Back to top

The current mutation

ID: V442
DNA: 1175G>A
Protein: G392D
Position: 1440








COV2Var annotation categories







Summary information of mutation (1175G>A)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   1440
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 1175G>A
  Ref Seq: G
  Mut Seq: A
  Protein Level   Protein 1-letter Mutation: G392D
  Protein 3-letter Mutation: Gly392Asp

Overview of the genomic positions of Mutation.
Note: The annotated 12 genes were retrieved from GeneBank (Accession: NC_045512.2). "MP" represents genomic position of mutation.





Analyzing the distribution of mutation (1175G>A) across geographic regions, temporal trends, and lineages

The count of genome sequences harboring this mutation and its distribution across global regions offer insights into regional variations.
Note: The distribution of mutation across 218 geographical regions. Color representation of genome sequence counts. The data is obtained from GISAID's metadata, specifically capturing the regional distribution of genomic sequences.



The dynamic count of genome sequences containing this mutation over time.
Note: Clicking the "Count" or "Cumulative Count" button toggles the view. Count represents the number of genome sequences per month. Cumulative count represents the accumulated total count up to the respective month. The data is obtained from GISAID's metadata, specifically capturing the collection date of genomic sequences.



For every time point represented in the graph above, identifying the top 3 lineages with the highest count of genome sequences carrying this mutation aids in pinpointing noteworthy lineages for further analysis.
Note: Users can filter the lineages by entering a "Year-Month" term in the search box. For example, entering 2020-01 will display lineages that appeared in January 2020. The data is obtained from GISAID's metadata, specifically capturing the collection date of genomic sequences.

Collection date Lineage Total lineage monthly counts Lineage-specific monthly counts Lineage-specific monthly frequency
2020-10 B.1.36 6 4 6.67e-1
2020-10 B.1.1.216 6 1 1.67e-1
2020-10 B.3 6 1 1.67e-1
2020-11 B.1.36 5 3 6.00e-1
2020-11 B.1.177.6 5 1 2.00e-1
2020-11 B.1.499 5 1 2.00e-1
2020-12 B.1.1.216 6 2 3.33e-1
2020-12 B.1 6 1 1.67e-1
2020-12 B.1.1.7 6 1 1.67e-1
2020-02 B.3 15 15 1.00e+0
2020-03 B.3 1052 782 7.43e-1
2020-03 B.3.1 1052 265 2.52e-1
2020-03 B.1 1052 2 1.90e-3
2020-04 B.3.1 451 229 5.08e-1
2020-04 B.3 451 218 4.83e-1
2020-04 B.1 451 3 6.65e-3
2020-05 B.3.1 63 38 6.03e-1
2020-05 B.3 63 22 3.49e-1
2020-05 B.1 63 2 3.17e-2
2020-06 B.3 9 6 6.67e-1
2020-06 B.3.1 9 2 2.22e-1
2020-06 B.1.590 9 1 1.11e-1
2020-07 B.3 5 2 4.00e-1
2020-07 A 5 1 2.00e-1
2020-07 B.1 5 1 2.00e-1
2020-08 B.3 3 2 6.67e-1
2020-08 B.1.2 3 1 3.33e-1
2020-09 B.1.1.222 4 2 5.00e-1
2020-09 B.1.36 4 2 5.00e-1
2021-01 B.1.427 25 17 6.80e-1
2021-01 B.1.1.214 25 2 8.00e-2
2021-01 B.1.1.7 25 2 8.00e-2
2021-10 AY.4 64 14 2.19e-1
2021-10 AY.25 64 12 1.88e-1
2021-10 AY.4.4 64 11 1.72e-1
2021-11 AY.4.4 104 24 2.31e-1
2021-11 AY.3 104 23 2.21e-1
2021-11 AY.4 104 22 2.12e-1
2021-12 AY.4 120 30 2.50e-1
2021-12 AY.25 120 27 2.25e-1
2021-12 AY.3 120 14 1.17e-1
2021-02 B.1.427 32 19 5.94e-1
2021-02 B.1.1.7 32 10 3.12e-1
2021-02 B.1.2 32 1 3.12e-2
2021-03 B.1.1.7 41 22 5.37e-1
2021-03 B.1.427 41 8 1.95e-1
2021-03 B.3 41 5 1.22e-1
2021-04 B.1.1.7 23 14 6.09e-1
2021-04 P.1 23 6 2.61e-1
2021-04 B.1.351 23 1 4.35e-2
2021-05 B.1.1.7 32 21 6.56e-1
2021-05 P.1 32 9 2.81e-1
2021-05 B.1.617.1 32 1 3.12e-2
2021-06 B.1.1.7 12 7 5.83e-1
2021-06 P.1 12 3 2.50e-1
2021-06 AY.25 12 1 8.33e-2
2021-07 AY.19 33 12 3.64e-1
2021-07 AY.98.1 33 8 2.42e-1
2021-07 P.1 33 4 1.21e-1
2021-08 AY.98.1 50 20 4.00e-1
2021-08 AY.4 50 6 1.20e-1
2021-08 AY.75 50 5 1.00e-1
2021-09 AY.4 38 13 3.42e-1
2021-09 AY.25 38 8 2.11e-1
2021-09 AY.103 38 3 7.89e-2
2022-01 BA.1.1 41 18 4.39e-1
2022-01 BA.1 41 11 2.68e-1
2022-01 BA.1.15 41 2 4.88e-2
2022-10 BA.2.75.5 255 106 4.16e-1
2022-10 BN.3.1 255 101 3.96e-1
2022-10 BN.3 255 20 7.84e-2
2022-11 BN.3.1 347 273 7.87e-1
2022-11 BA.2.75.5 347 43 1.24e-1
2022-11 BN.3 347 7 2.02e-2
2022-12 BN.3.1 476 389 8.17e-1
2022-12 BA.2.75.5 476 25 5.25e-2
2022-12 BN.3 476 24 5.04e-2
2022-02 BA.1.1 44 13 2.95e-1
2022-02 BA.2 44 11 2.50e-1
2022-02 BA.1 44 8 1.82e-1
2022-03 BA.2 73 49 6.71e-1
2022-03 BA.1.1 73 10 1.37e-1
2022-03 BA.2.9 73 4 5.48e-2
2022-04 BA.2 53 41 7.74e-1
2022-04 BA.1.1 53 5 9.43e-2
2022-04 BA.2.1 53 2 3.77e-2
2022-05 BA.2 37 20 5.41e-1
2022-05 BA.2.29 37 6 1.62e-1
2022-05 BA.2.3.13 37 4 1.08e-1
2022-06 BA.2.9.4 8 4 5.00e-1
2022-06 BA.2 8 2 2.50e-1
2022-06 BA.2.29 8 2 2.50e-1
2022-07 BA.2.75.5 18 7 3.89e-1
2022-07 BA.2.75 18 4 2.22e-1
2022-07 BA.2 18 1 5.56e-2
2022-08 BA.2.75.5 90 62 6.89e-1
2022-08 BN.3 90 14 1.56e-1
2022-08 BA.2.75 90 3 3.33e-2
2022-09 BA.2.75.5 155 99 6.39e-1
2022-09 BN.3 155 17 1.10e-1
2022-09 BN.4 155 17 1.10e-1
2023-01 BN.3.1 298 257 8.62e-1
2023-01 BN.3 298 10 3.36e-2
2023-01 BQ.1.1.1 298 7 2.35e-2
2023-02 BN.3.1 75 65 8.67e-1
2023-02 CH.1.1 75 3 4.00e-2
2023-02 BN.3 75 2 2.67e-2

