Human APOBEC3 Variations and Viral Infection
Abstract
:1. Introduction
2. APOBEC3 Variations
2.1. APOBEC3A and APOBEC3B
2.2. APOBEC3C
2.3. APOBEC3D
2.4. APOBEC3F
2.5. APOBEC3G
2.6. APOBEC3H
3. Future Directions and Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Description | Allelic Frequency | Studied Populations and References | Effect | |||
---|---|---|---|---|---|---|
African | European | Asian | ||||
APOBEC3A/B | ||||||
rs12628403 (surrogate for ~30 kb APOBEC3B deletion) | ~30 kb deletion (Δ) of all APOBEC3B exons and introns except for exon 8; In-frame fusion to APOBEC3A. | n = 3394 Δ = 0.03 | n = 20,404 Δ = 0.08 | n = 116 Δ = 0.4 | Indonesian PMID: 26305823 | HIV-1 co-infections: Δ > reference |
Moroccan PMID: 24010642 | %Δ: HBV patients ~ healthy donors Progression to liver diseases: Δ > reference | |||||
Western Indian PMID: 27522954 | Risk of HIV-1 acquisition: Δ > reference | |||||
European Americans and African Americans PMID: 19698078 | HIV-1 acquisition, progression to AIDS, and viral set point: Δ/Δ > reference | |||||
Japanese and Indian PMID: 20684727 | %Δ: HIV-1 patients ~ healthy donors | |||||
Japanese PMID: 19788695 | %Δ: HBV patients ~ healthy donors Hypermutation context: Δ ~ reference | |||||
Japanese PMID: 24667791 | %Δ: HIV-1 patients ~ healthy donors HIV-1 co-infections: Δ ~ reference HIV-1 progression: Δ ~ reference | |||||
APOBEC3C | ||||||
rs112120857 | Missense (G > C / G > T) S188I | n = 3574 G = 0.94 C = 0.00 T = 0.06 | n = 37,290 G = 0.99962 C = 0.00003 T = 0.00035 | n = 168 G = 1.00 C = 0.00 T = 0.00 | PMIDs: 27732658, 30558640 | In vitro anti-HIV-1 activity: I > S |
APOBEC3D | ||||||
rs201709403 | Missense (A > G) T238A | n = 2898 A = 1.00 G = 0.00 | n = 9690 A = 1.00 G = 0.00 | n = 112 A = 1.00 G = 0.00 | Northern South African PMID: 30660178 | %G (238A): HIV-1 patients > 1000 Genomes Africans |
rs75858538 | Missense (C > T) R97C | n = 5146 C = 0.98 T = 0.02 | n = 180,258 C = 0.9999 T = 0.0001 | n = 6364 C = 0.9998 T = 0.0002 | Northern South African PMID: 30660178 | %T (97C): HIV-1 patients > 1000 Genomes Africans |
PMID: 23755966 | Protein expression: R ~ C Anti-HIV-1 activity: R > C Sensitivity to HIV-1 Vif: R ~ C Anti-Alu activity: R ~ C | |||||
rs61748819 | Missense (G > A) R248K | n = 3574 G = 0.91 A = 0.09 | n = 32,834 G = 0.9997 A = 0.00034 | n = 168 G = 1.00 A = 0.000 | PMID: 23755966 | Protein expression: R > K Anti-HIV-1 activity: R > K Sensitivity to HIV-1 Vif: R ~ K Anti-Alu activity: R > K |
APOBEC3F | ||||||
rs2020390 | Missense (G > T) A108S | n = 3512 G = 0.60 T = 0.40 | n = 37,024 G = 0.49 T = 0.51 | n = 168 G = 0.29 T = 0.71 | Northern South African PMID: 30660178 | %T (108S): HIV-1 patients > 1000 Genomes African populations |
rs12157816 | Missense (A > G) Y307C | n = 3574 A = 0.97 G = 0.03 | n = 37,264 A = 0.9881 G = 0.0119 | n = 168 A = 1.0 G = 0.0 | Northern South African PMID: 30660178 | %G (307C): HIV-1 patients > 1000 Genomes African populations |
rs2076101 | Missense (G > A) V231I | n = 8220 G = 0.73 A = 0.27 | n = 256,418 G = 0.48 A = 0.52 | n = 3812 G = 0.3 A = 0.7 | European American and African American PMID: 26942578 | Set-point viral load: I > V Progression to AIDS: I > V Pneumocystis pneumonia: I > V |
