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The current mutation

ID: V365
DNA: 889A>G
Protein: M297V
Position: 1154








COV2Var annotation categories







Summary information of mutation (889A>G)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   1154
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 889A>G
  Ref Seq: A
  Mut Seq: G
  Protein Level   Protein 1-letter Mutation: M297V
  Protein 3-letter Mutation: Met297Val

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 (889A>G) 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
2020-01 B.1.438 1 1 1.00e+0
2020-10 B.1.438 39 30 7.69e-1
2020-10 B.1.177 39 6 1.54e-1
2020-10 B.1.438.1 39 2 5.13e-2
2020-11 B.1.438.1 119 82 6.89e-1
2020-11 B.1.234 119 12 1.01e-1
2020-11 B.1.438.4 119 10 8.40e-2
2020-12 B.1.438.1 550 491 8.93e-1
2020-12 B.1.438.4 550 26 4.73e-2
2020-12 B.1.243 550 13 2.36e-2
2020-03 B.1.513 1 1 1.00e+0
2020-06 B.1.438 4 4 1.00e+0
2020-07 B.1.438 1 1 1.00e+0
2020-08 B.1.438 12 12 1.00e+0
2020-09 B.1.438 17 15 8.82e-1
2020-09 B.1.438.1 17 2 1.18e-1
2021-01 B.1.438.1 1322 1241 9.39e-1
2021-01 B.1.438.2 1322 47 3.56e-2
2021-01 B.1.438.4 1322 18 1.36e-2
2021-10 AY.4 102 47 4.61e-1
2021-10 AY.41 102 16 1.57e-1
2021-10 AY.127 102 10 9.80e-2
2021-11 AY.4 107 18 1.68e-1
2021-11 AY.4.2 107 13 1.21e-1
2021-11 AY.43 107 13 1.21e-1
2021-12 AY.118 111 24 2.16e-1
2021-12 AY.4 111 17 1.53e-1
2021-12 AY.43 111 15 1.35e-1
2021-02 B.1.438.1 1734 1671 9.64e-1
2021-02 B.1.177 1734 13 7.50e-3
2021-02 B.1.438 1734 12 6.92e-3
2021-03 B.1.438.1 2835 2785 9.82e-1
2021-03 B.1.2 2835 8 2.82e-3
2021-03 B.1 2835 7 2.47e-3
2021-04 B.1.438.1 1999 1978 9.89e-1
2021-04 P.1 1999 9 4.50e-3
2021-04 B.1.1.7 1999 5 2.50e-3
2021-05 B.1.438.1 582 565 9.71e-1
2021-05 B.1.1.7 582 6 1.03e-2
2021-05 P.1 582 5 8.59e-3
2021-06 B.1.438.1 225 203 9.02e-1
2021-06 AY.16 225 6 2.67e-2
2021-06 P.1 225 5 2.22e-2
2021-07 B.1.438.1 29 6 2.07e-1
2021-07 P.1 29 5 1.72e-1
2021-07 AY.102 29 3 1.03e-1
2021-08 AY.4 74 13 1.76e-1
2021-08 B.1.438 74 9 1.22e-1
2021-08 B.1.617.2 74 7 9.46e-2
2021-09 AY.41 50 12 2.40e-1
2021-09 AY.4 50 6 1.20e-1
2021-09 AY.103 50 5 1.00e-1
2022-01 BA.1.1 58 18 3.10e-1
2022-01 BA.1 58 7 1.21e-1
2022-01 BA.1.17.2 58 6 1.03e-1
2022-10 XBD 21 17 8.10e-1
2022-10 BA.2.75.2 21 1 4.76e-2
2022-10 BA.5.1.23 21 1 4.76e-2
2022-11 BF.7 10 2 2.00e-1
2022-11 XBD 10 2 2.00e-1
2022-11 BA.5.2.20 10 1 1.00e-1
2022-12 BA.1.1 9 1 1.11e-1
2022-12 BA.5.1.12 9 1 1.11e-1
2022-12 BE.9 9 1 1.11e-1
2022-02 BA.1.1 42 27 6.43e-1
2022-02 BA.1.1.1 42 4 9.52e-2
2022-02 BA.2 42 4 9.52e-2
2022-03 BA.2 51 36 7.06e-1
2022-03 BA.1.1 51 7 1.37e-1
2022-03 BA.2.9.2 51 3 5.88e-2
2022-04 BA.2.10 10 5 5.00e-1
2022-04 BA.2 10 2 2.00e-1
2022-04 BA.1 10 1 1.00e-1
2022-05 BA.2 12 7 5.83e-1
2022-05 BA.2.9 12 2 1.67e-1
2022-05 AY.126 12 1 8.33e-2
2022-06 BE.1.1 8 3 3.75e-1
2022-06 BA.2 8 2 2.50e-1
2022-06 BA.5.3 8 2 2.50e-1
2022-07 BA.2.36 9 2 2.22e-1
2022-07 BF.10 9 2 2.22e-1
2022-07 BA.4 9 1 1.11e-1
2022-08 BA.5.5 10 2 2.00e-1
2022-08 BF.5 10 2 2.00e-1
2022-08 BA.2.9.5 10 1 1.00e-1
2022-09 BE.1 13 4 3.08e-1
2022-09 XBD 13 3 2.31e-1
2022-09 BA.2.75.2 13 2 1.54e-1
2023-01 BA.5.2.28 8 2 2.50e-1
2023-01 BQ.1 8 2 2.50e-1
2023-01 BF.7 8 1 1.25e-1
2023-02 XBB.1.5 4 2 5.00e-1
2023-02 BF.7.14 4 1 2.50e-1
2023-02 BQ.1.1 4 1 2.50e-1

