SARS-CoV-2 Mutation Detail Information

Virus Mutation SARS-CoV-2 Mutation delH69/V70


Basic Characteristics of Mutations
Mutation Site delH69/V70
Mutation Site Sentence However; after convalescent plasma therapy; we observed large; dynamic shifts in the viral population; with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (DeltaH69/DeltaV70) in the S1 N-terminal domain of the spike protein.
Mutation Level Amino acid level
Mutation Type Deletion
Gene/Protein/Region S
Standardized Encoding Gene S  
Genotype/Subtype -
Viral Reference MN908947.3
Functional Impact and Mechanisms
Disease COVID-19    
Immune -
Target Gene -
Clinical and Epidemiological Correlations
Clinical Information Y
Treatment -
Location England
Literature Information
PMID 33545711
Title SARS-CoV-2 evolution during treatment of chronic infection
Author Kemp SA,Collier DA,Datir RP,Ferreira IATM,Gayed S,Jahun A,Hosmillo M,Rees-Spear C,Mlcochova P,Lumb IU,Roberts DJ,Chandra A,Temperton N,Sharrocks K,Blane E,Modis Y,Leigh KE,Briggs JAG,van Gils MJ,Smith KGC,Bradley JR,Smith C,Doffinger R,Ceron-Gutierrez L,Barcenas-Morales G,Pollock DD,Goldstein RA,Smielewska A,Skittrall JP,Gouliouris T,Goodfellow IG,Gkrania-Klotsas E,Illingworth CJR,McCoy LE,Gupta RK
Journal Nature
Journal Info 2021 Apr;592(7853):277-282
Abstract The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein(1) and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (DeltaH69/DeltaV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment. In vitro, the spike double mutant bearing both DeltaH69/DeltaV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. The spike deletion mutant DeltaH69/DeltaV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals.
Sequence Data SAMN16976824 - SAMN16976846
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.