Ive were cloned and sequenced (Vartanian et al., 2010). G-to-A mutations were

Ive were cloned and sequenced (BQ-123 site Vartanian et al., 2010). G-to-A mutations were observed in HBV minus strands with a sequence context consistent with A3G activity. The remainder of the mutations showed a sequence context more typical of A3C, rather than AID (Vartanian et al., 2010). Deep sequencing also was performed on PCR products obtained in reactions with a 95 denaturation. Four of five samples showed G-to-A hypermutation varying from 10 to 35 in the X gene, which is single-stranded in virions (Vartanian et al., 2010). Taken together with the fact that mutated sequences are rarely recovered by normal high denaturation temperature PCR, the level of HBV hypermutation appears to be significantly lower than that reported for a number of retroviruses. Data from several laboratories have indicated that loss of the pre-capsid (core) antigen may be due to APOBEC-mediated editing (Noguchi et al., 2007; Turelli et al., 2004; Vartanian et al., 2010). Serum samples from 47 HBeAg-positive and 33 HBeAg-negative treatment-na e patients were subjected to deep sequencing (Beggel et al., 2013). Hypermutation rates were ca. 15-fold greater in HBeAg-negative patients and were preferentially in the HBV virionassociated single-stranded region. Similar to other studies, the context of the G-to-A mutations suggested editing by A3G (Beggel et al., 2013; Vartanian et al., 2010). Because pre-core antigen expression is associated with high viremia and the coding region contains several optimal sites for APOBEC-mediated mutation, seroconversion to HBeAg negativity may well represent innate immune selection for particular HBV variants (Beggel et al., 2013; Vartanian et al., 2010). Interestingly, transfusion-transmitted virus (TTV) found in the blood of healthy patients and in HBV carriers contains G-to-A hypermutations, indicating that viruses that lack reverse transcriptase can be subjected to APOBEC family restriction (Tsuge et al., 2010). TTV is a single-stranded negative-sense DNA virus, which is predicted to be a good target for A3 enzymes (Irshad et al., 2006). In addition, single-stranded DNA viruses belonging to the parvovirus family can be restricted by APOBEC, particularly A3A (Chen et al., 2006; Narvaiza et al., 2009). Curiously, two different parvoviruses are inhibited by A3A, suggesting a conserved mechanism, yet inhibition appears independent of catalytic activity (Narvaiza et al., 2009).Author Manuscript Author Manuscript Author Manuscript Author ManuscriptVirology. Author manuscript; available in PMC 2016 May 01.Harris and DudleyPageDouble-stranded DNA viruses also may also be substrates for APOBEC family members. Double-stranded DNA viruses may yield exposed single-stranded DNA during transcription or genome replication. Human GW9662 chemical information papilloma viruses (HPVs) for example are sexually transmitted, and about 24 of the 300 genotypes are associated with human cancers (zur Hausen, 2008). HPV types 1a and 16 in plantar skin warts and precancerous cervical lesions were shown to have hypermutations (Vartanian et al., 2008). A3A, A3B, and A3H are expressed in keratinocytes, where HPV has been shown to replicate. Further, co-transfection experiments have shown that overexpression of these enzymes could induce HPV hyperediting (Vartanian et al., 2008). Recent studies also have documented APOBEC-mediated 5-TC-to-TT hypermutation signatures in numerous cancers, including HPV-associated cervical and head-and-neck squamous cell carcinomas (HNSCCs) (Alexandrov et al.,.Ive were cloned and sequenced (Vartanian et al., 2010). G-to-A mutations were observed in HBV minus strands with a sequence context consistent with A3G activity. The remainder of the mutations showed a sequence context more typical of A3C, rather than AID (Vartanian et al., 2010). Deep sequencing also was performed on PCR products obtained in reactions with a 95 denaturation. Four of five samples showed G-to-A hypermutation varying from 10 to 35 in the X gene, which is single-stranded in virions (Vartanian et al., 2010). Taken together with the fact that mutated sequences are rarely recovered by normal high denaturation temperature PCR, the level of HBV hypermutation appears to be significantly lower than that reported for a number of retroviruses. Data from several laboratories have indicated that loss of the pre-capsid (core) antigen may be due to APOBEC-mediated editing (Noguchi et al., 2007; Turelli et al., 2004; Vartanian et al., 2010). Serum samples from 47 HBeAg-positive and 33 HBeAg-negative treatment-na e patients were subjected to deep sequencing (Beggel et al., 2013). Hypermutation rates were ca. 15-fold greater in HBeAg-negative patients and were preferentially in the HBV virionassociated single-stranded region. Similar to other studies, the context of the G-to-A mutations suggested editing by A3G (Beggel et al., 2013; Vartanian et al., 2010). Because pre-core antigen expression is associated with high viremia and the coding region contains several optimal sites for APOBEC-mediated mutation, seroconversion to HBeAg negativity may well represent innate immune selection for particular HBV variants (Beggel et al., 2013; Vartanian et al., 2010). Interestingly, transfusion-transmitted virus (TTV) found in the blood of healthy patients and in HBV carriers contains G-to-A hypermutations, indicating that viruses that lack reverse transcriptase can be subjected to APOBEC family restriction (Tsuge et al., 2010). TTV is a single-stranded negative-sense DNA virus, which is predicted to be a good target for A3 enzymes (Irshad et al., 2006). In addition, single-stranded DNA viruses belonging to the parvovirus family can be restricted by APOBEC, particularly A3A (Chen et al., 2006; Narvaiza et al., 2009). Curiously, two different parvoviruses are inhibited by A3A, suggesting a conserved mechanism, yet inhibition appears independent of catalytic activity (Narvaiza et al., 2009).Author Manuscript Author Manuscript Author Manuscript Author ManuscriptVirology. Author manuscript; available in PMC 2016 May 01.Harris and DudleyPageDouble-stranded DNA viruses also may also be substrates for APOBEC family members. Double-stranded DNA viruses may yield exposed single-stranded DNA during transcription or genome replication. Human papilloma viruses (HPVs) for example are sexually transmitted, and about 24 of the 300 genotypes are associated with human cancers (zur Hausen, 2008). HPV types 1a and 16 in plantar skin warts and precancerous cervical lesions were shown to have hypermutations (Vartanian et al., 2008). A3A, A3B, and A3H are expressed in keratinocytes, where HPV has been shown to replicate. Further, co-transfection experiments have shown that overexpression of these enzymes could induce HPV hyperediting (Vartanian et al., 2008). Recent studies also have documented APOBEC-mediated 5-TC-to-TT hypermutation signatures in numerous cancers, including HPV-associated cervical and head-and-neck squamous cell carcinomas (HNSCCs) (Alexandrov et al.,.