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
V365 B.1.438 9.92e-1 120 2020-1-10 2021-8-7
V365 B.1.438.1 9.98e-1 9030 2020-9-16 2021-12-7
V365 B.1.438.2 1.00e+0 53 2021-1-6 2021-2-15
V365 B.1.438.3 1.00e+0 13 2020-12-9 2021-3-18
V365 B.1.438.4 1.00e+0 64 2020-10-19 2021-3-23
V365 XBD 7.33e-2 22 2022-8-25 2023-2-7






Examining mutation (889A>G) 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 (889A>G) 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 3.85e+1 2.60e+5 1.48e-4 1.00e+0 Increase
Deceased 3.73e-14 4.41e+5 8.46e-20 1.00e+0 Increase
Homebound 3.73e-14 4.41e+5 8.46e-20 1.00e+0 Increase
Hospitalized 1.26e+1 1.58e+3 7.98e-3 9.94e-1 Increase
Mild 1.49e+1 2.76e+3 5.39e-3 9.96e-1 Increase
Recovered -1.34e+0 5.55e+5 -2.42e-6 1.00e+0 Decrease

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 5.25e+0 1.27e+0 4.14e+0 3.41e-5 Increase
18-39 -1.57e+0 6.52e-1 -2.41e+0 1.58e-2 Decrease
40-64 -1.21e+0 6.35e-1 -1.91e+0 5.62e-2 Decrease
65-84 2.62e+0 9.57e-1 2.74e+0 6.14e-3 Increase
>=85 2.15e+0 1.65e+0 1.30e+0 1.92e-1 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 2.63e-1 6.00e-1 4.38e-1 6.62e-1 Increase





Investigating natural selection at mutation (889A>G) 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

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

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




Alterations in protein physicochemical properties induced by mutation (889A>G)

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 489956.85 6.04 543550 89.05 -0.023
Reference ORF1ab_pp1a 489988.91 6.04 543550 88.99 -0.023




Alterations in protein stability induced by mutation (889A>G)

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
M297V ORF1ab_pp1a Point 297 -0.68 Decrease 7 25 Environment
M297V ORF1ab_pp1a Point 297 -0.69 Decrease 7.4 37 Internal




Impact on protein function induced by mutation (889A>G)

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
M297V ORF1ab_pp1a Point 0.16 Altered Cytoplasmic_loop (Pr = 0.25 | P = 1.7e-03)
Gain of ADP-ribosylation at R301 (Pr = 0.17 | P = 0.08)
Altered Calmodulin_binding (Pr = 0.11 | P = 0.10)




Exploring mutation (889A>G) 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 (889A>G)

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
M297V ORF1ab_pp1a 1154 Proteinase K DGFVGRIRSV (pos: 297)
 NA
M297V ORF1ab_pp1a 1154 Chymotrypsin-low specificity NA
 DGFMGRIRSV (pos: 297)
M297V ORF1ab_pp1a 1154 CNBr NA
 DGFMGRIRSV (pos: 297)




Impact of spike protein mutation (889A>G) 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 (889A>G) 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).

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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.

