The Viruses

Dr. Akepati S. Reddy School of Energy and Environment Thapar University Patiala (PUNJAB) 147001 INDIA

Viruses and life

Virus originates from Latin word poison First used by Pasteur to describe infectious agent for rabies First virus discovered was tobacco mosaic disease virus (TMV)
Characteristics of life Have cells Grow and maintain their structure by taking up nutrients and energy from the environment and generate wastes Respond to their external environment Reproduce and pass on their organization to their offspring Evolve and adopt to their environment Viruses Themselves do not possess a cell - Noncellular or acellular Obligate intracellular parasites Have no ATP generating system Have no means for protein synthesis (ribosomes) ?

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Extraordinarily simple in physical and chemical properties Appear as non-living but have some properties of living things - Do not metabolize, do not utilize energy, do not produce waste, do not grow, and do not adapt to environment, but reproduce in living cells

Size, Structure and Morphology

Size
Very small entities (20 to 300 nm polio virus and poxvirus smallest bacteria measures 200 nm) Can not be observed by light microscope needs electron microscope its invention (1940s) started virology development Discovered in early 1900s as filterable particles - bacteria are not filterable

Structure
Nucleic acid (genome) encased in a layer of protein (capsid) Some have membrane like envelope Genome + capsid = nucleo-capsid (virus particle and virion)

Nucleic acid
DNA or RNA (never both) single or double stranded continuous or segmented molecule takes over the host cell metabolism and produces new virus particles

Size, Structure and Morphology

Capsid
Single type or many types of proteins Organized into a series of repeating units (capsomers) Many but fixed even number of identical capsomers chemically bound together to form capsid 252 in Herpes simplex Protects viral genome and gives shape to virus Involved in procuring new host cells (has binding sites)

Envelope
Not all viruses are enveloped envelope is common in animal viruses (pox virus, herpes simplex) naked virus (no envelope) Derived from host cell membrane but differ from it (have certain viral specified proteins) In some, envelop has spikes (glycoprotein projections on envelope) responsible for attachment Enhances transmission through protecting from drying

Susceptibility to chemical agents

Detergents or lipid solvents can react with envelope Phenols can react with capsid protein Formaldehyde can alter genome

Size, Structure and Morphology

Morphology
Helical
Genome is in the form of spiral coil Capsid follows this spiral arrangement Rabies virus & tobacco mosaic virus (TMV) are examples

Polyhedral (icosahedral)
Icosahedral has 20 equilateral trinagular pieces joined together to form 12 edges and 12 points Adeno virus, mumps virus, chickenpox virus, herpes simplex are examples Certain viruses have neither icosahedral nor helical symmetry Pox virus has box like arrangement - ultramicroscopic rods cover the surface

Size, Structure and Morphology

Enveloped
Appear spherical because of the envelope Helical and polyhedral are enveloped Rabies virus is helical and enveloped Herpes virus is icosahedral and enveloped Influenza virus is 8 helical nucleocapsids enclosed in an envelope Viruses without envelope are known as naked viruses

Complex
Bacterio-phages Has a head region, contractile tail region, a set of tail fibers and a base plate with tail pins

Host range and specificity

Supposedly all cellular life forms have associated viruses All viruses are limited in their host range - for some the range is limited to a single species (in some cases not even the entire species) Binding Sites on the viral capsid or envelope should match with Receptor Sites on host cell membrane Restriction-modification systems as well as biochemical incompatibilities can limit the phage host range
through mutations host-range barriers can be overcome and can change the host range changes in host range, through transduction, allow gene exchange between distantly related bacteria

When the range is wide usually more closely related host species are included in the range Have limited tissue or cell specificity
Dermotropic, Neurotropic (Polio virus on nerve cells), Pneumotropic (Adenovirus on upper respiratory Tract), Lymphotropic, Viscerotropic (Liver, heart, spleen, etc.) Differences in surface markers or in physiologies of host cells may be responsible

Viral Replication/ Infection cycle

Involves penetration of host cell, and utilization of its metabolism for producing new virus particles
In the process the host cell is destroyed, tissues are progressively deteriorated and disease development occurs

Burst size: number of viruses released by host cell upon lytic cycle Virus has capacity to increase in number at a rate much higher than their cellular hosts
hence has ability to cause disease

Replication cycle can be considered to include the following steps

Adsorption/attachment Penetration Uncoating Synthesis Assembly/maturation Release

Infection/replication cycle

Infection/replication cycle

Viral Replication/ Infection cycle

Viruses are termed as Lytic if they destroy the host cells to release their progeny - have no mechanism
for progeny virus release except poking holes in the membrane to avoid making and release of progeny virus

