34 Viruses. Viruses are parasites that afflict every twig on the tree of KEY CONCEPTS

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1 FREEMC34_ _FP_ /28/04 9:24 AM Page Viruses KEY CONCEPTS Viruses are tiny, noncellular parasites that infect virtually every type of cell known. They cannot perform metabolism on their own meaning outside a parasitized cell and are not considered to be alive. Different types of viruses are specialized for infecting particular species and types of cells. Viruses are highly diverse in overall morphology and in the nature of their genetic material. The genomes of viruses may consist of double-stranded DNA, single-stranded DNA, double-stranded RNA, or one of several types of singlestranded RNA. The viral infection cycle can be broken down into five steps: (1) entry into a host cell, (2) replication of the viral genome, (3) the production of viral proteins, (4) the assembly of a new generation of virus particles, and (5) exit from the infected cell. Photomicrograph created by treating seawater with a fluorescing compound that binds to nucleic acids. The smallest, most abundant dots are viruses. The larger, numerous spots are bacteria and archaea. The largest splotches are protists. Viruses are parasites that afflict every twig on the tree of life. They are not cells and are not made up of cells, so they are not considered organisms. They cannot manufacture their own ATP or carbon-containing compounds, and they cannot make copies of themselves. Viruses enter a host cell, take over its biosynthetic machinery, and use that machinery to manufacture a new generation of viruses. Outside of cells, viruses simply exist they cannot do anything. A virus is an obligate, intracellular parasite. The adjective obligate is appropriate because viruses cannot replicate unless they enter the inside of a cell. Because they are not organisms, viruses are referred to as particles or agents and are not given scientific 1genus + species2 names. Most biologists would argue that viruses are not even alive. Yet viruses have a genome, they are superbly adapted to exploit the metabolic capabilities of their host cells, and they evolve. Table 34.1 summarizes some characteristics of viruses. The diversity and abundance of viruses almost defy description. Nearly all organisms examined thus far are parasitized by at least one kind of virus. The bacterium Escherichia coli, which resides in the human intestine, is afflicted by more than a dozen types of bacteriophage (literally, bacteria-eater ). A bacteriophage is a virus that infects bacteria. The ocean s plankton teems with bacteria and archaea, yet viruses outnumber them in this habitat by a factor of 10 to 1. A wine bottle filled with seawater taken from the ocean s surface contains about 10 billion virus particles almost double the world s population of humans. 780

2 FREEMC34_ _FP_ /28/04 9:24 AM Page 781 Chapter 34 Viruses 781 TABLE 34.1 Characteristics of Viruses versus Characteristics of Organisms Viruses Organisms Hereditary DNA or RNA; can DNA; always material be single stranded double stranded or double stranded Plasma No Yes membrane present? Can carry out No even if a viral Yes transcription independently? polymerase is present, transcription of viral genome requires use of ATP and nucleotides provided by host cell Can carry out No Yes translation independently? Metabolic Virtually none Extensive capabilities synthesis of ATP, reduced carbon compounds, vitamins, lipids, nucleic acids, etc. Brain and CNS encephalitis rabies polio herpes zoster yellow fever Ebola dengue West Nile Lymphatic system Epstein-Barr HIV paramyxovirus (e.g., measles) Trachea and lungs parainfluenza RSV influenza adenovirus Heart coxsackie 34.1 Why Do Biologists Study Viruses? Any study of life s diversity would be incomplete unless it included a look at the acellular parasites that exploit that diversity. But viruses are also important from a practical standpoint. To health-care workers, agronomists, and foresters, these parasites are a persistent and sometimes catastrophic source of misery and economic loss. The nature of viruses has been understood only since the 1940s, but they have been the focus of intense research ever since. Biologists study viruses because they cause illness and death. In the human body, virtually every system, tissue, and cell can be infected by one or more kinds of virus (Figure 34.1). Research on viruses is motivated by the desire to minimize the damage they can cause. In addition, biologists study viruses with the goal of exploiting their ability to enter cells. Recall from Chapter 19 that viruses are being tested as possible therapeutic agents in the treatment of genetic diseases. If viruses can be engineered to carry normal copies of human genes into the cells of patients, it is possible that the gene products could cure symptoms. Recent Viral Epidemics in Humans Physicians and researchers use the term epidemic ( uponpeople ) to describe a disease that affects a large number of people at the same time. Viruses have caused the most devastating epidemics in recent human history. During the eighteenth and nineteenth centuries, it was not unusual for Native American tribes to lose 90 percent of their members over the course Digestive tract and liver hepatitis A, B, C, D, E rotavirus Blood vessels and blood cells erythrovirus Ebola hantavirus Reproductive organs herpes 2 papillomavirus Skin rubella variola papillomavirus herpes 1 molluscum contagiosum Skeletal muscles coxsackie Peripheral nerves rabies FIGURE 34.1 Human Organs and Systems That Are Parasitized by Viruses EXERCISE Choose two viruses that you are familiar with. Next to each, write the symptoms caused by an infection with this virus.

