Lecture VII_Introduction to virology.pdf

CK TEDAM UNIVERSITY OF TECHNOLOGY & APPLIED SCIENCES INTRODUCTION TO VIROLOGY Eugene Dogkotenge Kuugbee (PhD)  OBJECTIVES At the end of the lecture, students will understand 1. The morphology and characteristics of viruses 2. The classification of viruses 3. The...

CK TEDAM UNIVERSITY OF TECHNOLOGY & APPLIED SCIENCES INTRODUCTION TO VIROLOGY Eugene Dogkotenge Kuugbee (PhD)  OBJECTIVES At the end of the lecture, students will understand 1. The morphology and characteristics of viruses 2. The classification of viruses 3. The various DNA and RNA viruses and the diseases they cause 4. The replication of viruses and 5. The pathogenesis of viruses  INTRODUCTION Viruses are obligate intracellular parasites that can only replicate (or multiply) inside a living cell. Viruses were discovered when bacteria free filtrate, with no particulate material present, was shown to causing disease. The agent causing the disease was named Virus, which means poison. Three main hypothesis explains the origin of viruses: 1. Regressive hypothesis (Reduction or degeneracy hypothesis) : Viruses are remnants of cellular organisms. Viruses may have existed as small cells that parasitized larger cells, and lost the genes required for parasitism over time. 2. Cellular origin hypothesis (Vagrancy, escape, progressive hypothesis): viruses arose from genetic materials that acquired the ability to move between cells. Viruses may have evolved from pieces of DNA or RNA that escaped from genes of larger organisms.  INTRODUCTION 3. Co-evolution hypothesis (virus first hypothesis) : viruses predates or co- evolved with their current cellular host. Viruses might have evolved from complex molecules of protein and nucleic acid at the same time that the first cell appeared on earth. The characteristics of viruses include: 1. Viruses contain a single type of nucleic acid, either RNA or DNA but never both, and contain a protein coat that surrounds the nucleic acid. 2. Viruses are small(20-150 nm), multiply inside living cells using the host synthetic machinery, and totally dependent on living cells for existence 3. They have a receptor binding protein for attaching or docking to cells. They cannot grow on artificial cell free medium 4. They lack proper cellular organization, multiply by complex method, and lack enzymes for protein and nucleic acid synthesis. They lack cell wall, cell membrane, or cellular organelles, and are not susceptible to antibacterial antibiotics  MORPHOLOGY OF VIRUSES The structure of the virus consist of the following: 1. Nucleic acid 2. Capsid 3. Envelope 4. Surface proteins and lipids  MORPHOLOGY OF VIRUSES The viruses are made of nucleic acids and proteins. The viral genome consists of a single nucleic acid containing the genetic information for multiplication. The genome is surrounded by a protein coat called the Capsid made up of polypeptides called capsomeres. The genome and the capsid are collectively called Nucleocapsid. The nucleic acid may be RNA or DNA; double stranded or single stranded; linear or circular; plus polarity or minus polarity; segmented or unsegmented. A nucleic acid that encodes the information for making viral protein is termed positive sense nucleic acid. A nucleic acid made up of complementary base to those of a positive sense nucleic acid is called negative sense nucleic acid. The naked nucleic acid of some viruses is infectious (e.g. Picornavirus, Togavirus, PapovaVirus, Adenovirus, Herpsevirus)  MORPHOLOGY OF VIRUSES-Capsid The function of the capsid includes: To protect the viral genome from external harmful factors, To introduce the viral genome into the host cells, Its antigenic and specific for each virus. Based on the arrangement of the capsomeres around the nucleic acid, three types of symmetry exist for viruses: Icosahedral or cubical symmetry, Helical symmetry and Complex symmetry. MORPHOLOGY OF VIRUSES-envelope Viruses are either enveloped or non-enveloped. The envelope surrounds the nucleocapsid, and is made of lipoprotein. The lipid part is from host cell membrane. The protein part is virus coded, made of PEPLOMERS, projecting as spikes. Peplomers are antigenic, can also bind to surface receptors facilitating entry. Envelope viruses are susceptible to heat and lipid solvents like ether MORPHOLOGY OF VIRUSES- Viral Proteins There are two types: 1. Structural proteins:- present in the coat of the viruses 2. Non-structural (functional) proteins:- these are viral enzymes and haemagglutinins Four groups of enzymes have been detected in viruses: 1. Neuraminidase or sialidase 2. RNA polymerase: copies DNA into RNA 3. Reverse transcriptase (RNA dependent DNA polymerase): transcribes RNA into DNA 4. Enzymes of cellular origin.  