Virology
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TABLE OF CONTENTS Preface........................................................................................................ 1 Chapter One: Virus Foundations ................................................................. 5 The Study of Virology....................................................................................................... 5 History of Virology ........................................................................................................... 8 Viruses in Evolution ....................................................................................................... 10 Viral Structures ............................................................................................................... 11 Viral Genomes and their Implications in Disease ..........................................................17 Viral Taxonomy of Human Pathogens .......................................................................... 19 Virus Life Cycles ............................................................................................................. 20 Key Takeaways ............................................................................................................... 24 Quiz ................................................................................................................................ 25 Chapter Two: Viral Infection Basics .......................................................... 28 Viral Pathogenesis.......................................................................................................... 28 Viral Host Responses in Humans .................................................................................. 33 Portals of Entry .............................................................................................................. 37 Diagnostics in Viral Infections ...................................................................................... 39 Key Takeaways ............................................................................................................... 41 Quiz ................................................................................................................................ 42 Chapter Three: DNA Viruses ..................................................................... 45 Papovaviruses ................................................................................................................ 45 Adenoviruses .................................................................................................................. 49 Herpesviruses ................................................................................................................ 52
Poxvirus.......................................................................................................................... 57 Parvovirus ...................................................................................................................... 58 Key Takeaways ............................................................................................................... 59 Quiz ................................................................................................................................ 60 Chapter Four: Positive-strand RNA Viruses and Double-stranded RNA Viruses ..................................................................................................... 63 Picornaviruses ................................................................................................................ 63 Alphaviruses ................................................................................................................... 66 Coronaviruses ................................................................................................................ 69 Norwalk Virus .................................................................................................................71 Double-stranded RNA Viruses ...................................................................................... 72 Key Takeaways ............................................................................................................... 76 Quiz ................................................................................................................................ 77 Chapter Five: Negative-strand RNA Viruses .............................................. 79 Filoviruses ...................................................................................................................... 79 Rhabdovirus ................................................................................................................... 82 Influenza Viruses ........................................................................................................... 84 Other Negative-strand Viruses ...................................................................................... 87 Key Takeaways ............................................................................................................... 94 Quiz ................................................................................................................................ 95 Chapter Six: Reverse Transcribing Viruses and Hepatitis Viruses ............. 97 Retroviruses ................................................................................................................... 97 Hepatitis Viruses .......................................................................................................... 103 Key Takeaways ............................................................................................................. 109 Quiz ...............................................................................................................................110
Chapter Seven: Viral Mutations ............................................................... 113 Basics of Viral Mutations .............................................................................................. 113 Novel or Emerging Viruses ........................................................................................... 117 Zoonotic Viruses ........................................................................................................... 119 Key Takeaways ............................................................................................................. 123 Quiz .............................................................................................................................. 124 Chapter Eight: Virus Epidemiology .......................................................... 127 Learning from Pandemics.............................................................................................127 Recent Viral Pandemics ............................................................................................... 130 Studying Viral Epidemics ............................................................................................ 135 Basic Reproductive Number .........................................................................................137 Genetic Drift in Viral Infections ...................................................................................137 Key Takeaways ............................................................................................................. 139 Quiz .............................................................................................................................. 140 Chapter Nine: Subviral Infections ........................................................... 143 Satellite Viruses............................................................................................................ 143 Infectious Prion Diseases............................................................................................. 146 Key Takeaways ............................................................................................................. 150 Quiz ............................................................................................................................... 151 Chapter Ten: Virus Vectors ..................................................................... 154 Recombinant DNA Vectors .......................................................................................... 154 Virus Vectors in Cloning ...............................................................................................155 Gene Expression Vectors ..............................................................................................157 Gene Therapy Vectors .................................................................................................. 158
