This section of the book includes a more diverse collection of infectious agents when compared to the first section. But, in contrast to the acute nature of most RNA virus infections, all of these persist, sometimes over many decades of a host's life.

Two retroviruses are included that primarily infect peripheral cells, but in a minority of patients the retroviruses are brought into the brain as passengers on circulating cells that cross the microvascular endothelium to reach distinct cell types in the central nervous system (CNS). These diseases, HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and neuro-AIDS, caused by human T cell leukemia virus-1 (HTLV-1) (Chapter 8) and human immunodeficiency virus (HIV) (Chapter 9), respectively, are serious clinical problems involving millions of patients. In HTLV-1, it is the host's immune response that leads to the pathology, while with HIV, the progressive loss of immune function leads to susceptibility to opportunistic infections and tumors. Like RNA viruses, the RNA-dependent DNA polymerase (reverse transcriptase) lacks the proofreading function of host DNA replication, and mutations are frequently inserted, which leads to evasion of both host defenses and antiviral drug treatment.

JC virus is a ubiquitous small DNA virus, a papovavirus, but it causes disease in immunocompromised patients (Chapter 10). Most patients today are comorbidly infected with HIV given the sheer numbers of patients with that disease.