SARS-CoV-2 Mutation Detail Information

Virus Mutation SARS-CoV-2 Mutation A701V


Basic Characteristics of Mutations
Mutation Site A701V
Mutation Site Sentence Table 1
Mutation Level Amino acid level
Mutation Type Nonsynonymous substitution
Gene/Protein/Region S
Standardized Encoding Gene S  
Genotype/Subtype B.1.1.7
Viral Reference NC_045512.2
Functional Impact and Mechanisms
Disease COVID-19    
Immune -
Target Gene -
Clinical and Epidemiological Correlations
Clinical Information -
Treatment -
Location Iran
Literature Information
PMID 37543926
Title Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations
Author Zare Ashrafi F,Mohseni M,Beheshtian M,Fattahi Z,Ghodratpour F,Keshavarzi F,Behravan H,Kalhor M,Jalalvand K,Azad M,Koshki M,Jafarpour A,Ghaziasadi A,Abdollahi A,Kiani SJ,Ataei-Pirkooh A,Rezaei Azhar I,Bokharaei-Salim F,Haghshenas MR,Babamahmoodi F,Mokhames Z,Soleimani A,Ziaee M,Javanmard D,Ghafari S,Ezani A,Ansari Moghaddam A,Shahraki-Sanavi F,Hashemi Shahri SM,Azaran A,Yousefi F,Moattari A,Moghadami M,Fakhim H,Ataei B,Nasri E,Poortahmasebi V,Varshochi M,Mojtahedi A,Jalilian F,Khazeni M,Moradi A,Tabarraei A,Piroozmand A,Yahyapour Y,Bayani M,Aboofazeli A,Ghafari P,Keramat F,Tavakoli M,Jalali T,Pouriayevali MH,Salehi-Vaziri M,Khorram Khorshid HR,Najafipour R,Malekzadeh R,Kahrizi K,Jazayeri SM,Najmabadi H
Journal Archives of Iranian medicine..
Journal Info 2023 Feb 1;26(2):69-75
Abstract BACKGROUND: Global real-time monitoring of SARS-CoV-2 variants is crucial to controlling the COVID-19 outbreak. The purpose of this study was to set up a Sanger-based platform for massive SARS-CoV-2 variant tracking in laboratories in low-resource settings. METHODS: We used nested RT-PCR assay, Sanger sequencing and lineage assignment for 930-bp of the SARS-CoV-2 spike gene, which harbors specific variants of concern (VOCs) mutations. We set up our platform by comparing its results with whole genome sequencing (WGS) data on 137 SARS-CoV-2 positive samples. Then, we applied it on 1028 samples from March-September 2021. RESULTS: In total, 125 out of 137 samples showed 91.24% concordance in mutation detection. In lineage assignment, 123 out of 137 samples demonstrated 89.78% concordance, 65 of which were assigned as VOCs and showed 100% concordance. Of 1028 samples screened by our in-house method, 78 distinct mutations were detected. The most common mutations were: S:D614G (21.91%), S:P681R (12.19%), S:L452R (12.15%), S:T478K (12.15%), S:N501Y (8.91%), S:A570D (8.89%), S:P681H (8.89%), S:T716I (8.74%), S:L699I (3.50%) and S:S477N (0.28%). Of 1028 samples, 980 were attributed as VOCs, which include the Delta (B.1.617.2) and Alpha (B.1.1.7) variants. CONCLUSION: Our proposed in-house Sanger-based assay for SARS-CoV-2 lineage assignment is an accessible strategy in countries with poor infrastructure facilities. It can be applied in the rapid tracking of SARS-CoV-2 VOCs in the SARS-CoV-2 pandemic.
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.