GENERAL PROPERTIES OF VIRUSES
Viruses are the smallest infectious agents ranging from about 20 nm to 300 nm in diameter.
They have nucleic acid that is encased in a protein shell, which may be surrounded by a lipid-containing membrane. The entire infectious unit is termed a virion.
Viruses belong to an independent status because of several distinguishing features which set them apart from other familiar microbial agents:
1. They are acellular
2. They replicate by a self-assemblage process and not by binary fision, budding etc., as associated with other microbes.
3. They are obligate intracellular parasite that infect virtually all types of cells (plant, animal & bacteria)
4. They contain either RNA or DNA as their genetic materials (but not both)
5. They lack an energy generating system and so, they do not demonstrate any significant metabolic activity.
6. They depend on their host biosynthetic machinery for survival.
7. Viruses are specific in the type of cell and host they infect.
8. They show variation in size and shapes, structure, genome organization and expression, strategies of replication and transmission.
TERMS RELATED TO VIRAL PROPERTIES
a) Capsid: They are symmetric protein shell or coat that encloses the nucleic genome
b) Nucleocapsid: This represents the capsid together with the enclosed nucleic acids
c) Capsomere: They are morphologic units seen in the electron microscope on the surface of virus particles. It represents clusters of polypeptides, which when completely assembled, form the capsid
d) Virion: This is a complete infective virus particle
e) Envelope: A lipid-containing membrane that surrounds some virus particles. It is acquired during viral maturation by budding process through a cellular membrane.
f) Defective virus: A virus particle that is functionally deficient in some aspect of replication.
g) Subunit: A single folded viral polypeptide chain.
STRUCTURE OF VIRUSES
Most viruses are extremely adapted to their host organism; hence virus structure varies greatly. However, there are some general structural characteristics that all viruses share in common.
All viruses have a protein capsid that contains its genetic materials (Nucleic Acid). The capsid is made of protein called protomers. Capsid construction varies greatly among viruses with most being specialized for a particular virus’s host organism. Some viruses, mostly those that affect animals and man have membranous envelope surrounding their capsid. This allows the virus to penetrate host cells through membrane fusion.
The virus genetic materials rest inside the capsid, this genetic material can be either DNA or RNA and never both. The type of genetic material a virus contains is used in viral classification. In addition to the nucleocapsid, some viruses mostly those that infect bacteria have a tail region which is often an elaborate protein structure that aids in the binding of the virus to the surface of a susceptible host cell and eventual release of the viral genetic material into it.
VARIATIONS IN SIZE AND SHAPES
Viruses come in an amazing variety of shapes and sizes. They are very small and are measured in nanometer (i.e. one-billionth of a meter 10-9). Megaviruses, Mimiviruses and Pandoraviruses are some of the largest known viruses which range from 1 - 2.5 mb (1mb = 1,000,000bp of DNA).
The amount and arrangement of the proteins and nucleic acid of viruses determined their size and shapes. The Nucleic Acid and proteins of each class of viruses assemble themselves into a structure called Nucleoproteins/Nucleocapsid.
Some viruses have more than one layer of protein surrounding the nucleic acid; others have a lipoprotein membrane called an envelope which is derived from the membrane of the host cell that surrounds the nucleocapsid core penetrating the membrane (It is common to animal viruses e.g. Hepatitis C)
Animal viruses exhibit extreme variation in size and shape. The smallest animal viruses belong to the families Parvovaviridae and Picornaviridae which measure about 20nm and 30nm in diameter respectively. Viruses of these two families are icosahedrons in shape and contain nucleic acid with limited genetic information. Viruses of the family Poxviridae are about 250-400nm in diameter and they are neither polygons nor filamentous. Poxviruses are structurally more complex than simple bacteria.
Animal viruses that have rod-shaped (helical) nucleocapsids are those enclosed in an envelope; these viruses are found in the families – Paramyxoviridae, Orthomyxoviridae, Coronaviridae and Rhabdoviridae. Not all enveloped viruses contain helical nucleocapsids e.g. those of the families Herpesviridae, Retroviridae and Togaviridae have polygonal nucleocapsids.
