SARS-CoV-2 Mutation Detail Information

Virus Mutation SARS-CoV-2 Mutation T28144C


Basic Characteristics of Mutations
Mutation Site T28144C
Mutation Site Sentence Sequences within lineage B had nucleotide substitution T28144C,rendering the L84S amino acid change in the Orf8 protein.
Mutation Level Nucleotide level
Mutation Type Nonsynonymous substitution
Gene/Protein/Region ORF8
Standardized Encoding Gene ORF8  
Genotype/Subtype B
Viral Reference MN908947
Functional Impact and Mechanisms
Disease COVID-19    
Immune -
Target Gene -
Clinical and Epidemiological Correlations
Clinical Information -
Treatment -
Location Mexico
Literature Information
PMID 32641486
Title Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico
Author Taboada B,Vazquez-Perez JA,Munoz-Medina JE,Ramos-Cervantes P,Escalera-Zamudio M,Boukadida C,Sanchez-Flores A,Isa P,Mendieta-Condado E,Martinez-Orozco JA,Becerril-Vargas E,Salas-Hernandez J,Grande R,Gonzalez-Torres C,Gaytan-Cervantes FJ,Vazquez G,Pulido F,Araiza-Rodriguez A,Garces-Ayala F,Gonzalez-Bonilla CR,Grajales-Muniz C,Borja-Aburto VH,Barrera-Badillo G,Lopez S,Hernandez-Rivas L,Perez-Padilla R,Lopez-Martinez I,Avila-Rios S,Ruiz-Palacios G,Ramirez-Gonzalez JE,Arias CF
Journal Journal of virology
Journal Info 2020 Aug 31;94(18):e01056-20
Abstract The coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to enabling implementation of effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage A/G, containing mostly sequences from North America, and lineage B/S, containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized 14 independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represented local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described for the country. Within this local transmission cluster, we also identified an H49Y amino acid change in the Spike protein. This mutation represents a homoplasy occurring independently through time and space and may function as a molecular marker to follow any further spread of these viral variants throughout the country. Our results provide a general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts.IMPORTANCE Understanding the introduction, spread, and establishment of SARS-CoV-2 within distinct human populations as well as the evolution of the pandemics is crucial to implement effective control strategies. In this work, we report that the initial virus strains introduced in Mexico came from Europe and the United States and that the virus was circulating locally in the country as early as mid-March. We also found evidence for early local transmission of strains with a H49Y mutation in the Spike protein, which could be further used as a molecular marker to follow viral spread within the country and the region.
Sequence Data EPI_ISL_424345;EPI_ISL_424348;EPI_ISL_424625;EPI_ISL_424626;EPI_ISL_424627;EPI_ISL_424731;EPI_ISL_424666;EPI_ISL_424667;EPI_ISL_424670;EPI_ISL_424672;EPI_ISL_424673;EPI_ISL_426361;EPI_ISL_426362;EPI_ISL_426363;EPI_ISL_426364;EPI_ISL_426365;EPI_ISL_412972
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.