Key Takeaways ............................................................................................................. 162 Quiz .............................................................................................................................. 163 Chapter Eleven: Persistent Viruses and Tumor Viruses .......................... 166 Persistent Viruses ........................................................................................................ 166 Tumor Viruses............................................................................................................... 171 Key Takeaways ............................................................................................................. 174 Quiz ...............................................................................................................................175 Chapter Twelve: Viral Detection Strategies and Viral Therapeutics ..........178 Methods of Viral Detection .......................................................................................... 178 Antiviral Therapies ...................................................................................................... 184 Vaccines for Viral Infections ........................................................................................ 186 Viral Eradication .......................................................................................................... 187 Key Takeaways ............................................................................................................. 190 Quiz ............................................................................................................................... 191 Summary ................................................................................................ 194 Course Questions and Answers ............................................................... 198 Answers to Quiz ...................................................................................... 241 Answers to Chapter One .............................................................................................. 241 Answers to Chapter Two .............................................................................................. 243 Answers to Chapter Three ........................................................................................... 244 Answers to Chapter Four ............................................................................................. 245 Answers to Chapter Five .............................................................................................. 246 Answers to Chapter Six ................................................................................................ 247 Answers to Chapter Seven ........................................................................................... 248
Answers to Chapter Eight ............................................................................................ 249 Answers to Chapter Nine ............................................................................................. 250 Answers to Chapter Ten ............................................................................................... 251 Answers to Chapter Eleven .......................................................................................... 252 Answers to Chapter Twelve ......................................................................................... 253 Answers to Course Quiz ............................................................................................... 254
PREFACE The purpose of this audio-course is to provide you with a solid and thorough education on virology as it applies mainly to human diseases. While scientists have long suspected that there were infectious particles we now know to be viruses causing some human infections, the actual finding of viruses, their structures, and functions have been relatively recent because of medical research. In recent years, there has been an explosion of what medical researchers and doctors know about viral diseases and their effect on human health, leading to interventions that have greatly reduced the impact of these types of infections on our lives. In this audio-course, the focus will be on how viruses cause disease, the human host response to viral infections, and the pathophysiology of the many different viral infections that affect all humans throughout the world. Many viruses are wellestablished and have caused the same known infections for millennia, while others are novel infections that continue to cause epidemics and pandemics, even in the modern medical era when we think we have the answers to all types of human diseases. Some viruses cause cancer because of their effect on the human cell genome, while others are used to treat human diseases in unique ways. We will also talk about the different approaches to managing viral infections, such as antiviral drug therapy and immunizations used to provide primary intervention against viral diseases. Chapter one in the course introduces the study of viruses and virology by looking at what viruses are, how we have come to understand them, and how it is believed that viruses fit into the evolution of life on earth. Viruses have different structures and several choices in the types of genetic material in them that affect how they behave in an infection. In this chapter, we will also talk about the taxonomy of viruses as well as about the typical viral life cycle during a cellular infection. Chapter two furthers the discussion of viruses by looking at viral infections in general. The basics of viral pathogenesis are discussed along with the typical immune response to viral infections, which leads to the majority of symptoms. Viruses with different
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portals of entry lead to different host infectious diseases, which are also covered. The ways that viral infections are detected, called viral diagnostics, is also covered in this chapter. The focus of chapter three in the course is the different types of DNA viruses as they apply mainly to human diseases. These include papovavirus infections, which include polyomaviruses and papillomaviruses, which share some common characteristics. Adenovirus infections also involve DNA viruses and herpesviruses are also major sources of DNA viral infections. We will also talk about poxviruses and parvoviruses, which aren’t as common in humans but still represent classifications of DNA viruses. Chapter four is about the different positive-strand RNA viruses plus the various doublestranded RNA viruses causing human diseases. These include the different picornaviruses, such as poliovirus and other enteroviruses, coxsackie viruses, flaviviruses, and togaviruses. Coronaviruses are also positive-strand RNA viruses that can lead to both minor and severe respiratory infections. A variety of double-stranded RNA viruses cause human diseases, including rotaviruses and several tick-borne viruses. Each of these is covered in this chapter in terms of their clinical presentation and the pathophysiology of their disease processes in humans. Chapter five in the course focuses on the different negative-strand RNA viruses, which are otherwise a diverse group of viruses. Filoviruses are discussed, including those that cause hemorrhagic diseases in humans. Influenza viruses, which are much more common causes of human disease, are also covered in this chapter. Rabies is a rhabdovirus that also causes severe disease in humans. There are several paramyxoviruses covered in this chapter, including those that cause mumps, measles, and respiratory syncytial virus infections. The two main topics of chapter six are the reverse transcribing viruses called retroviruses and the different hepatitis viruses. Among reverse transcribing viruses are the retrovirus that causes HIV disease and human T cell leukemia viruses. Hepatitis viruses can be picornaviruses, such as hepatitis A or Hepadnaviruses, such as hepatis B and hepatitis C, which are discussed in this chapter. There are several minor types of hepatitis viruses, which are also covered in the chapter.
