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The current mutation

ID: V2020
DNA: 10054C>T
Protein: L3352F
Position: 10319








COV2Var annotation categories







Summary information of mutation (10054C>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   10319
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 10054C>T
  Ref Seq: C
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: L3352F
  Protein 3-letter Mutation: Leu3352Phe

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 (10054C>T) 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.1.2 4 4 1.00e+0
2020-10 B.1.2 8192 7521 9.18e-1
2020-10 B.1.595 8192 259 3.16e-2
2020-10 B.1.587 8192 132 1.61e-2
2020-11 B.1.2 17334 16270 9.39e-1
2020-11 B.1.595 17334 296 1.71e-2
2020-11 B.1.587 17334 173 9.98e-3
2020-12 B.1.2 22643 20960 9.26e-1
2020-12 B.1.595 22643 581 2.57e-2
2020-12 B.1.577 22643 342 1.51e-2
2020-02 B.1.2 2 2 1.00e+0
2020-03 B.1.595 209 180 8.61e-1
2020-03 B.1 209 15 7.18e-2
2020-03 B.1.589 209 4 1.91e-2
2020-04 B.1.595 349 294 8.42e-1
2020-04 B.1.595.4 349 26 7.45e-2
2020-04 B.1.577 349 8 2.29e-2
2020-05 B.1.595 386 292 7.56e-1
2020-05 B.1.595.4 386 61 1.58e-1
2020-05 B.1.2 386 12 3.11e-2
2020-06 B.1.2 1525 672 4.41e-1
2020-06 B.1.595 1525 480 3.15e-1
2020-06 B.1.595.4 1525 157 1.03e-1
2020-07 B.1.2 3335 2302 6.90e-1
2020-07 B.1.595 3335 674 2.02e-1
2020-07 B.1 3335 98 2.94e-2
2020-08 B.1.2 2750 2135 7.76e-1
2020-08 B.1.595 2750 279 1.01e-1
2020-08 B.1 2750 81 2.95e-2
2020-09 B.1.2 4004 3684 9.20e-1
2020-09 B.1.595 4004 131 3.27e-2
2020-09 B.1 4004 57 1.42e-2
2021-01 B.1.2 32829 30799 9.38e-1
2021-01 B.1.596 32829 562 1.71e-2
2021-01 B.1.595 32829 424 1.29e-2
2021-10 AY.4 140 17 1.21e-1
2021-10 AY.25.1 140 16 1.14e-1
2021-10 AY.43 140 15 1.07e-1
2021-11 AY.4 140 46 3.29e-1
2021-11 AY.122 140 15 1.07e-1
2021-11 AY.46.5 140 15 1.07e-1
2021-12 AY.103 169 28 1.66e-1
2021-12 AY.4.2 169 21 1.24e-1
2021-12 B.1.617.2 169 19 1.12e-1
2021-02 B.1.2 24987 23506 9.41e-1
2021-02 B.1.596 24987 472 1.89e-2
2021-02 B.1.588 24987 326 1.30e-2
2021-03 B.1.2 17893 16841 9.41e-1
2021-03 B.1.596 17893 433 2.42e-2
2021-03 B.1.588 17893 160 8.94e-3
2021-04 B.1.2 4374 3955 9.04e-1
2021-04 B.1.1.7 4374 116 2.65e-2
2021-04 P.1 4374 104 2.38e-2
2021-05 B.1.2 540 349 6.46e-1
2021-05 B.1.1.7 540 97 1.80e-1
2021-05 P.1 540 48 8.89e-2
2021-06 AY.4 186 66 3.55e-1
2021-06 B.1.2 186 49 2.63e-1
2021-06 B.1.1.7 186 34 1.83e-1
2021-07 B.1.2 166 50 3.01e-1
2021-07 AY.39.1 166 21 1.27e-1
2021-07 AY.4 166 16 9.64e-2
2021-08 AY.25 239 43 1.80e-1
2021-08 B.1.2 239 35 1.46e-1
2021-08 AY.4 239 29 1.21e-1
2021-09 B.1.2 168 27 1.61e-1
2021-09 AY.103 168 19 1.13e-1
2021-09 AY.25.1 168 16 9.52e-2
2022-01 BA.1.1 212 76 3.58e-1
2022-01 BA.1 212 32 1.51e-1
2022-01 BA.1.15 212 31 1.46e-1
2022-10 BF.7.4 166 64 3.86e-1
2022-10 BA.5.2.44 166 32 1.93e-1
2022-10 BA.5.2.35 166 16 9.64e-2
2022-11 BA.5.2.35 236 97 4.11e-1
2022-11 BF.7.4 236 63 2.67e-1
2022-11 BA.5.2.44 236 18 7.63e-2
2022-12 BA.5.2.35 243 87 3.58e-1
2022-12 BF.7.4 243 68 2.80e-1
2022-12 BQ.1.1 243 11 4.53e-2
2022-02 BA.1.1 254 81 3.19e-1
2022-02 BA.2 254 73 2.87e-1
2022-02 BA.1.17.2 254 21 8.27e-2
2022-03 BA.2 249 166 6.67e-1
2022-03 BA.1.1 249 19 7.63e-2
2022-03 BA.1 249 8 3.21e-2
2022-04 BA.2 145 87 6.00e-1
2022-04 BA.2.9 145 21 1.45e-1
2022-04 BA.4.8 145 9 6.21e-2
2022-05 BA.2 168 89 5.30e-1
2022-05 BA.4.8 168 30 1.79e-1
2022-05 BA.2.9 168 17 1.01e-1
2022-06 BA.2 96 28 2.92e-1
2022-06 BA.5.5 96 11 1.15e-1
2022-06 BA.4 96 9 9.38e-2
2022-07 BA.5.5 106 20 1.89e-1
2022-07 BA.4 106 17 1.60e-1
2022-07 BF.21 106 10 9.43e-2
2022-08 BA.5.5 115 39 3.39e-1
2022-08 BE.1 115 10 8.70e-2
2022-08 BF.5 115 10 8.70e-2
2022-09 BA.5.5 97 21 2.16e-1
2022-09 BA.5.2.44 97 13 1.34e-1
2022-09 BA.4.1 97 8 8.25e-2
2023-01 BF.7.4 135 31 2.30e-1
2023-01 BA.5.2.35 135 26 1.93e-1
2023-01 CH.1.1.1 135 14 1.04e-1
2023-02 XBB.1.5 18 8 4.44e-1
2023-02 BF.7.4 18 4 2.22e-1
2023-02 BA.5.2.35 18 2 1.11e-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
V2020 B.1.1.244 1.46e-2 2 2020-4-7 2021-3-19
V2020 B.1.1.312 1.05e-2 5 2020-8-13 2021-3-17
V2020 B.1.1.335 4.41e-1 15 2020-4-3 2021-3-16
V2020 B.1.2 9.83e-1 129228 2020-1-4 2022-7-29
V2020 B.1.397 1.07e-2 2 2020-4-7 2021-9-14
V2020 B.1.567 9.82e-1 266 2020-3-23 2021-4-3
V2020 B.1.574 2.57e-2 11 2020-6-7 2021-1-2
V2020 B.1.577 9.93e-1 1471 2020-4-6 2022-3-24
V2020 B.1.587 1.00e+0 627 2020-4-23 2021-7-20
V2020 B.1.588 9.99e-1 1211 2020-8-5 2022-4-20
V2020 B.1.588.1 1.00e+0 24 2020-11-28 2020-11-28
V2020 B.1.589 9.84e-1 125 2020-3-15 2020-8-31
V2020 B.1.591 1.00e+0 134 2020-8-17 2021-3-28
V2020 B.1.595 9.87e-1 4197 2020-3-9 2022-5-17
V2020 B.1.595.1 1.00e+0 163 2020-5-16 2021-1-18
V2020 B.1.595.2 1.00e+0 29 2020-6-14 2020-11-5
V2020 B.1.595.3 1.00e+0 37 2020-6-27 2021-1-7
V2020 B.1.595.4 1.00e+0 281 2020-4-20 2021-3-15
V2020 B.1.596 7.58e-1 2005 2020-4-11 2021-9-22
V2020 BA.4.8 3.36e-1 41 2022-3-8 2022-9-17
V2020 BA.5.2.35 6.70e-2 228 2022-8-3 2023-2-20
V2020 BA.5.2.44 5.85e-2 73 2022-6-4 2023-2-7
V2020 BE.4.1.1 4.29e-2 9 2022-8-7 2023-2-6
V2020 BF.7.4 3.99e-2 241 2022-6-14 2023-2-17
V2020 CV.1 1.24e-2 6 2022-9-16 2023-2-17
V2020 DC.1 1.82e-2 4 2022-8-8 2023-1-9
V2020 P.6 1.21e-2 3 2020-12-2 2021-4-25






