Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351.
Result: On the other hand, the N gene D3L mutation is strongly associated with variant B.1.1.7 and is not associated with other currently dominant variants.
Result: The 5'p region of the variant B.1.1.7 SC-2 N gene contains a complete codon substitution, translated into D3L amino acid substitution.
Result: This reaction was termed N gene D3L reaction:ND3L.
Discussion: A few commercial kits partially address the detection of these SC-2 variants, but they target general mutations, such as N501Y and E484K in the spike protein, and not variant-specific mutations, such as the N protein D3L substitution or t
Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation.
Result: nPCR product B contains codon GAT at nucleotide position 28280, which changes to CTA in B.1.1.7 lineage viruses, resulting in the amino acid substitution aspartic acid to leucine at residue 3 of the nucleocapsid (N) protein.
SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay.
PMID: 34044153
2021
Clinical microbiology and infection
Introduction: B.1.1.7 has also a specific single nucleotide polymorphism in the N gene (D3L) which can be
Method: For validation of D3L polymorphism specific Ct shift in the N gene, each plasmid was diluted to an initial copy number of 1,25*10 8 and, subsequently diluted to 1:10, 1:100 and 1:1000 dilutions.
Result: This confirmed that the D3L mutation can be identified by the Allplex SARS-CoV-2/FluA/FluB/RSV assay, but not by the Allplex 2019-nCoV test (Figure 2).
Result: To elucidate the underlying molecular mechanism resulting in the observed N gene dropout or Ct value shift, we cloned the N gene coding sequence with and without D3L mutation into pCR -TOPO vectors which were then used for PCR analysis.
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.
Result: For example, the B.1.1.7 lineage includes mutations C5388A (orf1ab:A1708D) in a string of 7 perfectly conserved amino acids in a well-conserved region of nsp3, C14676T, a synonymous change in a large SCE in RdRp (situated between two conserved structures predicted by RNAz so possibly part of a containing structure too large for the prediction algorithm), T24506G (spike:S982A) in an extremely well-conserved region of S2, a three-nucleotide mutation at position 28280 (nucleocapsid:D3L) which weakens the initiation context of ORF9b, and C27972T (
Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern.
Result: Moreover, the UK-VOC contains several aa substitutions in other genomic regions, including NSP3: T183I, A890D, I1412T, NSP12: P323L, NS8: R52I, Y73C, and N-protein; D3L, R203K, G204R, S235F.
Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications.
Result: The D3L and T205I, S235F mutations in the N protein occur outside the dimer and RNA interaction interfaces, in the unstructured regions in its NTD and linker regions, respectively (Figure S10).
SARS_CoV_2 mutation literature information.
PMID: 
2021
Microbiology spectrum
Browser Board
Co-occurred Entities
Filtrator
ViMRT