Virus An important biomolecule in Bio-engineering

Md. Hasib Al Mahbub Student ID: 0902045 Email: mahbub1332@gmail.com Abstract Virus is one of the most important biomolecules which are used in bio-engineering. It is acellular, non-cytoplasmic infectious agents. They may be spherical or golf ball-like, rodshaped, tadpole-like, helical or polyhedral. It replicates inside the living cells of other organisms and outside the cell, they behave like inert chemicals. Viruses contain only a single type of nucleic acid either DNA or RNA. They are host specific that they infect only a single species and definite cells of the host organisms. They cause highly infectious diseases to animals including human beings, angiosperms, bacteria and fungi. Human diseases like common cold, influenza, chickenpox, Ebola, AIDS, avian influenza, SARS are caused by viruses. Virus has a major application in microbiology, medicine and nanotechnology in production of vaccines, recombinant DNA etc. and has a great economic importance. This article contains fundamental information about virus on structure, classification, life cycle, major human diseases and its application in different sectors. Keyword: Virus, DNA, RNA, Capsid, Genome, Replication. Introduction Viruses are a unique group of biological entities known to infect every type of cell, including bacteria, algae, fungi, protozoa, plants, and animals. They are the simplest form of life. Indeed they are so simple that they exist on the borderline between the living and the inanimate, non-biological world as they are unable to replicate on their own. [1] They are obligate parasites in the sense that they can only replicate after they have invaded and parasitized a host cell and usually causes death or loss of function of that cell. [1] Most viruses have either RNA or DNA as their genetic material. The nucleic acid may be single- or double-stranded. The entire infectious virus particle, called a virion, consists of the nucleic acid and an outer shell of protein. The simplest viruses contain only enough RNA or DNA to encode four proteins. The most complex can encode 100 200 proteins. [2] Virus is not cellular in nature and structure is very compact and economical. Viruses have played key roles in shuffling and redistributing genes among organisms and by causing diseases in animals and plants. Viruses are important to the study of molecular and cell biology as they provide simple systems that can be used to manipulate and investigate the functions of cells. For example, viruses have been useful in the study of genetics and helped our understanding of the basic mechanisms of molecular genetics, such as DNA replication, transcription, RNA processing, translation, protein transport, and immunology. [2] Viruses are important in medical research for finding cures for common diseases. Also, viruses are source of vaccines that prevent common infections. Viruses are beneficial Gene therapy, Cancer prevention and control of harmful or damaging organisms, in both agriculture and medicine. History and origin of viruses The concept of a virus as a distinct entity dates back only to the very late 1800s. [1] By the end of the 19th century, viruses were 1

defined in terms of their infectivity. The first images of viruses were obtained upon the invention of electron microscopy in 1931 by the German engineers Ernst Ruska and Max Knoll. [3] The true nature of viruses was discovered in 1933, when the biologist Wendell Stanley prepared an extract of a plant virus called tobacco mosaic virus (TMV) and attempted to purify it. [4] The second half of the 20th century was the golden age of virus discovery and most of the over 2,000 recognized species of animal, plant, and bacterial viruses were discovered during these years. [5] Three main hypotheses that describe the origin of viruses are [6] - 1. The progressive, or escape, hypothesis states that viruses arose from genetic elements that gained the ability to move between cells; 2. The regressive, or reduction, hypothesis asserts that viruses are remnants of cellular organisms; and 3. the virus-first hypothesis states that viruses may have evolved from complex molecules of protein and nucleic acid at the same time as cells first appeared on Earth and would have been dependent on cellular life for billions of years. Structure Viruses vary greatly in appearance and size. The smallest are only about 17 nanometers in diameter, and the largest are up to 1000 nanometers (1 micrometer) in their greatest dimension. [6] The largest viruses are barely visible with a light microscope, but viral morphology is best revealed using the electron microscope. Viruses are so small that they are comparable to molecules in size. A hydrogen atom is about 0.1 nanometer in diameter, and a large protein molecule is several hundred nanometers in its greatest dimension. [2] All viruses have the same basic structure: a core of nucleic acid surrounded by protein. Individual viruses contain only a single type