Examining mutation (10054C>T) 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
Felis catus B.1.577 USA 2020-7-29 EPI_ISL_699509
Felis catus B.1.2 USA 2020-8-13 EPI_ISL_3148878
Felis catus B.1.2 USA 2020-10-6 EPI_ISL_3128552
Odocoileus virginianus B.1.596 USA 2020-12-9 EPI_ISL_5804741
Odocoileus virginianus B.1.2 USA 2020-12-7 EPI_ISL_5804744
Odocoileus virginianus B.1.2 USA 2020-12-7 EPI_ISL_5804745
Odocoileus virginianus B.1.2 USA 2020-12-5 EPI_ISL_5804746
Odocoileus virginianus B.1.2 USA 2020-12-5 EPI_ISL_5804747
Odocoileus virginianus B.1.2 USA 2020-12-7 EPI_ISL_5804749
Odocoileus virginianus B.1.2 USA 2020-12-8 EPI_ISL_6425279
Odocoileus virginianus B.1.2 USA 2020-12-7 EPI_ISL_6425275
Odocoileus virginianus B.1.2 USA 2020-11-6 EPI_ISL_5804757
Odocoileus virginianus B.1.2 USA 2020-12-28 EPI_ISL_5804754
Odocoileus virginianus B.1.2 USA 2020-11-15 EPI_ISL_6425285
Odocoileus virginianus B.1.2 USA 2020-11-30 EPI_ISL_6425269
Odocoileus virginianus B.1.2 USA 2020-11-29 EPI_ISL_5804755
Odocoileus virginianus B.1.2 USA 2020-10-28 EPI_ISL_5804756
Odocoileus virginianus B.1.2 USA 2020-11-7 EPI_ISL_5804759
Odocoileus virginianus B.1.2 USA 2020-11-8 EPI_ISL_5804760
Odocoileus virginianus B.1.2 USA 2020-11-17 EPI_ISL_6425286
Odocoileus virginianus B.1.2 USA 2020-11-24 EPI_ISL_5804761
Odocoileus virginianus B.1.2 USA 2020-12-5 EPI_ISL_5804762
Odocoileus virginianus B.1.2 USA 2020-12-10 EPI_ISL_5804763
Odocoileus virginianus B.1.2 USA 2020-12-2 EPI_ISL_6425270
Odocoileus virginianus B.1.2 USA 2020-9-28 EPI_ISL_6425284
Odocoileus virginianus B.1.2 USA 2020-10-8 EPI_ISL_5804764
Odocoileus virginianus B.1.2 USA 2020-11-24 EPI_ISL_5804766
Odocoileus virginianus B.1.2 USA 2020-11-24 EPI_ISL_5804767
Odocoileus virginianus B.1.2 USA 2020-11-24 EPI_ISL_5804768
Odocoileus virginianus B.1.2 USA 2020-11-24 EPI_ISL_5804769
Odocoileus virginianus B.1.2 USA 2020-11-24 EPI_ISL_5804770
Odocoileus virginianus B.1.2 USA 2020-11-24 EPI_ISL_5804771
Odocoileus virginianus B.1.2 USA 2020-11-24 EPI_ISL_6425283
Odocoileus virginianus B.1.2 USA 2020-11-24 EPI_ISL_6425276
Odocoileus virginianus B.1.2 USA 2020-11-24 EPI_ISL_5804772
Odocoileus virginianus B.1.2 USA 2020-11-24 EPI_ISL_5804773
Odocoileus virginianus B.1.2 USA 2020-11-24 EPI_ISL_5804775
Odocoileus virginianus B.1.2 USA 2020-12-10 EPI_ISL_5804776
Odocoileus virginianus B.1.2 USA 2020-12-10 EPI_ISL_5804777
Odocoileus virginianus B.1.2 USA 2020-12-10 EPI_ISL_5804778
Odocoileus virginianus B.1.2 USA 2020-12-10 EPI_ISL_5804779
Odocoileus virginianus B.1.2 USA 2020-12-10 EPI_ISL_5804780
Odocoileus virginianus B.1.2 USA 2020-12-10 EPI_ISL_5804781
Odocoileus virginianus B.1.2 USA 2020-12-10 EPI_ISL_5804782
Odocoileus virginianus B.1.2 USA 2020-12-10 EPI_ISL_5804783
Odocoileus virginianus B.1.2 USA 2020-12-10 EPI_ISL_5804784
Odocoileus virginianus B.1.2 USA 2020-12-23 EPI_ISL_5804785
Odocoileus virginianus B.1.2 USA 2020-11-17 EPI_ISL_5804786
Odocoileus virginianus B.1.2 USA 2020-11-17 EPI_ISL_5804787
Odocoileus virginianus B.1.2 USA 2020-12-17 EPI_ISL_6425267
Odocoileus virginianus B.1.2 USA 2020-11-5 EPI_ISL_13610581
Canis lupus familiaris B.1.2 USA 2020-9-14 EPI_ISL_3128555
Canis lupus familiaris B.1.577 USA 2020-9-24 EPI_ISL_3128553
Canis lupus familiaris B.1.2 USA 2020-10-22 EPI_ISL_8317060
Neovison vison B.1.2 USA 2020-11-24 EPI_ISL_1527630
Neovison vison B.1.2 USA 2020-11-24 EPI_ISL_1527631
Neovison vison B.1.2 USA 2020-11-24 EPI_ISL_1527632
Neovison vison B.1.2 USA 2020-11-24 EPI_ISL_1527633
Panthera uncia B.1.2 USA 2020-12-4 EPI_ISL_2928447
Panthera tigris jacksoni B.1.2 USA 2020-10-19 EPI_ISL_2928444
Panthera tigris jacksoni B.1.2 USA 2020-10-19 EPI_ISL_2928445
Panthera tigris jacksoni B.1.2 USA 2020-10-27 EPI_ISL_2928446
Felis catus B.1.2 USA 2021-1-7 EPI_ISL_2958984
Felis catus B.1.2 USA 2021-1-26 EPI_ISL_2958981
Felis catus B.1.2 USA 2021-2-22 EPI_ISL_1218882
Felis catus B.1.2 USA 2021-2-22 EPI_ISL_1218884
Felis catus B.1.2 USA 2021-1-4 EPI_ISL_2958986
Felis catus B.1.2 USA 2021-4-23 EPI_ISL_8897004
Odocoileus virginianus B.1.2 USA 2021-11-7 EPI_ISL_13610658
Odocoileus virginianus B.1.2 USA 2021-2-1 EPI_ISL_4878315
Odocoileus virginianus B.1.2 USA 2021-2-1 EPI_ISL_4847031
Odocoileus virginianus B.1.596 USA 2021-2-2 EPI_ISL_4878316
Odocoileus virginianus B.1.2 USA 2021-2-16 EPI_ISL_4847032
Odocoileus virginianus B.1.2 USA 2021-2-24 EPI_ISL_4847033
Odocoileus virginianus B.1.596 USA 2021-2-25 EPI_ISL_4878317
Odocoileus virginianus B.1.596 USA 2021-2-25 EPI_ISL_4878318
Odocoileus virginianus B.1.596 USA 2021-2-25 EPI_ISL_4878319
Odocoileus virginianus B.1.596 USA 2021-2-25 EPI_ISL_4878320
Odocoileus virginianus B.1.596 USA 2021-2-25 EPI_ISL_4878321
Odocoileus virginianus B.1.596 USA 2021-2-25 EPI_ISL_4878322
Canis lupus familiaris B.1.2 USA 2021-2-12 EPI_ISL_1241386
Panthera tigris sondaica B.1.2 USA 2021-2-2 EPI_ISL_2928450