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Chapter seven in the course talks about viral genome mutations and how these are most likely to occur. Certain viral genomes are more likely to be mutagenic than others, which has implications for viral epidemics and the evolution of viral pandemics. Viral mutations in both humans and animals are important factors in the development of novel viruses that become problematic in humans who do not have the immunity to the new form of the virus. Chapter eight looks more carefully at issues related to virus epidemiology. A great deal about the epidemiology of viruses and their epidemics can be learned from past epidemics and pandemics. In this chapter, we talk about the different recent viral pandemics in the world and the ways in which each was unique as well as how each was handled. The ways in which viral epidemics are studied is discussed in this chapter, as well as commonly used terminology in epidemics, such as the basic reproductive number and the issues of antigenic drift versus antigenic shift. Chapter nine in the course introduces satellite viruses or viroids and prion diseases, which are both representative of infectious particles that are considered to be subviral in their presentation. Subviral particles like viroids cannot reproduce by themselves and often need a helper virus in order to be infectious in humans. The chapter also talks about prion diseases, which can be infectious to humans. Prions contain no genetic material; their infectious component is made from an abnormal protein that causes disease in the cells they occupy. Viruses have medical applications as one of several vectors used to treat diseases, which is the main focus of chapter ten. It involves making recombinant DNA technology that combines human genes with viral genomes for different purposes. These gene products can be used to make DNA libraries used for cloning and to used viral infections to add missing genes to a cell, such as would be used for the different gene therapies being studied throughout the world in the management of common single-gene disorders. Chapter eleven in the course discusses issues seen in persistent viral infections and in infections secondary to tumor viruses, which have the potential to cause cancer or tumors in the cells they infect. As you will see, certain viruses are more prone to causing
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persistent infections than others. The same is true for viruses that seem more likely to cause tumors or cancer compared to other viruses. The focus of chapter twelve includes the different methods by which doctors and epidemiologists use viral detection strategies to detect an active or resolved viral infection. There are techniques used in acute situations and others that can say if an infection has largely resolved. The different antiviral therapies, including vaccines are covered in this chapter. Ideally, viruses that can be eradicated should be managed this way but it hasn’t been done in the vast majority of viral infections.
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CHAPTER ONE: VIRUS FOUNDATIONS This chapter introduces the study of viruses and virology by looking at what viruses are, how we have come to understand them, and how it is believed that viruses fit into the evolution of life on earth. Viruses have different structures and several choices in the types of genetic material in them that affect how they behave in an infection. In this chapter, we will also talk about the taxonomy of viruses as well as about the typical viral life cycle during a cellular infection.
THE STUDY OF VIROLOGY Viruses are important to study because they involve a significant healthcare burden and a contribute greatly to the infectious disease burden throughout the world. Viral infections can affect humans as early as in the prenatal period through vertical transmission of the virus from mother to child. In fact, a viral infection this early in development has a great impact on the fetus that can lead to fetal death or birth defects in the child. Viral infections are a big part of childhood and is the time when most people become immune to the many viruses they catch during this period of life. While most viral diseases are not serious, there are episodic periods in history where a novel viral pathogen emerges, leading to widespread epidemics and pandemics affecting people of all ages and in all parts of the world. Those most susceptible to dying from these types of viral infections are those who have chronic diseases, poor immune systems, malnutrition, and those at the extremes of age. Viruses are different from the cellular organisms that define life in general. According to established guidelines about what constitutes a form of life, an organism is considered a living thing if it has a cell membrane containing cytoplasm and genetic material and if it has its own metabolic processes and ability to divide through sexual or asexual means. Viruses do not qualify because they do not have cytoplasm and do not have metabolic
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capabilities themselves. They also do not have true cell membranes, even though some have an outer lipid envelope. Viruses may have either RNA or DNA as their genome but not both. The fact that some have RNA makes viruses unique from life forms in another way as well. It is possible for viruses to have either single-stranded or double-stranded nucleic acids. With singlestranded RNA, it can be considered positive-sense RNA or negative-sense RNA. Positive-sense RNA is no different from messenger RNA because it gets translated unchanged into viral proteins, while negative-sense RNA must be altered in ways we will talk about later in order to be translated. Viruses in general only code for a few proteins for replication and require host DNA to complete the process. There are some terms you should be familiar with before we discuss viruses and virology further. For example, the term “virion” is the same thing as a virus particle. All viruses are covered with a protein coat called a capsid, which is usually made from subunits of protein called capsomers. When we talk of the virus’s nucleocapsid, we are referring to both the genome and the capsid of the virus together. Some are covered also with an envelope made from lipids, similar to the bacterial or eukaryotic cell membrane. Peplomers are the different proteins in the viral envelope; these are almost always glycoproteins consisting of both sugars and proteins. Because viruses are obligate parasites, they can infect every known type of living thing without exception. Viruses do have cell tropism, which means they are limited in the type of cell or organism they can infect. The right receptor on the cell itself must be present in order for the virus to be infectious to the cell. We will talk much more about routes of entry of viruses in humans but basically these can be inhaled, inoculated through the skin or mucous membranes, ingested, or passed through exchange of bodily fluids. One commonly overlooked method of transmission is that of vertical transmission from mother to fetus in utero. Viral infections in humans and other multicellular organisms can remain completely localized in the host or can become disseminated throughout the host. Dissemination is usually through the presence of viremia or spread through the lymphatic system of the host. There are those that will cause more generalized disease in the beginning but the