CLASSIFICATION OF VIRUSES There are various methods for classification of viruses: 1. Holmes Classification: based on host 3 groups: group I (phagines-attack bacteria), group II (phytophagines- attack plants) and group III(zoophagines (attack animals) 2. International committee for Taxonomy of Viruses (ICTV): Viruses are grouped into family(-viridae) based on morphology, genome structure, strategy of replication. Families are further classified into genera(- virus) based on physicochemical and serological difference 3. Baltimore Classification: Based on genome and replication strategy. CLASSIFICATION OF VIRUSES- (ICTV) CLASSIFICATION OF VIRUSES- (Baltimore Classification)  CLASSIFICATION OF VIRUSES https://www.youtube.com/watch?v=Df_qAFF58Ec https://www.youtube.com/watch?v=rOBXsZ8Xfm0  VIRAL REPLICATION Viruses undergo a complex way of cell division called replication. Six steps are involved: 1. Attachment or adsorption: using viral attachment proteins to receptors. Determines tropism 2. Penetration: translocation, fusion or endocytosis 3. Uncoating: capsid removed, viral genome exposed 4. Biosynthesis: gene expression of the virus 5. Assembly: either in the nucleus or cytoplasm 6. Release and maturation: by lysis (kills cell) or budding (may kill the cell) VIRAL REPLICATION VIRAL REPLICATION  VIRAL REPLICATION 1. ATTACHMENT OR ADSORPTION It is the first and most specific step of viral replication and involves receptor interaction. Viruses have attachment sites on their envelope or capsid protein that bind to complementary site on the host cell. Susceptibility of the host to infection depends on the presence or absence of receptors on the cell surface. E.g. HIV (gp120) binds CD4 on cells; Hemagglutinin of influenza binds Sialic acid on respiratory epithelium 2. PENETRATION After attachment, the virus penetrates into the host cell by: Phagocytosis, viropexis or endocytosis (virus enters in the form of a cytoplasmic vesicle(phagosome); usually non- enveloped viruses); Membrane fusion (direct fusion between envelope of a virus particle and the cell’s plasma membrane after which nucleocapsid is released into the cell; envelope viruses mostly); Translocation (whole non-envelope virus enters the host by moving across the cell membrane); Injection of nucleic acid (Usually by bacteriophages when they cannot cross the cell wall of the bacteria)  VIRAL REPLICATION 3. UNCOATING The viral capsid is separated by lysosomal enzymes for the release of the nucleic acid into the cytoplasm. It varies depending on the nature of the virus: Uncoating by lysosomal enzymes in phagocytic vacuole or Golgi vesicle which degrades the protein of the viral capsid OR Uncoating exclusively by enzymes in the cytoplasm of the host. Infectivity is lost (why?) – proteins on cell or capsid needed to bind to receptor. 4. BIOSYNTHESIS The viral components are synthesized in this step and include the nucleic acid, capsid protein, enzymes for replication, regulatory proteins to shut down host cell metabolism. DNA viruses: replication occurs in the nucleus (EXCEPT poxvirus which synthesize its DNA in the cytoplasm), mRNA transcription and protein translation takes place in the cytoplasm RNA Viruses: replication occurs in the cytoplasm (EXCEPT Retroviruses and Orthomyxoviruses which synthesizes their RNA in the nucleus).  VIRAL REPLICATION BIOSYNTHESIS OF DNA VIRUSES The following steps are involved: 1. The parental DNA is transcribed into early mRNA 2. The early mRNA is translated to produce non-structural proteins 3. Early non-structural proteins shut down the host metabolism and helps in replication of parental DNA to form copies of progeny DNA 4. Progeny DNA undergoes transcription to form late mRNA which are further translated to form late structural proteins (capsid and envelope proteins)  VIRAL REPLICATION BIOSYNTHESIS OF RNA VIRUSES This depends on the RNA genome; TYPE II (Negative sense ssRNA positive or negative sense RNA, Viruses): single or double stranded. The RNA is opposite in polarity to a TYPE I (Positive sense ssRNA mRNA, and hence cannot be directly Viruses): translated to form early proteins The RNA is same polarity with a mRNA, and hence can be directly The (-)ssRNA is first transformed to translated to form early proteins (+)ssRNA using RNA polymerase. The early proteins have RNA The (+) ssRNA is then translated to form polymerase activity that directs the proteins. Also, it acts as a template and replication of the progeny RNA undergoes replication to form copies of the progeny (-)ssRNA (+)ssRNA -→ (-)ssRNA -→ (+)ssRNA. Late proteins are formed by translation of the (+)ssRNA  VIRAL REPLICATION TYPE III (double stranded RNA TYPE IV (Retroviruses): Viruses): Retroviruses have two copies of (+)ssRNA and the enzymes reverse transcriptase and integrase. In the cell, the ssRNA is The dsRNA (reoviridae) have each reverse transcribed to form ssDNA by segment coding for protein. reverse transcriptase. The (+) strand RNA can acts as a The ssDNA is conversated to dsDNA by mRNA and transcribes proteins using DNA polymerase activity of the reverse viral enzymes transcriptase. Both