of nucleic acid, either DNA or RNA. The DNA or RNA genome may be linear or circular, and single-stranded or doublestranded. [7] Nearly all viruses form a protein sheath, or capsid, around their nucleic acid core. The capsid is composed of one to a few different protein molecules repeated many times. In some viruses, specialized enzymes are stored within the capsid. Many animal viruses form an envelope around the capsid rich in proteins, lipids, and glycoprotein molecules. While some of the material of the envelope is derived from the host cells membrane, the envelope does contain proteins derived from viral genes as well. [8] Viral Components: Capsids, Nucleic Acids, and Envelopes A complete virus particle, known as a virion, consists of nucleic acid surrounded by a protective coat of protein called a capsid. [6] These are formed from identical protein subunits called capsomers. Viruses can have a lipid "envelope" derived from the host cell membrane. Virus components can be represented with a flowchart: [7]
Capsid Covering Envelope (not found in all viruses) Nucleic acid molecule(s) (DNA or RNA) Matrix proteins enzymes (not found in all viruses)

Virus Particle Central Core

All viruses have a protein capsid, or shell, that surrounds the nucleic acid in the central core. Together the capsid and the nucleic acid are referred to as the nucleocapsid. [9] Members of 13 of the 20 families of animal viruses possess an additional covering external to the capsid called an envelope, which is usually a modified piece of the hosts cell membrane. Viruses that consist of 2

only a nucleocapsid are considered naked viruses. As we shall see later, the enveloped viruses also differ from the naked viruses in the way that they enter and leave a host cell. A fully formed virus that is able to establish an infection in a host cell is often called a virion. [10] Viral Capsid In general, the capsid of any virus is constructed from a number of identical protein subunits called capsomers. The capsomers can spontaneously self-assemble into the finished capsid. Depending on how the capsomers are shaped and arranged, this assembly results in two different types: helical and icosahedral. [8] The simpler helical capsids have rod-shaped capsomers that bind together to form a series of hollow discs. These can be short and highly rigid, or long and very flexible. The genetic material, in general, single-stranded RNA, but ssDNA in some cases, is bound into the protein helix by interactions between the negatively charged nucleic acid and positive charges on the protein. Enveloped helical nucleocapsids are more flexible and tend to be arranged as a looser helix within the envelope. [11] This type of morphology is found in several enveloped human viruses, including those of influenza, measles, and rabies. The capsids of a number of major virus families are arranged in an icosahedron a three-dimensional, 20-sided figure with 12

evenly spaced corners. [9] The arrangements of the capsomers vary from one virus to another. The Viral Envelope Many types of virus have a glycoprotein envelope surrounding the nucleocapsid. The envelope is composed of two lipid layers interspersed with protein molecules of lipoprotein bilayer and may contain material from the membrane of a host cell as well as that of viral origin. [6] The virus obtains the lipid molecules from the cell membrane during the viral budding process. However, the virus replaces the proteins in the cell membrane with its own proteins, creating a hybrid structure of cell-derived lipids and virus-derived proteins. Many viruses also develop spikes made of glycoprotein on their envelopes that help them to attach to specific cell surfaces. [12] Nucleic Acids Just as in cells, the nucleic acid of each virus encodes the genetic information for the synthesis of all proteins. While the doublestranded DNA is responsible for this in prokaryotic and eukaryotic cells, only a few groups of viruses use DNA. [9] Most viruses maintain all their genetic information with the single-stranded RNA. There are two types of RNA based viruses. In most, the genomic RNA is termed a plus strand because it acts as messenger RNA for direct synthesis of viral protein. A few, however, have negative strands of RNA. In these cases,