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virus will become localized in a body area and remain dormant there, as is the case with herpesvirus infections like herpes simplex and varicella—both of which harbor in the nerves. All viral infections have an incubation period, which is from the moment of exposure to the time of clinical disease onset. Those viruses that are localized have shorter incubation periods of less than seven days, while disseminated infections have a longer incubation period. There are host factors in viral infections we will talk about. The host will release many immune cells, cytokines, and interferons that cause most of the viral symptoms seen in a viral infection. These things are apart from the actual tissue damage caused by cell lysis during an active infection of each cell actually invaded upon by the virion. As these cells lyse, they release factors that contribute to further inflammation and advancement of the immune response. The host response to virus infections involves many factors, including T cell activation and antibody production by B cells. The T cells are responsible for destroying host cells that have become infected with the virus, while antibodies aid the immune response by tagging virus particles for easier removal. Antibodies are less actively involved in the host response to an active infection but are more involved in preventing a re-infection with the virus at a later time. While the majority of viruses are self-limited, we will talk about those that lead to chronic infections and cancer as side effects of not being able to clear the virus from the body. About fifteen percent of all human cancers have some viral component to their etiology. These are largely from chronic and persistent virus infections but not all patients with a chronic viral infection will get cancer from this type of infection. As you’ll see, the most common viruses linked to cancer include hepatitis B, hepatitis C, human papillomavirus, human herpesvirus 8, and Epstein-Barr viruses.
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HISTORY OF VIROLOGY The term virus has been used in medical texts since 1599, when the term actually meant “venom”. Primitive vaccination has existed for thousands of years in China where vaccination was called variolation. The process involved mixing body fluids from those with smallpox with those who did not have the disease in order to immunize those uninfected. This was further advanced in the western world in the late 1700s, when cowpox was used instead to immunize patients against the related smallpox vaccine. Rabies vaccines have existed since 1886, even though viruses themselves were unknown entities. Viruses were attempted to be extracted since the 1800s. Biologist Dmitry Ivanovsky demonstrated that filtering leaf extracts from tobacco plants that had been infected with the tobacco mosaic disease did not trap the infectious agent. It was then proposed that a very small particle or toxin was involved in these types of infections. Others determined that the filterable substance was able to be passed from one generation to another and that it was infectious rather than toxic in nature. The first suggestion that viruses were cancer-causing happened in 1903 and was essentially proven a few years later when a virus-like agent was found to transmit chicken-related leukemia. It was nearly at the same time when chicken sarcoma was found to be infectious in nature. This was caused the Rous sarcoma virus 1—later found to be a type of retrovirus. While we don’t think of bacterial viruses, called bacteriophages, affect humans but they do in fact have an impact on us. The first bacteriophages were recognized in 1911 and, because bacteria grow easily, the understanding of these infections has helped the study of virology overall. It was later determined that, while scarlet fever is bacterial in origin, it depends on one that is itself infected with a bacteriophage. Animal virus research was expanded greatly when it was discovered that these viruses could infect chicken eggs. This fact has since led to the development of many vaccines against human viruses, such as the influenza virus vaccines. Yellow fever vaccine came
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out of chicken egg research and has since saved the lives of millions who would have become infected throughout the world. The tobacco mosaic virus was the first to be crystalized so that its structure could be analyzed using electron microscopy as of 1935. It was since shown that the virus was still infectious after it had been crystalized, further showing that these were not truly life forms. The self-assembly of viruses was later demonstrated in 1955, although it was only proposed at the time that this was what happens inside cells. The first retrovirus was discovered in 1965, which is an RNA virus that is reverse transcribed to make complementary DNA that potentially could integrate into the host’s genome. Infectious human retroviruses were first discovered in 1974 and the role of reverse transcriptase in these infections was uncovered. It was only later discovered that reverse transcriptase is not an enzyme specific to these viruses but that it also is a part of the physiology of retrotransposons in eukaryotic DNA. Cancer research as it applies to virology became clarified in the mid-1970s when it was discovered that not all cancers from viruses were because of viral oncogenes. Instead, some viruses, including the Rous sarcoma virus, also activated proto-oncogenes within the genomes of eukaryotic cells. The proto-oncogene was found to turn into an oncogene in order to lead to cancer. While viral outbreaks had been seen for a very long time, the first Ebola outbreak began in 1974 as an emerging or novel viral infection. Five years later, the World Health Organization announced that smallpox had been eradicated worldwide. Prions as infectious agents were discovered in 1982 and the HIV virus was first reported as an infectious disease in 1981. HIV has become the best-studied virus in the world. This has led to the first antiretroviral drug treatments for the disease. Gene therapy has been studied with regard to viruses since the 1980s. This came at the same time that it was determined that retroviruses were able to insert themselves into the human genome. The success of this therapy is not yet what is probable in the future, although a few patients with severe combined immunodeficiency disease or SCID have been successfully treated with viral vector-based gene therapy.