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        Show interface residues:





Impact of mutation (889A>G) 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 (889A>G) 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
V3001 17819T>C missense_variant ORF1ab_pp1ab I5940T 7.09e-1 AY.4.2
V2847 16711G>T missense_variant ORF1ab_pp1ab V5571F 8.02e-1 AY.98
V3014 17896G>A missense_variant ORF1ab_pp1ab D5966N 8.00e-1 B.1.2
V9476 294T>C synonymous_variant ORF7a S98S 7.07e-1 BA.1.15.1
V1844 8590T>C missense_variant ORF1ab_pp1a F2864L 1.00e+0 AY.10
V7081 9144A>G synonymous_variant ORF1ab_pp1a V3048V 1.00e+0 AY.10
V7246 10377G>T synonymous_variant ORF1ab_pp1a T3459T 1.00e+0 AY.10
V7966 16059C>T synonymous_variant ORF1ab_pp1ab C5353C 7.07e-1 AY.10
V9279 195G>T synonymous_variant E L65L 1.00e+0 AY.10
V553 1625G>A missense_variant ORF1ab_pp1a R542H 6.71e-1 AY.112
V5776 *4358G>A downstream_gene_variant S None 7.07e-1 AY.112
V2605 14264G>A missense_variant ORF1ab_pp1ab S4755N 9.71e-1 AY.118
V7734 14265C>T synonymous_variant ORF1ab_pp1ab S4755S 9.57e-1 AY.118
V8267 18306C>T synonymous_variant ORF1ab_pp1ab L6102L 9.06e-1 AY.118
V858 2897C>T missense_variant ORF1ab_pp1a S966F 7.07e-1 AY.120
V7809 14784C>T synonymous_variant ORF1ab_pp1ab I4928I 8.11e-1 AY.127
V4720 8A>G missense_variant M D3G 7.74e-1 AY.134
V3680 519G>T missense_variant S Q173H 6.32e-1 AY.14
V8435 19617C>T synonymous_variant ORF1ab_pp1ab D6539D 7.30e-1 AY.16
V8872 1908T>C synonymous_variant S Y636Y 6.79e-1 AY.16
V693 2167T>C missense_variant ORF1ab_pp1a S723P 8.16e-1 AY.34.1
V7373 11502C>T synonymous_variant ORF1ab_pp1a S3834S 1.00e+0 AY.36
V694 2168C>T missense_variant ORF1ab_pp1a S723F 7.07e-1 AY.39.1.4
V8259 18219C>T synonymous_variant ORF1ab_pp1ab H6073H 7.07e-1 AY.39.1.4
V1387 5840A>G missense_variant ORF1ab_pp1a Y1947C 1.00e+0 AY.41
V2983 17700G>T missense_variant ORF1ab_pp1ab M5900I 9.72e-1 AY.41
V3266 19630G>T missense_variant ORF1ab_pp1ab A6544S 8.59e-1 AY.41
V3423 20666C>T missense_variant ORF1ab_pp1ab T6889M 7.67e-1 AY.41
V9195 318C>T synonymous_variant ORF3a L106L 9.85e-1 AY.41
V9394 645C>T synonymous_variant M D215D 6.17e-1 AY.41
V1154 4295C>T missense_variant ORF1ab_pp1a A1432V 7.07e-1 AY.46.6
V905 3050C>T missense_variant ORF1ab_pp1a T1017I 8.16e-1 AY.46.6
V8477 20025A>G synonymous_variant ORF1ab_pp1ab E6675E 7.07e-1 AY.4.6
V9628 345T>C synonymous_variant N T115T 7.07e-1 AY.4.6
V301 577C>T missense_variant ORF1ab_pp1a P193S 1.00e+0 AY.71
V3551 76C>T missense_variant S P26S 1.00e+0 AY.71
V4446 262G>T missense_variant ORF3a V88L 7.07e-1 AY.71
V2995 17764G>T missense_variant ORF1ab_pp1ab A5922S 1.00e+0 AY.85
V7942 15837C>T synonymous_variant ORF1ab_pp1ab Y5279Y 1.00e+0 AY.85
V3047 18034A>G missense_variant ORF1ab_pp1ab I6012V 1.00e+0 AY.98.1
V9769 996C>A synonymous_variant N T332T 1.00e+0 B.1.1.519