The count of genome sequences and the frequency of this mutation in each lineage.
Note: Displaying mutation frequencies (>0.01) among 2,735 lineages. Mutation Count represents the count of sequences carrying this mutation. Users can filter the lineages by entering a search term in the search box. For example, entering "A.1" will display A.1 lineages. The data is obtained from GISAID's metadata, specifically capturing the lineage of genomic sequences. Mutation count: Count of sequences carrying this mutation.

Mutation ID Lineage Mutation frequency Mutation count Earliest lineage emergence Latest lineage emergence
V442 AY.19 2.03e-2 8 2021-4-5 2022-5-7
V442 AY.4.4 1.27e-2 44 2021-1-19 2022-2-22
V442 B.1.590 1.54e-2 3 2020-3-15 2020-11-20
V442 B.3 9.86e-1 1054 2020-2-20 2021-4-1
V442 B.3.1 9.93e-1 534 2020-1-21 2021-11-16
V442 BA.2.75.5 1.86e-1 346 2022-7-1 2023-2-1
V442 BN.2 1.13e-2 2 2022-7-10 2023-1-31
V442 BN.3 1.00e+0 95 2022-3-11 2023-2-10
V442 BN.3.1 9.95e-1 1088 2022-9-21 2023-2-22
V442 BN.4 9.00e-1 45 2022-8-23 2023-1-13






Examining mutation (1175G>A) found in abundant sequences of non-human animal hosts

Exploring mutation presence across 35 non-human animal hosts for cross-species transmission.
Note: We retained the mutation that appear in at least three non-human animal hosts' sequences. The data is obtained from GISAID's metadata, specifically capturing the host of genomic sequences.

Animal host Lineage Source region Collection date Accession ID




Association between mutation (1175G>A) and patients of different ages, genders, and statuses

Note: The logistic regression model was employed to examine changes in patient data before and after the mutation. The logistic regression model was conducted using the glm function in R. The data is obtained from GISAID's metadata, specifically capturing the patient status, gender, and age of genomic sequences.

Analyzing the association between mutation and patient status.
Note: we categorized the data into different patient statuses (ambulatory, deceased, homebound, hospitalized, mild, and recovered) based on GISAID classifications. In the analysis exploring the association between mutation and patient status, the model included mutation, patient status, patient age, gender, sequence region of origin, and sequence collection time point. In the 'increase' direction of the mutation, it means that when this mutation occurs, it increases the corresponding effect proportion. In the 'decrease' direction of the mutation, it means that when this mutation occurs, it decreases the corresponding effect proportion. A p-value lower than 0.001 signifies a notable differentiation between the population with and without the mutation.

Attribute Effect Estimate SE Z-value P-value Direction
Patient status Ambulatory -7.80e-1 1.26e+0 -6.18e-1 5.37e-1 Decrease
Deceased -4.71e+0 1.20e+0 -3.91e+0 9.12e-5 Decrease
Homebound -4.22e+1 2.90e+4 -1.45e-3 9.99e-1 Decrease
Hospitalized 1.80e+0 5.03e-1 3.57e+0 3.59e-4 Increase
Mild 8.64e-1 8.51e-1 1.02e+0 3.10e-1 Increase
Recovered 1.91e-1 7.65e-1 2.50e-1 8.02e-1 Increase

Analyzing the association between mutation and patient status.
Note: we categorized the data into different patient age (0-17, 18-39, 40-64, 65-84, and 85+). In the analysis exploring the association between mutation and patient age, the model included mutation, patient age, gender, sequence region of origin, and sequence collection time point. In the 'increase' direction of the mutation, it means that when this mutation occurs, it increases the corresponding effect proportion. In the 'decrease' direction of the mutation, it means that when this mutation occurs, it decreases the corresponding effect proportion. A p-value lower than 0.001 signifies a notable differentiation between the population with and without the mutation.

