Background and Aims HBV can integrate in the host genome of the hepatocyte and recent findings suggest that integrated HBV contributes to the persistent production of viral proteins. Here, we quantified the levels of integrated HBV in patients with chronic hepatitis B (CHB) and analyzed the relation between HBV integration, virological activity (plasma HBV DNA and HBsAg levels), and clinical outcomes. Approach and Results We developed and validated a multistep Arthrobacter luteus (Alu)‐PCR that specifically amplifies integrated HBV and RT‐Alu‐PCR detecting mRNA transcripts derived from integrated HBV. Pretreatment liver biopsy samples and baseline characteristics of 124 patients with CHB either treated for 48 weeks with pegylated interferon plus adefovir or tenofovir or receiving no treatment were available for analysis. Integrated HBV sequences containing open reading frame S and X (but not C) and S and X mRNA transcripts derived from integrated HBV could be detected and quantified in liver biopsies. Integrated HBV levels correlated with HBV DNA, HBsAg, alanine aminotransferase plasma levels, and the liver histology activity index but not to levels of intrahepatic covalently closed circular DNA (cccDNA), plasma pregenomic RNA, or hepatitis B core‐related antigen. Multivariable logistic regression analysis showed that lower baseline HBV integration levels were independently associated with HBsAg loss (functional cure) within 5 years follow‐up. Conclusions Integrated HBV levels are strongly correlated with surrogate markers for virological activity but not to cccDNA levels and are predictive for HBsAg loss. Our data suggest that integrated HBV is closely related to HBV replication and may therefore be an important tool in the evaluation and development of treatment modalities aiming to cure CHB.

Anti-phage defence systems in bacterial genomes have a vast intra- and inter-species diversity. Here we investigated whether combinations of defence systems are selected for or against due to the effects of anti-phage protection. Analysis of defence system co-occurrence in Escherichia coli genomes revealed that positive and negative co-occurrences are common, and surprisingly both can provide synergistic anti-phage activities. Furthermore, we did not find conserved patterns of defence system co-occurrence across bacterial taxa. This suggests that the selection of strains carrying defence system combinations is more likely a consequence of environmental conditions than mechanistic incompatibilities between defence systems. Additionally, we showed that Gabija and Zorya type II can sense the anti-restriction protein Ocr to activate defence, and that phages also make use of these shared sensing mechanisms to evade multiple defence systems with a single escape strategy. Together, our results highlight the complex co-evolutionary dynamics of phage defence and anti-defence.