3 FREEMC34_ _FP_ /28/04 9:24 AM Page Unit 6 The Diversification of Life of a few years to measles, smallpox, and other viral diseases spread by contact with European settlers. In terms of global impact, the influenza outbreak of , called Spanish flu, qualifies as the most devastating epidemic recorded to date. Influenza is a virus that infects the upper respiratory tract. The strain of influenza virus that emerged in 1918 infected people worldwide and was particularly virulent meaning it tended to cause severe disease. Within hours of showing symptoms, the lungs of previously healthy people often became so heavily infected that affected individuals suffocated to death. Most victims were between the ages of 20 and 40. The viral outbreak occurred just as World War I was drawing to a close and killed far more people than did the conflict itself. For example, ten times as many Americans died of influenza than were killed in combat in the war. Worldwide, the Spanish flu may have killed over 50 million people. Current Viral Epidemics in Humans: HIV In terms of the total number of people affected, the measles and smallpox epidemics among native peoples and the 1918 influenza outbreak are almost certain to be surpassed by the incidence of AIDS. Acquired immune deficiency syndrome (AIDS) is an affliction caused by the human immunodeficiency virus (HIV; Figure 34.2). Relatively little is known about the strain of influenza that caused the Spanish flu epidemic of , but HIV is far and away the most intensively studied of all viruses. Since the early 1980s, governments and private corporations from around the world have spent hundreds of millions of dollars on HIV research. More biologists 1 µm FIGURE 34.2 The Human Immunodeficiency Virus (HIV) Colorized scanning electron micrograph showing HIV particles (red) emerging from an infected human T cell (green). Helper T cells in bloodstream (cells per mm 3 blood) Acute phase Rapid decline Chronic phase Gradual decline AIDS Onset of AIDS Onset Death Weeks Years FIGURE 34.3 T-Cell Counts Decline during an HIV Infection Graph of changes in the number of T cells that are present in the bloodstream over time, based on data from a typical patient infected with HIV. The acute phase of infection occurs immediately after infection and is sometimes associated with symptoms such as fever. Infected people usually show no disease symptoms in the chronic phase, even though their T-cell counts are in slow, steady decline. AIDS typically occurs when T-cell counts dip below 200/mm 3 of blood. are working on HIV than on any other type of virus. Given this virus s current and projected impact on human populations around the globe, the investment is justified. How Does HIV Cause Disease? Like other viruses, HIV parasitizes specific types of cells. The cells most affected by HIV are called helper T cells and macrophages. These cells are components of the immune system, which is the body s defense system against disease. Chapter 49 explains just how crucial helper T cells and macrophages are to the immune system s response to invading bacteria and viruses. If an HIV particle succeeds in infecting one of these cells and reproducing inside, however, the cell dies as hundreds of new particles break out and infect more cells. Although the body continually replaces helper T cells and macrophages, the number produced does not keep pace with the number being destroyed by HIV. As a result, the total number of helper T cells in the bloodstream gradually declines as an HIV infection proceeds (Figure 34.3). When the T-cell count drops, the immune system s responses to invading bacteria and viruses become less and less effective. Eventually, too few helper T cells are left to fight off pathogens efficiently, and pathogenic bacteria and viruses begin to multiply unchecked. In almost all cases, one or more of these infections prove fatal. HIV kills people indirectly by making them susceptible to pneumonia, fungal infections, and unusual types of cancer. What Is the Scope of the AIDS Epidemic? Researchers with the United Nation s AIDS program estimate that AIDS

4 FREEMC34_ _FP_ /28/04 9:25 AM Page 783 Chapter 34 Viruses 783 North America 1,000,000 Eastern Europe and Central Asia 1,300,000 Caribbean 430,000 Western Europe 580,000 North Africa and Middle East 480,000 Asia and Pacific Islands 7,400,000 Latin America 1,600,000 Australia and Sub-Saharan Africa 25,000,000 New Zealand 32,000 Total infected: 37,800,000 FIGURE 34.4 Geographic Distribution of HIV Infections Data, compiled by the World Health Organization, showing the numbers of people living with HIV in July 2004, by geographic area. has already killed 25 million people worldwide. HIV infection rates have been highest in east and central Africa, where one of the greatest public health crises in history is now occurring (Figure 34.4). In Botswana and elsewhere, blood-testing programs have confirmed that up to a third of all adults carry HIV. Although there may be a lag of as much as 8 12 years between the initial infection and the onset of illness, virtually all people who become infected with the virus will die of AIDS. Currently, the UN estimates the total number of HIV-infected people worldwide at about 38 million. An additional 5 million people are infected each year, and the epidemic is growing. Researchers are particularly alarmed because the focus of the epidemic is shifting from its historical center of incidence central and southern Africa to south and east Asia. Infection rates are growing as much as 17 percent per year in some of the world s most populous countries particularly India, China, Russia, Ethiopia, and Nigeria. If present trends continue, 80 million more people will be infected by Most viral and bacterial diseases afflict the very young and the very old. But because HIV is a sexually transmitted disease, young adults are most likely to contract the virus and die. People who become infected in their late teens or twenties die of AIDS in their twenties or thirties. Tens of millions of people are being lost in the prime of their lives. Physicians, politicians, educators, and aid workers all use the same word to describe the epidemic s impact: staggering How Do Biologists Study Viruses? Researchers who study viruses focus on two goals: (1) developing vaccines that allow hosts to fight off disease if they become infected and (2) developing antiviral drugs that prevent a virus from replicating efficiently inside the host. Both types of research begin with attempts to isolate the virus in question. Isolating viruses takes researchers into the realm of nanobiology, in which structures are measured in billionths of a meter. (One nanometer, abbreviated nm, is 10-9 meter. ) Viruses are typically 50 to 100 nm in diameter. They are dwarfed by eukaryotic cells; millions of viruses can fit on the head of a pin. If virus-infected cells can be grown in culture or harvested from a host individual, researchers can usually isolate the virus by passing the cells through a filter. The filters used to study viruses have pores that are large enough for viruses to pass through but are too small to admit cells. To test the hypothesis that the solution that passes through the filter contains viruses that cause a specific disease, researchers expose uninfected host cells to this filtrate. If the virus-causation hypothesis is correct, then exposing host cells to the filtrate will result in infection. In this way, researchers can isolate a virus and confirm that it is the causative agent of infection. Recall from Chapter 27 that these steps are inspired by Koch s postulates, which established the criteria for linking a specific infectious agent with a specific disease.