Attribute Effect Estimate SE Z-value P-value Direction
Patient age, years 0-17 -9.55e-1 1.67e-1 -5.72e+0 1.06e-8 Decrease
18-39 -2.32e-1 7.23e-2 -3.21e+0 1.31e-3 Decrease
40-64 6.79e-2 6.79e-2 1.00e+0 3.17e-1 Increase
65-84 2.62e-1 8.01e-2 3.28e+0 1.06e-3 Increase
>=85 7.95e-1 1.50e-1 5.30e+0 1.19e-7 Increase

Analyzing the association between mutation and patient status.
Note: we categorized the data into different patient gender (male and female). In the analysis exploring the association between mutation and patient gender, the model included mutation, patient gender, patient age, sequence region of origin, and sequence collection time point. In the 'increase' direction of the mutation, it means that when this mutation occurs, it increases the corresponding effect proportion. In the 'decrease' direction of the mutation, it means that when this mutation occurs, it decreases the corresponding effect proportion. A p-value lower than 0.001 signifies a notable differentiation between the population with and without the mutation.

Attribute Effect Estimate SE Z-value P-value Direction
Patient gender Male 1.09e-1 6.65e-2 1.65e+0 9.99e-2 Increase





Investigating natural selection at mutation (1175G>A) site for genetic adaptation and diversity

Note: Investigating the occurrence of positive selection or negative selection at this mutation site reveals implications for genetic adaptation and diversity.

The MEME method within the HyPhy software was employed to analyze positive selection. MEME: episodic selection.
Note: List of sites found to be under episodic selection by MEME (p < 0.05). "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site P-value Lineage Method
nsp2 806 2719 638 212 1.00e-2 BA.2.10.1 MEME
nsp2 806 2719 638 212 0.00e+0 BA.2.24 MEME
nsp2 806 2719 638 212 1.00e-2 BA.2.75.5 MEME
nsp2 806 2719 638 212 0.00e+0 BA.5.2.28 MEME
nsp2 806 2719 638 212 1.00e-2 BA.5.2.2 MEME
nsp2 806 2719 638 212 1.00e-2 BA.5.2.43 MEME
nsp2 806 2719 638 212 1.00e-2 BQ.1.10 MEME
nsp2 806 2719 638 212 5.00e-2 BQ.1.1.1 MEME
nsp2 806 2719 638 212 0.00e+0 BQ.1.13.1 MEME
nsp2 806 2719 638 212 2.00e-2 BQ.1.1.6 MEME
nsp2 806 2719 638 212 4.00e-2 AY.95 MEME
nsp2 806 2719 638 212 0.00e+0 B.1.1.50 MEME
nsp2 806 2719 638 212 0.00e+0 B.1.36 MEME
nsp2 806 2719 638 212 0.00e+0 B.1.2 MEME
nsp2 806 2719 638 212 1.00e-2 B.1.427 MEME
nsp2 806 2719 638 212 1.00e-2 BA.1.1.2 MEME
nsp2 806 2719 638 212 0.00e+0 BA.1.17 MEME
nsp2 806 2719 638 212 0.00e+0 BA.5.2 MEME
nsp2 806 2719 638 212 3.00e-2 BE.1.1 MEME
nsp2 806 2719 638 212 1.00e-2 BQ.1.12 MEME
nsp2 806 2719 638 212 1.00e-2 P.1 MEME
nsp2 806 2719 638 212 1.00e-2 AY.3 MEME
nsp2 806 2719 638 212 1.00e-2 AY.46 MEME
nsp2 806 2719 638 212 2.00e-2 B.1.1.214 MEME
nsp2 806 2719 638 212 2.00e-2 AY.19 MEME
nsp2 806 2719 638 212 1.00e-2 CG.1 MEME
nsp2 806 2719 638 212 1.00e-2 XAM MEME

The FEL method within the HyPhy software was employed to analyze both positive and negative selection. FEL: pervasive selection on samll datasets.
Note: List of sites found to be under pervasive selection by FEL (p < 0.05). A beta value greater than alpha signifies positive selection, while a beta value smaller than alpha signifies negative selection. "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site Alpha Beta P-value Lineage Method
nsp2 806 2719 638 212 0.00 19.96 0.00e+0 BA.2.75.5 FEL
nsp2 806 2719 638 212 0.00 7.39 3.00e-2 BQ.1.1.1 FEL
nsp2 806 2719 638 212 6.98 0.00 4.00e-2 A.2.5 FEL
nsp2 806 2719 638 212 0.00 22.83 3.00e-2 AY.95 FEL
nsp2 806 2719 638 212 0.00 11.98 3.00e-2 B.1.1.50 FEL
nsp2 806 2719 638 212 0.39 276.35 5.00e-2 B.3.1 FEL
nsp2 806 2719 638 212 0.00 58.88 5.00e-2 AY.19 FEL
nsp2 806 2719 638 212 0.00 127.33 3.00e-2 XAM FEL

