In Silico Analysis of Hepatitis B Virus Occult Associated Mutations in Botswana Using a Novel Algorithm
Abstract
:1. Introduction
2. Materials and Methods
2.1. Population
2.2. Determination of OBI-Associated Mutations
2.3. Ethical Considerations
2.4. In Silico Methods
2.5. Data Analysis
3. Results
OBI-Associated Mutations Phenotypic Results
Phyre2 Results
4. Discussion
Author Contributions
Funding
Conflicts of Interest
References
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Variant | Genotype | PROVEAN Prediction # | PROVEAN Prediction * | SNAP2 Prediction | PolyPhen2 | References |
---|---|---|---|---|---|---|
sN146D, sC147Y, sY100C, sG130R, sC138Y, sP142S, sG145R, sG145E, sN146S, sC147R, sC149Y, sD144G | A | ✔ | ✔ | ✔ | ✔ | [81,82] |
sS132P, sT114R, sT115A, sK141E | A | ✔ | ✔ | ✔ | [71,81] | |
sC121A, sC124A, sQ129H, sC147A | A | ✔ | ✔ | ✔ | [81] | |
sP120T | A | ✔ | ✔ | ✔ | [81] | |
sP127S | A | ✔ | ✔ | [81] | ||
sC149A | A | ✔ | ✔ | [81] | ||
sC124R, sS136P, sC139R, sT140I, sD144A, sG145R, sG145A, sG145W, sG145I, sG145P, sG145N, sG145D, sK122I | B | ✔ | ✔ | ✔ | ✔ | [49] [83] [61] |
sK141E, sK160N, sT123N | B | ✔ | ✔ | ✔ | [49,84] | |
sQ129R | B | ✔ | [49] | |||
sP120T | B | ✔ | ✔ | ✔ | [49] | |
sA159G | B | ✔ | [84] | |||
sG119R, sC124R, sC124Y, sS136P, sC139R, sK141E, sL21R, sT131I, sP142S | C | ✔ | ✔ | ✔ | ✔ | [49] [85] [86] |
sG145R, sG145A | C | ✔ | ✔ | ✔ | [86] | |
sL95W | C | ✔ | ✔ | ✔ | [85] | |
sD144A | C | ✔ | ✔ | ✔ | [49] | |
sT140I, sP120T, sE2G | C | ✔ | ✔ | [49] [85] | ||
sL98V | C | ✔ | ✔ | [85] | ||
sD99G | C | ✔ | ✔ | ✔ | [87] | |
sQ129R | C | ✔ | [49] | |||
sM133T | C | ✔ | ✔ | [88] | ||
sI126S | C | [49] | ||||
sT116N | D | ✔ | ✔ | ✔ | [66] | |
sP120T | D | ✔ | ✔ | ✔ | [80] | |
sR122P, sG145R | D | ✔ | ✔ | ✔ | [66] [85] | |
sT125M | D | ✔ | ✔ | ✔ | ✔ | [89] |
Total (Effect) | 52 (76.5%) | 65 (95.6%) | 55(80.1%) | 52 (76.5%) | ||
Total (Neutral) | 16 | 3 | 13 | 16 |
Variant | Region | Genotype | PROVEAN Prediction # | PROVEAN Prediction * | SNAP2 | PolyPhen2 | Reference |
---|---|---|---|---|---|---|---|
sM103I | S | A | ✔ | ✔ | [44] | ||
sK122R | S | A | [44] | ||||
tpP100S | TP | A | ✔ | ✔ | ✔ | [45] | |
sP111S, sS154P, sK122P, sK122W | S | B | ✔ | ✔ | ✔ | ✔ | [83,90] |
sG112E, sG119E, sW165R, sK122G, sK122L, sK122D | S | B | ✔ | ✔ | ✔ | [83,90] | |
sQ129R | S | B | ✔ | [90] | |||
sI150T | S | B | ✔ | ✔ | ✔ | [90] | |
sK122M, sK122H | S | B | ✔ | ✔ | ✔ | [83] | |
sK122Q | S | B | [83] | ||||
sK122T, sK122E, sK122N | S | B | ✔ | ✔ | [83] | ||
tpQ177H | TP | B | ✔ | [45] | |||
tpR27L | TP | B | ✔ | ✔ | [45] | ||
sC121Y | S | C | ✔ | ✔ | ✔ | ✔ | [87] |
sR24K, sT47A, sT47K, sI126S, sF134Y | S | C | [85,86,87] | ||||
sQ101R | S | D | ✔ | [66] | |||
sS167L | S | D | ✔ | ✔ | ✔ | [66] | |
sS143L | S | D | ✔ | ✔ | [66] | ||
total | 18 (56.3%) | 8 (25%) | 11 (34.4%) | 23 (71.9%) |
Variant | ORF | Genotype | Final Result |
---|---|---|---|
sL97P, sT114I, sC124Y *, sN131K *, sP217L * | S | A1 | Deleterious |
sQ129H * | S | D3 | Deleterious |
PreS1S78N | PreS1 | D3 | Deleterious |
PreS2F22P, PreS2F22H | PreS2 | D3 | Deleterious |
xS11A, xV15I | X | A1 | Neutral |
xS31A, xS101P, xL116V | X | D3 | Neutral |
xP11S, xQ87L | X | D3 | Deleterious |
cS26P, cD32G, cP45S, cE46D, cR127H | Core | A1 | Deleterious |
cI59L | Core | A1 | Neutral |
cV74N, cS87N, cF97I | Core | D3 | Neutral |
cD2A, D4Y, cI3R, cE64K, cW102V, cF103V | Core | D3 | Deleterious |
tpN120Y, tpK155R | Pol-TP | A1 | Deleterious |
spS91T, spS133G | Pol-Spacer | A1 | Neutral |
rtL140I, rtA329T | Pol-RT | A1 | Neutral |
rtT225A | Pol-RT | A1 | Deleterious |
rhI81M | Pol-RH | A1 | Neutral |
spW64R, spP103S | Pol-Spacer | D3 | Neutral |
rtY257F | Pol-RT | D3 | Neutral |
rtT128I | Pol-RT | D3 | Deleterious |
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Anderson, M.; Choga, W.T.; Moyo, S.; Bell, T.G.; Mbangiwa, T.; Phinius, B.B.; Bhebhe, L.; Sebunya, T.K.; Makhema, J.; Marlink, R.; et al. In Silico Analysis of Hepatitis B Virus Occult Associated Mutations in Botswana Using a Novel Algorithm. Genes 2018, 9, 420. https://doi.org/10.3390/genes9090420
Anderson M, Choga WT, Moyo S, Bell TG, Mbangiwa T, Phinius BB, Bhebhe L, Sebunya TK, Makhema J, Marlink R, et al. In Silico Analysis of Hepatitis B Virus Occult Associated Mutations in Botswana Using a Novel Algorithm. Genes. 2018; 9(9):420. https://doi.org/10.3390/genes9090420
Chicago/Turabian StyleAnderson, Motswedi, Wonderful T. Choga, Sikhulile Moyo, Trevor Graham Bell, Tshepiso Mbangiwa, Bonolo B. Phinius, Lynette Bhebhe, Theresa K. Sebunya, Joseph Makhema, Richard Marlink, and et al. 2018. "In Silico Analysis of Hepatitis B Virus Occult Associated Mutations in Botswana Using a Novel Algorithm" Genes 9, no. 9: 420. https://doi.org/10.3390/genes9090420