5 FREEMC34_ _FP_ /28/04 9:25 AM Page Unit 6 The Diversification of Life (a) Virus particles (green dots) (b) Bacterial cells (c) Eukaryotic cell 0.2 µm 1 µm 1 µm Relative sizes FIGURE 34.5 Viruses Are Tiny (a) Viruses are much smaller than (b) bacterial cells or (c) eukaryotic cells. Notice the scale bars on each micrograph. Once biologists have isolated a virus, how do they study and characterize it? Let s begin with morphological traits, then consider how viral life cycles vary. Analyzing Morphological Traits To see a virus, researchers usually rely on transmission electron microscopy (Figure 34.5). Only the very largest viruses, such as the smallpox virus, are visible with a light microscope. Electron microscopy has revealed that viruses come in a wide variety of shapes, and many viruses can be identified by shape alone (Figure 34.6). In overall structure, however, they fall into just two general categories. Viruses can either be (1) enclosed by just a shell of protein called a capsid or (2) enclosed by both a capsid and a membrane-like envelope. Regarding their morphology, then, the important distinction among viruses is whether they are nonenveloped or enveloped. Nonenveloped viruses have an extremely simple structure. They consist of genetic material and possibly one or more enzymes inside a capsid a protein coat. The nonenveloped virus illustrated in Figure 34.7a is an adenovirus. You undoubtedly have adenoviruses on your tonsils or in other parts of your upper respiratory passages right now. (a) Tobacco mosaic virus (d) Bacteriophage T nm (b) Adenovirus (c) Influenza virus 100 nm 25 nm 50 nm FIGURE 34.6 Viruses Vary in Size and Shape Virus shapes include (a) rods, (b) polyhedrons, (c) spheres, and (d) complex shapes with heads and tails.

6 FREEMC34_ _FP_ /28/04 9:25 AM Page 785 Chapter 34 Viruses 785 (a) Nonenveloped virus (b) Enveloped virus Genome Capsid (protein) Enveloped viruses are slightly more complex. They also have genetic material inside a capsid, but the capsid is surrounded by an envelope. The envelope consists of a phospholipid bilayer with a mixture of viral proteins and proteins derived from the plasma membrane of a host cell specifically, the host cell in which the virus particle was manufactured. The enveloped virus illustrated in Figure 34.7b is HIV. Once a virus has been isolated and its overall morphology characterized, researchers usually focus on understanding the nature of the virus s replication cycle and on attempts to develop a vaccine. A vaccine is a preparation that primes a host s immune system to respond to a specific type of virus. Box 34.1 explains how vaccines work and why it has not been possible to develop a vaccine for certain viruses particularly the cold virus or HIV. Here let s focus on variation in virus replication cycles. Genome Capsid (protein) Envelope (phospholipid bilayer) FIGURE 34.7 Viruses Are Nonenveloped or Enveloped (a) A protein coat forms the exterior of nonenveloped viruses. (b) In enveloped viruses, the exterior is composed of a membranous sphere. Inside this envelope, the hereditary material is enclosed by a protein coat. Analyzing Variation in Replication Cycles: Lytic and Lysogenic Growth Although it is likely that millions of types of virus exist, they all infect their host cells in one of two general ways: lytic growth or lysogenic growth. All viruses undergo lytic growth; some can grow lysogenically as well. Both types of viral infection begin when part or all of a virus particle enters the interior of a host cell. Figure 34.9a shows a lytic replication cycle. During lytic growth, the viral genome enters the host cell and viral or host enzymes make copies of it, using nucleotides and ATP provided by the host. The host cell also manufactures viral proteins. When synthesis of the viral genome and viral proteins is complete, a new generation BOX 34.1 How Are Vaccines Developed? As Chapter 49 will show, one of the primary ways that an individual s immune system responds to parasite attack is through the production of antibodies. An antibody ( against-body ) is a protein that binds with high specificity to a particular site on another molecule. That is, an antibody will bind only to one particular site on one particular compound. Any molecule that elicits the production of antibodies is considered to be an antigen ( against-produce ). Vaccines contain antigens. The antigens are usually components of a virus s exterior the capsid from a nonenveloped virus or the envelope proteins from an enveloped virus. Exterior proteins are effective antigens because they are the part of the virus that is seen by the immune system cells. To vaccinate a person or a domestic animal, viral antigens are injected or swallowed. Once inside the individual, the antigens stimulate immune system cells called B cells (see Chapter 49), which produce antibodies to the antigen (Figure 34.8, page 786). Once antigens are coated with antibodies, the antigens are destroyed by other cells and components of the immune system. Vaccinations are like fire drills or earthquake preparedness drills they prepare the immune system to respond to a specific type of threat. In effect, they are a faked infection. Immune system cells that are stimulated to produce antibodies by a vaccination remain active in the vaccinated person for a long time often for life. If a vaccinated person is later exposed to active virus particles, the immune system can respond quickly and effectively enough to stop the infection before it threatens the individual s health. In many cases, vaccines have been spectacularly successful at curbing or (Continued on next page)