Temperate, if they are entering into a lysogenic relationship with their host
Chronic infection: Release of virions occur without lysis of host cells, and the latter multiply while continuously leaking virions

A lytic cycle is considered to include Eclipse period (starts with phage adsorption and ends with maturation of phage progeny in the infected cell) Latent period spans from phage adsorption to cell lysis Lysis: Mechanism of host cell destruction involves following
virus terminates its infection to release progeny phages Poking of holes in the plasma membrane occurs Enzymatic destruction of the host cell wall can also occur

Viral Replication/ Infection cycle

Adsorption/Attachment
Needs attachment sites on virus surface and receptor sites on host cell surface Involves interaction between viral proteins (either capsomer or envelope proteins) and host cell receptor sites - spikes on envelope can act as attachment sites Antibodies produced by host cells can cover the attachment sites and unable this step

Penetration
Involves entry of virus genome into host cell and may involve
Dissolution of host cell membrane (bacteriophages) Phagocytosis in non-enveloped virus (human and animal cells) Union of envelope with host cell membrane (enveloped viruses)

Uncoating (eclipse)
involves setting free of viral core or genome in the host cell cytoplasm - Cellular enzymes dissolve the protein coat

Entry step of bacteriophage

Entry of Enveloped virus

Viral Replication/ Infection cycle

Synthesis
Can be divided into two periods
Early period synthesis of proteins required for replication of viral genetic material occurs Late period nucleic acid replication and synthesis of capsid and envelope proteins

Involves synthesis of viral proteins and replication of viral nucleic acid Nucleic acid of viral genome directs synthesis
Encodes new enzyme proteins that interfere with host cells gene expression

Energy and building blocks needed for the synthesis (amino acids and nucleotides) are supplied by the host cells

Transcription and protein synthesis

All necessary genetic information is brought into host cells by the viral genome
Some of the genes specify the proteins used in the viral synthesis and some other genes direct the protein synthesis

Viral Replication/ Infection cycle

Transcription and protein synthesis
Host cell ribosomes are used in the protein synthesis In case of RNA virus, the viral RNA directly serves as mRNA in protein synthesis (if it is an anti-sense RNA, then it is used as template for mRNA synthesis)
In case of DNA virus, the viral DNA provides genetic code for the mRNA synthesis

In certain cases, viral DNA, instead of immediate replication, may proceed to nucleus and integrate into host cell chromosome (lysogeny lisogenic or provirus) and at later stage encoding of synthesis of viral particles is initiated temperate virus
RNA virus can also be lysogenic viral RNA is used as template for complementary DNA synthesis and this DNA becomes lysogenic (HIV virus)

Transcription

Viral Replication/ Infection cycle

Replication of viral genome
In case of DNA viruses, the DNA core goes into the nucleus and replicates there In case of RNA virus, the RNA core remains in the cytoplasm and produce m-RNA or m-RNA complementary In case of Retrovirus, Reverse Transcriptase enzyme is produced and reverse transcription occurs
The RNA genome acts as a template for the production of one strand of DNA this in turn acts as template and viral DNA synthesized Synthesized viral DNA enters the nucleus to direct viral replication

Viral Replication/ Infection cycle

Assembly (maturation)
Combining of replicated viral nucleic acid with viral capsid proteins and acquisition of envelope Place of assembly may differ from virus to virus
in many it occurs in cytoplasm in some genome synthesis occurs in nucleus and capsid synthesis in cytoplasm capsids go into nucleus for assembly assembled nucleo-capsids migrate back to cytoplasm

In case of DNA viruses, capsomeres are transported into the nucleus, and assembly occurs in nucleus In case of RNA virus, the RNA core is replicated in the host cell cytoplasm and the assembly also occurs in the cytoplasm

Viral Replication/ Infection cycle

Release:
Intracellular virus particles exit host cells to the extracellular environment For some viruses it is part of the maturation - Enveloped virus acquires the envelope during this stage
Nucleo-capsid moves to the membrane and forces its way through membrane by budding process Host cell membrane surrounds the nucleo-capsid and then the membrane is modified with viral proteins The enveloped virus then pinches off and creates a hole (which may later be sealed)

Release can be host cell lysis release or chronic release virulent viruses or lytic type
During release lysozyme enzymes may breakdown host cell wall Interrupted host cell metabolism may lead to spontaneous decay of the host cell