The FUBAR method within the HyPhy software was employed to analyze both positive and negative selection. FUBAR: pervasive selection on large datasets.
Note: List of sites found to be under pervasive selection by FUBAR (prob > 0.95). A prob[alpha < beta] value exceeding 0.95 indicates positive selection, while a prob[alpha > beta] value exceeding 0.95 indicates negative selection. "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site Prob[alpha>beta] Prob[alpha<beta] Lineage Method
nsp2 806 2719 638 212 1.00e-2 9.70e-1 BA.2.43 FUBAR
nsp2 806 2719 638 212 0.00e+0 1.00e+0 BA.2.75.5 FUBAR
nsp2 806 2719 638 212 1.00e-2 9.70e-1 BA.5.1.16 FUBAR
nsp2 806 2719 638 212 2.00e-2 9.60e-1 BA.5.2.43 FUBAR
nsp2 806 2719 638 212 2.00e-2 9.60e-1 BQ.1.1.1 FUBAR
nsp2 806 2719 638 212 9.60e-1 2.00e-2 A.2.5 FUBAR
nsp2 806 2719 638 212 0.00e+0 9.90e-1 AY.95 FUBAR
nsp2 806 2719 638 212 1.00e-2 9.80e-1 B.1.1.50 FUBAR
nsp2 806 2719 638 212 9.60e-1 2.00e-2 B.1.311 FUBAR
nsp2 806 2719 638 212 9.70e-1 2.00e-2 B.1.391 FUBAR
nsp2 806 2719 638 212 3.00e-2 9.50e-1 BA.1.1.2 FUBAR
nsp2 806 2719 638 212 2.00e-2 9.60e-1 BA.5.2 FUBAR
nsp2 806 2719 638 212 1.00e-2 9.80e-1 AY.19 FUBAR
nsp2 806 2719 638 212 2.00e-2 9.70e-1 B.1.459 FUBAR
nsp2 806 2719 638 212 2.00e-2 9.70e-1 B.1.540 FUBAR
nsp2 806 2719 638 212 9.60e-1 2.00e-2 B.1.627 FUBAR
nsp2 806 2719 638 212 2.00e-2 9.70e-1 CG.1 FUBAR
nsp2 806 2719 638 212 1.00e-2 9.80e-1 XAM FUBAR




Alterations in protein physicochemical properties induced by mutation (1175G>A)

Understanding the alterations in protein physicochemical properties can reveal the evolutionary processes and adaptive changes of viruses
Note: ProtParam software was used for the analysis of physicochemical properties. Significant change threshold: A change exceeding 10% compared to the reference is considered a significant change. "GRAVY" is an abbreviation for "grand average of hydropathicity".

Group Protein name Molecular weight Theoretical PI Extinction coefficients Aliphatic index GRAVY
Mutation ORF1ab_pp1a 490046.95 6.02 543550 88.99 -0.024
Reference ORF1ab_pp1a 489988.91 6.04 543550 88.99 -0.023




Alterations in protein stability induced by mutation (1175G>A)

The impact of mutations on protein stability directly or indirectly affects the biological characteristics, adaptability, and transmission capacity of the virus
Note: iMutant 2.0 was utilized to analyze the effects of mutations on protein stability. pH 7 and a temperature of 25°C are employed to replicate the in vitro environment. pH 7.4 and a temperature of 37°C are utilized to simulate the in vivo environment.

Mutation Protein name Mutation type Position ΔDDG Stability pH Temperature Condition
G392D ORF1ab_pp1a Point 392 -1.15 Decrease 7 25 Environment
G392D ORF1ab_pp1a Point 392 -1.09 Decrease 7.4 37 Internal




Impact on protein function induced by mutation (1175G>A)

The impact of mutations on protein function
Note: The MutPred2 software was used to predict the pathogenicity of a mutation and gives the molecular mechanism of pathogenicity. A score above 0.5 indicates an increased likelihood of pathogenicity. "Pr" is the abbreviation for "proportion. P" is the abbreviation for "p-value.

Mutation Protein name Mutation type Score Molecular mechanisms
G392D ORF1ab_pp1a Point 0.247 Loss of Strand (Pr = 0.28 | P = 6.4e-03)
Loss of Loop (Pr = 0.27 | P = 0.03)
Altered Cytoplasmic_loop (Pr = 0.26 | P = 1.0e-03)
Gain of Acetylation at K394 (Pr = 0.16 | P = 0.08)
Gain of N-linked_glycosylation at N389 (Pr = 0.09 | P = 0.01)




Exploring mutation (1175G>A) distribution within intrinsically disordered protein regions

Intrinsically Disordered Proteins (IDPs) which refers to protein regions that have no unique 3D structure. In viral proteins, mutations in the disordered regions s are critical for immune evasion and antibody escape, suggesting potential additional implications for vaccines and monoclonal therapeutic strategies.
Note: The iupred3 software was utilized for analyzing IDPs. A score greater than 0.5 is considered indicative of an IDP. In the plot, "POS" represents the position of the mutation.





Alterations in enzyme cleavage sites induced by mutation (1175G>A)

Exploring the impact of mutations on the cleavage sites of 28 enzymes.
Note: The PeptideCutter software was used for detecting enzymes cleavage sites. The increased enzymes cleavage sites refer to the cleavage sites in the mutated protein that are added compared to the reference protein. Conversely, the decreased enzymes cleavage sites indicate the cleavage sites in the mutated protein that are reduced compared to the reference protein.

