SARS-CoV-2 Mutation Detail Information

Virus Mutation SARS-CoV-2 Mutation A1493G


Basic Characteristics of Mutations
Mutation Site A1493G
Mutation Site Sentence In silico analysis suggested that the N501Y-RT-LAMP and Q493R-RT-LAMP assays would distinguish N501Y (A1501U) and Q493R (A1478G)/Q498R (A1493G) strains from all coronaviruses lacking the target mutations (Supplementary Figure S3).
Mutation Level Nucleotide level
Mutation Type Nonsynonymous substitution
Gene/Protein/Region S
Standardized Encoding Gene S  
Genotype/Subtype BA.1;BA.2
Viral Reference NC_045512.2
Functional Impact and Mechanisms
Disease COVID-19    
Immune -
Target Gene -
Clinical and Epidemiological Correlations
Clinical Information -
Treatment -
Location -
Literature Information
PMID 37445876
Title A New Method to Detect Variants of SARS-CoV-2 Using Reverse Transcription Loop-Mediated Isothermal Amplification Combined with a Bioluminescent Assay in Real Time (RT-LAMP-BART)
Author Iijima T,Sakai J,Kanamori D,Ando S,Nomura T,Tisi L,Kilgore PE,Percy N,Kohase H,Hayakawa S,Maesaki S,Hoshino T,Seki M
Journal International journal of molecular sciences
Journal Info 2023 Jun 27;24(13):10698
Abstract Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), of which there are several variants. The three major variants (Alpha, Delta, and Omicron) carry the N501Y, L452R, and Q493R/Q498R mutations, respectively, in the S gene. Control of COVID-19 requires rapid and reliable detection of not only SARS-CoV-2 but also its variants. We previously developed a reverse transcription loop-mediated isothermal amplification assay combined with a bioluminescent assay in real time (RT-LAMP-BART) to detect the L452R mutation in the SARS-CoV-2 spike protein. In this study, we established LAMP primers and peptide nucleic acid probes to detect N501Y and Q493R/Q498R. The LAMP primer sets and PNA probes were designed for the N501Y and Q493R/Q498R mutations on the S gene of SARS-CoV-2. The specificities of RT-LAMP-BART assays were evaluated using five viral and four bacterial reference strains. The sensitivities of RT-LAMP-BART assays were evaluated using synthetic RNAs that included the target sequences, together with RNA-spiked clinical nasopharyngeal and salivary specimens. The results were compared with those of conventional real-time reverse transcription-polymerase chain reaction (RT-PCR) methods. The method correctly identified N501Y and Q493R/Q498R. Within 30 min, the RT-LAMP-BART assays detected up to 100-200 copies of the target genes; conventional real-time RT-PCR required 130 min and detected up to 500-3000 copies. Surprisingly, the real-time RT-PCR for N501Y did not detect the BA.1 and BA.2 variants (Omicron) that exhibited the N501Y mutation. The novel RT-LAMP-BART assay is highly specific and more sensitive than conventional real-time RT-PCR. The new assay is simple, inexpensive, and rapid; thus, it can be useful in efforts to identify SARS-CoV-2 variants of concern.
Sequence Data "EPI_ISL_601443 (Alpha), EPI_ISL_660190 (Beta), EPI_ISL_906081 (Gamma), EPI_ISL_1419152 (Delta), EPI_ISL_8750789 (Epsilon), EPI_ISL_8005633 (Zeta), EPI_ISL_1083809 (Eta), EPI_ISL_8158591 (Iota), EPI_ISL_8259884 (Mu), EPI_ISL_6841980 (Omicron BA.1), EPI_ISL_9097416 (Omicron BA.2), EPI_ISL_13241867 (Omicron BA.4), EPI_ISL_12703378 (Omicron BA.5)], SARS-CoV-1 (NC_004718.3), MERS-CoV (NC_019843.3)], and four human coronaviruses [α-coronaviruses AF304460.1 (229E) and AY567487.2 (NL63), and β-coronaviruses AY391777.1 (OC43) and NC_006577.2 (HKU1)"
Mutation Information
Note
Basic Characteristics of Mutations
  • Mutation Site: The specific location in a gene or protein sequence where a change occurs.
  • Mutation Level: The level at which a mutation occurs, including the nucleotide or amino acid level.
  • Mutation Type: The nature of the mutation, such as missense mutation, nonsense mutation, synonymous mutation, etc.
  • Gene/Protein/Region: Refers to the specific region of the virus where the mutation occurs. Including viral genes, viral proteins, or a specific viral genome region. If the article does not specifically indicate the relationship between the mutation and its correspondence, the main
  • Gene/Protein/Region studied in the article is marked.
  • Genotype/Subtype: Refers to the viral genotype or subtype where the mutation occurs. If the article does not specifically indicate the relationship between the mutation and its correspondence, the main Genotype/Subtype studied in the article is marked.
  • Viral Reference: Refers to the standard virus strain used to compare and analyze viral sequences.
Functional Impact and Mechanisms
  • Disease: An abnormal physiological state with specific symptoms and signs caused by viral infection.
  • Immune: The article focuses on the study of mutations and immune.
  • Target Gene: Host genes that viral mutations may affect.
Clinical and Epidemiological Correlations
  • Clinical Information: The study is a clinical or epidemiological study and provides basic information about the population.
  • Treatment: The study mentioned a certain treatment method, such as drug resistance caused by mutations. If the study does not specifically indicate the relationship between mutations and their correspondence treatment, the main treatment studied in the article is marked.
  • Location: The source of the research data.
Literature Information
  • Sequence Data: The study provides the data accession number.