Willems L, Gillet NA. APOBEC3 Interference during Replication of Viral Genomes. Viruses. 2015; 7: 2999-3018. https://doi.org/10.3390/v7062757 PMID: 26110583
Salter JD, Bennett RP, Smith HC. The APOBEC Protein Family: United by Structure, Divergent in Function. Trends Biochem Sci. 2016; 41: 578-594. https://doi.org/10.1016/j.tibs.2016.05.001 PMID: 27283515
Münk C, Willemsen A, Bravo IG. An ancient history of gene duplications, fusions and losses in the evolution of APOBEC3 mutators in mammals. BMC Evol Biol. 2012; 12: 71. https://doi.org/10.1186/1471-2148-12-71 PMID: 22640020
Taylor BJ, Nik-Zainal S, Wu YL, Stebbings LA, Raine K, Campbell PJ, et al. DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis. Stamatoyannopoulos J, editor. eLife. 2013; 2: e00534. https://doi.org/10.7554/eLife.00534 PMID: 23599896
Sheehy AM, Gaddis NC, Choi JD, Malim MH. Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature. 2002; 418: 646-650. https://doi.org/10.1038/nature00939 PMID: 12167863
Sasada A, Takaori-Kondo A, Shirakawa K, Kobayashi M, Abudu A, Hishizawa M, et al. APOBEC3G targets human T-cell leukemia virus type 1. Retrovirology. 2005; 2: 32. https://doi.org/10.1186/1742-4690-2-32 PMID: 15943885
Turelli P, Mangeat B, Jost S, Vianin S, Trono D. Inhibition of Hepatitis B Virus Replication by APOBEC3G. Science. 2004; 303: 1829-1829. https://doi.org/10.1126/science.1092066 PMID: 15031497
Lecossier D, Bouchonnet F, Clavel F, Hance AJ. Hypermutation of HIV-1 DNA in the Absence of the Vif Protein. Science. 2003; 300: 1112-1112. https://doi.org/10.1126/science.1083338 PMID: 12750511
Mangeat B, Turelli P, Caron G, Friedli M, Perrin L, Trono D. Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature. 2003; 424: 99-103. https://doi.org/10.1038/nature01709 PMID: 12808466
Mahieux R, Suspène R, Delebecque F, Henry M, Schwartz O, Wain-Hobson S, et al. Extensive editing of a small fraction of human T-cell leukemia virus type 1 genomes by four APOBEC3 cytidine deaminases. J Gen Virol. 2005; 86: 2489-2494. https://doi.org/10.1099/vir.0.80973-0 PMID: 16099907
Fan J, Ma G, Nosaka K, Tanabe J, Satou Y, Koito A, et al. APOBEC3G Generates Nonsense Mutations in Human T-Cell Leukemia Virus Type 1 Proviral Genomes In Vivo. J Virol. 2010; 84: 7278-7287. https://doi.org/10.1128/JVI.02239-09 PMID: 20463074
Suspène R, Guétard D, Henry M, Sommer P, Wain-Hobson S, Vartanian J-P. Extensive editing of both hepatitis B virus DNA strands by APOBEC3 cytidine deaminases in vitro and in vivo. Proc Natl Acad Sci U S A. 2005; 102: 8321-8326. https://doi.org/10.1073/pnas.0408223102 PMID: 15919829
Henry M, Guétard D, Suspène R, Rusniok C, Wain-Hobson S, Vartanian J-P. Genetic Editing of HBV DNA by Monodomain Human APOBEC3 Cytidine Deaminases and the Recombinant Nature of APOBEC3G. PLoS ONE. 2009; 4. https://doi.org/10.1371/journal.pone.0004277 PMID: 19169351
Suspène R, Aynaud M-M, Koch S, Pasdeloup D, Labetoulle M, Gaertner B, et al. Genetic Editing of Herpes Simplex Virus 1 and Epstein-Barr Herpesvirus Genomes by Human APOBEC3 Cytidine Deaminases in Culture and In Vivo. J Virol. 2011; 85: 7594-7602. https://doi.org/10.1128/JVI.00290-11 PMID: 21632763
Vartanian J-P, Guétard D, Henry M, Wain-Hobson S. Evidence for Editing of Human Papillomavirus DNA by APOBEC3 in Benign and Precancerous Lesions. Science. 2008; 320: 230-233. https://doi.org/10.1126/science.1153201 PMID: 18403710
Verhalen B, Starrett GJ, Harris RS, Jiang M. Functional Upregulation of the DNA Cytosine Deaminase APOBEC3B by Polyomaviruses. J Virol. 2016; 90: 6379-6386. https://doi.org/10.1128/JVI.00771-16 PMID: 27147740
