Chapter 6- An Introduction to Viruses* *Lecture notes are to be used as a study guide only and do not represent the comprehensive information you will need to know for the exams. 6.1 Overview of Viruses Early Searches for the Tiniest Microbes Viruses are smaller than the cells they infect. The existence of viruses was postulated by Louis Pasteur. In the late 1890 s Ivanoski and Beijerinck showed the existence of the tobacco mosaic virus, along with Loeffler and Frosch s experiment with the virus that causes foot-and-mouth disease in cattle. Years of experiments after these initial discoveries showed that viruses have unique sizes, shapes, and chemical structures. Virology is now a sub-discipline of Microbiology. See 6.1 Making Connections The Position of Viruses in the Biological Spectrum Viruses can infect all types of cells in each Domain. The early history of viruses is unknown, however, it is widely accepted that viruses have been in existence for billions of years. It is estimated that there are more viruses on Earth than even bacterial cells. Viruses have had an important impact on the evolution of the cells in the three (3) Domains. Viruses are described as obligate intracellular parasites that use a specific host cell to replicate. As a result, viruses cause serious damage and disease to the cells they infect. See Table 6.1. There are conflicting theories on what viruses are and are not, but suffice it to say, viruses can cause disease, so they must be dealt with in terms of human health. 6.2 The General Structure of Viruses Size Range Viruses are ultramicroscopic, you need an electron microscope to see them (figure 6.1). Negative staining techniques are used to visualize their external structure and positive staining techniques can visualize proteins and nucleic acids. See Monster Viruses (figure 6.2). 1
Viral Components: Capsids, Nucleic Acids, and Envelopes Viruses lack many of the components seen in cells, even the simplest cell. Viruses contain a nucleic acid core, either DNA or RNA, surrounded by a protein coat. Some viruses have an additional outer layer called an envelope. Also, some viruses carry enzymes in their internal structure that assists them during their infectious process. A nucleocapsid virus is composed of a nucleic acid core and a surrounding protein capsid. These viruses are also called naked viruses (figure 6.4a). Many animal viruses have an envelope, and are called enveloped viruses (figure 6.4b). See also figure 6.10. The Viral Capsid: The Protective Outer Shell The capsid is a prominent geometric feature. The capsid is comprised of smaller units called capsomers. The capsomers can form the shapes helical (rod shaped, figure 6.5 and 6.6), and icosahedral (figure 6.7 and figure 6.8). The Viral Envelope Animal viruses are mostly enveloped viruses, and when they release, they take some of the host cell membrane with them, with the addition of viral membrane proteins. Spikes are extensions from the surface of the virus envelope, and are used to attach to the host cell. Functions of the Viral Capsid/Envelope - Protect the nucleic acid core. - Assist penetration of the host cells - Stimulate an immune response Complex Viruses: Atypical Viruses The poxviruses are covered by lipoproteins and coarse fibrils and the bacteriophages have polyhedral head and tail fibers (figure 6.9). Nucleic Acids: At the Core of a Virus The genome of organisms is expressed through nucleic acids, DNA, RNA. Viruses contain either DNA or RNA, but not both in the viral particle. The structure of the nucleic acid in a virus can vary, ds, ss, segmented, 2
circular. RNA viruses that are immediately translated upon infection of the host cell is called a positive sense RNA virus. An RNA virus that must convert its RNA to a translatable form is called a negative sense RNA virus. Viruses carry just the amount of nucleic acid they need to be infectious in a host cell. Other Substances in the Viral Particle Viruses can carry with them specific enzymes they need to be infectious in a host cell. Enzymes such as polymerases, replicases, and reverse transcriptase in HIV. 6.3 How Viruses Are Classified and Named Viruses are not classified in a Kingdom and/or Domain systems. Viruses are grouped into orders, families, and genera. The common English name is widely used to designate a virus. See Table 6.2. 6.4 Modes of Viral Multiplication Viruses will completely take-over a host cell once it enters. The virus will use the machinery of the host cell to make more viral particles. Multiplication Cycles in Animal Viruses Viruses are intracellular obligate parasites unable to replicate outside of a host cell. Fully formed viruses capable of infecting new host cells are referred to as virions. Once the virion nucleic acid has penetrated the host cell, the replication cycle can proceed via two pathways: the lytic cycle or the lysogenic cycle. Figure 6.11, illustrates the one thing fundamental for all viral pathogens: They must enter a living cell before they can multiply. Viruses have different methods for replicating (once inside a host cell) depending on what type of nucleic acid they carry and whether or not they will be enveloped. 1. Adsorption and Host Range- Viruses adhere to host cell membranes via recognition between spikes and receptors of the host cell (fig. 6.12). The range of host cells that viruses can infect is called host range. This limits the cells viruses can infect. Viruses can also have tropisms, a preference for a cell type. 2. Penetration/Uncoating of Animal Viruses - The entire virus is taken into the animal cell in most cases. With enveloped viruses, the envelope fuses with the cell membrane and the genome and capsid enter the cell. For 3