V1387 5840A>G missense_variant ORF1ab_pp1a Y1947C 1.00e+0 B.1.1.63
V1938 9296C>T missense_variant ORF1ab_pp1a S3099L 1.00e+0 B.1.1.63
V2212 11257T>G missense_variant ORF1ab_pp1a F3753V 1.00e+0 B.1.1.63
V4597 670G>C missense_variant ORF3a G224R 1.00e+0 B.1.1.63
V6958 8124C>T synonymous_variant ORF1ab_pp1a N2708N 1.00e+0 B.1.1.63
V7155 9702C>T synonymous_variant ORF1ab_pp1a L3234L 1.00e+0 B.1.1.63
V9672 540T>C synonymous_variant N S180S 1.00e+0 B.1.1.63
V8324 18682C>T synonymous_variant ORF1ab_pp1ab L6228L 9.17e-1 B.1.234
V1667 7491G>T missense_variant ORF1ab_pp1a K2497N 8.09e-1 B.1.243
V7531 12705C>T synonymous_variant ORF1ab_pp1a N4235N 7.83e-1 B.1.243
V8569 20859G>T synonymous_variant ORF1ab_pp1ab G6953G 7.54e-1 B.1.243
V2027 10076C>T missense_variant ORF1ab_pp1a P3359L 1.00e+0 B.1.36.8
V2143 10957G>T missense_variant ORF1ab_pp1a V3653F 7.07e-1 B.1.36.8
V382 945G>A missense_variant ORF1ab_pp1a M315I 1.00e+0 B.1.36.8
V4546 524C>T missense_variant ORF3a T175I 1.00e+0 B.1.36.8
V7141 9612T>C synonymous_variant ORF1ab_pp1a Y3204Y 1.00e+0 B.1.36.8
V7429 11856A>G synonymous_variant ORF1ab_pp1a P3952P 1.00e+0 B.1.36.8
V8378 19116C>T synonymous_variant ORF1ab_pp1ab Y6372Y 7.07e-1 B.1.36.8
V9607 210A>G synonymous_variant N Q70Q 1.00e+0 B.1.36.8
V9388 606C>T synonymous_variant M G202G 6.71e-1 B.1.427
V2813 16441G>T missense_variant ORF1ab_pp1ab V5481L 1.00e+0 B.1.466.2
V7571 12987C>T synonymous_variant ORF1ab_pp1a Y4329Y 7.07e-1 B.1.621
V8418 19491T>C synonymous_variant ORF1ab_pp1ab N6497N 1.00e+0 B.1.621
V3375 20255A>G missense_variant ORF1ab_pp1ab D6752G 1.00e+0 B.1.637
V3520 13C>T missense_variant S L5F 6.53e-1 BA.2.9.2
V9178 234C>T synonymous_variant ORF3a H78H 1.00e+0 BA.2.9.2
V2965 17486C>T missense_variant ORF1ab_pp1ab A5829V 7.07e-1 BA.2.9.5
V9564 39C>T synonymous_variant N P13P 7.07e-1 BA.2.9.5
V3814 968C>T missense_variant S T323I 7.07e-1 BA.4.1.4
V6069 1473G>T synonymous_variant ORF1ab_pp1a V491V 1.00e+0 BA.4.1.4
V2817 16477G>T missense_variant ORF1ab_pp1ab V5493F 7.07e-1 BA.5.1.12
V5914 411C>T synonymous_variant ORF1ab_pp1a G137G 1.00e+0 BA.5.1.12
V8345 18852A>G synonymous_variant ORF1ab_pp1ab K6284K 7.07e-1 BA.5.1.23
V8530 20526C>T synonymous_variant ORF1ab_pp1ab V6842V 1.00e+0 BA.5.1.3
V3082 18256G>A missense_variant ORF1ab_pp1ab V6086I 1.00e+0 BA.5.2.28
V5927 486C>T synonymous_variant ORF1ab_pp1a N162N 7.07e-1 BA.5.2.28
V6336 3297G>A synonymous_variant ORF1ab_pp1a V1099V 8.16e-1 BA.5.2.28
V7105 9327C>T synonymous_variant ORF1ab_pp1a Y3109Y 7.07e-1 BA.5.2.28
V8283 18417C>T synonymous_variant ORF1ab_pp1ab A6139A 7.07e-1 BA.5.2.28
V7556 12915T>C synonymous_variant ORF1ab_pp1a G4305G 1.00e+0 BE.1
V5665 -15G>C upstream_gene_variant ORF10 None 1.00e+0 BE.4
V1320 5407C>T missense_variant ORF1ab_pp1a P1803S 7.07e-1 BE.9
V7450 12018T>C synonymous_variant ORF1ab_pp1a D4006D 1.00e+0 BE.9