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VIRUSES IN EVOLUTION Viruses are considered somewhere between life forms and inanimate objects by some researchers. Perhaps the one thing that viruses do that are most similar to life forms is that they contain genetic material that has the capacity to mutate over time. They have added to the diversity of all life forms because they add to the genome of these life forms. The diseases they cause also lead to changes in populations. Despite this, viruses themselves have confusing taxonomy that changes more dramatically than other types of organisms. Their evolution must be deduced because there are no fossil records. There are three prevailing views about the origin of viruses on earth. One proposes that viruses existed before cells and gave rise to cell life in general. They have unique genomes unlike the sequences seen in any life form. But because they need hosts themselves, cells are believed to have existed as long as viruses themselves in other theories on their origin. There is the belief that viruses essentially de-evolved or reduced themselves from more advanced parasites and is called the reduction hypothesis. This is supported by the fact that there are giant viruses overlapping cell life forms in some aspects. Still others suggest the “escape process”, meaning that viruses once escaped cellular genomes through horizontal gene transfer. It doesn’t explain, though, the uniqueness of their genomes. Viruses may have mediated the ability of eukaryotes to make RNA from DNA through transcription. Because of the major theories of viral evolution being so divergent, there are those that believe the true evolution of viruses has been a composite of these theories. Both megaviruses and mimiviruses are giant forms that have a partial ability to make what’s necessary for the translation process. Viruses have appeared to coexist along all evolutionary lines. It is possible that the last universal common ancestor of life in the universe gave birth to a minimum of two descendants. These were the last universal cellular ancestor and an archaic virocell ancestor. The cellular ancestor evolved into the different life forms, while the virocell ancestor did not evolve to have its own ribosomal machinery, forcing them to be cellular parasites.
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Some suggest that virocells must have predated the current modern cells because they can infect both prokaryotes and eukaryotes. The current data indicate that viruses originated back when cells were so primitive that they lacked ribosomes as well. Without ribosomes, the ability to reproduce independently was impossible as we know it. Capsid proteins were probably acquired after the genetic material was created, indicating that the first genomes were possibly intracellular. The fact that viruses are parasitic may have also been a late finding in these organisms. For this to be true, the ancient viruses must have had more genes in their genome and must have gradually lost some of these genes that necessitated their parasitic nature. In that sense, the reduction of genomes might have been a driving force in evolution rather than genome expansion. Genome reduction probably started in viruses but also occurred in other organisms later on. The most primordial viruses may have once been able to have their own metabolism.
VIRAL STRUCTURES As mentioned, all viruses have a genome and a protein capsid, while some have a lipid envelope. In their totality, each viral particle is called a virion. Those virions without a lipid envelope are called naked viruses. The protein capsid has the capability of recognizing and surrounding just viral DNA. It is suggested that there is a packaging sequence or signal on the viral genome that indicates the necessity of capsids to surround them. Capsids are made of repeating capsomeres that, in most non-phage viruses, are either helical or icosahedral. Each capsomere is usually but not always a single polypeptide chain, also called a structural subunit or protomer. The first helical capsid to be studied is that of the tobacco mosaic virus, which is shown in figure 1:
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Figure 1
This virus has single-stranded RNA with pieces of RNA fitting into one groove of each protein subunit. Some other viruses have more complex helical capsids that involve more than one polypeptide subunit. Helices have two parameters, including an amplitude and pitch. Pitch is the distance covered by each turn of this helix. Many of these viruses are very stable but can come together or dissociate, depending on the environmental circumstances. There are no real covalent bonds between these subunits so they can easily dissociate. Some animal viruses also have helical nucleocapsids and all are enveloped viruses, including the human influenza virus and rabies. Icosahedral capsids are also made of subunits that form structures that appear to be spherical but are not truly spherical. The genome is contained within this icosahedral structure. One icosahedron has twenty identical equilateral triangle faces shaped into a roughly spherical shape. Figure 2 shows the icosahedral virus shape:
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Figure 2.