Mutation Protein name Genome position Enzyme name Increased cleavage sites Decreased cleavage sites
G392D ORF1ab_pp1a 1440 Thermolysin NA
 NESGLKTILR (pos: 392)
G392D ORF1ab_pp1a 1440 Asp-N endopeptidase HNESDLKTIL (pos: 391)
 NA
G392D ORF1ab_pp1a 1440 Formic acid NESDLKTILR (pos: 392)
 NA
G392D ORF1ab_pp1a 1440 Asp-N endopeptidase + N-terminal Glu HNESDLKTIL (pos: 391)
 NA




Impact of spike protein mutation (1175G>A) on antigenicity and immunogenicity

Investigating the impact of mutations on antigenicity and immunogenicity carries important implications for vaccine design and our understanding of immune responses.
Note: An absolute change greater than 0.0102 (three times the median across sites) in antigenicity score is considered significant. An absolute changegreater than 0.2754 (three times the median across sites) in immunogenicity score is considered significant. The VaxiJen tool was utilized for antigenicity analysis. The IEDB tool was used for immunogenicity analysis. Antigens with a prediction score of more than 0.4 for this tool are considered candidate antigens. MHC I immunogenicity score >0, indicating a higher probability to stimulate an immune response.

Group Protein name Protein region Antigenicity score Immunogenicity score




Impact of mutation (1175G>A) on viral transmissibility by the affinity between RBD and ACE2 receptor

Unraveling the impact of mutations on the interaction between the receptor binding domain (RBD) and ACE2 receptor using deep mutational scanning (DMS) experimental data to gain insights into their effects on viral transmissibility.
Note: The ΔBinding affinity represents the disparity between the binding affinity of a mutation and the reference binding affinity. A positive Δbinding affinity value (Δlog10(KD,app) > 0) signifies an increased affinity between RBD and ACE2 receptor due to the mutation. Conversely, a negative value (Δlog10(KD,app) < 0) indicates a reduced affinity between RBD and ACE2 receptor caused by the mutation. A p-value smaller than 0.05 indicates significance. "Ave mut bind" represents the average binding affinity of this mutation. "Ave ref bind" refers to the average binding affinity at a site without any mutation (reference binding affinity).

;
Mutation Protein name Protein region Mutation Position Ave mut bind Ave ref bind ΔBinding affinity P-value Image


The interface between the receptor binding domain (RBD) and ACE2 receptor is depicted in the crystal structure 6JM0.
Note: The structure 6M0J encompasses the RBD range of 333 to 526. The binding sites (403-406, 408, 417, 439, 445-447, 449, 453, 455-456, 473-478, 484-498, and 500-506) on the RBD that interface with ACE2 are indicated in magenta. The binding sites on the RBD that have been identified through the interface footprints experiment. The ACE2 binding sites within the interface are shown in cyan, representing residues within 5Å proximity to the RBD binding sites. The mutation within the RBD range of 333 to 526 is depicted in red.

        Show as:

        Show interface residues:





Impact of mutation (1175G>A) on immune escape by the affinity between RBD and antibody/serum

By utilizing experimental data from deep mutational scanning (DMS), we can uncover how mutations affect the interaction between the receptor binding domain (RBD) and antibodies/serum. This approach provides valuable insights into strategies for evading the host immune response.
Note: We considered a mutation to mediate strong escape if the escape score exceeded 0.1 (10% of the maximum score of 1). A total of 1,504 antibodies/serum data were collected for this analysis. "Condition name" refers to the name of the antibodies/serum. "Mut escape score" represents the escape score of the mutation in that specific condition. "Avg mut escape score" indicates the average escape score of the mutation site in that condition, considering the occurrence of this mutation and other mutations. Class 1 antibodies bind to an epitope only in the RBD “up” conformation, and are the most abundant. Class 2 antibodies bind to the RBD both in “up” and “down” conformations. Class 3 and class 4 antibodies both bind outside the ACE2 binding site. Class 3 antibodies bind the RBD in both the open and closed conformation, while class 4 antibodies bind only in the open conformation.

Mutation Condition name Condition type Condition subtype Condition year Mut escape score Avg mut escape score




Investigating the co-mutation patterns of mutation (1175G>A) across 2,735 viral lineages

Investigating the co-mutation patterns of SARS-CoV-2 across 2,735 viral lineages to unravel the cooperative effects of different mutations. In biological research, correlation analysis of mutation sites helps us understand whether there is a close relationship or interaction between certain mutations.
Note: The Spearman correlation coefficient is used to calculate the correlation between two mutations within each Pango lineage. Holm–Bonferroni method was used for multiple test adjustment. We retained mutation pairs with correlation values greater than 0.6 or less than -0.6 and Holm–Bonferroni corrected p-values less than 0.05.