V3602 250C>A missense_variant S L84I 7.07e-1 BF.7.14
V7966 16059C>T synonymous_variant ORF1ab_pp1ab C5353C 7.07e-1 BF.7.14
V1212 4654A>G missense_variant ORF1ab_pp1a T1552A 7.07e-1 BM.1.1.1
V1911 9095C>T missense_variant ORF1ab_pp1a T3032I 7.07e-1 BM.1.1.1
V2094 10712C>T missense_variant ORF1ab_pp1a A3571V 7.07e-1 BM.1.1.1
V2185 11140G>A missense_variant ORF1ab_pp1a V3714I 7.07e-1 BM.1.1.1
V3698 544A>G missense_variant S K182E 7.07e-1 BM.1.1.1
V459 1243G>A missense_variant ORF1ab_pp1a G415S 7.07e-1 BM.1.1.1
V4886 106T>C missense_variant ORF7a S36P 7.07e-1 BM.1.1.1
V5656 1250C>T missense_variant N T417I 7.07e-1 BM.1.1.1
V6517 4734C>T synonymous_variant ORF1ab_pp1a N1578N 7.07e-1 BM.1.1.1
V7190 9921C>T synonymous_variant ORF1ab_pp1a C3307C 7.07e-1 BM.1.1.1
V7802 14700A>G synonymous_variant ORF1ab_pp1ab K4900K 7.07e-1 BM.1.1.1
V8462 19851C>T synonymous_variant ORF1ab_pp1ab V6617V 7.07e-1 BM.1.1.1
V3607 284C>A missense_variant S T95N 1.00e+0 BN.1.5
V6168 2145A>G synonymous_variant ORF1ab_pp1a G715G 7.07e-1 BN.1.5
V2975 17558C>T missense_variant ORF1ab_pp1ab P5853L 7.07e-1 BQ.1.28
V4786 562G>A missense_variant M A188T 8.16e-1 C.37
V3357 20164C>T missense_variant ORF1ab_pp1ab P6722S 1.00e+0 CM.2
V6467 4368C>T synonymous_variant ORF1ab_pp1a G1456G 8.16e-1 CM.8.1
V428 1127C>T missense_variant ORF1ab_pp1a S376L 1.00e+0 P.1.15
V8941 2448A>G synonymous_variant S S816S 1.00e+0 P.1.15
V2831 16595C>T missense_variant ORF1ab_pp1ab A5532V -1.00e+0 AY.18
V3953 1715C>T missense_variant S T572I 1.00e+0 AY.18
V8435 19617C>T synonymous_variant ORF1ab_pp1ab D6539D 1.00e+0 AY.18
V9120 3714C>T synonymous_variant S T1238T -1.00e+0 AY.18
V4100 2533G>T missense_variant S A845S 1.00e+0 AY.3.2
V3343 20120C>T missense_variant ORF1ab_pp1ab A6707V 1.00e+0 B.1.227
V3782 764C>T missense_variant S S255F 1.00e+0 B.1.227
V4011 2025G>T missense_variant S Q675H 1.00e+0 B.1.227
V4406 171G>T missense_variant ORF3a Q57H 1.00e+0 B.1.227
V4456 285G>T missense_variant ORF3a L95F 1.00e+0 B.1.227
V4560 555G>T missense_variant ORF3a Q185H 1.00e+0 B.1.227
V4626 766G>T missense_variant ORF3a V256F -6.89e-1 B.1.227
V6338 3318C>T synonymous_variant ORF1ab_pp1a S1106S 1.00e+0 B.1.227
V6742 6381A>G synonymous_variant ORF1ab_pp1a L2127L 1.00e+0 B.1.227
V8063 16803T>C synonymous_variant ORF1ab_pp1ab Y5601Y 1.00e+0 B.1.227
V8814 1467C>T synonymous_variant S Y489Y 1.00e+0 B.1.227
V9396 12C>T synonymous_variant ORF6 L4L 1.00e+0 B.1.227
V9479 315G>A synonymous_variant ORF7a A105A 1.00e+0 B.1.227
V9546 300G>A synonymous_variant ORF8 V100V 1.00e+0 B.1.227
V4558 550T>C missense_variant ORF3a Y184H 7.57e-1 XBD
V5897 318C>T synonymous_variant ORF1ab_pp1a V106V 1.00e+0 XBD
V903 3043G>A missense_variant ORF1ab_pp1a E1015K 1.00e+0 XBD





Manual curation of mutation (889A>G)-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