Peretti A, Geoghegan EM, Pastrana DV, Smola S, Feld P, Sauter M, et al. Characterization of BK polyomaviruses from kidney transplant recipients suggests a role for APOBEC3 in driving in-host virus evolution. Cell Host Microbe. 2018; 23: 628-635.e7. https://doi.org/10.1016/j.chom.2018.04.005 PMID: 29746834
Milewska A, Kindler E, Vkovski P, Zeglen S, Ochman M, Thiel V, et al. APOBEC3-mediated restriction of RNA virus replication. Sci Rep. 2018; 8: 5960. https://doi.org/10.1038/s41598-018-24448-2 PMID: 29654310
Fehrholz M, Kendl S, Prifert C, Weissbrich B, Lemon K, Rennick L, et al. The innate antiviral factor APOBEC3G targets replication of measles, mumps and respiratory syncytial viruses. J Gen Virol. 2012; 93: 565-576. https://doi.org/10.1099/vir.0.038919-0 PMID: 22170635
Peng Z-G, Zhao Z-Y, Li Y-P, Wang Y-P, Hao L-H, Fan B, et al. Host apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide-like 3G is an innate defensive factor and drug target against hepatitis C virus. Hepatol Baltim Md. 2011; 53: 1080-1089. https://doi.org/10.1002/hep.24160 PMID: 21480314
Stenglein MD, Harris RS. APOBEC3B and APOBEC3F inhibit L1 retrotransposition by a DNA deamination-independent mechanism. J Biol Chem. 2006; 281: 16837-16841. https://doi.org/10.1074/jbc. M602367200 PMID: 16648136
Tsuge M, Noguchi C, Akiyama R, Matsushita M, Kunihiro K, Tanaka S, et al. G to A hypermutation of TT virus. Virus Res. 2010; 149: 211-216. https://doi.org/10.1016/j.virusres.2010.01.019 PMID: 20138932
Chen H, Lilley CE, Yu Q, Lee DV, Chou J, Narvaiza I, et al. APOBEC3A Is a Potent Inhibitor of Adeno-Associated Virus and Retrotransposons. Curr Biol. 2006; 16: 480-485. https://doi.org/10.1016/j.cub.2006.01.031 PMID: 16527742
Narvaiza I, Linfesty DC, Greener BN, Hakata Y, Pintel DJ, Logue E, et al. Deaminase-independent inhibition of parvoviruses by the APOBEC3A cytidine deaminase. PLoS Pathog. 2009; 5: e1000439. https://doi.org/10.1371/journal.ppat.1000439 PMID: 19461882
Yu X, Yu Y, Liu B, Luo K, Kong W, Mao P, et al. Induction of APOBEC3G ubiquitination and degradation by an HIV-1 Vif-Cul5-SCF complex. Science. 2003; 302: 1056-1060. https://doi.org/10.1126/science. 1089591 PMID: 14564014
Derse D, Hill SA, Princler G, Lloyd P, Heidecker G. Resistance of human T cell leukemia virus type 1 to APOBEC3G restriction is mediated by elements in nucleocapsid. Proc Natl Acad Sci. 2007; 104: 2915-2920. https://doi.org/10.1073/pnas.0609444104 PMID: 17299050
Cheng AZ, Yockteng-Melgar J, Jarvis MC, Malik-Soni N, Borozan I, Carpenter MA, et al. Epstein-Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity. Nat Microbiol. 2019; 4: 78-88. https://doi.org/10.1038/s41564-018-0284-6 PMID: 30420783
Warren CJ, Van Doorslaer K, Pandey A, Espinosa JM, Pyeon D. Role of the host restriction factor APOBEC3 on papillomavirus evolution. Virus Evol. 2015; 1. https://doi.org/10.1093/ve/vev015 PMID: 27570633
Anwar F, Davenport MP, Ebrahimi D. Footprint of APOBEC3 on the Genome of Human Retroelements. J Virol. 2013; 87: 8195-8204. https://doi.org/10.1128/JVI.00298-13 PMID: 23698293
Jern P, Russell RA, Pathak VK, Coffin JM. Likely Role of APOBEC3G-Mediated G-to-A Mutations in HIV-1 Evolution and Drug Resistance. PLoS Pathog. 2009; 5. https://doi.org/10.1371/journal.ppat. 1000367 PMID: 19343218
Ebrahimi D, Anwar F, Davenport MP. APOBEC3 Has Not Left an Evolutionary Footprint on the HIV-1 Genome!. J Virol. 2011; 85: 9139-9146. https://doi.org/10.1128/JVI.00658-11 PMID: 21697498