7 FREEMC34_ _FP_ /28/04 9:25 AM Page Unit 6 The Diversification of Life (Box 34.1 continued) even eliminating viral diseases in humans and domestic animals. In humans alone, effective vaccines have been developed against smallpox, yellow fever, polio, measles, and some forms of hepatitis. These diseases used to kill or sicken hundreds of thousands of people each year. There Are Two General Types of Vaccines Successful vaccines consist of inactivated viruses or attenuated viruses. An inactivated virus is not capable of causing an infection, because its genes have been damaged by chemical treatments often exposure to formaldehyde or irradiation with ultraviolet light. If you have been vaccinated for hepatitis A or flu, you have received an inactivated virus. Attenuated viruses are also called live virus vaccines, because they consist of complete virus particles. The adjective attenuated means that they lack virulence. Researchers can make a virus harmless to a host by culturing the virus on cells from species other than that host. In adapting to growth on the atypical cells, viral strains usually lose the ability to grow rapidly in their normal host cells. Although attenuated viruses still provoke a strong immune response, they are not capable of sustaining an infection in a vaccinated individual. The smallpox, polio, and measles vaccines consist of attenuated viruses. Researchers have not succeeded in developing vaccines against the common cold or HIV and have been only moderately successful in developing a vaccine against flu viruses. The reason is that cold and flu viruses and HIV have exceptionally high mutation rates. HIV actually has the highest mutation rate observed in any organism or virus. Why does a high mutation rate make vaccine development so difficult? Recall from Chapter 16 that a mutation is defined as a change in DNA. Because the enzymes that copy the genes found in cold and flu viruses and HIV are exceptionally error prone, many of the mature virus particles (virions) that are produced contain mutations in the genes for the virus s envelope proteins. When this DNA is transcribed and translated, the envelope proteins that result are likely to have an altered structure. Due to the high mutation rates of cold and flu viruses and HIV, the envelope proteins in these viruses constantly change through time. Stated another way, new strains of these viruses are constantly evolving. The antibodies HOW VACCINATION WORKS The antigens are usually protein components of a virus capsid or envelope produced against the envelope proteins of earlier strains do not work against strains that appear later, because the envelope proteins of the strains are different. A vaccination that protected an individual against certain strains of cold or flu virus or HIV would not help against other strains. To date, it has not been possible to design antigens from the cold or flu viruses or HIV that protect vaccinated individuals effectively. In the fight against HIV, drugs that inhibit viral enzymes and thus stop or slow viral replication have been much more successful than vaccination efforts. 1. Viral antigens are introduced into the body. 2. Certain immune system cells recognize antigens. 3. These cells stimulate other immune system cells to produce antibodies to the virus. Why Isn t There a Vaccine for Cold Virus, HIV, and the Flu Viruses? The cells that produce these specific antibodies remain active for a long time often for life 4. Later, if the host is exposed to live virus particles, the particles will be coated with antibodies and destroyed by immune system cells. FIGURE 34.8 Vaccination Induces a Response from the Immune System The immune system cells that respond to a vaccination are immortalized, meaning that they stay active for a long time. Thus, the body can respond quickly to any future infections by the same virus.

8 FREEMC34_ _FP_ /28/04 9:25 AM Page 787 Chapter 34 Viruses of virus particles assembles inside the host. A mature virus particle is called a virion. The infection ends when the viral agents exit the cell usually killing the host cell in the process. Figure 34.9b diagrams a lysogenic replication cycle, or lysogeny. Only certain types of viruses are capable of lysogenic growth. Although HIV and some other viruses that infect humans are capable of lysogeny, most lysogenic viruses infect bacteria. Recall that viruses that infect bacteria are called bacteriophages. In these viruses, lysogeny is an important variation on the lytic replication cycle. During lysogenic growth, viral DNA becomes incorporated into the host s chromosome. Often this integration occurs without serious damage to the host cell. Once the viral genome is in place, it is replicated by the host s DNA polymerase each time the cell divides. Copies of the viral genome are passed on to daughter cells just like one of the host s own genes. In the lysogenic state, a virus is usually latent, or quiescent. This means that no new particles are being produced and no unrelated cells are being infected. The virus is transmitted from one generation to the next along with the host s genes. In bacteriophages, lysogenic growth is typical when an infected bacterium is growing and dividing rapidly; the viral population then grows along with the bacterial population. But if the infected bacterium is damaged by sunlight or a toxin or if the host begins to starve, then the virus switches from lysogenic to lytic growth. To explain this observation, biologists point to the adaptive value of the switch between lytic and lysogenic replication cycles. If a bacterium is growing and dividing rapidly, then a virus s fitness is maximized through lysogenic growth. But if a bacterium is likely to stop growing or die, then a virus s fitness is maximized through lytic growth. It is not possible to treat a lysogenic infection with drugs, because the viruses are quiescent they just sit there. But even lytic infections are notoriously difficult to treat, because viruses use so many of the host cell s enzymes during the lytic replication cycle. Drugs that disrupt these enzymes usually harm the host much more than they harm the virus. To understand viral diversity and how antiviral drugs are developed, let s consider each phase of the lytic cycle in more detail. (a) LYTIC REPLICATION RESULTS IN A NEW GENERATION OF VIRUS PARTICLES AND THE DEATH OF THE HOST CELL. Host-cell genome Virus particle DNA mrna 1. Viral genome enters host cell. 2. Viral genome is replicated and transcribed. DNA Protein Free particles in tissue or environment 3. Viral mrnas are translated, and proteins processed. 5. Particles exit to exterior. 4. Particles assemble inside host. (b) LYSOGENIC REPLICATION RESULTS IN VIRUS GENES BEING TRANSMITTED TO DAUGHTER CELLS OF THE HOST. 1. Viral genome enters host cell. 2. Viral genome integrates into hostcell genome Host-cell DNA polymerase copies chromosome. 4. Cell divides. Virus is transmitted to daughter cells. FIGURE 34.9 Viruses Replicate via Lytic or Lysogenic Cycles, or Both (a) All viruses follow the same general lytic replication cycle. (b) Some viruses are also capable of lysogeny, meaning that their genome can become integrated into the host-cell chromosome. EXERCISE Compare and contrast a lysogenic virus to the transposable elements introduced in Chapter 20.