Association between mutation (10054C>T) 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 8.33e-3 5.12e-1 1.63e-2 9.87e-1 Increase
Deceased 3.31e-1 5.98e-1 5.54e-1 5.79e-1 Increase
Homebound -1.76e+1 7.27e+3 -2.42e-3 9.98e-1 Decrease
Hospitalized -1.22e+0 4.10e-1 -2.98e+0 2.84e-3 Decrease
Mild -1.40e+0 5.04e-1 -2.78e+0 5.45e-3 Decrease
Recovered 3.28e+0 8.19e-1 4.01e+0 6.15e-5 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 1.07e+0 1.13e-1 9.45e+0 3.26e-21 Increase
18-39 9.95e-2 4.93e-2 2.02e+0 4.35e-2 Increase
40-64 1.01e-1 5.00e-2 2.01e+0 4.39e-2 Increase
65-84 -6.19e-1 6.40e-2 -9.67e+0 3.96e-22 Decrease
>=85 -7.09e-1 1.24e-1 -5.72e+0 1.04e-8 Decrease

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 -3.57e-2 4.81e-2 -7.42e-1 4.58e-1 Decrease





Investigating natural selection at mutation (10054C>T) 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
3C 10055 10972 306 89 4.00e-2 BF.7 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

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
3C 10055 10972 306 89 9.50e-1 2.00e-2 BF.14 FUBAR
3C 10055 10972 306 89 0.00e+0 9.80e-1 B.1.596 FUBAR
3C 10055 10972 306 89 0.00e+0 9.80e-1 B.1.2 FUBAR




Alterations in protein physicochemical properties induced by mutation (10054C>T)

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 490022.93 6.04 543550 88.9 -0.024
Reference ORF1ab_pp1a 489988.91 6.04 543550 88.99 -0.023




Alterations in protein stability induced by mutation (10054C>T)

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
L3352F ORF1ab_pp1a Point 3352 0.46 Increase 7 25 Environment
L3352F ORF1ab_pp1a Point 3352 0.5 Increase 7.4 37 Internal




Impact on protein function induced by mutation (10054C>T)

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
L3352F ORF1ab_pp1a Point 0.343 Altered Cytoplasmic_loop (Pr = 0.29 | P = 2.1e-04)
Gain of Strand (Pr = 0.28 | P = 9.6e-03)
Altered PPI_residue (Pr = 0.27 | P = 0.05)
Gain of Relative_solvent_accessibility (Pr = 0.25 | P = 0.03)
Altered DNA_binding (Pr = 0.15 | P = 0.04)
Altered Stability (Pr = 0.12 | P = 0.03)
Loss of Disulfide_linkage at C3348 (Pr = 0.05 | P = 0.08)




Exploring mutation (10054C>T) 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 (10054C>T)

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
L3352F ORF1ab_pp1a 10319 Chymotrypsin-high specificity VLKFKVDTAN (pos: 3352)
 NA