Martinez T, Shapiro M, Bhaduri-McIntosh S, MacCarthy T. Evolutionary effects of the AID/APOBEC family of mutagenic enzymes on human gamma-herpesviruses. Virus Evol. 2019; 5: vey040. https://doi.org/10.1093/ve/vey040 PMID: 30792902
Woo PCY, Wong BHL, Huang Y, Lau SKP, Yuen K-Y. Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Virology. 2007; 369: 431-442. https://doi.org/10.1016/j.virol.2007.08.010 PMID: 17881030
Chen J, MacCarthy T. The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes. PLoS Comput Biol. 2017; 13. https://doi.org/10.1371/journal.pcbi.1005471 PMID: 28362825
Shapiro M, Meier S, MacCarthy T. The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. BMC Bioinformatics. 2018; 19: 163. https://doi.org/10.1186/s12859-018-2161-y PMID: 29716522
LaRue RS, Jónsson SR, Silverstein KA, Lajoie M, Bertrand D, El-Mabrouk N, et al. The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals. BMC Mol Biol. 2008; 9: 104. https://doi.org/10.1186/1471-2199-9-104 PMID: 19017397
Karlin S, Doerfler W, Cardon LR. Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses? J Virol. 1994; 68: 2889-2897. https://doi.org/10.1128/JVI.68.5.2889-2897.1994 PMID: 8151759
Muramatsu M, Kinoshita K, Fagarasan S, Yamada S, Shinkai Y, Honjo T. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell. 2000; 102: 553-563. https://doi.org/10.1016/s0092-8674(00)00078-7 PMID: 11007474
Powell LM, Wallis SC, Pease RJ, Edwards YH, Knott TJ, Scott J. A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine. Cell. 1987; 50: 831-840. https://doi.org/10.1016/ 0092-8674(87)90510-1 PMID: 3621347
Davidson NO, Innerarity TL, Scott J, Smith H, Driscoll DM, Teng B, et al. Proposed nomenclature for the catalytic subunit of the mammalian apolipoprotein B mRNA editing enzyme: APOBEC-1. RNA N Y N. 1995; 1: 3.
Moris A, Murray S, Cardinaud S. AID and APOBECs span the gap between innate and adaptive immunity. Front Microbiol. 2014; 5. https://doi.org/10.3389/fmicb.2014.00534 PMID: 25352838
Larijani M, Frieder D, Basit W, Martin A. The mutation spectrum of purified AID is similar to the mutability index in Ramos cells and in ung(-/-)msh2(-/-) mice. Immunogenetics. 2005; 56: 840-845. https://doi.org/10.1007/s00251-004-0748-0 PMID: 15650878
Warren CJ, Xu T, Guo K, Griffin LM, Westrich JA, Lee D, et al. APOBEC3A functions as a restriction factor of human papillomavirus. J Virol. 2015; 89: 688-702. https://doi.org/10.1128/JVI.02383-14 PMID: 25355878
Mori S, Takeuchi T, Ishii Y, Yugawa T, Kiyono T, Nishina H, et al. Human Papillomavirus 16 E6 Upregulates APOBEC3B via the TEAD Transcription Factor. J Virol. 2017; 91. https://doi.org/10.1128/JVI. 02413-16 PMID: 28077648
Westrich JA, Warren CJ, Klausner MJ, Guo K, Liu C-W, Santiago ML, et al. Human Papillomavirus 16 E7 Stabilizes APOBEC3A Protein by Inhibiting Cullin 2-Dependent Protein Degradation. J Virol. 2018; 92. https://doi.org/10.1128/JVI.01318-17 PMID: 29367246
Starrett GJ, Serebrenik AA, Roelofs PA, McCann JL, Verhalen B, Jarvis MC, et al. Polyomavirus T Antigen Induces APOBEC3B Expression Using an LXCXE-Dependent and TP53-Independent Mechanism. mBio. 2019; 10. https://doi.org/10.1128/mBio.02690-18 PMID: 30723127
Vieira VC, Leonard B, White EA, Starrett GJ, Temiz NA, Lorenz LD, et al. Human Papillomavirus E6 Triggers Upregulation of the Antiviral and Cancer Genomic DNA Deaminase APOBEC3B. mBio. 2014; 5. https://doi.org/10.1128/mBio.02234-14 PMID: 25538195
Warren CJ, Westrich JA, Van Doorslaer K, Pyeon D. Roles of APOBEC3A and APOBEC3B in Human Papillomavirus Infection and Disease Progression. Viruses. 2017; 9. https://doi.org/10.3390/v9080233 PMID: 28825669