Because proteins are not shaped like equilateral triangles, each face has more than one strand of polypeptide. The simplest icosahedral virus has three protein subunits per face so there are sixty separate polypeptides per viral particle. Because most viruses have larger genomes than this can support, most of these viruses have some multiple of 60 as their total polypeptide molecule number. The viral envelope is made from a lipid bilayer, which actually comes from lipids derived from the host cells themselves. It will also contain proteins coded for by the virus themselves. Most of these are trans-membrane glycoproteins. These serve to bind with host receptors and play a role in cell entry and things like membrane fusion or channel formation in the virus membrane itself. Many of these envelopes contain matrix or internal proteins that tack the nucleocapsid to the envelope itself. These are not capsulated. There are also transcription factors and enzymes in low amounts in the viral envelope. The basis behind enveloped viruses is that they essentially bud out of the cell membranes of the cells they occupy. Rather than causing the cell itself to burst, these viruses take a piece of the cell membrane with them as they leave the cell but it is also
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possible that the membrane around them comes from the nucleus, Golgi apparatus, or endoplasmic reticulum. The glycoproteins that will make up the outside of the envelope are largely clustered in one region so that as many of these get onto the envelope during budding. There are within these structure types many different and diverse morphologies seen. The size variations among viruses are great, with a size range of between 20 nanometers and 300 nanometers, although there are filoviruses that have a length of up to 1400 nanometers but a width of only 80 nanometers. Figure 3 shows a typical filovirus, such as the Ebola virus:
Figure 3.
Scanning electron microscopes are necessary for the visualization of viruses. These are coated with tungsten metal salts that will allow visualization through the scattering of electrons. Some are treated with positive staining that highlights the viral particle or negative staining that stains the background only.
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Bacteriophages infect bacteria and these have unique shapes with a head that contains the nucleic acid and a tail plus added structures that allow the nucleic acid alone to be injected directly into the cell itself. Figure 4 shows the basic structure of a bacteriophage:
Figure 4.
There are other complex viruses that do not have the traditional shapes. For example, the poxviruses are large and complex with a central nucleoid consisting of proteins and two lateral bodies that have no known function. It can range in shape from being ovoid to brick-shaped. Mimiviruses are quite large and have protein filamentous structures coming out of their surface. It is large enough to be seen under a light microscope. Figure 5 shows what a mimivirus looks like:
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Figure 5.
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VIRAL GENOMES AND THEIR IMPLICATIONS IN DISEASE There doesn’t seem much rhyme or reason why some viruses have one type of genome and others have yet another type altogether. In some cases, the genome type determines what the virus can do inside an infected cell and how it causes disease. One commonly studied virus that does not have major implications in human diseases is the T phage that infects E. coli bacteria. It consists of one molecule of double-stranded DNA. These viruses have an icosahedral head and a helical protein tail. The DNA is injected into the cell, where it can make about a hundred new virions every twenty minutes. The cell then lyses to release these phages. Within 20 minutes of infection, the metabolic processes in the cell will be turned over to make phage proteins only. Temperate phages like the lambda phage in E. coli are also well-studied. These are double-stranded DNA viruses that might become circular to create ordinary progeny that are released through lysing. They might also enter the genome of the bacterium to assume a lysogenic cycle that does not involve immediate lysing. We will talk more about this in a minute. The environment around the cell will determine what type of life cycle happens in the cell. Small DNA phages generally only code for less than twelve proteins and have also been extensively studied with regard to their life cycle. These are simple viruses that require a great deal of help from the host in order to make the proteins necessary to make the phage progeny. Research on these small DNA phages has helped researchers determine which cellular proteins are necessary to participate in DNA replication. RNA phages also infect E. coli but have an RNA genome. Most of these have their genomes directly made into proteins as is the case with eukaryotic messenger RNA. The phage RNA can make many but not all of the proteins necessary for the making of phage proteins. Some will just make RNA polymerase to transcribe viral RNA, an enzyme that dissolves cell walls of bacteria, and two capsid proteins used to make the phage capsids. As you learn about the animal viruses and, in particular, the human viruses, you’ll see that these are largely randomly named or named after the diseases they cause in the human host. It can be confusing because, in the case of respiratory viruses, the