(a) Naked Nucleocapsid Virus

(b) Enveloped Virus

Figure 1: Generalized structure of viruses. [7]

the virion has an enzyme, called RNA dependent RNA polymerase (transcriptase), which must first catalyze the production of complementary messenger RNA from the virion genomic RNA before viral protein synthesis can occur. [11] Genome An enormous variety of genomic structures can be seen among viral species; as a group, they contain more structural genomic diversity than plants, animals, archaea, or bacteria. [13] There are millions of different types of viruses, although only about 5,000 of them have been described in detail. [6] Genomic diversity among viruses are found on the basis of following properties and parameters: Table 1: Genomic diversity among viruses. [12]
Property Nucleic acid

CTV system and Baltimore classification system, which places viruses into one of seven groups. [14] Accompanying this broad method of classification are specific naming conventions and further classification guidelines set out by the International Committee on Taxonomy of Viruses. The International Committee on Taxonomy of Viruses began to devise and implement rules for the naming and classification of viruses early in the 1970s. Currently (2012), seven orders, 96 families, 22 subfamilies, 420 genera, and 2,618 species of viruses have been defined by the ICTV. This universal virus classification system employ the hierarchical levels of Order, Family, Subfamily, Genus, and Species. [15] The Baltimore system of virus classification provides a useful guide with regard to the various mechanisms of viral genome replication. The central theme here is that all viruses must generate positive strand mRNAs from their genomes, in order to produce proteins and replicate themselves. The precise mechanisms whereby this is achieved differ for each virus family. [16] This classification places viruses into seven groups: [16] i. ii. iii. iv. v. vi. vii. Double-stranded DNA Single-stranded (+)sense DNA Double-stranded RNA Single-stranded (+) sense RNA Single-stranded (-) sense RNA Single-stranded (+) sense RNA with DNA intermediate in life-cycle Double-stranded DNA with RNA intermediate

Shape

Strandedness

Sense

Parameters DNA RNA Both DNA and RNA (at different stages in the life cycle) Linear Circular Segmented Single-stranded Double-stranded Double-stranded with regions of singlestrandedness Positive sense (+) Negative sense () Ambisense (+/)

Virus classification Viruses are mainly classified by phenotypic characteristics, such as morphology, nucleic acid type, mode of replication, host organisms, and the type of disease they cause. Currently there are two main schemes used for the classification of viruses: the

Viral life cycle The general phases in the life cycle of animal viruses are adsorption, penetration, uncoating, synthesis, assembly, and release from the host cell. The length of the entire multiplication cycle varies from 8 hours in polioviruses to 36 hours in herpesviruses. [7] 4

1. Adsorption: The virus attaches to its host cell by specific binding of its spikes to cell receptors. 2. Penetration: The virus is engulfed into a vesicle by endocytocis. 3. Uncoating: The envelope of the virus is removed, and the RNA is freed into the cytoplasm. 4. Synthesis: Replication and Protein Production. Under the control of viral genes, the cell synthesizes the basic components of new viruses: RNA molecules, capsomers, and spikes.

Figure 2. Penetration of a bacterial cell by a T-even bacteriophage. [17]

Figure 3. Events in the multiplication cycle of T-even bacteriophages. The lytic cycle (17) involves full completion of viral infection through lysis and release of virions. Occasionally the virus enters a reversible state of lysogeny (left) and is incorporated into the hosts genetic material. [17]