the (+) and (-) strands serve as The dsDNA is transported to the nucleus, templates for the synthesis of integrated into the host chromosome by complementary strands to form the viral integrase, and serve as template for double stranded RNA production of mRNA and genomic progeny RNA  VIRAL REPLICATION BIOSYNTHESIS OF RNA VIRUSES  VIRAL REPLICATION BIOSYNTHESIS OF RNA VIRUSES  VIRAL REPLICATION 5. ASSEMBLY Here, the viral nucleic acid and proteins are assembled together to form the progeny virus (Nucleocapsid) and takes place in the cytoplasm or the nucleus of the host cell. DNA viruses are assembled in the nucleus EXCEPT Hepadnavirus and Poxvirus. RNA viruses are assembled in the cytoplasm 6. MATURATION and RELEASE Maturation of the viruses takes place after assembly, and occurs in the nucleus or cytoplasm or membranes (golgi, endoplasmic or plasma membrane) Release of the virus occurs by LYSIS (as shown by non-enveloped viruses and bacteriophages) OR Budding (as shown by enveloped viruses. The envelope is acquired from the plasma membrane or nuclear membrane)  VIRAL PATHOGENESIS Viral pathogenesis is the sequence of events during the course of viral infection within the host, and the mechanism giving rise to these events. Its simply the process by which virus causes diseases. The capacity of a virus to cause disease is its virulence or pathogenicity. Viral diseases results from (a)viral replication and direct damage to the host cells (cytopathogenesis) or (b)the immune response to the host (immunopathogenesis) The determinants of viral disease include: 1. The strain of the virus (virulence) 2. The target tissue (where it enters the body, ability to gain access to target tissue, viral tropism, permissiveness of cell) 3. Ability of the infection to kill the cell (cytotoxic effect) 4. Quantity of virus inoculated, duration of infection, and immune response of the host VIRAL PATHOGENESIS-Infection process Important events of the virus to cause infection: 1. Virus must invade the host, establish and replicate at site of inoculation 2. Overcome the local defense mechanism and Spread from the site of inoculation to other sites via blood stream 3. Undergo further replication in target organs (local or general) 4. Exit from the host in large numbers to infect other susceptible host cells For an infection to be initiated, three(3) requirements must be satisfied: 1. There must be an inoculum with sufficient viable virus to establish an infection (ID50, LD50, TCID50) 2. The virus must first reach and interact with susceptible cells capable of supporting viral replication 3. The host innate immunity, and pre-existing adaptive immunity must be insufficient to immediately abort the infection.  VIRAL INFECTION Most viral infections progress through the following steps in the body: 1. Transmission (entry into the host) 2. Primary site replication 3. Spread to secondary site 4. Manifestation of the diseases NB: INITIATION, ESTABLISHMENT, OUTCOME OF INFECTION VIRAL INFECTION-ROUTES  VIRAL INFECTION-ROUTES RESPIRATORY TRACT It is the most important entry site of viruses into the body. The cells are protected by the cleansing effect of the MUCUS and the CILIA via a process called mucuciliary escalation Viruses in droplets 5um or less may reach the lungs causing infection. 5-10um are trapped in the bronchioles and trachea, and 10um or more are trapped in the nasal mucosae  VIRAL INFECTION-ROUTES ALIMENTARY TRACT (ORAL) Viruses may be swallowed, or infect cells in the oropharynx to reach the intestinal tract. The Alimentary tract is protected by mucus, some with secretory antibodies (IgA). Viruses are inactivated by bile, stomach acid, proteolytic enzymes, and protected by the buffering action of milk in babies.  VIRAL INFECTION-ROUTES GENITOURINARY TRACT Its protected by mucosal lining, and low pH of vagina. Minute tears and abrasions to vagina, rectal and urethral epithelium facilitates entry. Infection is further facilitated by exchange of body fluids during sex.  VIRAL INFECTION-ROUTES THE SKIN The outer keratinized layer of the skin (stratum corneum) is impermeable to viruses Viruses gain access to the skin when its breached mechanically by trauma, insect bite, animal bite, various inoculations or transfusion procedures.  VIRAL INFECTION-ROUTES THE EYES/CONJUNCTIVA The conjunctiva is cleansed by secreted tears and eyelids. Infection occurs when there is abrasion to the conjunctiva or cornea (e.g. dusty environment). Infection occurs usually by aerosols, rubbing with contaminated fingers, ophthalmic procedures etc.  