Impact of spike protein mutation (10054C>T) 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 (10054C>T) 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 (10054C>T) 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 (10054C>T) 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
V7183 9885T>C synonymous_variant ORF1ab_pp1a L3295L 8.07e-1 BA.5.5
V1667 7491G>T missense_variant ORF1ab_pp1a K2497N 7.75e-1 P.1
V2875 16871C>T missense_variant ORF1ab_pp1ab P5624L 7.98e-1 P.1
V5985 837C>T synonymous_variant ORF1ab_pp1a S279S 8.08e-1 P.1
V7052 8901C>T synonymous_variant ORF1ab_pp1a T2967T 7.87e-1 P.1
V8468 19914C>T synonymous_variant ORF1ab_pp1ab V6638V 7.08e-1 P.1
V1551 6541A>G missense_variant ORF1ab_pp1a T2181A 8.77e-1 AY.125
V4967 280C>T stop_gained ORF7a Q94* 7.16e-1 AY.125
V3848 1154C>T missense_variant S T385I 7.30e-1 AY.20
V9467 256C>T synonymous_variant ORF7a L86L 6.22e-1 AY.20
V2738 15644G>T missense_variant ORF1ab_pp1ab G5215V 8.21e-1 B.1.1
V8866 1860C>T synonymous_variant S V620V 7.77e-1 B.1.1
V6659 5787G>A synonymous_variant ORF1ab_pp1a K1929K 6.50e-1 B.1
V4406 171G>T missense_variant ORF3a Q57H 7.07e-1 A.1
V5092 71C>T missense_variant ORF8 S24L 7.07e-1 A.1
V8740 826C>T synonymous_variant S L276L 1.00e+0 A.1
V5092 71C>T missense_variant ORF8 S24L 7.07e-1 A.3
V1980 9731C>T missense_variant ORF1ab_pp1a S3244L 7.07e-1 AY.106
V3895 1426G>A missense_variant S G476S 7.07e-1 AY.106
V2401 12667C>T missense_variant ORF1ab_pp1a P4223S 1.00e+0 AY.107
V5103 91T>C missense_variant ORF8 Y31H 1.00e+0 AY.107
V6979 8382T>C synonymous_variant ORF1ab_pp1a H2794H 1.00e+0 AY.107
V8578 20925T>C synonymous_variant ORF1ab_pp1ab N6975N 1.00e+0 AY.107
V7741 14310T>C synonymous_variant ORF1ab_pp1ab P4770P 1.00e+0 AY.112.2
V8679 348C>T synonymous_variant S S116S 8.16e-1 AY.112.2
V3037 17995A>G missense_variant ORF1ab_pp1ab I5999V 8.16e-1 AY.116
V4287 3775G>C missense_variant S D1259H 8.16e-1 AY.116
V4510 400C>T missense_variant ORF3a R134C 7.07e-1 AY.116
V5497 644G>T missense_variant N G215V 1.00e+0 AY.116
V87 -42T>C upstream_gene_variant ORF1ab_pp1a None 1.00e+0 AY.116
V9470 261C>T synonymous_variant ORF7a F87F 8.16e-1 AY.116
V8407 19338C>T synonymous_variant ORF1ab_pp1ab N6446N 7.07e-1 AY.117
V1796 8332C>T missense_variant ORF1ab_pp1a L2778F 1.00e+0 AY.119.2
V7550 12850C>T synonymous_variant ORF1ab_pp1a L4284L 1.00e+0 AY.122.6
V194 252_254delTAT disruptive_inframe_deletion ORF1ab_pp1a M85del 7.07e-1 AY.123
V6170 2151C>T synonymous_variant ORF1ab_pp1a Y717Y 1.00e+0 AY.123
V1807 8380C>T missense_variant ORF1ab_pp1a H2794Y 7.07e-1 AY.1
V3388 20330C>T missense_variant ORF1ab_pp1ab T6777I 7.07e-1 AY.1
V6890 7671G>T synonymous_variant ORF1ab_pp1a A2557A 7.07e-1 AY.2
V4848 7A>G missense_variant ORF7a I3V 6.55e-1 AY.33
V4336 74C>T missense_variant ORF3a P25L 1.00e+0 AY.34
V8662 249C>T synonymous_variant S V83V 1.00e+0 AY.38
V9672 540T>C synonymous_variant N S180S 1.00e+0 AY.43.3
V7087 9180T>C synonymous_variant ORF1ab_pp1a L3060L 1.00e+0 AY.46.1
V4187 3301C>T missense_variant S H1101Y 7.70e-1 AY.46.5
V4769 292G>T missense_variant M A98S 6.49e-1 AY.46.5
V7374 11511C>T synonymous_variant ORF1ab_pp1a A3837A 8.90e-1 AY.46.5
V1358 5659G>A missense_variant ORF1ab_pp1a V1887I 1.00e+0 AY.4.7
V5713 88G>T missense_variant ORF10 V30L 7.74e-1 AY.48
V5074 23G>A missense_variant ORF8 G8E 1.00e+0 AY.82
V1980 9731C>T missense_variant ORF1ab_pp1a S3244L 7.07e-1 AY.83
V3895 1426G>A missense_variant S G476S 1.00e+0 AY.83
V5958 660C>T synonymous_variant ORF1ab_pp1a D220D 1.00e+0 AY.83
V6624 5481C>T synonymous_variant ORF1ab_pp1a Y1827Y 1.00e+0 AY.85
V7935 15759T>C synonymous_variant ORF1ab_pp1ab S5253S 1.00e+0 AY.91
V1659 7463C>T missense_variant ORF1ab_pp1a S2488F 1.00e+0 AY.99.1
V4843 -4G>C upstream_gene_variant ORF7a None 1.00e+0 AY.99.1
V3895 1426G>A missense_variant S G476S 7.07e-1 AY.99
V7511 12558C>T synonymous_variant ORF1ab_pp1a S4186S 1.00e+0 AY.99
V9580 105G>A synonymous_variant N A35A 1.00e+0 AY.99
V5597 1087T>C missense_variant N F363L 1.00e+0 B.1.111
V7507 12550C>T synonymous_variant ORF1ab_pp1a L4184L 1.00e+0 B.1.111
V2537 13730C>T missense_variant ORF1ab_pp1ab A4577V 1.00e+0 B.1.1.1
V4716 4G>T missense_variant M A2S 7.07e-1 B.1.1.1
V5513 702G>T missense_variant N M234I 7.07e-1 B.1.1.1
V8158 17481C>T synonymous_variant ORF1ab_pp1ab N5827N 1.00e+0 B.1.1.216
V8284 18423C>T synonymous_variant ORF1ab_pp1ab C6141C 7.07e-1 B.1.1.216
