SARS-CoV-2 Mutation Detail Information

Virus Mutation SARS-CoV-2 Mutation P251L


Basic Characteristics of Mutations
Mutation Site P251L
Mutation Site Sentence AY.4 was the most detected sublineage, representing 61 5% (95% CI 57 0-65 7) of the sequenced samples, and there were seven samples with single spike mutations of interest as defined by Public Health England (now the UK Health Security Agency): Glu484Lys, Asn501Tyr, Phe490Ser, Arg246Gly, Val483Phe, Pro251Leu, and Gln613His (appendix p 6).
Mutation Level Amino acid level
Mutation Type Nonsynonymous substitution
Gene/Protein/Region S
Standardized Encoding Gene S  
Genotype/Subtype -
Viral Reference -
Functional Impact and Mechanisms
Disease COVID-19    
Immune -
Target Gene -
Clinical and Epidemiological Correlations
Clinical Information Y
Treatment -
Location England
Literature Information
PMID 35085490
Title SARS-CoV-2 infection and vaccine effectiveness in England (REACT-1): a series of cross-sectional random community surveys
Author Chadeau-Hyam M,Wang H,Eales O,Haw D,Bodinier B,Whitaker M,Walters CE,Ainslie KEC,Atchison C,Fronterre C,Diggle PJ,Page AJ,Trotter AJ,Ashby D,Barclay W,Taylor G,Cooke G,Ward H,Darzi A,Riley S,Donnelly CA,Elliott P
Journal The Lancet. Respiratory medicine
Journal Info 2022 Apr;10(4):355-366
Abstract BACKGROUND: England has experienced a third wave of the COVID-19 epidemic since the end of May, 2021, coinciding with the rapid spread of the delta (B.1.617.2) variant, despite high levels of vaccination among adults. Vaccination rates (single dose) in England are lower among children aged 16-17 years and 12-15 years, whose vaccination in England commenced in August and September, 2021, respectively. We aimed to analyse the underlying dynamics driving patterns in SARS-CoV-2 prevalence during September, 2021, in England. METHODS: The REal-time Assessment of Community Transmission-1 (REACT-1) study, which commenced data collection in May, 2020, involves a series of random cross-sectional surveys in the general population of England aged 5 years and older. Using RT-PCR swab positivity data from 100 527 participants with valid throat and nose swabs in round 14 of REACT-1 (Sept 9-27, 2021), we estimated community-based prevalence of SARS-CoV-2 and vaccine effectiveness against infection by combining round 14 data with data from round 13 (June 24 to July 12, 2021; n=172 862). FINDINGS: During September, 2021, we estimated a mean RT-PCR positivity rate of 0.83% (95% CrI 0.76-0.89), with a reproduction number (R) overall of 1.03 (95% CrI 0.94-1.14). Among the 475 (62.2%) of 764 sequenced positive swabs, all were of the delta variant; 22 (4.63%; 95% CI 3.07-6.91) included the Tyr145His mutation in the spike protein associated with the AY.4 sublineage, and there was one Glu484Lys mutation. Age, region, key worker status, and household size jointly contributed to the risk of swab positivity. The highest weighted prevalence was observed among children aged 5-12 years, at 2.32% (95% CrI 1.96-2.73) and those aged 13-17 years, at 2.55% (2.11-3.08). The SARS-CoV-2 epidemic grew in those aged 5-11 years, with an R of 1.42 (95% CrI 1.18-1.68), but declined in those aged 18-54 years, with an R of 0.81 (0.68-0.97). At ages 18-64 years, the adjusted vaccine effectiveness against infection was 62.8% (95% CI 49.3-72.7) after two doses compared to unvaccinated people, for all vaccines combined, 44.8% (22.5-60.7) for the ChAdOx1 nCov-19 (Oxford-AstraZeneca) vaccine, and 71.3% (56.6-81.0) for the BNT162b2 (Pfizer-BioNTech) vaccine. In individuals aged 18 years and older, the weighted prevalence of swab positivity was 0.35% (95% CrI 0.31-0.40) if the second dose was administered up to 3 months before their swab but 0.55% (0.50-0.61) for those who received their second dose 3-6 months before their swab, compared to 1.76% (1.60-1.95) among unvaccinated individuals. INTERPRETATION: In September, 2021, at the start of the autumn school term in England, infections were increasing exponentially in children aged 5-17 years, at a time when vaccination rates were low in this age group. In adults, compared to those who received their second dose less than 3 months ago, the higher prevalence of swab positivity at 3-6 months following two doses of the COVID-19 vaccine suggests an increased risk of breakthrough infections during this period. The vaccination programme needs to reach children as well as unvaccinated and partially vaccinated adults to reduce SARS-CoV-2 transmission and associated disruptions to work and education. FUNDING: Department of Health and Social Care, England.
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.