SARS-CoV-2 Mutation Detail Information

Virus Mutation SARS-CoV-2 Mutation G446S


Basic Characteristics of Mutations
Mutation Site G446S
Mutation Site Sentence We also confirmed that the lineage NWL7 (N = 21529 reads) actually contains the S:G446S substitution encoded by the mutation G22898A, that the lineage NWL29 (N = 13874 reads) carries S:F490S and S:E484A and that the reads of the lineage NWL15 (N = 26915 reads) do not have any nucleotide substitution that could account for the S:F490S mutation.
Mutation Level Amino acid level
Mutation Type Nonsynonymous substitution
Gene/Protein/Region S
Standardized Encoding Gene S  
Genotype/Subtype Omicron
Viral Reference -
Functional Impact and Mechanisms
Disease COVID-19    
Immune -
Target Gene -
Clinical and Epidemiological Correlations
Clinical Information -
Treatment -
Location Norway
Literature Information
PMID 39881253
Title Unsupervised detection of novel SARS-CoV-2 mutations and lineages in wastewater samples using long-read sequencing
Author Garcia I,Riis RK,Moen LV,Rohringer A,Madslien EH,Bragstad K
Journal BMC genomics
Journal Info 2025 Jan 29;26(1):87
Abstract The COVID-19 pandemic has underscored the importance of virus surveillance in public health and wastewater-based epidemiology (WBE) has emerged as a non-invasive, cost-effective method for monitoring SARS-CoV-2 and its variants at the community level. Unfortunately, current variant surveillance methods depend heavily on updated genomic databases with data derived from clinical samples, which can become less sensitive and representative as clinical testing and sequencing efforts decline.In this paper, we introduce HERCULES (High-throughput Epidemiological Reconstruction and Clustering for Uncovering Lineages from Environmental SARS-CoV-2), an unsupervised method that uses long-read sequencing of a single 1 Kb fragment of the Spike gene. HERCULES identifies and quantifies mutations and lineages without requiring database-guided deconvolution, enhancing the detection of novel variants.We evaluated HERCULES on Norwegian wastewater samples collected from July 2022 to October 2023 as part of a national pilot on WBE of SARS-CoV-2. Strong correlations were observed between wastewater and clinical sample data in terms of prevalence of mutations and lineages. Furthermore, we found that SARS-CoV-2 trends in wastewater samples were identified one week earlier than in clinical data.Our results demonstrate HERCULES' capability to identify new lineages before their detection in clinical samples, providing early warnings of potential outbreaks. The methodology described in this paper is easily adaptable to other pathogens, offering a versatile tool for environmental surveillance of new emerging pathogens.
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.