V862 2911C>T missense_variant ORF1ab_pp1a P971S 1.00e+0 B.1.1.216
V5460 605G>T missense_variant N S202I 7.07e-1 B.1.1.222
V5342 199C>T missense_variant N P67S 7.07e-1 B.1.1.28
V3102 18389G>T missense_variant ORF1ab_pp1ab R6130L 1.00e+0 B.1.1.294
V3447 20813C>T missense_variant ORF1ab_pp1ab T6938I 7.06e-1 B.1.1.294
V4334 71C>T missense_variant ORF3a T24I 8.16e-1 B.1.1.294
V5868 201C>T synonymous_variant ORF1ab_pp1a P67P 1.00e+0 B.1.1.294
V7228 10242C>T synonymous_variant ORF1ab_pp1a N3414N 6.31e-1 B.1.1.294
V1333 5459C>T missense_variant ORF1ab_pp1a T1820I 7.07e-1 B.1.1.301
V1517 6386C>T missense_variant ORF1ab_pp1a A2129V 7.07e-1 B.1.1.301
V1783 8237C>T missense_variant ORF1ab_pp1a T2746I 7.07e-1 B.1.1.301
V3598 238G>T missense_variant S D80Y 7.07e-1 B.1.1.301
V4406 171G>T missense_variant ORF3a Q57H 7.07e-1 B.1.1.301
V4539 515G>T missense_variant ORF3a G172V 7.07e-1 B.1.1.301
V5013 10C>T missense_variant ORF7b L4F 7.07e-1 B.1.1.301
V8429 19575T>C synonymous_variant ORF1ab_pp1ab N6525N 7.07e-1 B.1.1.301
V8747 888C>T synonymous_variant S L296L 7.07e-1 B.1.1.301
V6563 5025T>C synonymous_variant ORF1ab_pp1a Y1675Y 6.66e-1 B.1.1.306
V8893 2028T>C synonymous_variant S T676T 8.16e-1 B.1.1.306
V1158 4312C>T missense_variant ORF1ab_pp1a L1438F 1.00e+0 B.1.1.318
V2343 12275C>T missense_variant ORF1ab_pp1a A4092V 8.15e-1 B.1.1.348
V4842 -5C>T upstream_gene_variant ORF7a None 7.07e-1 B.1.1.432
V5116 116T>C missense_variant ORF8 I39T 7.07e-1 B.1.1.432
V5614 1129G>T missense_variant N D377Y 7.07e-1 B.1.1.432
V5853 105G>T synonymous_variant ORF1ab_pp1a V35V 7.07e-1 B.1.1.432
V2639 14610G>T missense_variant ORF1ab_pp1ab K4870N 1.00e+0 B.1.1.50
V3067 18167C>T missense_variant ORF1ab_pp1ab T6056I 8.66e-1 B.1.1.50
V4297 3790G>T missense_variant S V1264L 1.00e+0 B.1.1.50
V8630 75C>T synonymous_variant S P25P 6.49e-1 B.1.1.519
V6227 2508C>T synonymous_variant ORF1ab_pp1a Y836Y 7.07e-1 B.1.1.529
V2782 16129C>T missense_variant ORF1ab_pp1ab P5377S 7.06e-1 B.1.160.16
V2996 17765C>T missense_variant ORF1ab_pp1ab A5922V 8.66e-1 B.1.160.16
V5199 316G>C missense_variant ORF8 E106Q 7.74e-1 B.1.160.16
V9382 555G>A synonymous_variant M Q185Q 1.00e+0 B.1.1.70
V3390 20339C>T missense_variant ORF1ab_pp1ab S6780L 1.00e+0 B.1.177.56
V3953 1715C>T missense_variant S T572I 1.00e+0 B.1.177.56
V7185 9891C>T synonymous_variant ORF1ab_pp1a D3297D 7.07e-1 B.1.177.56
V7920 15687C>T synonymous_variant ORF1ab_pp1ab I5229I 1.00e+0 B.1.177.56
V433 1139C>T missense_variant ORF1ab_pp1a P380L 7.07e-1 B.1.232
V601 1770G>T missense_variant ORF1ab_pp1a L590F 6.32e-1 B.1.232
V8227 18048C>T synonymous_variant ORF1ab_pp1ab V6016V 7.07e-1 B.1.232
V9261 18G>A synonymous_variant E S6S 7.07e-1 B.1.232
V3211 19138C>T missense_variant ORF1ab_pp1ab H6380Y 1.00e+0 B.1.241
V4310 35C>T missense_variant ORF3a T12I 1.00e+0 B.1.265
V5092 71C>T missense_variant ORF8 S24L 1.00e+0 B.1.349
V2029 10103G>A missense_variant ORF1ab_pp1a R3368H 7.07e-1 B.1.36.1
V6954 8109A>G synonymous_variant ORF1ab_pp1a V2703V 1.00e+0 B.1.36.1
V8403 19320T>C synonymous_variant ORF1ab_pp1ab D6440D 7.07e-1 B.1.36.1
V1763 8069C>T missense_variant ORF1ab_pp1a A2690V 7.07e-1 B.1.36.8
V1885 8855C>T missense_variant ORF1ab_pp1a T2952I 7.07e-1 B.1.375
V7264 10524C>T synonymous_variant ORF1ab_pp1a D3508D -8.16e-1 B.1.375
V8459 19821A>G synonymous_variant ORF1ab_pp1ab V6607V 7.07e-1 B.1.375
V192 253_258delATGGTT conservative_inframe_deletion ORF1ab_pp1a M85_V86del 7.07e-1 B.1.400
V1172 4487C>T missense_variant ORF1ab_pp1a T1496I 8.16e-1 B.1.466.2
V3259 19598C>T missense_variant ORF1ab_pp1ab A6533V 1.00e+0 B.1.466.2
V7042 8853C>T synonymous_variant ORF1ab_pp1a D2951D 8.16e-1 B.1.466.2
V8301 18543C>T synonymous_variant ORF1ab_pp1ab N6181N 1.00e+0 B.1.466.2
V8903 2076C>T synonymous_variant S I692I 6.32e-1 B.1.466.2
V1682 7586C>T missense_variant ORF1ab_pp1a A2529V 1.00e+0 B.1.509
V2830 16589G>T missense_variant ORF1ab_pp1ab G5530V 6.32e-1 B.1.509
V371 905C>T missense_variant ORF1ab_pp1a S302F 8.65e-1 B.1.524
V3987 1919C>T missense_variant S S640F 8.65e-1 B.1.524
V4382 134G>T missense_variant ORF3a W45L 1.00e+0 B.1.524
V7161 9723C>T synonymous_variant ORF1ab_pp1a F3241F -6.72e-1 B.1.595
V7368 11482C>T synonymous_variant ORF1ab_pp1a L3828L -6.17e-1 B.1.595
V9272 91C>T synonymous_variant E L31L -6.58e-1 B.1.595
V9630 348G>T synonymous_variant N G116G -6.30e-1 B.1.595
