Comprehensive genetic and epigenetic analysis of occult hepatitis B from liver tissue samples

Background. Occult infection with hepatitis B virus (HBV) is a type of chronic HBV infection that is characterized by the absence of a detectable hepatitis B surface antigen in the blood and by very low levels of HBV DNA in the blood and liver. The mechanisms leading to occult HBV infection remain poorly understood but include possible genetic mutations and deletions. Recently, it has been shown that HBV has CpG islands that are methylated, raising the possibility that epigenetic changes may also be important. Methods. The full-length genomes of isolates from 5 cases of occult HBV infection were cloned and analyzed for mutations and deletions. Additional studies were performed to examine for APOBEC3G (1 member of a family of deaminating proteins that are part of the innate immune system's defense against viral infection) hyperediting and methylation of viral DNA. Results. Numerous mutations and deletions were found in the genomes of occult HBV. However, similar types and locations of polymorphisms were also noted in the genome sequences of HBV isolated from control liver tissue samples obtained from individuals with nonoccult HBV infection. Evidence of APOBEC3G hyperediting was found in 1 case of occult HBV infection, but hyperedited sequences made up only a small proportion of the viral sequences. Methylation of HBV CpG islands 1 and 2 was evident in both occult and nonoccult HBV sequences, with island 2 more densely methylated in occult HBV sequences and island 1 more densely methylated in nonoccult HBV sequences. Conclusion. Deletions and mutations are common in occult HBV but are also found in control nonoccult HBV, and no unique genetic signature for occult HBV was found. Methylation patterns differ between cases of occult and nonoccult HBV infection, suggesting that epigenetic changes may be relevant to occult HBV. Together, these findings suggest that multiple mechanisms can contribute to occult HBV infection.