5. Assembly: Viral spike proteins are inserted into the cell membrane for the viral envelope; nucleocapsid is formed from RNA and capsomers. 6. Release: Enveloped viruses bud off of the membrane, carrying away an envelope with the spikes. This complete virus or virion is ready to infect another cell. The range of structural and biochemical effects that viruses have on the host cell is extensive. These are called cytopathic effects. [12] Most virus infections eventually result in the death of the host cell. The causes of death include cell lysis, alterations to the cell's surface membrane and apoptosis. Often cell death is caused by termination of its normal activities because of suppression by virus-specific proteins, not all of which are components of the virus particle. Stages in the multiplication cycle of T-even bacteriophages is shown in figure 3. Role of virus in human disease There are many types of viruses that cause a wide variety of viral infections or viral diseases. For example, there are over 200 different viruses that can cause a cold or an upper respiratory infection. [18] Other common viruses include the influenza virus, which causes influenza or the flu. Some viruses can cause serious diseases, including AIDS, SARS, Hepatitis, Herpes Simplex etc. The transmission may be by air, water, body contact, food, different arthropods and parasites etc. [12] Some viruses can cause lifelong or chronic infections, where the viruses continue to replicate in the body despite the host's defense mechanisms. This is common in hepatitis B virus and hepatitis C virus infections. People chronically infected are known as carriers, as they serve as reservoirs of infectious virus. In populations with a high proportion of carriers, the disease is said to be endemic. [19]

A list of very common diseases and its responsible viruses are listed in table 2. Table 2: List of diseases caused by viruses [2]
Disease Name Influenza Herpes Simplex Chicken pox (Varicella) Measles (Rubeola) German Measles (Rubella) Mumps (Epidemic Parotitis) Small Pox (Variola) Yellow Fever Dengue Fever Hepatitis A Hepatitis B NANB Hepatitis Viral Gastroenteritis Viral Fevers AIDS Rabies Polio Virus Type RNA DNA DNA RNA RNA Organs Affected Respiratory Tract Skin, Pharynx, Genital organs Skin, Nervous System Respiratory Tract, Skin Skin

RNA

Salivary Glands, Blood Skin, Blood Liver, Blood Blood, Muscles Liver Liver Liver Intestine Blood T lymphocytes Brain, Spinal cord Intestine, Brain, Spinal Cord

DNA RNA RNA RNA DNA RNA RNA RNA Retrovirus ( RNA) RNA RNA

At the beginning of the twentieth century, 0.8% of the population died each year from infectious diseases. [18] During the last century, progress in the control of infectious diseases through improved sanitation, safer water supplies, the development of antibiotics and vaccines, and better medical care have dramatically reduced the threat to human health from these agents, especially in 6

developed countries. Today the rate is less than one-tenth as great. [7] The use of vaccines has led to effective control of the most dangerous of the viruses. Smallpox virus has been eradicated worldwide by means of an ambitious and concerted effort, sponsored by the World Health Organization, to vaccinate all people at risk for the disease. Poliovirus and measles virus have been eliminated from the Americas by intensive vaccination programs. Death rate from infectious diseases in the United States, 19001996. The death rate dropped over the twentieth century from around 800 deaths per 100,000 population per year to about 50. [7] Significant milestones in public health are shown. After dropping steadily for 80 years, interrupted only by the influenza pandemic of 19181919, the death rate began to rise in 1980 with the advent of the AIDS (acquired immunodeficiency syndrome) epidemic. [7] Deaths worldwide due to infectious disease are shown in Figure. 4, divided into six categories. In 2002 more than 3 million

deaths occurred as a result of acute respiratory disease, much of which is caused by viruses. More than 2 million deaths were attributed to diarrheal diseases, about half of which are due to viruses. AIDS killed 3 million people worldwide in 2002, and measles is still a significant killer in developing countries. The incidence of disease in various parts of the world caused by a number of widespread viruses. In the Americas and, for most viruses, Europe as well, widespread use of vaccines has almost eliminated disease caused by viruses for which vaccines exist. [21] In developing countries, measles, poliovirus, yellow fever virus, and rabies virus, as well as others, still cause serious problems although good vaccines exist. However, developed countries as well as developing countries suffer from viruses for which no vaccines exist to the current time. Human immunodeficiency virus (HIV) is the most striking example of the appearance of a virus that has recently entered the human