9 FREEMC34_ _FP_ /28/04 9:25 AM Page Unit 6 The Diversification of Life WEB TUTORIAL 34.1 The HIV Life Cycle Analyzing the Phases of the Lytic Cycle Five phases are common to lytic growth in virtually all viruses: (1) entry into a host cell, (2) replication and transcription of the viral genome, (3) production and processing of viral proteins, (4) assembly of a new generation of virions, and (5) exit from the infected cell. Each virus has a particular way of entering a host cell and completing the subsequent phases of the lytic cycle. Let s take a closer look. How Do Viruses Enter a Cell? The replication cycle of a virus begins when a free viral particle enters a target cell. This is no simple task. All cells are protected by a plasma membrane, and many cells also have a cell wall. How do viruses breach these defenses, insert themselves into the cytoplasm inside, and begin an infection? Most plant viruses enter host cells after a sucking insect, such as an aphid, has disrupted the cell wall with its mouthparts. In contrast, viruses that parasitize bacterial cells or that attack animal cells gain entry by binding to a specific molecule on the cell wall or plasma membrane. In response to this binding event, the genome of a nonenveloped virus enters the host cell, while the capsid remains on the cell wall or plasma membrane. When enveloped viruses bind to a host cell, the capsid enters the cell. To appreciate how investigators identify the proteins that viruses use to enter host cells, consider research on HIV. In 1981 right at the start of the AIDS epidemic biomedical researchers realized that people with AIDS had few or no T cells possessing CD4, a particular membrane protein. These cells are symbolized CD4 +. This discovery led to the hypothesis that CD4 functions as the doorknob that HIV uses to enter host cells. The doorknob hypothesis predicts that if CD4 is blocked, then HIV will not be able to enter host cells. Two teams used the same experimental strategy to test this hypothesis (Figure 34.10). They began by growing large populations of helper T cells in culture. Then they took a sample of the cells and added an antibody to one of the cell-surface proteins found on helper T cells, along with HIV particles. They repeated this experiment 160 times but used a different sample of cells and added a different antibody each time. The key point here is that each of the 160 antibodies bound to and effectively blocked a different cell-surface protein. If one of the antibodies used in the experiment happened to bind to the receptor used by HIV, that antibody would cover up the receptor. In this way, the antibody would prevent HIV from entering the cell and protect that cell from infection. This approach led both research teams to reach exactly the same result: Only antibodies to CD4 protected the cells from viral entry. Later work confirmed that HIV particles can enter cells only if the virions bind to a second membrane protein, called a coreceptor, in addition to CD4. In most individuals, proteins called CXCR4 and CCR5 function as co-receptors. The discovery of these co-receptors inspired a search for compounds that would block them and prevent HIV from entering cells. A drug com- pany recently announced the development of a compound that blocks CCR5. Early reports suggest that the new drug is providing some relief for people infected with HIV. If an HIV particle successfully binds to both CD4 and a co-receptor, however, the lipid bilayers of the particle s envelope and the plasma membrane of the helper T cell fuse. When fusion occurs, HIV has breached the cell boundary. The contents of the virus then enter the cytoplasm, and infection proceeds. How Do Viruses Copy Their Genomes? Viruses must copy their genes to make a new generation of particles and continue an infection. Many viruses use their own DNA polymerase enzyme to accomplish that crucial step. This protein uses nucleotides provided by the host in synthesizing copies of the viral genome. In some viruses, however, genes consist of RNA. In most viruses that have an RNA genome, copies of the genome are synthesized by the viral enzyme RNA replicase, which is an RNA polymerase. RNA replicase synthesizes RNA from an RNA template, using ribonucleotides provided by the host cell. In other RNA viruses, however, the genome is transcribed from RNA to DNA by a viral enzyme called reverse transcriptase. This enzyme is a DNA polymerase that makes a single-stranded complementary DNA, or cdna, from a single-stranded RNA template (see Chapter 19). Reverse transcriptase then catalyzes the synthesis of a complementary DNA strand, resulting in a double-stranded DNA. Viruses that reverse-transcribe their genome in this way are called retroviruses ( backward viruses ). The name is apt because the flow of genetic information in this type of virus goes from RNA back to DNA. HIV is a retrovirus. Two copies of the RNA genome and about 50 molecules of reverse transcriptase lie inside the capsid of each particle. The first antiviral drugs that were developed to combat HIV act by inhibiting reverse transcriptase. After reverse transcriptase makes a cdna copy of the viral genome, another viral enzyme inserts the copy into a stretch of host-cell chromosome. At this point, HIV is lysogenic. Although it may stay in the lysogenic state for a period, lytic growth is more common. For lytic growth to occur, the viral genes have to be transcribed to mrna and then translated into proteins by the host cell s ribosomes. Producing Viral Proteins Viruses cannot make the ribosomes and trnas necessary for translating their own mrnas into proteins. For a virus to make the proteins required to produce a new generation of virus particles, it must exploit the host cell s biosynthetic machinery. Viral mrnas and proteins are produced and processed in one of two ways, depending on whether the proteins end up in the outer envelope of a particle or in the capsid. RNAs that code for a virus s envelope proteins follow a route through the cell identical to that of the RNAs of the cell s own

10 FREEMC34_ _FP_ /28/04 9:25 AM Page 789 Chapter 34 Viruses 789 Question: Does the CD4 protein function as the doorknob that HIV uses to enter host cells? Hypothesis: CD4 is the membrane protein that HIV uses to enter cells. Null hypothesis: CD4 is not the membrane protein that HIV uses to enter cells. Experimental setup: 1. Start with many identical populations of helper T cells growing in culture. Antibodies block specific membrane proteins Add antibody to CD4 protein Add HIV Add antibody to 2ND protein Add HIV Add antibody to 3RD protein Add HIV Prediction: HIV will not infect cells with antibody to CD4 but will infect other cells. Prediction of null hypothesis: HIV will infect cells with antibody to CD4. Results: Add antibody to 160TH protein Add HIV 2. Add antibodies to the proteins found on helper T cells a different antibody for each sample of cells. 3. Add a constant number of HIV virions to all cultures. Incubate cultures under conditions optimal for virus entry. NO cells infected Many cells infected Many cells infected Many cells infected Conclusion: HIV uses CD4 proteins as the doorknob to enter helper T cells. Thus, only cells with CD4 on their surface can be infected by HIV. FIGURE Experiments Confirmed that CD4 Is the Receptor Used by HIV to Enter Host Cells In this experiment, the antibodies added to each culture bound to a specific protein found on the surface of helper T cells. Antibody binding blocked the membrane protein, so the protein could not be used by HIV to gain entry to the cells. membrane proteins. How these viral mrnas are translated by ribosomes attached to the endoplasmic reticulum (ER) is diagrammed in Figure 34.11a (page 790). Afterward the resulting proteins are transported to the Golgi apparatus, where carbohydrate groups are attached, producing glycoproteins. The finished glycoproteins are then inserted into the plasma membrane, where they are ready to be assembled into new virions. In contrast, a different route is taken by RNAs that code for proteins that make up the capsid or inner core of a virus particle, illustrated in Figure 34.11b. These RNAs are translated by ribosomes, but in the cytoplasm, just as non-membranebound cellular mrnas are. The long polypeptide sequences that result are later cut into functional proteins by a viral enzyme called protease. This enzyme cleaves viral polypeptides at specific locations a critical step in the production of finished viral proteins. The resulting protein fragments are assembled into a new viral core near the host cell s plasma membrane. The discovery that HIV produces its own protease triggered a search for drugs that would block the enzyme. This search got a huge boost when researchers succeeded in visualizing the threedimensional structure of HIV s protease, using the X-ray crystallographic techniques introduced in Chapter 4. The molecule has an opening in its interior that is adjacent to the active site,

