Taiwan, T1); MT066176 (Taiwan, T2); MT192759 (Taiwan, T3); MT198652 (Spain, SP); LC528232 (Japan, J1); LC528233 (Japan, J2); MT093571 (Sweden, SW); MT066156 (Italy, IT); and MT050493 (India, In) Clustalw tools was used for Multiple Sequence Alignment
32773643
(J Chin Med Assoc)
PMID
32773643
Date of Publishing: 2020 Aug
Title Genomic variance of Open Reading Frames (ORFs) and Spike protein in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Author(s) nameTsai PH, Wang ML et al.
Journal J Chin Med Assoc
Impact factor
3.9
Citation count: 8