VIRAL INFECTION-ROUTES VERTICAL TRANSMISSION It’s the transmission of infection from mother to the child. Transmission occurs in three (3) situations: 1. Transmission of viral genomic DNA in ova or sperms which may predispose infants to disease later in life 2. Transplacental spread where infection is passed from infected mother to fetus during pregnancy, and usually involves infected placenta. E.g. HIV, Hepatitis B, Zika virus 3. Perinatal transmission from contamination with infected genital secretions or bowel content during delivery. E.g. Herpes 1,2  SPREAD OF VIRUSES Primary viraemia: viruses spread to the blood stream either from the primary site or from lymph nodes. Primary viraemia is associated with lymphocytes and macrophages in plasma Secondary site replication: viruses are transported from blood stream to the reticuloendothelial system (RES; bone marrow, spleen, liver, endothelial cells) where further multiplication takes place. The RES is the central foci of viral replication. Secondary viraemia: from the RES, viruses spread over into the blood stream leading to secondary viraemia, and results in the onset of non-specific symptoms Target organs: through the blood stream, viruses reach their target organs depending on their tropism. The ability of viruses to infect certain organs determines the pattern of systemic illness.  VIRUS SHEDDING The shedding of viruses is essential to maintain the viruses in the host and the environment Shedding may occur in various stages of the disease: 1. Portal of entry: for viruses that produce local infection 2. Blood: for viruses that spread through vector bite (arboviruses), blood transfusion, needle pricks 3. Near target tissue or organ and 4. No viral shedding: humans are the end stage of certain viruses. MANIFESTATION OF INFECTION The interval between the entry of the virus into the host and appearance of the first clinical manifestation is the INCUBATION PERIOD. The incubation period depends on the distance between the site of entry and the target organ, and also on the immune response and nature of the viruses. Based on clinical outcome, viral infections are categorized into Inapparent (subclinical), Apparent (Clinical or overt) and Latent or persistent infection. Apparent infection could be: Acute, sub-acute or chronic VIRAL PATHOGENESIS AT THE CELL LEVEL Three types of infection can be produced at the cellular level by a virus: 1. Failed or abortive infection 2. Infection leading to cell death (cytocidal or lytic infection) 3. Infection without cell death :2 types (a) Steady state infection (no cell injury) and (b) Persistent viral infection (involves a period of latency) Viruses kills the host cell by several mechanisms including: (a) Inhibition of host cell DNA (b) Inhibition of protein synthesis (c)Fusion of cells (Syncytia formation) (d) Disruption of cell cytoskeleton (e) Immune mediated lysis (f) Induction of apoptosis and (g) Release of progeny viruses by lysis VIRAL PATHOGENESIS AT THE CELL LEVEL Some viruses also induce some morphological characteristics that change the staining properties of the host cell. The changes could be by: 1. Damage to the host cell chromosome (e.g. chromatin dot) 2. Formation of inclusion bodies: aggregates of virion or viral proteins or products of viral replication that confer altered staining property i. Intracytoplasmic: acidophilic/pink ii. Intranuclear: basophilic iii. Both intracytoplasmic or intranuclear VIRAL PATHOGENESIS AT THE CELL LEVEL HOST RESPONSE TO VIRAL INFECTIONS The human body exerts some resistance to viruses on entry to prevent them from causing disease. Two types of resistance is been exerted by the body: (1) Non-specific resistance (Innate response) and (2) Specific immune response : Antibody mediated immunity and Cell mediated Immunity The non-specific immune response include: Phagocytosis, Interferon, Nutrition, Age, Body temperature, Hormones and stress. The main innate response to viral infections is the production of interferons which inhibits viral replication in infected and uninfected cells. Specific immune response is by antibody mediated immunity and cell mediated immunity. Antibodies which protect against viral infection are IgG, IgA and IgM. The IgG and IgM activity is via neutralizing process of viral attachment, penetration and uncoating. IgA is produced by plasma cells locally in mucous membranes of respiratory and digestive tract. It prevents spread of viruses from local surfaces HOST RESPONSE TO VIRAL INFECTIONS Cell mediated immune response is by T-cells due to presence of viral specific receptors on their surfaces. T-cells on encounter with viruses gets activated into lymphoblast and secrete soluble factors known as lymphokines Other cells include NK cells, Killer cells and macrophages which directly attack viruses (mostly in innate response) The immune response exerted by the host leads to three events: 1. Destruction of infected cells 2. Production of interferons to interfere with viral replication 3. Neutralization of viral infectivity HOST RESPONSE TO VIRAL INFECTIONS PREVENTION OF VIRAL INFECTIONS Immunoprophylaxis is mainly applied in prevention of viral diseases using: 1. Vaccines I. Live Vaccines II. Killed or inactivated vaccines 2. Antisera or immunoglobulins I. Heterologous II. Homologous