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symptoms might be the same while the virus causing it might be very different from another virus causing the same symptoms. The type of nucleic acid in the cell makes a very big difference in its overall life cycle in the host cell. It also provides some way of classifying the different viral particles. Viral mRNA can have a plus strand or a minus strand. The plus strand is able to be quickly translated into proteins but the minus strand cannot do this without some intermediate step. Any strand of DNA that is complementary to a positive RNA viral strand is also considered a minus strand. All plus strands that are not already part of the genome must have a minus strand of either DNA or RNA as templates. This leads to six possible classes of animal viruses used in virology. Class I and class II DNA viruses are both based on DNA as the major genome. Class I viruses are all double-stranded DNA viruses. The viral DNA gets into the cell nucleus of the infected cell, gets transcribed into viral messenger RNA to make viral proteins. Some examples are human adenoviruses that cause GI and respiratory system infections, SV40 simian virus found in monkey kidney cells, herpesviruses to include those that cause cold sores, shingles, and chickenpox, and chickenpox, and human papillomaviruses that cause warts, including genital warts. Poxviruses are class I viruses, including smallpox virus or variola, which has been eradicated. Class II viruses are known as parvoviruses. These are single-stranded DNA viruses, some of which have both plus or minus strands held in different virions, while others just have minus strands. Either way, the DNA must get made into double-stranded DNA before it can become messenger RNA for the cell. RNA viruses are from classes III through VI. These cause a great variety of human and other animal viral infections. Class III viruses have double-stranded RNA as their genome. There will be a minus strand that acts solely as a template for the making of plus strands or messenger RNA strands. They contain many strands of up to twelve separate double-stranded RNA strands each. One strand will code for just one to two polypeptides. Because of this unique structure, these have segmented genomes. Many of these have enough capacity to make a full complement of enzymes.
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Class IV viruses have just a single plus strand of RNA in their genome. These viruses basically have viral messenger RNA in each virion. The RNA in the particle is by itself infectious, which isn’t true of other types of viruses. There is a minus strand made from the viral genome that gets utilized to make even more plus strands, acting as a template. Two types of these viruses are known, including polioviruses, which makes a long strand of protein that later gets cleaved to make several proteins. Others are those that cause yellow fever and viral encephalitis among humans. These make more than one messenger RNA molecule that both get translated into proteins. Class V viruses are all single negative strand RNA viruses, which are directly complementary to viral messenger RNA. These genomic strands do not themselves code for protein. There are two types, such as those represented by measles and mumps, which have one molecule of RNA per virion. Each has its own RNA polymerase to make positive strands that will code for one protein each. Another type is the influenza virus that has segmented genomes that each are templates for a single messenger RNA molecule. Some will be creative in that they can be read either way in order to make separate proteins with the same RNA strand. Class VI viruses are of a special category of enveloped viruses that have two identical plus-strands of RNA in them. These are retroviruses, simply because their genome will direct the formation of a DNA molecule that itself will synthesize viral messenger RNA. It takes reverse transcriptase to make a minus strand of the DNA molecule plus a complementary positive-sense strand. This makes a double strand of DNA that gets integrated into the cell. From there, this DNA gets made into viral messenger RNA to make viral proteins. Budding is used to allow these viruses to leave each cell, which makes them automatically enveloped viruses.
VIRAL TAXONOMY OF HUMAN PATHOGENS Taxonomy is the process of classifying and naming the different life forms, designed to group similar organisms together. It is not a simple process and involves the observations from many different researchers and constant reevaluation of the process. There are different organizations that keep track of the different prospective changes in
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nomenclature. The Internationals Committee on Taxonomy of Viruses will keep track of these things in viruses. All recommendations are disseminated to the scientific community at large. Viruses can be classified in different ways, including their genome types, the viral capsid structure, whether there is an envelope of not, the host range, the pathogenicity of the virus, the similarity in gene sequences, and the range of host. There are certain orders, families, genuses, and species that get clustered together. For example, all viruses of the Picornavirales order have no envelopes, have icosahedral structures, and have a genome with positive-sense RNA. There are many families and genuses under these categories. Once you get to the genus level, the viruses in the same genus are the most similar to one another.