PMID: 30448640 | HIV-1 restriction: V > I Protection against HIV-1 Vif: V > I Level of viral encapsidation: V > I | |||||
APOBEC3FΔ2 | Isoform lacking exon 2 | PMID: 20624919 | Sensitivity to Vif: main isoform > APOBEC3FΔ2 Viral packaging: main isoform > APOBEC3FΔ2 Antiviral activity: main isoform > APOBEC3FΔ2 Deamination: main isoform > APOBEC3FΔ2 | |||
APOBEC3FΔ2-4 | Isoform lacking exons 2, 3 and 4 | PMID: 20624919 | Sensitivity to Vif: APOBEC3FΔ2–4 > main isoform Viral packaging: main isoform > APOBEC3FΔ2–4 Antiviral activity: Main isoform > APOBEC3FΔ2–4 deamination: main isoform > APOBEC3FΔ2–4 | |||
APOBEC3G | ||||||
rs5757463 | -571G/C upstream (G > C) | n = 106 G = 0.29 C = 0.71 | n = 6564 G = 0.06 C = 0.94 | n = 4 G = 0.0 C = 1.0 | African Americans and European Americans PMID: 15452227 | Susceptibility to HIV-1 infection: G ~ C |
Brazilian PMID: 20874421 | CD4 T-cell count: CC > CG and GG | |||||
West Indian PMID: 29864532 | %CG: HIV patients > healthy donors %(GC + CC): HIV patients > healthy donors | |||||
Zimbabwean PMID: 27245545 | Susceptibility to HIV-1 infection: G ~ C | |||||
rs34550797 | -199G/A upstream (G > A) | n = 2816 G = 0.995 A = 0.005 | n = 7618 G = 0.9992 A = 0.0008 | n = 108 G = 1.0 A = 0.0 | African Americans and European Americans PMID: 15452227 | Susceptibility to HIV-1 infection: G ~ A |
rs5750743 | -90C/G upstream/5′UTR (C > G) | n = 276 C = 1.00 G = 0.00 | n = 5330 C = 0.54 G = 0.46 | n = 8 C = 1.0 G = 0.0 | African Americans and European Americans PMID: 15452227 | Susceptibility to HIV-1 infection: C ~ G |
West Indian PMID: 29864532 | %CG: HIV-1 patients > healthy donors %GG: healthy donors > HIV patients | |||||
Zimbabwean PMID: 27245545 | Susceptibility to HIV-1 infection: C ~ G | |||||
rs5757465 | Synonymous (T > C) F119F | n = 11,214 T = 0.90 C = 0.10 | n = 248,594 T = 0.56 C = 0.44 | n = 3908 T = 0.76 C = 0.24 | African Americans and European Americans PMID: 15452227 | Susceptibility to HIV-1 infection: T ~ C |
Diverse populations PMID: 23138837 | HIV-1 disease progression: T > C CNS impairment: T > C | |||||
rs3736685 | 197193T/C intron (T > C) | n = 7982 T = 0.63 C = 0.37 | n = 223,498 T = 0.97 C = 0.03 | n = 3870 T = 0.92 C = 0.08 | African Americans and European Americans PMID: 15452227 | Susceptibility to HIV-1 infection: T ~ C |
Zimbabwean PMID: 27245545 | Susceptibility to HIV-1 infection: T ~ C | |||||
rs2294367 | 199376G/C intron (C > G) | n = 2036 C = 0.99 G = 0.01 | n = 8254 C = 0.57 G = 0.43 | n = 16 C = 0.75 G = 0.25 | African Americans and European Americans PMID: 15452227 | Susceptibility to HIV-1 infection: C ~ G Progression to AIDS: G > C |
Zimbabwean PMID: 27245545 | Susceptibility to HIV-1 infection: C ~ G | |||||
rs8177832 | Missense (A > G) H186R | n = 11,678 A = 0.66 G = 0.34 | n = 252,598 A = 0.97 G = 0.03 | n = 6820 A = 0.92 G = 0.08 | African Americans and European Americans PMID: 15452227 | Susceptibility to HIV-1 infection: H ~ R Rate of CD4 T cell loss: R > H Progression to AIDS: R > H |
PMID: 27064995 | Antiviral activity: H > R Counteraction by Vif: H ~ R | |||||
Diverse populations PMID: 23138837 | HIV-1 disease progression: R > H CNS impairment: R > H | |||||
South Africans PMID: 19996938 | Viral load: R > H CD4 T cell count: H > R | |||||