11 FREEMC34_ _FP_ /28/04 9:25 AM Page Unit 6 The Diversification of Life (a) PRODUCTION OF ENVELOPE PROTEINS Plasma membrane mrna Protein 1. Viral mrnas are translated by ribosomes attached to rough ER. 2. Resulting proteins are transported to Golgi apparatus, where carbohydrates are attached. 3. Resulting glycoproteins are inserted into plasma membrane. (b) PRODUCTION OF CORE PROTEINS Protein Protease mrna Ribosome Core proteins 1. Viral mrnas are translated by ribosomes in the cytoplasm. 2. Resulting polypeptides are cut into functional proteins by protease. 3. Resulting core proteins are assembled near plasma membrane. FIGURE Production of Viral Proteins (a) After being synthesized on the rough ER, envelope proteins are inserted into the plasma membrane. (b) After being synthesized by ribosomes in the cytoplasm and processed, core proteins assemble near the host cell s plasma membrane. as Figure 34.12a shows. Polypeptides fit into the opening and are cleaved at the active site. Based on these data, researchers immediately began searching for molecules that could fit into the opening and prevent protease from functioning by binding to and blocking the active site (Figure 34.12b). Several HIV protease inhibitors are now on the market. Box 34.2 (page 792) explains why they are often prescribed in combination with other antiviral drugs. (a) HIV s protease enzyme (b) Could a drug block the active site? Protease inhibitor Active site of protease FIGURE The Three-Dimensional Structure of Protease (a) Ribbon diagram depicting the three-dimensional shape of HIV s protease enzyme. (b) Once protease s structure was solved, researchers began looking for compounds that would fit into the active site and prevent the enzyme from working.

12 FREEMC34_ _FP_ /28/04 9:25 AM Page 791 Chapter 34 Viruses 791 How Are Viruses Transmitted to New Hosts? Viruses leave a host cell in one of two ways: by budding from the plasma membrane or by bursting out of the cell. Viruses that bud from the host cell s plasma membrane take some of that membrane with them. As a result, they incorporate host-cell phospholipids and membrane proteins into their envelope, along with membrane proteins encoded by the viral genome (Figure 34.13a). Most budding viruses infect host cells that lack a cell wall. In contrast, viruses that burst erupt from the cell surface, breaking the host cell open in the process, in most cases killing the host cell (Figure 34.13b). Most viruses that burst infect host cells that have a cell wall. Once particles are released, the infection cycle is over. Thousands or millions of newly assembled virions are now in extracellular space. What happens next? If the host cell is part of a multicellular organism, the new generation of particles begins traveling through the body via the bloodstream or lymph system. There, they may be bound by antibodies produced by the immune system. In vertebrates, this binding marks the particles for destruction. But if a particle contacts an appropriate host cell before it encounters antibodies, then the particle will infect that cell. This starts the replication cycle anew. What if the virus has infected a unicellular organism, or if the virus leaves a multicellular host entirely? For example, when people cough, sneeze, spit, or wipe a runny nose, they help rid their body of viruses and bacteria. But they also project the pathogens into the environment, sometimes directly onto an uninfected host. From the virus s point of view, this new host represents an unexploited habitat brimming with resources in the (a) Budding of enveloped viruses Cell interior Cell exterior Viral core Host cell s membrane protein Viral envelope proteins 100 nm (b) Bursting of nonenveloped viruses Cell interior Cell exterior Lysed cell 100 nm FIGURE Viruses Leave Infected Cells by Budding or Bursting (a) Enveloped viruses bud from a host cell, taking with them a lipid bilayer containing their envelope proteins. (b) Nonenveloped viruses burst from a host cell. This event ruptures the plasma membrane (and cell wall, if there is one). QUESTION Both budding and bursting kill the host cell. Propose a hypothesis to explain why infection with a budding virus is fatal.

