Chapter 5: Viruses

Virology encompasses the study of viruses as obligate intracellular parasites that rely entirely on host cell machinery to replicate and survive, a fundamental distinction that defines viral biology. Viruses are classified through multiple systems, including the hierarchical ICTV framework that organizes viruses into orders and families, and the Baltimore classification scheme that categorizes viruses based on genome composition (DNA or RNA configurations and their polarity) and the intermediary steps required to generate messenger RNA for protein synthesis. Structurally, all virions contain a genome surrounded by a protein capsid composed of individual capsomere units, with enveloped viruses additionally possessing a lipid membrane derived from host cells and embedded with glycoprotein spike structures that mediate initial contact with target cells. Viral replication pathways differ significantly between bacteriophages and animal viruses; bacteriophages either enter a lytic cycle that terminates in host cell rupture and phage release, or establish lysogeny through integration of the prophage into the bacterial chromosome for dormant persistence. Animal virus infection follows a sequential progression involving adsorption to host receptors, membrane penetration, uncoating to release the genome into the cytoplasm, replication of genetic material and protein components, assembly of progeny virions, and eventual cell exit through budding or lysis. Infections manifest along a spectrum from acute lytic infections causing rapid cell death with visible cytopathic effects to chronic and latent persistent infections where viral replication continues or remains dormant within host cells. Major viral families include DNA viruses such as herpesviruses and poxviruses, as well as RNA viruses including orthomyxoviruses and retroviruses that employ reverse transcriptase to synthesize DNA from an RNA template. Beyond conventional viruses, the chapter addresses subviral agents including viroids as small circular RNA plant pathogens, virusoids as defective particles requiring co-infection by helper viruses, and prions as infectious proteinaceous particles that cause transmissible spongiform encephalopathies through aberrant protein misfolding and propagation within nervous tissue.