Associated mutation ID DNA mutation Mutation type Protein name Protein mutation correlation coefficient Lineage
V4641 785C>T missense_variant ORF3a P262L 6.11e-1 AY.4
V6393 3798T>C synonymous_variant ORF1ab_pp1a D1266D 7.17e-1 AY.4
V440 1174G>A missense_variant ORF1ab_pp1a G392S 7.78e-1 AY.3
V8385 19177C>T synonymous_variant ORF1ab_pp1ab L6393L 7.00e-1 AY.3
V440 1174G>A missense_variant ORF1ab_pp1a G392S 7.07e-1 BA.1.1.2
V440 1174G>A missense_variant ORF1ab_pp1a G392S 7.30e-1 BA.1.17
V9622 327T>C synonymous_variant N Y109Y 6.67e-1 BA.1.17
V440 1174G>A missense_variant ORF1ab_pp1a G392S 9.23e-1 P.1
V7336 11232C>T synonymous_variant ORF1ab_pp1a Y3744Y 7.07e-1 BF.7
V1732 7866G>T missense_variant ORF1ab_pp1a K2622N 7.07e-1 A
V5599 1091C>T missense_variant N P364L 7.07e-1 A
V9264 42T>C synonymous_variant E V14V 1.00e+0 A
V1948 9400C>T missense_variant ORF1ab_pp1a P3134S 1.00e+0 AY.101
V1967 9595_9597delTTA conservative_inframe_deletion ORF1ab_pp1a L3199del 6.67e-1 AY.118
V756 2402C>T missense_variant ORF1ab_pp1a A801V 8.16e-1 AY.118
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 AY.124.1
V6839 7194G>T synonymous_variant ORF1ab_pp1a V2398V 1.00e+0 AY.25.2
V9287 15C>T synonymous_variant M N5N 7.07e-1 AY.25.2
V9290 39T>C synonymous_variant M L13L 1.00e+0 AY.30
V2984 17705A>G missense_variant ORF1ab_pp1ab D5902G 1.00e+0 AY.34.1
V636 1891C>T missense_variant ORF1ab_pp1a L631F 1.00e+0 AY.4.2.1
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 AY.42
V3598 238G>T missense_variant S D80Y 7.31e-1 AY.4.4
V3897 1430G>T missense_variant S S477I 9.65e-1 AY.4.4
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 AY.46
V3310 19870G>T missense_variant ORF1ab_pp1ab V6624L 1.00e+0 AY.67
V332 695G>T missense_variant ORF1ab_pp1a R232L 1.00e+0 AY.67
V8737 807T>C synonymous_variant S Y269Y 1.00e+0 AY.67
V9813 1245C>T synonymous_variant N D415D 1.00e+0 AY.67
V2676 15063G>T missense_variant ORF1ab_pp1ab M5021I 7.56e-1 AY.99.2
V3872 1332G>C missense_variant S K444N 7.07e-1 AY.99.2
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 B.1.1.214
V4419 193C>T missense_variant ORF3a L65F 7.07e-1 B.1.1.222
V8989 2796C>A synonymous_variant S G932G 1.00e+0 B.1.1.318
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 B.1.1.50
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 B.1.1.529
V8359 18922C>T synonymous_variant ORF1ab_pp1ab L6308L 1.00e+0 B.1.177.6
V9721 816A>G synonymous_variant N Q272Q 1.00e+0 B.1.351
V4024 2042C>T missense_variant S P681L 7.78e-1 B.1.36
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 B.1.36
V5779 *4359C>T downstream_gene_variant S None 7.69e-1 B.1.36
V5847 81C>T synonymous_variant ORF1ab_pp1a L27L 7.39e-1 B.1.36
V8530 20526C>T synonymous_variant ORF1ab_pp1ab V6842V 8.89e-1 B.1.36
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 B.1.427
V328 679G>A missense_variant ORF1ab_pp1a G227S 1.00e+0 B.1.470
V527 1535C>T missense_variant ORF1ab_pp1a T512I 1.00e+0 B.1.470
V5533 755C>T missense_variant N A252V 7.07e-1 B.1.470
V9722 822C>T synonymous_variant N F274F 7.07e-1 B.1.470
V2902 17038G>T missense_variant ORF1ab_pp1ab V5680F 1.00e+0 B.1.499
V3031 17961G>T missense_variant ORF1ab_pp1ab M5987I 1.00e+0 B.1.499
V3749 679G>T missense_variant S V227L 1.00e+0 B.1.499
V8041 16653G>T synonymous_variant ORF1ab_pp1ab L5551L 1.00e+0 B.1.499
V9323 279C>T synonymous_variant M L93L 1.00e+0 B.1.499
V8972 2637G>A synonymous_variant S A879A 1.00e+0 B.1.617.1
V4072 2338G>C missense_variant S E780Q 1.00e+0 BA.1.1.13
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 BA.2.10.1
V6160 2094T>C synonymous_variant ORF1ab_pp1a A698A 1.00e+0 BA.2.10.1
V1585 6772G>T missense_variant ORF1ab_pp1a G2258C 1.00e+0 BA.2.1
V5427 553C>T missense_variant N R185C 8.16e-1 BA.2.1
V9199 339C>T synonymous_variant ORF3a Y113Y 8.16e-1 BA.2.1
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 BA.2.24
V5677 -3C>T upstream_gene_variant ORF10 None 7.50e-1 BA.2.29
V7715 14136G>A synonymous_variant ORF1ab_pp1ab V4712V 8.94e-1 BA.2.56
V1374 5767G>T missense_variant ORF1ab_pp1a A1923S 1.00e+0 BA.2.75.3
V1577 6740C>T missense_variant ORF1ab_pp1a T2247I 1.00e+0 BA.5.2.19