Wallace NA, Münger K. The curious case of APOBEC3 activation by cancer-associated human papillomaviruses. PLOS Pathog. 2018; 14: e1006717. https://doi.org/10.1371/journal.ppat.1006717 PMID: 29324878
Qiu J, Söderlund-Venermo M, Young NS. Human Parvoviruses. Clin Microbiol Rev. 2017; 30: 43-113. https://doi.org/10.1128/CMR.00040-16 PMID: 27806994
Chen KC, Shull BC, Lederman M, Stout ER, Bates RC. Analysis of the termini of the DNA of bovine parvovirus: demonstration of sequence inversion at the left terminus and its implication for the replication model. J Virol. 1988; 62: 3807-3813. https://doi.org/10.1128/JVI.62.10.3807-3813.1988 PMID: 2843676
Sharma S, Patnaik SK, Kemer Z, Baysal BE. Transient overexpression of exogenous APOBEC3A causes C-to-U RNA editing of thousands of genes. RNA Biol. 2017; 14: 603-610. https://doi.org/10.1080/15476286.2016.1184387 PMID: 27149507
Sharma S, Wang J, Alqassim E, Portwood S, Cortes Gomez E, Maguire O, et al. Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells. Genome Biol. 2019; 20: 37. https://doi.org/10.1186/s13059-019-1651-1 PMID: 30791937
Perelygina L, Chen M, Suppiah S, Adebayo A, Abernathy E, Dorsey M, et al. Infectious vaccine-derived rubella viruses emerge, persist, and evolve in cutaneous granulomas of children with primary immunodeficiencies. PLOS Pathog. 2019; 15: e1008080. https://doi.org/10.1371/journal.ppat.1008080 PMID: 31658304
Wang S-M, Wang C-T. APOBEC3G cytidine deaminase association with coronavirus nucleocapsid protein. Virology. 2009; 388: 112-120. https://doi.org/10.1016/j.virol.2009.03.010 PMID: 19345973
Giorgio SD, Martignano F, Torcia MG, Mattiuz G, Conticello SG. Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2. Sci Adv. 2020; eabb5813. https://doi.org/10.1126/sciadv. abb5813 PMID: 32596474
van der Hoek L. Human coronaviruses: what do they cause? Antivir Ther. 2007; 12: 651-658. PMID: 17944272
Hayward JA, Tachedjian M, Cui J, Cheng AZ, Johnson A, Baker ML, et al. Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity. Mol Biol Evol. 2018; 35: 1626-1637. https://doi.org/10.1093/molbev/msy048 PMID: 29617834
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020; 1-13. https://doi.org/10.1038/s41586-020-2286-9 PMID: 32353859
Zhang W, Wang H, Li Z, Liu X, Liu G, Harris RS, et al. Cellular Requirements for BIV Vif-Mediated Inactivation of Bovine APOBEC3 Proteins. J Virol. 2014. https://doi.org/10.1128/JVI.02072-14 PMID: 25142583
Cagliani R, Forni D, Clerici M, Sironi M. Coding potential and sequence conservation of SARS-CoV-2 and related animal viruses. Infect Genet Evol. 2020; 83: 104353. https://doi.org/10.1016/j.meegid.2020. 104353 PMID: 32387562
Cheng AZ, Moraes SN de, Attarian C, Yockteng-Melgar J, Jarvis MC, Biolatti M, et al. A Conserved Mechanism of APOBEC3 Relocalization by Herpesviral Ribonucleotide Reductase Large Subunits. bioRxiv. 2019; 765735. https://doi.org/10.1101/765735
Nagaraju T, Sugden AU, Sugden B. Four-dimensional analyses show that replication compartments are clonal factories in which Epstein-Barr viral DNA amplification is coordinated. Proc Natl Acad Sci. 2019; 116: 24630-24638. https://doi.org/10.1073/pnas.1913992116 PMID: 31744871
Hoopes JI, Cortez LM, Mertz TM, Malc EP, Mieczkowski PA, Roberts SA. APOBEC3A and APOBEC3B Preferentially Deaminate the Lagging Strand Template during DNA Replication. Cell Rep. 2016; 14: 1273-1282. https://doi.org/10.1016/j.celrep.2016.01.021 PMID: 26832400
