SARS-CoV-2 Mutation Detail Information

Virus Mutation SARS-CoV-2 Mutation D5584Y


Basic Characteristics of Mutations
Mutation Site D5584Y
Mutation Site Sentence These mutations comprised known clade/lineage defining mutations such as ORF1ab V86F (leader protein), A3529T (nsp5), A4977V (RdRp), A5376V and D5584Y (helicase), in Spike IHV68I, N501T and H655Y, in ORF8 L84S, and in nucleocapsid A35V and S202N, in addition to P2110S (nsp3), ORF3a S171L and Spike P681R.
Mutation Level Amino acid level
Mutation Type Nonsynonymous substitution
Gene/Protein/Region NSP13
Standardized Encoding Gene ORF1b  
Genotype/Subtype -
Viral Reference NC_045512.2
Functional Impact and Mechanisms
Disease COVID-19    
Immune -
Target Gene -
Clinical and Epidemiological Correlations
Clinical Information Y
Treatment -
Location Egypt
Literature Information
PMID 36008511
Title SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study
Author Jalal D,Elzayat MG,El-Shqanqery HE,Diab AA,Yahia A,Samir O,Bakry U,Amer K,ElNaqeeb M,Hassan W,Talat HS,Farawela HM,Hamdy MS,Soliman MS,El Sissy MH,Ezzelarab MH,El Khateeb SM,Soliman LH,Haddad SE,Hatem A,Ismail MS,Hossam M,Mansour T,Shalaby L,Soliman S,Hassan R,Hammad M,Abdo I,Magdeldin S,ElHaddad A,Abouelnaga S,Sayed AA
Journal Scientific reports
Journal Info 2022 Aug 25;12(1):14511
Abstract A serious global public health emergency emerged late November 2019 in Wuhan City, China, by a new highly pathogenic virus, SARS-CoV-2. The virus evolution spread has been tracked by three developing databases: GISAID, Nextstrain and PANGO to understand its circulating variants. In this study, 110 diagnosed positive COVID-19 patient's samples, were collected from Kasr Al-Aini Hospital and the Children Cancer Hospital Egypt 57357 between May 2020 and January 2021, with clinical severity ranging from mild to severe. The viral genomes were sequenced by next generation sequencing, and phylogenetic analysis was performed to understand viral transmission dynamics. According to Nextstrain clades, most of our sequenced samples belonged to clades 20A and 20D, which in addition to clade 20B were present from the beginning of sample collection in May 2020. Clades 19A and 19B, on the other hand, appeared in the mid and late 2020 respectively, followed by the disappearance of clade 20B at the end of 2020. We identified a relatively high prevalence of the D614G spike protein variant and novel patterns of mutations associated together and with different clades. We also identified four mutations, spike H49Y, ORF3a H78Y, ORF8 E64stop and nucleocapsid E378V, associated with higher disease severity. Altogether, our study contributes genetic, phylogenetic, and clinical correlation data about the spread of the SARS-CoV-2 pandemic in Egypt.
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.