V4263 3682G>T missense_variant S V1228L 6.57e-1 B.1.596
V5092 71C>T missense_variant ORF8 S24L 8.17e-1 B.1.596
V5342 199C>T missense_variant N P67S 8.90e-1 B.1.596
V5452 596C>T missense_variant N P199L 6.36e-1 B.1.596
V1443 6139G>T missense_variant ORF1ab_pp1a V2047F 1.00e+0 B.1.617.1
V2329 12194C>T missense_variant ORF1ab_pp1a T4065I 7.63e-1 B.1.617.1
V5366 303G>T missense_variant N M101I 8.16e-1 B.1.621.1
V1667 7491G>T missense_variant ORF1ab_pp1a K2497N 7.07e-1 B.1.621
V4982 304_309delCTTATT conservative_inframe_deletion ORF7a L102_I103del 7.07e-1 B.1.621
V9625 336C>T synonymous_variant N Y112Y 7.07e-1 B.1.621
V4762 247G>A missense_variant M A83T 1.00e+0 B.6.6
V617 1829C>T missense_variant ORF1ab_pp1a S610L 8.16e-1 B.6.6
V7933 15750G>A synonymous_variant ORF1ab_pp1ab R5250R 1.00e+0 B.6.6
V9182 252G>T synonymous_variant ORF3a L84L 1.00e+0 B.6.6
V9520 105C>T synonymous_variant ORF8 D35D 8.16e-1 B.6.6
V8045 16675T>C synonymous_variant ORF1ab_pp1ab L5559L 7.07e-1 BA.1.1.14
V3884 1354C>A missense_variant S L452M 7.07e-1 BA.1.13.1
V9388 606C>T synonymous_variant M G202G 1.00e+0 BA.1.13.1
V9672 540T>C synonymous_variant N S180S 1.00e+0 BA.1.13.1
V7947 15909C>T synonymous_variant ORF1ab_pp1ab N5303N 1.00e+0 BA.1.14.2
V4519 439C>T missense_variant ORF3a L147F 1.00e+0 BA.1.6
V4800 13G>T missense_variant ORF6 V5F 6.65e-1 BA.1.6
V8485 20091A>G synonymous_variant ORF1ab_pp1ab L6697L 1.00e+0 BA.1.6
V8356 18906C>T synonymous_variant ORF1ab_pp1ab F6302F 1.00e+0 BA.1.9
V2908 17072C>T missense_variant ORF1ab_pp1ab T5691I 7.07e-1 BA.2.10.1
V1763 8069C>T missense_variant ORF1ab_pp1a A2690V 7.07e-1 BA.2.13
V143 119C>T missense_variant ORF1ab_pp1a S40L 7.07e-1 BA.2.36
V5117 118C>T missense_variant ORF8 H40Y 7.07e-1 BA.2.36
V5633 1161G>T missense_variant N K387N 6.45e-1 BA.2.37
V310 619C>T missense_variant ORF1ab_pp1a R207C 6.17e-1 BA.2.38
V3484 21040C>A missense_variant ORF1ab_pp1ab R7014S 7.07e-1 BA.2.52
V3486 21041G>A missense_variant ORF1ab_pp1ab R7014H 7.07e-1 BA.2.52
V513 1442C>T missense_variant ORF1ab_pp1a S481F 7.07e-1 BA.2.52
V9138 21C>T synonymous_variant ORF3a I7I 1.00e+0 BA.2.53
V1471 6227T>C missense_variant ORF1ab_pp1a I2076T 1.00e+0 BA.2.56
V4002 1983G>T missense_variant S E661D 1.00e+0 BA.2.56
V5116 116T>C missense_variant ORF8 I39T 6.32e-1 BA.2.56
V6445 4179G>T synonymous_variant ORF1ab_pp1a V1393V 6.32e-1 BA.2.56
V1576 6737C>T missense_variant ORF1ab_pp1a S2246L 1.00e+0 BA.2.65
V2405 12746C>T missense_variant ORF1ab_pp1a T4249I 7.07e-1 BA.2.65
V6453 4275C>T synonymous_variant ORF1ab_pp1a Y1425Y 7.07e-1 BA.2.65
V1424 6077A>G missense_variant ORF1ab_pp1a D2026G 1.00e+0 BA.2.75.1
V516 1451C>T missense_variant ORF1ab_pp1a T484I 7.07e-1 BA.2.75.1
V6114 1783C>T synonymous_variant ORF1ab_pp1a L595L 1.00e+0 BA.2.75.1
V4452 277C>T missense_variant ORF3a H93Y 1.00e+0 BA.2.75.5
V4603 686C>A missense_variant ORF3a T229N 1.00e+0 BA.2.75.5
V8823 1524C>T synonymous_variant S Y508Y 7.07e-1 BA.2.75.5
V5167 209C>T missense_variant ORF8 P70L 1.00e+0 BA.2.75
V7179 9870T>A synonymous_variant ORF1ab_pp1a L3290L 1.00e+0 BA.2.75
V5916 418C>T synonymous_variant ORF1ab_pp1a L140L 7.07e-1 BA.4.1.1
V7295 10809C>T synonymous_variant ORF1ab_pp1a F3603F 1.00e+0 BA.4.2
V5157 197G>A missense_variant ORF8 G66D 1.00e+0 BA.4.6.1
V9141 60C>T synonymous_variant ORF3a I20I 7.00e-1 BA.5.1.12
V5926 480C>T synonymous_variant ORF1ab_pp1a N160N 7.07e-1 BA.5.1.16
V2447 13166C>T missense_variant ORF1ab_pp1a P4389L 7.07e-1 BA.5.1.25
V3179 18892C>T missense_variant ORF1ab_pp1ab H6298Y 7.07e-1 BA.5.1.2
V7562 12951T>C synonymous_variant ORF1ab_pp1a D4317D 1.00e+0 BA.5.1.5
V5600 1093C>T missense_variant N P365S 8.24e-1 BA.5.2.18
V8705 558C>T synonymous_variant S F186F 8.24e-1 BA.5.2.18
V924 3127G>A missense_variant ORF1ab_pp1a A1043T 8.75e-1 BA.5.2.18
V1333 5459C>T missense_variant ORF1ab_pp1a T1820I 7.07e-1 BA.5.2.20
V425 1114G>A missense_variant ORF1ab_pp1a A372T 6.32e-1 BA.5.2.21
V7693 13971C>T synonymous_variant ORF1ab_pp1ab Y4657Y 1.00e+0 BA.5.2.23
V3026 17922G>A missense_variant ORF1ab_pp1ab M5974I 6.03e-1 BA.5.2.26
V9137 6T>C synonymous_variant ORF3a D2D 6.83e-1 BA.5.2.26
V3706 551G>T missense_variant S G184V 6.54e-1 BA.5.2.27
V8390 19212A>G synonymous_variant ORF1ab_pp1ab L6404L 7.74e-1 BA.5.2.27
V8479 20046T>C synonymous_variant ORF1ab_pp1ab Y6682Y 8.16e-1 BA.5.2.28
V8758 1002C>T synonymous_variant S N334N 8.16e-1 BA.5.2.28