Seplyarskiy VB, Soldatov RA, Popadin KY, Antonarakis SE, Bazykin GA, Nikolaev SI. APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication. Genome Res. 2016; 26: 174-182. https://doi.org/10.1101/gr.197046.115 PMID: 26755635
Haradhvala NJ, Polak P, Stojanov P, Covington KR, Shinbrot E, Hess JM, et al. Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair. Cell. 2016; 164: 538-549. https://doi.org/10.1016/j.cell.2015.12.050 PMID: 26806129
Kazanov MD, Roberts SA, Polak P, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, et al. APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions. Cell Rep. 2015; 13: 1103-1109. https://doi.org/10.1016/j.celrep.2015.09.077 PMID: 26527001
Vartanian J-P, Henry M, Marchio A, Suspène R, Aynaud M-M, Guétard D, et al. Massive APOBEC3 editing of hepatitis B viral DNA in cirrhosis. PLoS Pathog. 2010; 6: e1000928. https://doi.org/10.1371/journal.ppat.1000928 PMID: 20523896
Kramvis A, Kostaki E-G, Hatzakis A, Paraskevis D. Immunomodulatory Function of HBeAg Related to Short-Sighted Evolution, Transmissibility, and Clinical Manifestation of Hepatitis B Virus. Front Microbiol. 2018; 9. https://doi.org/10.3389/fmicb.2018.02521 PMID: 30405578
Casey JL. Control of ADAR1 Editing of Hepatitis Delta Virus RNAs. In: Samuel CE, editor. Adenosine Deaminases Acting on RNA (ADARs) and A-to-I Editing. Berlin, Heidelberg: Springer; 2012. pp. 123-143. https://doi.org/10.1007/82_2011_146 PMID: 21732238
Nair S, Zlotnick A. Asymmetric Modification of Hepatitis B Virus (HBV) Genomes by an Endogenous Cytidine Deaminase inside HBV Cores Informs a Model of Reverse Transcription. J Virol. 2018; 92. https://doi.org/10.1128/JVI.02190-17 PMID: 29491156
Henderson S, Chakravarthy A, Su X, Boshoff C, Fenton TR. APOBEC-Mediated Cytosine Deamination Links PIK3CA Helical Domain Mutations to Human Papillomavirus-Driven Tumor Development. Cell Rep. 2014; 7: 1833-1841. https://doi.org/10.1016/j.celrep.2014.05.012 PMID: 24910434
Smith NJ, Fenton TR. The APOBEC3 genes and their role in cancer: insights from human papillomavirus. J Mol Endocrinol. 2019; 62: R269-R287. https://doi.org/10.1530/JME-19-0011 PMID: 30870810
Tang K-W, Alaei-Mahabadi B, Samuelsson T, Lindh M, Larsson E. The landscape of viral expression and host gene fusion and adaptation in human cancer. Nat Commun. 2013; 4: 1-9. https://doi.org/10.1038/ncomms3513 PMID: 24085110
Starrett GJ, Buck CB. The case for BK polyomavirus as a cause of bladder cancer. Curr Opin Virol. 2019; 39: 8-15. https://doi.org/10.1016/j.coviro.2019.06.009 PMID: 31336246
Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SAJR, Behjati S, Biankin AV, et al. Signatures of mutational processes in human cancer. Nature. 2013; 500: 415-421. https://doi.org/10.1038/ nature12477 PMID: 23945592
Howley PM, Pfister HJ. Beta genus papillomaviruses and skin cancer. Virology. 2015;479-480: 290-296. https://doi.org/10.1016/j.virol.2015.02.004 PMID: 25724416
Tommasino M. The biology of beta human papillomaviruses. Virus Res. 2017; 231: 128-138. https://doi.org/10.1016/j.virusres.2016.11.013 PMID: 27856220
Viarisio D, Müller-Decker K, Accardi R, Robitaille A, Dürst M, Beer K, et al. Beta HPV38 oncoproteins act with a hit-and-run mechanism in ultraviolet radiation-induced skin carcinogenesis in mice. PLOS Pathog. 2018; 14: e1006783. https://doi.org/10.1371/journal.ppat.1006783 PMID: 29324843
Adamson-Small LA, Ignatovich IV, Laemmerhirt MG, Hobbs JA. Persistent parvovirus B19 infection in non-erythroid tissues: Possible role in the inflammatory and disease process. Virus Res. 2014; 190: 8-16. https://doi.org/10.1016/j.virusres.2014.06.017 PMID: 24998884