The shape and size of any given virus is related to the size of the viral genome and to the nature of the capsid proteins. Some viral genomes are so small that they code for only a few structural proteins. For example, viruses that exhibit helical capsid symmetry have only one type of capsid protein, whereas viruses with other types of symmetry may have several types of capsid proteins.
Therefore, it is the interactions of these proteins subunits (bonding between their amino acid R-groups) that determine the specific geometric patterns of the virus capsid. On the basis of this, the following symmetry are identified:
i. Helical capsid symmetry
ii. Icosahedral capsid symmetry
iii. Complex or combined symmetry
Images of the three types of symmetry found in viruses
HELICAL SYMMETRY
This composed of a single type of capsomere stacked around a central axis to form a helical structure which has a central tube. This arrangement may result in rod shaped or filamentous virion. The identical protein subunit of helical capsids is arranged end to end in the shape of a rod with each turn of the rod possessing the same number of subunits. Non-covalent bond is formed between amino acids on adjacent subunits on the same turn of spiral as well as between adjacent turns of the spiral.
The vast number of non-covalent bonds gives the capsid tremendous structural stability, which is similar to the hydrogen bonding between strands of DNA molecule. This produces a filamentous appearance of the virus. A good example of a filamentous, naked plant virus with helical nucleocapsid is Tobacco Mosaic Virus (TMV) while an example of an enveloped helical animal virus is influenza virus.
ICOSAHEDRAL CAPSID SYMMETRY
Spherically shaped nucleocapsids are constructed according to an icosahedral (a polygon with 20 triangular faces). Capsomeres that are connected to five neighbouring capsomeres are called Pentamers while those with six neighbouring capsomeres are called hexamers. It is worthy of note that as the size of a virus increases, the numbers of capsomeres increases. For example adenoviruses have been shown to have about 252 capsomeres. Arrangement of nucleic acids in the core of icosahedral viruses appeared to be one tightly coiled unit in some viruses while in others it appeared to be coiled fragments.
These groups of viruses possess capsid that is neither purely helical nor purely icosahedral and may possess extra structures such as protein tail or a complex outer wall. These viruses have symmetric constructions that are complex or may be referred to as a combination of a helical and icosahedral symmetry. Examples of viruses in this category are poxviruses, orf virus, T- even phages (coliphages) etc. The T-even phages especially possess a collar structure located at the base of its head which connects to a tail assembly that is in the shape of a helical sheath surrounding an inner hollow core. It is through this core that DNA located in the head, can be injected into the bacterium during infection process.
Images of bacteriophage and influenza viruses showing their major component
VIRAL GENOME/ NUCLEIC ACID
The viral genome is the molecular blueprints for the building of intact virion. It may be DNA or RNA which may be double stranded (ds) or single stranded (ss), linear or circular. Viruses with RNA genomes are called ribo-viruses and those with DNA genomes are called deoxyviruses. Plants viruses for example, generally possess RNA genomes with a few exceptions such as cauliflower mosaic virus (CMV), which contains DNA. Animal viruses and bacteriophages on the other hand, generally possess DNA (only very rarely they possess RNA).
The nucleic acid of each virus encode the genetic information for the synthesis of proteins. In almost all free living organisms, the genetic information is in the form of ds DNA arranged along the length of the double helix molecule.
In viruses however, genetic information comes in variety of forms both on the basis of number of strands in the genome and the type of nucleic acid. The four major types of viruses recognized include:
a. Single stranded DNA - ss DNA viruses e.g. coliphages
b. Double stranded DNA - ds DNA viruses e.g. Herpes virus, smallpox virus, Vaccinia, T-even bacteriophages
c. Single stranded RNA - ss RNA viruses e.g. TMV, Polio virus
d. Double stranded RNA - ds RNA viruses e.g. Reo viruses
In ss RNA viruses, the genome may be plus – strand RNA (when it functions as m RNA) or minus- strand RNA (when it acts as complementary strands from which messenger RNA (mRNA) is synthesized). In some cases, virion possesses a segmented genome e.g. orthomyxoviruses which are minus-strand RNA molecules. Most ds RNA viruses have segmented genomes with each segment representing a single gene that encodes the information for the synthesis of a single protein. The virion of most plant viruses, many animal viruses and bacteria viruses are composed of ss RNA and in most of these viruses the genomic RNA is termed +ve strand. This is because the genomic RNA acts as mRNA for the direct synthesis (translation) of the viral protein.