Figure 4. Six leading infectious diseases as causes of death. Data are the totals for all ages worldwide in 1995. [7] 1998, and 2002. The data came from the World Health Organization

population and caused a plague of worldwide importance. The arrival of this virus in the United States caused a noticeable rise in the total number of deaths from infectious disease. Application of virus in different sectors Viruses have been useful to us as tools for the study of molecular and cellular biology. Further, the development of viruses as vectors for the expression of foreign genes has given them a new and expanded role in science and medicine, including their potential use in gene therapy. [21] The major application of virus is found in medicine, life science, material science, food microbiology and nanotechnology. The powerful techniques developed by life sciences are becoming the basis of engineering approaches towards nanomaterials, opening a wide range of applications far beyond biology and medicine. [22] Knowledge about mechanisms of viral replication has helped to modify viruses for various purposes. For instance, the ability of virions to introduce their contents into the cytoplasm and nuclei of infected cells has been adapted for use in DNA cloning and offers possibilities in the treatment of certain diseases. [11] Being useful in the study of genetics and it helped our understanding of the basic mechanisms of molecular genetics, such as DNA replication, transcription, RNA processing, translation, protein transport, and immunology. [23] In different industrial manufacturing processes use of different types of viruses are found. Which also proves the economic importance of virus also. Expression of heterologous proteins by viruses is the basis of several manufacturing processes that are currently being used for the production of various proteins such as vaccine antigens and antibodies. Industrial processes have been recently developed using viral vectors and a

number of pharmaceutical proteins are currently in pre-clinical and clinical trials. [6] Viruses are increasingly being used in as tools and building blocks for electronics, chemistry, and biomedical science. They have potential uses in a variety of nanotechnology applications. Vaccins for different types of deadly diseases are invented by the application of recombinent DNA technology. With the development of science virus has also become beneficial in the control of cancer. [12] Some viruses are innately able to target and destroy cancer cells, while other methods use molecular approaches based on viral vector systems to create specific therapeutics. For controlling insect pests Baculoviruses can be used which is a large group of viruses that infect insects and other arthropods. [23] Virus vectors is used for the expression of a missing protein as a cure for the genetic defect associated with its absence. Some of these monogenic diseases might be curable through the use of gene therapy. [7] To date, several hundred patients have been treated with vectors based on Moloney murine leukemia virus in clinical trials. Clinical trials have also been conducted that use adenovirus. adeno-associated virus, poxvirus, and herpesvirus vectors. [7] Virus can also be synthesized and the first synthetic virus was created in 2002. [24] The synthesized virus is rather a DNA genome (in case of a DNA virus), or a cDNA copy of its genome (in case of RNA viruses). [25] This technology is now being used to investigate vaccination processes. The ability to synthesize viruses has far reaching consequences, since viruses can no longer be regarded as extinct, as long as the information of their genome sequence is known and permissive cells are available. Currently, National Institutes of Health has

genome sequences of 2048 viruses in their online database publicly. [26] Conclusion Viruses influence the evolution of life form the prebiotic beginnings of replicator molecules and replicating programs, to the first cells; from the origin of the eukaryotic nucleus to multicellularity and from worms to humans. All life has been touched by viral influences. Virus are not only harmful but also beneficial in some cases. The knowledge of replication is evolutionary for production of different kind of vaccines. In all types of biological activities this kind of microbe plays a potential role. Development of vaccines, Food nutrition analysis, medicine, nanotechnology, agricultural invention etc. are followed by the continuous research on virus. Our knowledge of viruses continues to expand rapidly and in near future it is expected to have a wide range of application in gene therapy. References
[1] Koonin EV, Senkevich TG, Dolja VV. The ancient Virus World and evolution of cells. Biol. Direct. 2006; 1:29. [2] Gelderblom HR. Structure and Classification of Viruses. In: Baron S, editor. Medical Microbiology. 4th edition. Galveston (TX): University of Texas Medical Branch at Galveston; 1996. Chapter 41. Available from: http://www.ncbi.nlm.nih.gov/books/NBK8174/ [3] Steinhardt E, Israeli C, Lambert R.A. Studies on the cultivation of the virus of vaccinia. J. Inf Dis. 1913; 13(2):294300. [4] Stanley WM, Loring HS. The isolation of crystalline tobacco mosaic virus protein from diseased tomato plants. Science. 1936; 83(2143):85. [5] Norrby E. Nobel Prizes and the emerging virus concept. Arch. Virol. 2008; 153(6):1109 23.

