SARS-CoV-2 Mutation Detail Information

Virus Mutation SARS-CoV-2 Mutation E484K


Basic Characteristics of Mutations
Mutation Site E484K
Mutation Site Sentence Encouragingly, c/µ+Ka/Ks identified 32 top nonsynonymous mutations (in order of decreasing c/μ: D614G, P681H, N501Y, D1118H, T716I, A570D, S982A, L452R, T478K, D950N, T19R, E484K, K417N, L18F, G142D, V1176F, D138Y, T1027I, T95I, T20N, P26S, H655Y, A701V, R190S, D80A, D215G, A222V, S477N, F490S, N439K, R346K, and K440K) (Table 3, Fig. 3) and are all located within the S1 region (N-terminal domain/NTD and Receptor-binding domain/RBD) and S2 region (including Heptad-Repeat 1/HR1 and Heptad-Repeat 2/HR2).
Mutation Level Amino acid level
Mutation Type Nonsynonymous substitution
Gene/Protein/Region S
Standardized Encoding Gene S  
Genotype/Subtype -
Viral Reference Wuhan-Hu-1
Functional Impact and Mechanisms
Disease -
Immune -
Target Gene -
Clinical and Epidemiological Correlations
Clinical Information -
Treatment -
Location -
Literature Information
PMID 39584063
Title Enhanced detection and molecular modeling of adaptive mutations in SARS-CoV-2 coding and non-coding regions using the c/micro test
Author Paradis NJ,Wu C
Journal Virus evolution
Journal Info 2024 Nov 6;10(1):veae089
Abstract Accurately identifying mutations under beneficial selection in viral genomes is crucial for understanding their molecular evolution and pathogenicity. Traditional methods like the Ka/Ks test, which assesses non-synonymous (Ka) versus synonymous (Ks) substitution rates, assume that synonymous substitutions at synonymous sites are neutral and thus is equal to the mutation rate (micro). Yet, evidence suggests that synonymous sites in translated regions (TRs) and untranslated regions (UTRs) can be under strong beneficial selection (Ks > micro) and strongly conserved (Ks approximately 0), leading to false predictions of adaptive mutations from codon-by-codon Ka/Ks analysis. Our previous work used a relative substitution rate test (c/micro, c: substitution rate in UTR/TR, and micro: mutation rate) to identify adaptive mutations in SARS-CoV-2 genome without the neutrality assumption of the synonymous sites. This study refines the c/micro test by optimizing micro value, leading to a smaller set of nucleotide and amino acid sites under beneficial selection in both UTR (11 sites with c/micro > 3) and TR (69 nonsynonymous sites: c/micro > 3 and Ka/Ks > 2.5; 107 synonymous sites: Ks/micro > 3). Encouragingly, the top two mutations in UTR and 70% of the top nonsynonymous mutations in TR had reported or predicted effects in the literature. Molecular modeling of top adaptive mutations for some critical proteins (S, NSP11, and NSP5) was carried out to elucidate the possible molecular mechanism of their adaptivity.
Sequence Data -
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.