Several large families of animal viruses (Rhabdoviridae) particularly, contain genomic ssRNA termed –ve strand that is complementary to the mRNA. All –ve strand RNA viruses have an enzyme called an RNA-dependent RNA polymerase (transcriptase) which must first catalyse the synthesis of complementary mRNA from the virion genomic RNA before viral protein synthesis can occur. These variations in the nucleic acids of viruses form one central criterion for viral classification.
In ssRNA viral family called Retroviridae, the RNA of these viruses is +ve strand but the viruses are equipped with an enzyme called a reverse transcriptase that copies the ssRNA to form dsDNA. In some viral family, they contain genomes that are partially ds and partially ss example of such is Hepadnaviridae.
VIRAL PROTEINS
The proteins determine the antigenic characteristics of the virus. Hence, the host’s protective immune response is directed against antigenic determinants proteins or glycoproteins exposed on the surface of the virus particle.
It was earlier believed that viruses lack enzymes, but now some viruses have been discovered to contain enzymes. Some viruses carry enzymes (proteins) inside their virions. The spikes of enveloped viruses like influenza, measles and mumps contain the enzyme neuraminidase which facilitates their penetration into the host cell. In some cases, the spikes contain haemoglutinin that allows clumping of RBCs and help in adsorption to specific host cell, e.g. polio viruses, adenoviruses, influenza, measles and mumps etc. The tips of bacteriophage contain the enzyme lysosome which enhances its penetration into the host cell.
In retroviruses such as HIV, Rous Sarcoma Virus, an RNA-dependent DNA polymerase called reverse transcriptase is found associated with its genome which help in DNA synthesis from the viral RNA through the process called reverse transcription.
The structural proteins of viruses have several important functions and involved the following:
1. They facilitate the transfer of viral nucleic acid from one host cell to the other.
2. They protect the viral genome against inactivation by nucleases
3. They participate in the attachment of the viral particles to a susceptible host cell
4. They provide the structural symmetry of the virus particle.
A number of different viruses contain lipid envelopes as part of their structure. The lipid is acquired when the viral nucleocapsid buds through a cellular membrane during maturation. This process occurs where virus-specific proteins have been inserted into the host cell membrane (this is typical of many animal viruses). Phospholipid composition of any viral envelope is determined by the specific type of cell membrane involved in the budding process.
Viral envelopes also do contain glycoproteins which in contrast to lipids in viral membrane, are encoded and so they are not derived from the host cell. It is by means of which enveloped virus attaches itself to a target cell by interacting with a cellular receptor on the host’s cell surface (s).
REACTIONS OF VIRUSES TO PHYSICAL AND CHEMICAL AGENTS
There is great variation in the heat stability of different viruses which may be attributed to the symmetric arrangement of the capsid proteins. Viruses are known to be affected by physical factors such as; heat, salts, pH, Radiation and chemical agents like; ether, detergents, formaldehyde etc. For example, icosahedral viruses tend to be stable as they lose little infectivity after several hours at 37oC. However, enveloped viruses are much more heat labile. Viral infectivity is generally destroyed by heat at temperatures between 50 – 60oC within 30 minutes. Viral stability is a very important factor in vaccine production and administration. For example polio vaccine must be stored at freezing temperature to preserve its potency. Viruses are usually stable between pH values of 5.0 and 9.0 but majority of viruses are destroyed by alkaline conditions.
CRYSTALLIZATION OF VIRUSES
What is viral crystallization?