French PMID: 15609224 | Progression to AIDS: H ~ R | |||||
Caucasians PMID: 16988524 | Progression to AIDS: H ~ R | |||||
Argentinian PMID: 22145963 | Progression to AIDS: H ~ R Viral G-to-A mutation: H ~ R | |||||
Argentinian PMID: 21571098 | HIV-1 transmission: H ~ R Progression to AIDS: H ~ R Viral G-to-A mutation: H ~ R | |||||
Zimbabwean PMID: 27245545 | Susceptibility to HIV-1 infection: H ~ R | |||||
Morocco PMID: 24010642 | Risk of HBV acquisition: H ~ R | |||||
Burkina Fasoian PMID: 26741797 | Protection against HIV-1 infection: GGT [rs6001417, rs8177832 (H186R), rs35228531] > Other haplotypes Risk of HIV-1 infection: GGC and CGC > Other haplotypes | |||||
Burkina Fasoian PMID: 27449138 | HIV-1/HBV co-infection rate: other haplotypes > GGT [rs6001417, rs8177832 (H186R), rs35228531] | |||||
Western Indian PMID: 26853443 | Risk of HIV-1 acquisition: H ~ R Progression to AIDS: H ~ R | |||||
North Indian PMID: 18652534 | Absence of 186R variant | |||||
rs17496018 | C40693T Intron (C > T) | n = 4296 C = 0.94 T = 0.06 | n = 26,952 C = 0.93 T = 0.07 | n = 128 C = 0.97 T = 0.03 | Caucasians PMID: 16988524 | Risk of HIV-1 infection: T > C |
Argentinian PMID 22145963 | Progression to AIDS: H ~ R Viral G > A mutation: H ~ R | |||||
Argentinian PMID: 21571098 | HIV-1 transmission: H ~ R Progression to AIDS: H ~ R Viral G-to-A mutation: H ~ R C > T polymorphism was associated with Vif variation. | |||||
rs17496046 | Missense (C > G) Q275E | n = 4374 C = 0.87 G = 0.13 | n = 96,948 C = 0.93 G = 0.07 | n = 3326 C = 0.97 G = 0.03 | Caucasians PMID: 16988524 | Risk of HIV-1 infection: C ~ G |
Northern South African PMID: 30660178 | % G (275E): HIV-1 patients > 1000 Genomes Africans | |||||
rs6001417 | Intron (C > G) | n = 2960 C = 0.63 G = 0.37 | n = 16,474 C = 0.97 G = 0.03 | n = 112 C = 0.94 G = 0.06 | Burkina Fasoian PMID: 26741797 | Protection against HIV-1 infection: GGT [rs6001417, rs8177832 (H186R), rs35228531] > Other haplotypes Risk of HIV-1 infection: GGC and CGC > Other haplotypes |
Burkina Fasoian PMID: 27449138 | HIV-1/HBV co-infection rate: other haplotypes > GGT [rs6001417, rs8177832 (H186R), rs35228531] | |||||
rs35228531 | Downstream (C > T) | n = 1564 C = 0.994 T = 0.006 | n = 9814 C = 1.00 T = 0.00 | n = 112 C = 1.00 T = 0.00 | South African PMID: 19996938 | Viral load: T > C CD4 T-cell count: C > T |
Burkina Fasoian PMID: 26741797 | Protection against HIV-1 infection: GGT [rs6001417, rs8177832 (H186R), rs35228531] > Other haplotypes Risk of HIV-1 infection: GGC and CGC > Other haplotypes | |||||
Burkina Fasoian PMID: 27449138 | HIV-1/HBV co-infection rate: C > T HIV-1/HBV co-infection rate: Other haplotypes > GGT [rs6001417, rs8177832 (H186R), rs35228531] | |||||
rs5757467 | Intron (C > T) | n = 2946 C = 0.31 T = 0.69 | n = 15,414 C = 0.36 T = 0.64 | n = 112 C = 0.21 T = 0.79 | West Australian PMID: 16940537 | HIV-1 hypermutation: C > T |
APOBEC3H | ||||||
rs139292 (Previously rs140936762) | Indel (CAA/Δ) N15Δ | n = 3506 Δ = 0.32 | n = 20,264 Δ = 0.34 | n = 168 Δ = 0.23 | PMID: 32235597 | Antiviral activity: Reference > Δ |
Northern South African PMID: 30660178 | %Δ: HIV-1 patients >1000 Genomes Africans | |||||
Japanese PMID: 25721876 | Susceptibility to HIV-1 infection: Δ > reference | |||||