V9126 3762C>T synonymous_variant S C1254C 8.16e-1 BA.5.2.28
V2821 16498C>T missense_variant ORF1ab_pp1ab L5500F 1.00e+0 BA.5.2.2
V3318 19969C>T missense_variant ORF1ab_pp1ab P6657S 1.00e+0 BA.5.2.2
V2577 14002A>G missense_variant ORF1ab_pp1ab T4668A 1.00e+0 BA.5.2.33
V5576 980C>T missense_variant N S327L 7.07e-1 BA.5.2.33
V6549 4935G>A synonymous_variant ORF1ab_pp1a R1645R 1.00e+0 BA.5.2.33
V6630 5547C>T synonymous_variant ORF1ab_pp1a D1849D 7.07e-1 BA.5.2.33
V7389 11613C>T synonymous_variant ORF1ab_pp1a V3871V 1.00e+0 BA.5.2.33
V9766 987G>T synonymous_variant N T329T 1.00e+0 BA.5.2.33
V2267 11743C>T missense_variant ORF1ab_pp1a L3915F 7.07e-1 BA.5.2.34
V9139 24C>T synonymous_variant ORF3a F8F 9.52e-1 BA.5.2.35
V9175 219C>T synonymous_variant ORF3a L73L -6.61e-1 BA.5.2.35
V3532 55A>C missense_variant S T19P 7.20e-1 BA.5.2.44
V5850 99C>T synonymous_variant ORF1ab_pp1a D33D 9.63e-1 BA.5.2.44
V6095 1647C>T synonymous_variant ORF1ab_pp1a S549S 6.08e-1 BA.5.2.44
V6356 3471C>T synonymous_variant ORF1ab_pp1a D1157D 9.93e-1 BA.5.2.44
V9156 117C>T synonymous_variant ORF3a A39A 6.08e-1 BA.5.2.44
V9471 264C>T synonymous_variant ORF7a I88I 7.07e-1 BA.5.2.48
V1535 6451A>G missense_variant ORF1ab_pp1a S2151G 1.00e+0 BA.5.5.2
V6347 3357C>T synonymous_variant ORF1ab_pp1a G1119G 1.00e+0 BA.5.5.2
V8909 2145C>T synonymous_variant S P715P 1.00e+0 BA.5.5.2
V9257 816C>T synonymous_variant ORF3a S272S 1.00e+0 BA.5.5.2
V9754 942C>T synonymous_variant N F314F 1.00e+0 BE.1.1.2
V4246 3601C>A missense_variant S Q1201K 1.00e+0 BE.1.2.1
V9107 3600C>A synonymous_variant S L1200L 1.00e+0 BE.1.2.1
V2050 10367C>T missense_variant ORF1ab_pp1a A3456V 8.66e-1 BE.3
V2744 15718G>A missense_variant ORF1ab_pp1ab V5240I 1.00e+0 BF.1
V3606 283A>G missense_variant S T95A 8.94e-1 BF.1
V4354 101C>T missense_variant ORF3a T34M 7.07e-1 BF.27
V7553 12873C>T synonymous_variant ORF1ab_pp1a I4291I 7.07e-1 BF.27
V944 3208G>A missense_variant ORF1ab_pp1a G1070S 7.07e-1 BF.27
V6179 2197C>T synonymous_variant ORF1ab_pp1a L733L 7.07e-1 BF.3
V981 3337C>T missense_variant ORF1ab_pp1a H1113Y 7.07e-1 BF.3
V1670 7499C>T missense_variant ORF1ab_pp1a S2500F 8.74e-1 BF.7.4
V9764 981G>T synonymous_variant N S327S 7.07e-1 BF.7.6
V1369 5761C>T missense_variant ORF1ab_pp1a P1921S 7.07e-1 BF.8
V460 1249C>T missense_variant ORF1ab_pp1a H417Y 1.00e+0 BF.8
V5572 966G>A missense_variant N M322I 1.00e+0 BN.1.5
V6067 1464G>A synonymous_variant ORF1ab_pp1a V488V 9.13e-1 BN.1.5
V6630 5547C>T synonymous_variant ORF1ab_pp1a D1849D 6.78e-1 BN.1.5
V8050 16725C>T synonymous_variant ORF1ab_pp1ab G5575G 9.13e-1 BN.1.5
V1596 6800G>A missense_variant ORF1ab_pp1a R2267K 7.07e-1 BQ.1.1.11
V4800 13G>T missense_variant ORF6 V5F 1.00e+0 BQ.1.1.11
V5908 378C>T synonymous_variant ORF1ab_pp1a N126N 7.07e-1 BQ.1.1.1
V8766 1062C>T synonymous_variant S N354N 7.07e-1 BQ.1.1.1
V7855 15186C>T synonymous_variant ORF1ab_pp1ab G5062G 6.66e-1 BQ.1.1.28
V6457 4305C>T synonymous_variant ORF1ab_pp1a I1435I 7.07e-1 BQ.1.1.4
V6384 3747C>T synonymous_variant ORF1ab_pp1a L1249L 1.00e+0 BQ.1.16
V3969 1841A>G missense_variant S D614G -7.07e-1 BQ.1.9
V7079 9126C>T synonymous_variant ORF1ab_pp1a D3042D 7.07e-1 BQ.1.9
V7785 14574C>T synonymous_variant ORF1ab_pp1ab I4858I 6.32e-1 BQ.1
V5332 122G>A missense_variant N R41Q 9.25e-1 CR.1.1
V80 -47G>A upstream_gene_variant ORF1ab_pp1a None 7.07e-1 P.1.10
V4879 83C>T missense_variant ORF7a T28I 8.81e-1 P.1.17
V882 2977G>T missense_variant ORF1ab_pp1a G993C 1.00e+0 P.1.1
V5347 214G>A missense_variant N V72I 1.00e+0 Q.1
V6103 1716A>C synonymous_variant ORF1ab_pp1a G572G 7.07e-1 XBB
V7136 9592C>T synonymous_variant ORF1ab_pp1a L3198L 1.00e+0 AY.20.1
V8359 18922C>T synonymous_variant ORF1ab_pp1ab L6308L 1.00e+0 AY.20.1
V5092 71C>T missense_variant ORF8 S24L 1.00e+0 B.1.1.210
V4506 392G>C missense_variant ORF3a W131S 1.00e+0 B.1.1.231
V5783 *4361G>T downstream_gene_variant S None 1.00e+0 B.1.1.231
V5939 564C>T synonymous_variant ORF1ab_pp1a N188N 1.00e+0 B.1.1.231
V1991 9860C>T missense_variant ORF1ab_pp1a T3287I 8.13e-1 B.1.1.244
V195 253_255delATG conservative_inframe_deletion ORF1ab_pp1a M85del 1.00e+0 B.1.1.258
V5807 *4385C>T downstream_gene_variant S None 1.00e+0 B.1.1.258
V6144 1962C>T synonymous_variant ORF1ab_pp1a T654T 1.00e+0 B.1.1.258
V1049 3615G>T missense_variant ORF1ab_pp1a E1205D 1.00e+0 B.1.1.312
V1419 6062C>T missense_variant ORF1ab_pp1a T2021I 1.00e+0 B.1.1.312
