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Various patterns of replication as applied to specific viruses, as well as the effect of viral infections on the host cell and organism, are the subject of many of the following chapters in this book. The best way to begin to understand patterns of virus replication is to consider a simple general case: the productive infection cycle – this is shown schematically in Figure 2.2. A number of critical events are involved in this cycle. The basic pattern of replication is as follows:

1 The virus specifically interacts with the host cell surface, and the viral genome is introduced into the cell. This involves specific recognition between virus surface proteins and specific proteins on the cell surface (receptors) in animal and bacterial virus infections.

2 Viral genes are expressed using host cell processes. This viral gene expression results in synthesis of a few or many viral proteins involved in the replication process.

3 Viral proteins modify the host cell and allow the viral genome to replicate using host and viral enzymes. While this is a simple statement, the actual mechanisms by which viral enzymes and proteins can subvert a cell are manifold and complex. This is often the stage at which the cell is irreversibly modified and eventually killed. Much modern research in the molecular biology of virus replication is directed toward understanding these mechanisms.

4 New viral coat proteins assemble into capsids, and viral genomes are included. The process of assembly of new virions is relatively well understood for many viruses. The successful description of the process has resulted in a profound linkage of knowledge about the principles of macromolecular structures, the biochemistry of protein–protein and protein–nucleic acid interactions, and the thermodynamics of large macromolecule structures.Figure 2.2 The virus replication cycle. Most generally, virus replication can be broken into the stages shown: (a) initial recognition between virus and cell and introduction of viral genetic material into the host cell, (b) virus gene expression and induction of virus‐induced modification of host, allowing (c) virus genome replication. Following this, (d) virus‐associated proteins are expressed, and (e) new virus is assembled and released, often resulting in cell death.

5 Virus is released where it can infect new cells and repeat the process. This is the basis of virus spread, whether from cell to cell or from individual to individual. Understanding the process of virus release requires knowledge of the biochemical interactions between cellular organelles and viral structures. Understanding the process of virus spread between members of a population requires knowledge of the principles of epidemiology and public health.