Indian PMID: 26559750 | Susceptibility to HIV-1 infection: Δ > reference | |||||
rs139293 | Missense (G > T) R18L | n = 3158 G = 0.96 T = 0.04 | n = 36,146 G = 0.75 T = 0.25 | n = 166 G = 0.92 T = 0.08 | Northern South Africa PMID: 30660178 | %T(18L): HIV-1 patients > 1000 Genomes Africans |
rs139297 | Missense (G > C) G105R | n = 1308 G = 0.66 C = 0.34 | n = 35,022 G = 0.56 C = 0.44 | n = 148 G = 0.89 C = 0.11 | PMID: 32235597 | Ubiquitination: G (HapI) > R (HapII) |
PMID: 20519396 | Antiviral activity: R (HapII) > G (HapI) HIV-1 encapsidation: R (HapII) ~ G (HapI) Protein expression: R (HapII) > G (HapI) Interaction with Gag: R (HapII) with nucleocapsid; G (HapI) with C-terminal of matrix and N-terminal of capsid | |||||
Japanese PMID: 25721876 | Susceptibility to HIV-1 infection: G (HapI) > R (HapII) Progression to AIDS: G (HapI) > R (HapII) | |||||
Indian PMID: 26559750 | %15Δ-105R: HIV-1 patients > healthy donors | |||||
Diverse populations PMID: 21167246 | Rate of HIV-1 GA-to-AA mutation: R (HapII) > G (HapI) | |||||
rs139299 | Missense (G > C) K121D | n = 3574 G = 0.24 C = 0.76 | n = 37,158 G = 0.52 C = 0.48 | n = 168 G = 0.72 C = 0.28 | Diverse populations PMID: 21167246 | Rate of HIV-1 GA-to-AA mutation: D (HapII) > K (HapI) |
rs139298 | Missense (A > G) K121D | n = 11,188 A = 0.21 G = 0.79 | n = 252,052 A = 0.53 G = 0.47 | n = 6744 A = 0.69 G = 0.31 | Diverse populations PMID: 21167246 | Rate of HIV-1 GA-to-AA mutation: D (HapII) > K (HapI) |
rs139302 | Missense (G > C) E178D | n = 3882 G = 0.26 C = 0.74 | n = 97,472 G = 0.54 C = 0.46 | n = 3326 G = 0.67 C = 0.33 | PMID: 21167246 | Rate of HIV-1 GA-to-AA mutation: D (HapII) > E (HapI) |
Northern South African PMID: 30660178 | %C (178D): HIV-1 patients > 1000 Genomes Africans | |||||
PMID: 27534815 | Cytosine deamination: E (HapV) > D (other haplotypes) Methyl cytosine deamination: D (HapII) >> E (other haplotypes) DNA binding: all haplotypes are the same. | |||||
rs149229175 | Indel (CTC/Δ) intron | n = 3410 Δ = 0.32 | n = 18,142 Δ = 0.13 | n = 164 Δ = 0.08 | Diverse populations PMID: 30297863 | %SV200: Δ > CTC |
SV200, SV183, SV182, and SV154 | Splice variants with different C-terminals | Diverse populations PMID: 18945781 | Viral restriction: SV200 (HapII) > other variants | |||
Diverse populations PMID: 30297863 | Antiviral activity: HapII-SV200 > SV182/183 Viral encapsidation: HapII-SV182/183 > SV200 Protease processing: only HapII SV200 L1 fragment in transcript: only HapII SV200 | |||||
PMID: 27534815 | Cytosine and methyl cytosine deamination: HapI-SV182/183 > SV200 >> SV154 | |||||
PMID: 31400856 | HBV restriction: HapII SV183 > other variants |
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Sadeghpour, S.; Khodaee, S.; Rahnama, M.; Rahimi, H.; Ebrahimi, D. Human APOBEC3 Variations and Viral Infection. Viruses 2021, 13, 1366. https://doi.org/10.3390/v13071366
Sadeghpour S, Khodaee S, Rahnama M, Rahimi H, Ebrahimi D. Human APOBEC3 Variations and Viral Infection. Viruses. 2021; 13(7):1366. https://doi.org/10.3390/v13071366
Chicago/Turabian StyleSadeghpour, Shiva, Saeideh Khodaee, Mostafa Rahnama, Hamzeh Rahimi, and Diako Ebrahimi. 2021. "Human APOBEC3 Variations and Viral Infection" Viruses 13, no. 7: 1366. https://doi.org/10.3390/v13071366