13 FREEMC34_ _FP_ /28/04 9:25 AM Page Unit 6 The Diversification of Life BOX 34.2 HIV Drug Cocktails and the Evolution of Drug Resistance HIV protease inhibitors were dispensed widely in North America and Europe beginning in the mid-1990s, with spectacular results. After therapy, many patients no longer had detectable levels of HIV in their blood. The drugs knocked HIV populations down. Within two years, however, HIV levels in many of the patients taking protease inhibitors began to rebound. To investigate why this was happening, researchers sequenced the HIV protease gene in these patients. The researchers found that a series of mutations had occurred in the protease gene. These mutations led to changed amino acid sequences in the enzyme s active site. Because protease inhibitor molecules did not fit as well into the altered version of the active site, the enzyme could function reasonably well even in the presence of the inhibitor molecules. Almost as soon as a new protease inhibitor went into widespread use, researchers had documented the evolution of resistance to the drug. The scientific literature abounds with examples of bacteria that have evolved resistance to antibiotics and viruses that have evolved resistance to antiviral drugs. But perhaps no organism or virus has evolved resistance to control agents as quickly as HIV has. The leading hypothesis to explain this observation is that HIV s mutation rate is particularly high. Researchers who assay transcripts produced by HIV s reverse transcriptase find that, on average, the wrong base is inserted once every 8000 nucleotides. (In contrast, E. coli s DNA polymerase incorporates the wrong nucleotide about once in every 1 billion bases.) This means that, on average, a new mutant is generated every time HIV replicates its genome. Genetically, no two HIV particles are alike. Why is HIV s high mutation rate important? In infected individuals, approximately 10 billion new viral particles are produced daily. It is likely that, among the 10 billion, there are particles with a mutation in the active sites of reverse transcriptase or protease. As a result, HIV populations are almost certain to contain variants that are at least partially resistant to drugs that cripple most other particles in the population. The message to researchers and physicians is clear: Due to HIV s high mutation rate, the search for drug therapies promises to be an arms race a constant battle between novel drugs and novel, resistant strains of the virus. In attempting to keep ahead of drugresistant viruses, physicians prescribe combination therapy drug cocktails that include a protease inhibitor and one or more reverse transcriptase inhibitors. If patients begin to show signs of resistant strains, the physician will change the dosage or composition of the cocktail. Although it is extremely expensive, combination therapy has extended the life span and improved the quality of life for tens of thousands of AIDS patients. form of target cells. The situation is analogous to that of a multicellular animal dispersing to a new habitat and colonizing it. Viruses that successfully colonize a new host replicate and increase in number. The alleles carried by these successful colonists increase in frequency in the total population. In this way, natural selection favors alleles that allow viruses to do two things: (1) replicate within a host and (2) be transmitted to new hosts. For physicians and public health officials, reducing the likelihood of transmission is often an effective way to reduce the spread of a virus. HIV particles must be transmitted from person to person via body fluids such as blood, semen, or vaginal secretions. Faced with decades of disappointing results in drug and vaccine development, public health officials are aggressively promoting preventive medicine. Condom use reduces sexual transmission of HIV. Aggressive treatment of venereal diseases may also help; the lesions caused by chlamydia, genital warts, and gonorrhea encourage the transmission of HIV-contaminated blood during sexual intercourse. The most effective forms of preventive medicine are sexual abstinence or monogamy. Where blood supplies are routinely screened, HIV is rarely contracted by means other than unprotected sex with an infected person. The effectiveness of preventive medicine underscores one of this chapter s fundamental messages: Viruses are a fact of life. Every organism is victimized by viruses; every organism has defenses against them. But the tree of life will never be free of these parasites. Mutation and natural selection guarantee that viral genomes will continually adapt to the defenses offered by their hosts, regardless of whether those defenses are devised by an immune system or by biomedical researchers. Viruses are a constant threat for every organism alive. CHECK YOUR UNDERSTANDING All organisms and cell types are parasitized by some type of virus. Viruses may undergo lytic or lysogenic growth, or both, when they infect a host cell. You should be able to diagram generalized lytic and lysogenic replication cycles. Your lytic cycle should distinguish five phases: (1) entry into a host cell, (2) replication of the viral genome, (3) production of viral proteins, (4) assembly of a new generation of virions, and (5) exit from the infected cell. You should also be able to give an example of how each phase occurs in a particular virus.

14 FREEMC34_ _FP_ /28/04 9:25 AM Page 793 Chapter 34 Viruses What Themes Occur in the Diversification of Viruses? If viruses can infect virtually every type of organism and cell known, how can biologists possibly identify themes that help organize viral diversity? The answer is that, in addition to being identified as enveloped or nonenveloped, viruses can be categorized by the nature of their hereditary material in essence, the type of molecule their genes are made of. The single most important aspect of viral diversity is the variation that exists in their genetic material. Two other points are critical to recognize about viral diversity: (1) Biologists do not have a solid understanding of how viruses originate, but (2) it is certain that viruses will continue to diversify. After analyzing diversity in viral genes, let s consider hypotheses to explain where viruses come from and recent data on new or emerging viruses. The Nature of the Viral Genetic Material DNA is the hereditary material in all cells. As cells synthesize the molecules they need to function, information flows from DNA to mrna to proteins (Chapter 15). Although all cells follow this pattern, which is called the central dogma of molecular biology, some viruses break it. This conclusion traces back to work done in the 1950s, when biologists were able to separate the protein and nucleic acid components of a particle known as the tobacco mosaic virus, or TMV. Surprisingly, the nucleic acid portion of this virus consisted of RNA, not DNA. Later experiments demonstrated that the RNA of TMV, by itself, could infect plant tissues and cause disease. This was a confusing result, because it showed that, in this virus at least, RNA not DNA functions as the genetic material. Subsequent research revealed an amazing diversity of viral genome types. In some groups of viruses, such as the agents that cause measles and flu, the genome consists of RNA. In others, such as the particles that cause herpes and smallpox, the genome is composed of DNA. Further, the RNA and DNA genomes of viruses can be either single stranded or double stranded. The single-stranded genomes can also be classified as positive sense or negative sense or ambisense. In a positive-sense virus, the genome contains the same sequences as the mrna required to produce viral proteins. In a negative-sense virus, the base sequences in the genome are complementary to those in viral mrnas. In an ambisense virus, some sections of the genome are positive sense while others are negative sense. Finally, the number of genes found in viruses varies widely. The tymoviruses that infect plants contain as few as three genes, but the genome of smallpox can code for up to 343 proteins. Table 34.2 summarizes the diversity of viral genome types. TABLE 34.2 The Diversity of Viral Genomes Key: ss = single stranded; ds = double stranded; 1+2 = positive sense (genome sequence is the same as viral mrna); 1-2 = negative sense (genome sequence is complementary to viral mrna). Genome Example(s) Host Result of Infection Notes (+)ssrna (-)ssrna + TMV Tobacco plants Tobacco mosaic TMV was the first RNA virus disease (leaf wilting) to be discovered. Influenza Many mammal Influenza The negative-sense ssrna and bird species viruses transcribe their genomes to mrna via RNA replicase. dsrna + Phytovirus Rice, corn, Dwarfing Double-stranded RNA and other viruses are transmitted crop species from plant to plant by insects. Many can also replicate in their insect hosts. ssrna or + or Rous sarcoma Chickens Sarcoma (cancer of Rous sarcoma virus was (+)ssdna that virus connective tissue) identified as a cancerrequires reverse or causing agent in 1911, transcription for + decades before any virus replication was seen. ssdna can + w * 174 Bacteria Death of host cell The genome for w * 174 is or be (+), (-), or circular and was the first (+) and (-) complete genome ever sequenced. dsdna Baculovirus Insects Death These are the largest + Smallpox Humans Smallpox viruses in terms of genome Bacteriophage Bacteria Death size and overall size.

