SARS-CoV-2 Mutation Detail Information

Virus Mutation SARS-CoV-2 Mutation G339C


Basic Characteristics of Mutations
Mutation Site G339C
Mutation Site Sentence Such changes which are common for both global dataset without Indian and dataset of exclusive Indian sequences are R203M in Nucleocapsid for 20B, T85I and Q57H in NSP2 and ORF3a respectively for 20C while for exclusive Indian sequences such unique changes are A97V in RdRp, G339S and G339C in NSP2 in 19A and Q57H in ORF3a in 20A.
Mutation Level Amino acid level
Mutation Type Nonsynonymous substitution
Gene/Protein/Region NSP2
Standardized Encoding Gene ORF1a  
Genotype/Subtype 19A
Viral Reference NC_045512.2
Functional Impact and Mechanisms
Disease COVID-19    
Immune -
Target Gene -
Clinical and Epidemiological Correlations
Clinical Information -
Treatment -
Location India
Literature Information
PMID 34547443
Title Characterisation of SARS-CoV-2 clades based on signature SNPs unveils continuous evolution
Author Ghosh N,Saha I,Nandi S,Sharma N
Journal Methods (San Diego, Calif.)
Journal Info 2022 Jul;203:282-296
Abstract Since the emergence of SARS-CoV-2 in Wuhan, China more than a year ago, it has spread across the world in a very short span of time. Although, different forms of vaccines are being rolled out for vaccination programs around the globe, the mutation of the virus is still a cause of concern among the research communities. Hence, it is important to study the constantly evolving virus and its strains in order to provide a much more stable form of cure. This fact motivated us to conduct this research where we have initially carried out multiple sequence alignment of 15359 and 3033 global dataset without Indian and the dataset of exclusive Indian SARS-CoV-2 genomes respectively, using MAFFT. Subsequently, phylogenetic analyses are performed using Nextstrain to identify virus clades. Consequently, the virus strains are found to be distributed among 5 major clades or clusters viz. 19A, 19B, 20A, 20B and 20C. Thereafter, mutation points as SNPs are identified in each clade. Henceforth, from each clade top 10 signature SNPs are identified based on their frequency i.e. number of occurrences in the virus genome. As a result, 50 such signature SNPs are individually identified for global dataset without Indian and dataset of exclusive Indian SARS-CoV-2 genomes respectively. Out of each 50 signature SNPs, 39 and 41 unique SNPs are identified among which 25 non-synonymous signature SNPs (out of 39) resulted in 30 amino acid changes in protein while 27 changes in amino acid are identified from 22 non-synonymous signature SNPs (out of 41). These 30 and 27 amino acid changes for the non-synonymous signature SNPs are visualised in their respective protein structure as well. Finally, in order to judge the characteristics of the identified clades, the non-synonymous signature SNPs are considered to evaluate the changes in proteins as biological functions with the sequences using PROVEAN and PolyPhen-2 while I-Mutant 2.0 is used to evaluate their structural stability. As a consequence, for global dataset without Indian sequences, G251V in ORF3a in clade 19A, F308Y and G196V in NSP4 and ORF3a in 19B are the unique amino acid changes which are responsible for defining each clade as they are all deleterious and unstable. Such changes which are common for both global dataset without Indian and dataset of exclusive Indian sequences are R203M in Nucleocapsid for 20B, T85I and Q57H in NSP2 and ORF3a respectively for 20C while for exclusive Indian sequences such unique changes are A97V in RdRp, G339S and G339C in NSP2 in 19A and Q57H in ORF3a in 20A.
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.