VIRUS LIFE CYCLES Viruses in general have roughly the same life cycle although, with bacteriophages, there are both lytic and lysogenic cycles to consider. The basic driving force behind all viral infections and their ability to succeed as pathogens is to have attachment to the right host, the proper metabolic pathways to make new virus particles, and the ability to release those particles in ways that affect another host cell. They do not go through division but instead undergo replication. Figure 6 shows the typical viral life cycle:
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Figure 6.
Each virus has its own unique life cycle but they generally follow the same basic pattern of replication. It all starts with attachment, which depends on specific interactions between the capsid proteins and host cell receptors on the cell surface. The specificity determines the range of hosts. Each host cell will have a surface protein that interacts with the viral capsid protein. The success of the virus depends on being able to infect cells that will allow it to best replicate. If there is a viral envelope, it will often fuse in order to allow the viral genome to enter the cell. The next step is penetration of the virus itself or the viral genome into the host cell. This can happen in several ways. The bacteriophage will inject its genome only through the relatively thin cell wall of the organism. Plants are able to be accessed only through cell trauma because they have a thick and rigid cellulose wall. Once the virus gains entry, it 21
can travel from cell to cell through the plasmodesmata between the different cells. In animal cells, there is endocytosis, which is receptor-mediated, and membrane fusion. If any part of the capsid is taken up into the host cell itself, the capsid must be removed through the uncoating process. It can involve self-degradation using viral enzymes or using host enzymes or through simple dissociation processes. The viral nucleic acid is then a naked piece of RNA or DNA inside the cell. Once this has been accomplished, replication of the genome can begin. The replication of viruses means the copying of its genome in whatever way the virus need to do this. Viral messenger RNA is synthesized, viral proteins are made, and further viral genome replication is regulated. Sometimes, there are several rounds of messenger RNA synthesis before the nucleic acid is made to make new viral particles. The next step is viral particle assembly. It sometimes requires protein modification or maturation of virus particles before the particles get assembled in the cell cytoplasm. Finally, there is release of virus particles, usually by lysis of the host cell. It generally means that the cell dies. As mentioned, enveloped viruses like HIV leave through budding, which does not involve death of the infected cell. Lysogeny is what happens with some bacteriophage infections, creating a lysogenic cycle rather than a lytic cycle. During this type of cycle, the viral genome will incorporate its genome into the host cell genome or will form a circular plasmid inside the cell. The phage virus’s genetic material is called a prophage that gets transmitted genetically to the daughter cells. Certain events, such as chemicals or exposure to UV radiation, will revert the cycle back to a lytic one that will kill the cell and release particles of new viruses. This process does happen in eukaryotic infections but to a lesser degree. Bacteriophages that only allow for lytic cell replication are called virulent phages, while those that replicate during both types of virus life cycles are called temperate phages. Those daughter cells that contain the viral prophage are called lysogens. They do not die but will switch to the lytic cycle if induction occurs. When there is induction, the prophage is excised and new virus particles are made. Some lysogens have an evolutionary disadvantage, while others are advantageous because they have some gene inside them, for example, that confers resistance to their own host.
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Bacteriophage infections might not seem important to humans but, in fact, they can be very important. Bacteria can go from being non-virulent to highly virulent, just because of lysogenic conversion. This is because the virus that infects these bacteria contain what are called morons, which are genetic elements that confer some type of advantage to the bacterial cell. The examples of this include Corynebacterium diphtheriae infections, which only make diphtheria toxin when the bacterium is itself infected by its own phage. Vibrio cholerae, Streptococcus pyogenes, and Shigella species have the same issue where the organism makes a toxin that is only coded for by viral nucleic acids.
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KEY TAKEAWAYS •
Viruses are not technically forms of life because they lack the recognized features that identify life forms.
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Viruses are obligate parasites and cannot replicate without a host cell.
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Viruses have been studied and treated for thousands of years with the most information gotten in the last hundred years about these particles.
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Viruses have three distinct shapes in general but there are some variations in certain types.
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There are different theories of virus evolution, particularly as they relate to the origin of viruses themselves.
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The viruses have several different classifications based on the type of nucleic acid inside the cell.
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The viral life cycle proceeds the same for most infections but some will have a less typical lysogenic cycle that doesn’t immediately kill the cell.
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Bacteriophage infections indirectly affect animals and humans because some will cause the bacteria infected to be much more virulent in general.
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