15 FREEMC34_ _FP_ /28/04 9:25 AM Page Unit 6 The Diversification of Life Where Did Viruses Come From? No one knows where viruses originated, but many biologists suggest that they are closely related to the plasmids and transposable elements introduced in Chapter 19 and Chapter 20. Viruses, plasmids, and transposable elements are all acellular, mobile genetic elements that replicate with the aid of a host cell. Simple viruses are actually indistinguishable from plasmids except for one feature: The viruses have a protein coat or membrane-like envelope. Some biologists hypothesize that simple viruses, plasmids, and transposable elements represent escaped gene sets. This hypothesis states that mobile genetic elements are descended from clusters of genes that physically escaped from bacterial or eukaryotic chromosomes long ago. According to this hypothesis, the escaped gene sets took on a mobile, parasitic existence because they happened to encode the information needed to replicate themselves at the expense of the genomes that once held them. In the case of viruses, the hypothesis is that the escaped genes included the instructions for making a protein capsid and possibly envelope proteins. According to the escaped-gene hypothesis, it is likely that each of the distinct types of RNA viruses and single-stranded DNA viruses represents a distinct escape event. The same researchers contend that DNA viruses with large genomes originated in a very different manner, however. Here the hypothesis is that the large DNA viruses trace their ancestry back to free-living bacteria that once took up residence inside eukaryotic cells. The idea is that these organisms degenerated into viruses by gradually losing the genes required to synthesize ATP, nucleic acids, amino acids, and other compounds. Although this idea sounds speculative, it cannot be dismissed lightly. Chapter 27 introduced species in the genus Chlamydia, which are bacteria that live as parasites inside animal cells. And Chapter 28 provided evidence that the organelles called mitochondria and chloroplasts, which reside inside eukaryotic cells, originated as intracellular symbionts. Investigators contend that, instead of evolving into intracellular symbionts that aid their host cell, DNA viruses became parasites capable of destroying the host. To date, neither of these hypotheses has been tested rigorously. To support the escaped-genes hypothesis, researchers would probably have to discover a brand new virus that originated in this way, or viruses that had so recently derived from intact bacterial or eukaryotic genes that the viral DNA sequence still strongly resembled the DNA sequence of those genes. To support the degeneration hypothesis, researchers would probably have to find strong genetic homologies between viruses and parasitic species of bacteria that live inside cells. But currently, there is no widely accepted view of where viruses came from. Emerging Viruses, Emerging Diseases Although it is not known how the various types of virus originated, it is certain that viruses will continue to diversify. With alarming regularity, the front pages of newspapers carry accounts of deadly viruses that are infecting humans for the first time. In 1993 a hantavirus that normally infects mice suddenly afflicted dozens of people in the southwestern United States. Nearly half of the people who developed hantavirus pulmonary syndrome died. Still higher fatality rates were recorded in 1995 when the Ebola virus, a variant of a monkey virus, caused a wave of infections in the Democratic Republic of Congo. By the time the outbreak subsided, over 200 cases had been reported; 80 percent were fatal. During an Ebola outbreak in 1976, 90 percent of cases were fatal. Hantavirus pulmonary syndrome and Ebola are examples of emerging diseases: new illnesses that suddenly affect significant numbers of individuals in a host population. In these cases, the causative agents were considered emerging viruses because they had switched from their traditional host species to a new host humans. Many investigators consider HIV to be an emerging virus because it originated in chimps and was first transmitted to humans in the early to mid-twentieth century (see Box 34.3). Physicians become alarmed when they see a large number of patients with identical and unusual disease symptoms in the same geographic area over a short period of time. The physicians report these cases to public health officials, who take on two urgent tasks: (1) identifying the agent that is causing the new illness and (2) determining how the disease is being transmitted. Several strategies can be used to identify a pathogen. In the case of the outbreak of hantavirus pulmonary syndrome, officials recognized strong similarities between symptoms in the U.S. cases and symptoms caused by the Hantaan virus native to northeast Asia. The Hantaan virus rarely causes disease in humans; its normal host is rodents. To determine whether a Hantaan-like virus was responsible for the U.S. outbreak, researchers began capturing mice in the homes and workplaces of afflicted people. About a third of the captured rodents tested positive for the presence of a Hantaan-like virus. (The test that was done is explained in Chapter 49.) DNA sequencing studies confirmed that the virus was a previously undescribed type of hantavirus. Further, the sequences found in the mice matched those found in infected patients. Based on these results, officials were confident that a rodent-borne hantavirus was causing the wave of infections. The next step in the research program, identifying how the agent is being transmitted, is equally critical. If a virus that normally parasitizes a different species suddenly begins infecting humans, if it can be transmitted efficiently from person to