Crystallization is the process of transformation of viral components into organized solid particles. Crystallization of biological macro molecules including viral components is use to study structural characteristics. Direct visualization of viruses became possible after the evolution of electron microscopes in 1940. In 1935, TMV became the first virus to be crystallized followed by the successful crystallization of polio virus in 1955.
A virus crystal consists of thousands of viruses and because of its purity it is well suited for chemical studies. Dr Wendell Stanley achieved the first crystallization of viruses in 1935. However, he was not the first to try to purify TMV but the methods available were not adequate to produce virus samples pure enough to work with. Dr Stanley succeeded when he employed precipitation with lead acetate combined with a novel centrifugal method. The crystallized virus he achieved was strong enough that 1cm3 of a solution containing one part of its liquid would infect a tobacco plant. The crystallized virus was found to be 17million times greater than that of the heaviest known protein. Thereafter, other scientists later proved that the virus was not only a protein as Stanley proposed but a nucleoprotein. Hence, Stanley crystallized a living matter in a characteristically non-living form. This discovery was the basis of his Nobel prise for Chemistry in 1946.
TABLE 1 BELOW SHOWS THE LIST OF SOME VIRUSES BY NAME
S/N NAMES OF VIRUSES
1. Hantaan virus
2. Hendra virus
3. Hepatitis A virus
4. Hepatitis B virus
5. Hepatitis C virus
6. Hepatitis E virus
7. Hepatitis delta virus
8. Horsepox virus
9. Human adenovirus
10. Human astrovirus
11. Human coronavirus
12. Human cytomegalovirus
13. Human enterovirus 68, 70
14. Human herpesvirus 1
15. Human immunodeficiency virus
16. Human papillomavirus 1
17. Human parainfluenza
18. Human parvovirus B19
19. Human respiratory syncytial virus
20. Human rhinovirus
21. Human SARS coronavirus
22. Human spumaretrovirus
23. Human T-lymphotropic virus
24. Human torovirus
25. Influenza A virus
26. Influenza B virus
27. Influenza C virus
28. Isfahan virus
29. JC polyomavirus
30. Japanese encephalitis virus
31. Junin arenavirus
32. KI Polyomavirus
33. Kunjin virus
34. Lagos bat virus
35. Lake Victoria marburgvirus
36. Langat virus
37. Lassa virus
38. Lordsdale virus
39. Louping ill virus
40. Lymphocytic choriomeningitis virus
41. Machupo virus
42. Mayaro virus
43. MERS coronavirus
44. Measles virus
45. Mengo encephalomyocarditis virus
46. Merkel cell polyomavirus
47. Mokola virus
48. Molluscum contagiosum virus
49. Monkeypox virus
50. Mumps virus
51. Murray valley encephalitis virus
52. New York virus
53. Nipah virus
54. Norwalk virus
55. O'nyong-nyong virus
56. Orf virus
57. Oropouche virus
58. Pichinde virus
59. Poliovirus
60. Punta toro phlebovirus
61. Puumala virus
62. Rabies virus
63. Rift valley fever virus
64. Rosavirus A
65. Ross river virus
66. Rotavirus A
67. Rotavirus B
68. Rotavirus C
69. Rubella virus
70. Sagiyama virus
71. Salivirus A
72. Sandfly fever sicilian virus
73. Sapporo virus
74. SARS coronavirus 2
75. Semliki forest virus
76. Seoul virus
77. Simian foamy virus
78. Simian virus 5
79. Sindbis virus
80. Southampton virus
81. St. louis encephalitis virus
82. Tick-borne powassan virus
83. Torque teno virus
84. Toscana virus
85. Uukuniemi virus
86. Vaccinia virus
87. Varicella-zoster virus
88. Variola virus
89. Venezuelan equine encephalitis virus
90. Vesicular stomatitis virus
91. Western equine encephalitis virus
92. WU polyomavirus
93. West Nile virus
94. Yaba monkey tumor virus
95. Yaba-like disease virus
96. Yellow fever virus
97. Zika virus
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virology STM326