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 BA.5.2.19
V2967 17498C>T missense_variant ORF1ab_pp1ab A5833V 7.07e-1 BA.5.2.28
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 BA.5.2.28
V6942 8046C>T synonymous_variant ORF1ab_pp1a N2682N 6.54e-1 BA.5.2.28
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 BA.5.2.2
V306 607G>A missense_variant ORF1ab_pp1a D203N 1.00e+0 BA.5.2.3
V5912 399C>T synonymous_variant ORF1ab_pp1a G133G 8.16e-1 BA.5.2.3
V3159 18755C>T missense_variant ORF1ab_pp1ab P6252L 1.00e+0 BA.5.2.43
V3424 20668G>A missense_variant ORF1ab_pp1ab G6890S 1.00e+0 BA.5.2.43
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 BA.5.2.43
V6651 5721C>T synonymous_variant ORF1ab_pp1a F1907F 1.00e+0 BA.5.2.43
V1605 6836C>T missense_variant ORF1ab_pp1a A2279V 7.50e-1 BA.5
V5448 589T>C missense_variant N S197P 7.50e-1 BA.5
V18 -168C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 BE.4
V6818 7014C>T synonymous_variant ORF1ab_pp1a F2338F 7.07e-1 BE.4
V9057 3300A>G synonymous_variant S T1100T 1.00e+0 BE.4
V2963 17483C>T missense_variant ORF1ab_pp1ab P5828L 6.50e-1 BF.21
V79 -48C>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 B
V1351 5579A>G missense_variant ORF1ab_pp1a K1860R 7.07e-1 BM.1.1.1
V1796 8332C>T missense_variant ORF1ab_pp1a L2778F 7.07e-1 BM.1.1.1
V4061 2240C>T missense_variant S T747I 7.07e-1 BM.1.1.1
V440 1174G>A missense_variant ORF1ab_pp1a G392S 7.07e-1 BM.1.1.1
V583 1699A>G missense_variant ORF1ab_pp1a I567V 7.07e-1 BM.1.1.1
V5982 828C>T synonymous_variant ORF1ab_pp1a P276P 7.07e-1 BM.1.1.1
V841 2828C>T missense_variant ORF1ab_pp1a P943L 7.07e-1 BM.1.1.1
V9467 256C>T synonymous_variant ORF7a L86L 7.07e-1 BM.1.1.1
V9638 414C>T synonymous_variant N A138A 7.07e-1 BM.1.1.1
V5410 497C>T missense_variant N T166I 1.00e+0 BM.1.1.3
V6597 5277G>A synonymous_variant ORF1ab_pp1a Q1759Q 1.00e+0 BM.1.1.3
V7247 10380C>T synonymous_variant ORF1ab_pp1a D3460D 7.07e-1 BM.1.1.3
V7414 11760C>T synonymous_variant ORF1ab_pp1a S3920S 7.07e-1 BM.1.1.3
V9553 333T>C synonymous_variant ORF8 Y111Y 7.07e-1 BN.1.4
V8811 1425C>T synonymous_variant S A475A 1.00e+0 BN.1
V1267 4958C>T missense_variant ORF1ab_pp1a T1653I 1.00e+0 BQ.1.10
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 BQ.1.10
V440 1174G>A missense_variant ORF1ab_pp1a G392S 7.07e-1 BQ.1.1.18
V1249 4850C>T missense_variant ORF1ab_pp1a T1617I 1.00e+0 BQ.1.12
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 BQ.1.12
V1916 9142G>A missense_variant ORF1ab_pp1a V3048I 7.07e-1 BQ.1.13.1
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 BQ.1.13.1
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 BQ.1.1.6
V890 2999C>T missense_variant ORF1ab_pp1a T1000I 1.00e+0 BQ.1.1.6
V7881 15390C>T synonymous_variant ORF1ab_pp1ab D5130D 8.16e-1 BQ.1.26.1
V8036 16623C>T synonymous_variant ORF1ab_pp1ab Y5541Y 7.06e-1 BQ.1.26.1
V608 1796C>T missense_variant ORF1ab_pp1a A599V 1.00e+0 BQ.1.8
V6073 1497C>T synonymous_variant ORF1ab_pp1a F499F 6.76e-1 BQ.1
V6210 2397C>T synonymous_variant ORF1ab_pp1a Y799Y 1.00e+0 C.36.3
V7595 13161C>T synonymous_variant ORF1ab_pp1a R4387R 7.07e-1 C.36.3
V9063 3357C>T synonymous_variant S N1119N 7.07e-1 C.36.3
V1351 5579A>G missense_variant ORF1ab_pp1a K1860R 1.00e+0 CA.3
V3447 20813C>T missense_variant ORF1ab_pp1ab T6938I 1.00e+0 CA.3
V3832 1067A>C missense_variant S K356T 7.07e-1 CA.3
V4017 2036A>G missense_variant S N679S 1.00e+0 CA.3
V583 1699A>G missense_variant ORF1ab_pp1a I567V 1.00e+0 CA.3
V5982 828C>T synonymous_variant ORF1ab_pp1a P276P 1.00e+0 CA.3
V6978 8361C>T synonymous_variant ORF1ab_pp1a F2787F 1.00e+0 CA.3
V1241 4790C>T missense_variant ORF1ab_pp1a T1597I 1.00e+0 CH.1.1
V6368 3567C>T synonymous_variant ORF1ab_pp1a S1189S 8.66e-1 CH.1.1
V8292 18480C>T synonymous_variant ORF1ab_pp1ab Y6160Y 7.74e-1 CH.1.1
V7012 8595C>T synonymous_variant ORF1ab_pp1a V2865V 1.00e+0 R.1
V3687 532G>A missense_variant S D178N 1.00e+0 XBB.2
V444 1189C>T missense_variant ORF1ab_pp1a L397F 1.00e+0 XBB.2
V9736 871C>T synonymous_variant N L291L 7.07e-1 XBB.2
V2400 12659C>T missense_variant ORF1ab_pp1a P4220L 1.00e+0 AY.19
V2915 17107G>T missense_variant ORF1ab_pp1ab A5703S 1.00e+0 AY.19
