SARS-CoV-2 Mutation Detail Information

Virus Mutation SARS-CoV-2 Mutation C28087T


Basic Characteristics of Mutations
Mutation Site C28087T
Mutation Site Sentence Furthermore, the two mismatches closest to the 3' end of the N3 forward primer - C28087T and C28093T - were significantly associated with N3 target dropout (Fisher's exact, p = 0.0407 and p < 0.0001, respectively), but the mismatch at the first position was not significantly associated with N3 target dropout (Fisher's exact, p = 0.0914).
Mutation Level Nucleotide level
Mutation Type
Gene/Protein/Region
Standardized Encoding Gene
Genotype/Subtype B.1.1.7
Viral Reference -
Functional Impact and Mechanisms
Disease COVID-19    
Immune -
Target Gene -
Clinical and Epidemiological Correlations
Clinical Information -
Treatment -
Location America
Literature Information
PMID 34877674
Title Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach
Author Hernandez MM,Banu R,Gonzalez-Reiche AS,van de Guchte A,Khan Z,Shrestha P,Cao L,Chen F,Shi H,Hanna A,Alshammary H,Fabre S,Amoako A,Obla A,Alburquerque B,Patino LH,Ramirez JD,Sebra R,Gitman MR,Nowak MD,Cordon-Cardo C,Schutzbank TE,Simon V,van Bakel H,Sordillo EM,Paniz-Mondolfi AE
Journal Journal of medical virology
Journal Info 2022 Apr;94(4):1606-1616
Abstract The coronavirus disease 2019 (COVID-19) pandemic has sparked the rapid development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY(R) SARS-CoV-2 Panel combines reverse-transcription polymerase chain reaction and matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified data set of 1262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 to April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly specific for the Alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.
Sequence Data EPI_ISL_882805 – EPI_ISL_5336552
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.