[6] Dimmock, N.J; Easton, Andrew J; Leppard, Keith (2007) Introduction to Modern Virology sixth edition [7] Strauss, J. H., & Strauss, E. G. (2007). Viruses and human disease. Academic Press. [8] Imaging of viruses by atomic force microscopy. J Gen Virol. 2001; 82(9):2025 2034. [9] Caspar DL, Klug A. Physical principles in the construction of regular viruses. Cold Spring Harb. Symp. Quant. Biol. 1962; 27:124 [10] Crick FH, Watson JD. Structure of small viruses. Nature. 1956; 177(4506):4735. [11] Davidson, Michael W. Virus Structure, Florida State University. Available from: http://micro.magnet.fsu.edu/cells/virus.html. Retrived on: 16/2/2014 [12] Collier, Leslie; Balows, Albert; Sussman, Max (1998) Topley and Wilson's Microbiology and Microbial Infections ninth edition, Volume 1, Virology, volume editors: Mahy, Brian and Collier, Leslie. Arnold. [13] Breitbart M, Rohwer F. Here a virus, there a virus, everywhere the same virus. Trends Microbiol. 2005; 13(6):27884. [14] Lwoff A, Horne RW, Tournier P. A virus system. C. R. Hebd. Seances Acad. Sci. 1962; 254:42257. [15] King AMQ, Lefkowitz E, Adams MJ, Carstens EB. Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier; 2011. [16] Baltimore D. The strategy of RNA viruses. Harvey Lect. 1974; 70 Series: 5774. [17] Talaro, K. P. Foundations in Microbiology' 2007 Ed. (sixth Edition) 2007 Edition, Rex Bookstore, Inc. [18] Centers for Disease Control and Prevention (1998), Botulism in the United States 1899-1996: Handbook for Epidemiologists, Clinicians, and Laboratory Workers, Atlanta, Georgia. [19] Bertoletti A, Gehring A. Immune response and tolerance during chronic hepatitis B virus

infection. Hepatol. Res. 2007; 37 Suppl 3:S331 8. [20] Einstein MH, Schiller JT, Viscidi RP, Strickler HD, Coursaget P, Tan T, Halsey N, Jenkins D. Clinician's guide to human papillomavirus immunology: knowns and unknowns. The Lancet Infectious Diseases. 2009; 9(6):34756. [21] Matsuzaki S, Rashel M, Uchiyama J, Sakurai S, Ujihara T, Kuroda M, Ikeuchi M, Tani T, Fujieda M, Wakiguchi H, Imai S. Bacteriophage therapy: a revitalized therapy against bacterial infectious diseases. Journal of Infection and Chemotherapy: Official Journal of the Japan Society of Chemotherapy. 2005; 11(5):2119. [22] Fischlechner M, Donath E. Viruses as Building Blocks for Materials and Devices. Angewandte Chemie International Edition. 2007; 46(18):318493. [23] Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James (2008).Viruses: Structure, Function, and Uses. [24] Cello J, Paul AV, Wimmer E. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science. 2002; 297(5583):10168. [25] Coleman JR, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S. Virus attenuation by genome-scale changes in codon pair bias. Science. 2008; 320(5884):17847. [26] Genomes. "NIH viral genome database". Ncbi.nlm.nih.gov. Retrieved on 10/2/2014.

10