naked viruses, the virion is endocytosed, then within vesicles (or in the cytoplasm) the capsid breaks down and the nucleic acid is released (fig. 6.13). 3. Synthesis: Replication and Protein Production - RNA synthesis, protein synthesis, and genome replication occur. Because viral genomes are ssdna, dsdna, ssrna, or dsrna, there is a wide variety of methods for transcription, translation and replication. 4. Assembly of Animal Viruses: Host Cell as Factory - During this phase, newly synthesized viral capsids are package with the viral DNA, and virion assembly is completed. 5. Release of Mature Viruses - Many animal viruses become enveloped as they escape from the cell (fig. 6.14). Nonenveloped and complex viruses exit the cell through cell lysis. Enveloped viruses can exit by budding or exocytosis. A virion is a fully formed virus that is ready to infect a host cell. Visible Damage to the Host Cell The cytopathic effects (CPE) are defined as viral induced damages to the host cell. Damages such as: inclusion bodies and cancer (figure 6.15). See CLINICAL CONNECTIONS: PERSISTENT VIRAL INFECTIONS and Table 6.3. 6.5 The Multiplication Cycle in Bacteriophages Viruses that infect bacteria are called bacteriophages(figure 6.16). The most widely studied bacteriophages infect E. coli (figure 6.17 and figure 6.18). Bacteriophages go through similar steps of host cell infection like animal viruses. See Table 6.4. Lysogeny: The Silent Virus Infection When a DNA virus is inside the host cell, it can incorporate its DNA into the host chromosome, and now the virus is called a prophage. The condition in which the bacterial chromosome carries the phage DNA is called lysogeny. The virus can remove itself from the host chromosome in a process called induction. Some phages are responsible for bacteria being pathogenic. This is called lysogenic conversion, such as Vibrio cholera. 4
Once inside the cell, the viral nucleic can take one of two paths: (i) Lytic Phase (fig. 6.16) In the lytic phase, viral DNA is replicated by using host DNA polymerases and other enzymes. As viral DNA copies are being made, those DNA molecules are also being transcribed and translated (once again by using the host enzymes). At this point, the lytic stage proceeds directly to step 4: Assembly & Maturation Unless... a lysogenic state is induced (ii) Lysogenic State (fig. 6.16) In this scenario, the viral DNA does not get replicated and transcribed immediately upon viral penetration of the host cell. Rather, the viral DNA integrates into the host DNA and becomes silent. At this point the virus is called a provirus. Every time the host cell divides, it copies its DNA, and so the viral DNA is copied as well, and passed to each daughter cell. This can continue for many hundreds of generations. This is especially true of DNA viruses and retroviruses (like HIV). Note that this incorporation of viral DNA into host cell DNA can have severe ramifications including cancer in animals. When the time is right (usually cellular stress or a change in environmental conditions), the provirus will become active, the genes will be transcribed and translated and a lytic phase will begin. 6.6 Techniques in Cultivating and Identifying Animal Viruses Methods for culturing viruses are in vitro methods, such as in tissue culture, or in vivo methods, such as inoculating lab animals. The need for culturing viruses are: 1) isolate clinical samples, 2) prepare vaccines, and 3) research. Using Cell (Tissue) Culture Techniques Using isolated animal cells that are grown in sterile chambers called tissue culture flasks. Viruses can affect the cells in the tissue culture by lysing them and/or forming plaques (figure 6.19). 5
Using Bird Embryos Bird embryos are suitable for culturing viruses because they are an already enclosed, sterile system. Bird embryos are often used to make vaccines. Using Live Animal Inoculation Animals such as mice, rats, rabbits, and non-human primates can be used. 6.7 Viral Infection, Detection, and Treatment Viruses are a common cause of acute infections. Not all viral infections result in death, but some do have a high mortality rate such as HIV, Ebola, and rabies. It is essential to have the correct diagnosis for viral infections. Rapid tests, immunofluorescence, PCR, and cell culture techniques can be used to detect viruses in a patient sample. 6.8 Prions and Other Nonviral Infectious Particles Prions are abnormal naked proteins and cause a disease called transmissible spongiform encephalopathies (TSEs). Prions occur in several mammals, such as sheep and goats, cows and humans. Satellite viruses are dependent on other viruses for their replication, and can increase the severity of the primary viral infection. Plants are susceptible to an altered RNA particle called viroids. 6