V5905 354C>T synonymous_variant ORF1ab_pp1a Y118Y 1.00e+0 B.1.1.312
V6842 7263C>T synonymous_variant ORF1ab_pp1a V2421V 1.00e+0 B.1.1.312
V9159 129C>T synonymous_variant ORF3a F43F 8.43e-1 B.1.1.312
V9389 609C>T synonymous_variant M N203N 7.73e-1 B.1.1.312
V9776 1023C>T synonymous_variant N D341D 9.12e-1 B.1.1.312
V3340 20092G>T missense_variant ORF1ab_pp1ab G6698C 1.00e+0 B.1.1.334
V3520 13C>T missense_variant S L5F 6.32e-1 B.1.1.334
V3066 18160A>G missense_variant ORF1ab_pp1ab N6054D 1.00e+0 B.1.1.335
V3485 21040C>T missense_variant ORF1ab_pp1ab R7014C 8.86e-1 B.1.1.335
V4539 515G>T missense_variant ORF3a G172V 8.89e-1 B.1.1.335
V5092 71C>T missense_variant ORF8 S24L 8.89e-1 B.1.1.335
V5342 199C>T missense_variant N P67S 9.42e-1 B.1.1.335
V5452 596C>T missense_variant N P199L 9.42e-1 B.1.1.335
V8911 2169C>T synonymous_variant S T723T 1.00e+0 B.1.1.335
V61 -68G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.1.448
V9682 609G>A synonymous_variant N R203R 1.00e+0 B.1.160.14
V8315 18613C>T synonymous_variant ORF1ab_pp1ab L6205L 7.06e-1 B.1.210
V6061 1398C>T synonymous_variant ORF1ab_pp1a D466D 1.00e+0 B.1.284
V9389 609C>T synonymous_variant M N203N 1.00e+0 B.1.284
V3010 17867C>T missense_variant ORF1ab_pp1ab T5956I 1.00e+0 B.1.306
V3485 21040C>T missense_variant ORF1ab_pp1ab R7014C 1.00e+0 B.1.306
V4015 2031G>T missense_variant S Q677H 1.00e+0 B.1.306
V5092 71C>T missense_variant ORF8 S24L 1.00e+0 B.1.306
V5342 199C>T missense_variant N P67S 1.00e+0 B.1.337
V3259 19598C>T missense_variant ORF1ab_pp1ab A6533V 1.00e+0 B.1.36.24
V5675 -5G>T upstream_gene_variant ORF10 None 1.00e+0 B.1.36.24
V6095 1647C>T synonymous_variant ORF1ab_pp1a S549S 1.00e+0 B.1.36.24
V9126 3762C>T synonymous_variant S C1254C 1.00e+0 B.1.36.24
V3805 857C>T missense_variant S T286I 1.00e+0 B.1.397
V7351 11379C>T synonymous_variant ORF1ab_pp1a Y3793Y 8.14e-1 B.1.397
V7544 12807C>T synonymous_variant ORF1ab_pp1a F4269F 1.00e+0 B.1.397
V6676 5931C>T synonymous_variant ORF1ab_pp1a P1977P 7.05e-1 B.1.421
V7214 10134A>G synonymous_variant ORF1ab_pp1a L3378L -1.00e+0 B.1.421
V7345 11307C>T synonymous_variant ORF1ab_pp1a F3769F 1.00e+0 B.1.421
V5312 95G>A missense_variant N R32H 7.05e-1 B.1.448
V1732 7866G>T missense_variant ORF1ab_pp1a K2622N 7.06e-1 B.1.521
V5738 *4324C>T downstream_gene_variant S None 1.00e+0 B.1.521
V342 794C>T missense_variant ORF1ab_pp1a T265I 1.00e+0 B.1.550
V3485 21040C>T missense_variant ORF1ab_pp1ab R7014C 1.00e+0 B.1.550
V4406 171G>T missense_variant ORF3a Q57H 7.02e-1 B.1.550
V5092 71C>T missense_variant ORF8 S24L 7.02e-1 B.1.550
V5342 199C>T missense_variant N P67S 1.00e+0 B.1.550
V7038 8820A>G synonymous_variant ORF1ab_pp1a E2940E 1.00e+0 B.1.550
V7401 11691C>T synonymous_variant ORF1ab_pp1a D3897D 1.00e+0 B.1.550
V342 794C>T missense_variant ORF1ab_pp1a T265I 7.72e-1 B.1.567
V1808 8386A>C missense_variant ORF1ab_pp1a M2796L -7.04e-1 B.1.589
V213 295C>T missense_variant ORF1ab_pp1a R99C -7.04e-1 B.1.589
V2595 14144C>T missense_variant ORF1ab_pp1ab P4715L 7.04e-1 B.1.589
V342 794C>T missense_variant ORF1ab_pp1a T265I 7.04e-1 B.1.589
V3894 1424C>T missense_variant S A475V -7.04e-1 B.1.589
V4115 2612C>T missense_variant S A871V -7.04e-1 B.1.589
V8815 1473T>C synonymous_variant S P491P -7.04e-1 B.1.589
V2216 11272A>G missense_variant ORF1ab_pp1a I3758V 1.00e+0 B.45
V260 421_429delAAGTCATTT conservative_inframe_deletion ORF1ab_pp1a K141_F143del 1.00e+0 B.45
V6833 7155C>T synonymous_variant ORF1ab_pp1a I2385I 1.00e+0 B.45
V9557 360C>T synonymous_variant ORF8 F120F 1.00e+0 B.45
V6657 5775C>T synonymous_variant ORF1ab_pp1a F1925F 1.00e+0 BA.4.1.10
V1981 9763A>G missense_variant ORF1ab_pp1a T3255A 8.15e-1 BA.5.2.10
V2951 17414C>T missense_variant ORF1ab_pp1ab T5805M 9.00e-1 BE.4.1.1
V373 914C>T missense_variant ORF1ab_pp1a P305L 8.10e-1 BE.4.1.1
V1354 5621C>T missense_variant ORF1ab_pp1a T1874I 1.00e+0 C.13
V4596 668C>T missense_variant ORF3a T223I 7.05e-1 C.23
V5084 43G>A missense_variant ORF8 A15T 7.05e-1 C.23
V3997 1963C>T missense_variant S H655Y -7.06e-1 CA.5
V1070 3677A>G missense_variant ORF1ab_pp1a K1226R 1.00e+0 DS.1
V4742 187G>A missense_variant M A63T -1.00e+0 DS.1
V5985 837C>T synonymous_variant ORF1ab_pp1a S279S 1.00e+0 P.6
V7633 13461T>C synonymous_variant ORF1ab_pp1ab A4487A 1.00e+0 P.6





Manual curation of mutation (10054C>T)-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