V4016 2033C>T missense_variant S T678I 1.00e+0 AY.19
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 AY.19
V7870 15282C>T synonymous_variant ORF1ab_pp1ab A5094A 1.00e+0 AY.19
V7891 15468G>T synonymous_variant ORF1ab_pp1ab V5156V 1.00e+0 AY.19
V1167 4403C>T missense_variant ORF1ab_pp1a S1468F 1.00e+0 B.1.1.409
V2629 14522C>T missense_variant ORF1ab_pp1ab A4841V 7.05e-1 B.1.1.409
V792 2626G>A missense_variant ORF1ab_pp1a A876T 1.00e+0 B.1.1.409
V492 1342G>A missense_variant ORF1ab_pp1a D448N 1.00e+0 B.1.459
V709 2218A>G missense_variant ORF1ab_pp1a I740V 1.00e+0 B.1.459
V7273 10605G>T synonymous_variant ORF1ab_pp1a L3535L 1.00e+0 B.1.459
V7673 13836T>C synonymous_variant ORF1ab_pp1ab G4612G 1.00e+0 B.1.459
V8747 888C>T synonymous_variant S L296L 1.00e+0 B.1.459
V2803 16352C>A missense_variant ORF1ab_pp1ab T5451N 1.00e+0 B.1.540
V4068 2311G>T missense_variant S A771S 1.00e+0 B.1.540
V6197 2328T>C synonymous_variant ORF1ab_pp1a A776A 1.00e+0 B.1.540
V7403 11697C>T synonymous_variant ORF1ab_pp1a L3899L 1.00e+0 B.1.540
V1626 7034C>T missense_variant ORF1ab_pp1a A2345V 1.00e+0 BL.5
V3827 1038A>T missense_variant S R346S -1.00e+0 BL.5
V3832 1067A>C missense_variant S K356T 1.00e+0 BL.5
V3957 1721A>T missense_variant S D574V -1.00e+0 BL.5
V4405 171G>C missense_variant ORF3a Q57H 1.00e+0 BL.5
V4742 187G>A missense_variant M A63T -1.00e+0 BL.5
V5067 10C>T missense_variant ORF8 L4F -1.00e+0 BL.5
V5484 630G>T missense_variant N M210I 1.00e+0 BL.5
V5662 -18G>T upstream_gene_variant ORF10 None -6.96e-1 BL.5
V5738 *4324C>T downstream_gene_variant S None 1.00e+0 BL.5
V603 1772C>T missense_variant ORF1ab_pp1a A591V 1.00e+0 BL.5
V6111 1767T>C synonymous_variant ORF1ab_pp1a D589D 1.00e+0 BL.5
V6346 3354C>T synonymous_variant ORF1ab_pp1a V1118V 1.00e+0 BL.5
V8256 18207T>C synonymous_variant ORF1ab_pp1ab D6069D 1.00e+0 BL.5
V8292 18480C>T synonymous_variant ORF1ab_pp1ab Y6160Y 1.00e+0 BL.5
V9654 471C>T synonymous_variant N I157I -1.00e+0 BL.5
V982 3341G>T missense_variant ORF1ab_pp1a C1114F 1.00e+0 BL.5
V1271 4976C>T missense_variant ORF1ab_pp1a P1659L 7.05e-1 BN.2
V1351 5579A>G missense_variant ORF1ab_pp1a K1860R 7.05e-1 BN.2
V1796 8332C>T missense_variant ORF1ab_pp1a L2778F 7.05e-1 BN.2
V3201 19079C>T missense_variant ORF1ab_pp1ab A6360V 7.05e-1 BN.2
V3387 20314G>T missense_variant ORF1ab_pp1ab V6772L 7.05e-1 BN.2
V3447 20813C>T missense_variant ORF1ab_pp1ab T6938I 7.05e-1 BN.2
V3733 638T>A missense_variant S V213E 7.05e-1 BN.2
V3882 1348A>G missense_variant S N450D 7.05e-1 BN.2
V4081 2425C>T missense_variant S P809S 7.05e-1 BN.2
V4423 201G>C missense_variant ORF3a K67N 7.05e-1 BN.2
V583 1699A>G missense_variant ORF1ab_pp1a I567V 7.05e-1 BN.2
V5982 828C>T synonymous_variant ORF1ab_pp1a P276P 7.05e-1 BN.2
V7784 14571T>C synonymous_variant ORF1ab_pp1ab D4857D 7.05e-1 BN.2
V8159 17484T>C synonymous_variant ORF1ab_pp1ab P5828P 7.05e-1 BN.2
V3578 204_209delACATGT disruptive_inframe_deletion S H69_V70del -6.12e-1 BN.4
V1351 5579A>G missense_variant ORF1ab_pp1a K1860R 1.00e+0 BN.6
V1796 8332C>T missense_variant ORF1ab_pp1a L2778F 1.00e+0 BN.6
V2293 11875A>G missense_variant ORF1ab_pp1a T3959A -7.04e-1 BN.6
V3447 20813C>T missense_variant ORF1ab_pp1ab T6938I 1.00e+0 BN.6
V583 1699A>G missense_variant ORF1ab_pp1a I567V 1.00e+0 BN.6
V5982 828C>T synonymous_variant ORF1ab_pp1a P276P 1.00e+0 BN.6
V6639 5628C>T synonymous_variant ORF1ab_pp1a T1876T 7.06e-1 CB.1
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 CG.1
V440 1174G>A missense_variant ORF1ab_pp1a G392S 1.00e+0 XAM
V773 2525C>T missense_variant ORF1ab_pp1a T842I 1.00e+0 XAM





Manual curation of mutation (1175G>A)-related literature from PubMed

The pubmed.mineR and pubmed-mapper were utilized for extracting literature from PubMed, followed by manual filtering.
Note: PubMed: (COVID-19 [Title/Abstract] OR SARS-COV-2 [Title/Abstract]) AND (DNA mutation [Title/Abstract] OR Protein mutation-1 letter [Title/Abstract] OR Protein mutation-3 letter [Title/Abstract]).

DNA level Protein level Paper title Journal name Publication year Pubmed ID
1175G>A G392D Variant analysis of SARS-CoV-2 genomes Bull World Health Organ 2020 32742035