Replication cycle of bacteriophages

Lytic cycle (T-even bacteriophage)
Phages obligately lytic are known as virulent (tailed phages) Filamentous phages follow chronic infection Virus injects genetic material (DNA) into the cell and capsid remains outside Tail releases lysozyme No virions can be recovered from infected cells Capsids and DNA are assembled into complete virions and release of virions occurs through breaking of the plasma membrane Burst time (from attachment to release) is 20-40 minutes and burst size is 50 to 200

Lysogenic cycle (temperate phages- Lambda phage)

Injected linear phage DNA circularizes and enters either lytic or lysogenic cycle Phase DNA integrates with bacterial chromosome and becomes prophage and remains latent called as latent state Binary fission distributes prophage to both daughter cells Due to a stimulus prophage DNA is removed from the bacterial chromosome (known as excision) and lytic cycle is initiated

Replication cycle of Animal virus

Attachment to susceptible cell Penetration (Uptake of nucleocapsid into cell) - can be through direct fusion with cell membrane or through endocytosis Targeting of nucleo-capsid to site of reproduction Uncoating of nucleic acid from capsid (lysosomal, cytoplasmic or viral enzymes may be involved) Synthesis of viral proteins (in cytoplasm) Replication of nucleic acid (occurs in nucleus in case of DNA virus and in cytoplasm in case of RNA virus) Maturation of virion particles Virion release from cell - occurs through
lysis of cells - in case of naked virus - poliovirus Budding viral proteins get incorporated in specific areas of the membrane and enveloped virus buds through the membrane in those areas host cell does not necessarily die - HIV

Virus spread within host Exit of virus from host and transmission to new host

Retroviruses, Reverse Transcriptase and Reverse Transcription

Classification and Nomenclature

No universally accepted classification system Categorization of viruses can be based on Nucleic acid type
DNA or RNA double stranded or single strand if single stranded RNA whether it is positive or negative (can or can not act as mRNA) single stranded RNA can be iether positive or negative stranded Segmented nucleic acid and single continuous molecule

Capsid symmetry Presence or absence of envelope Host range and tropism (host specificity)
for some it is limited to a single species and for some it may extend to a group of most closely related species within a single species a virus may be limited to a particular type of cells or tissues compatibility of receptor sites influences the range

Infection physiology No binomial nomenclature is used - Still known by common names (polio virus, pox virus, etc.)

Growing of Viruses
Bacteriophages
Grow lawn of Bacteria on a Spread Plate Add Bacteriophages Infection will result in Plaques (clear zones on plate)

Animal Viruses
On living Animals (mice, rabbits, guinea pigs) On chicken Embryos (Eggs) - used to be most common method and still used to produce many vaccines On cell Cultures (most common method these days)

Cell Cultures
Primary Cell Lines (die out after a few generations) Diploid Cell Lines (derived from human embryos and maintained for up to 100 generations) Continuous Cell Lines - transformed cells (cancerous cells), may be maintained indefinitly

Detection of Viruses
Electron microscopy Immunologic Assays: Detect specific viral proteins or antibodies to them. Western Blotting ELISA Biological Assays: Detect cytopathic effects (CPE) caused by viral infection of cells. Plaque assays for lytic viruses Focus formation for transforming oncogenic viruses Hemagglutination Assay: Many viruses clump red blood cells. Molecular Assays: Assay for viral nucleic acids. PCR (Polymerase chain reaction) Southerns (DNA) or Northerns (RNA)

Viruses and Diseases and Symptoms

Effects of viruses on humans Liver (yellow fever or hepatitis) Respiratory tract (influenza, common cold and respiratory syncytial disease) Brain (rabies, encephalitis, polio) Gastrointestinal tract (gastroenteritis) Symptoms of infection (unique and differ with virus) Brain cells infected by rabies virus develop Negribodies WBC affected with mononucleosis virus become granulated and foamy and form characteristic downy cells Skin rashes are developed by measles, chickenpox virus etc. Viral infection can cause or develop
cells to fuse into larger bodies called syncytia cells to clump together (agglutination) intracellular aggregates (inclusions in cells - cytopathic effects: non lytic damage caused to host cells by virus)

Lysogenesis can stimulate cancerous growth (oncogenic virus) herpes viruses and Epstein-barr virus cause tumors & cancers Certain forms of leukemia can be stimulated by viruses Lambda phage (prophage) can change bacterial properties can supply genes to code exotoxins and convert non-pathogenic bacteria into pathogenic

Impacts of Animal Viruses on Cells

Mechanisms of Viral Pathology

Cytopathic effects
Negative effects of viral infection on individual cells Include cell abnormalities (biochemical and morphological) and/or cell death (cytocidal effects - deadly cytopathic effects) Different from the damage caused by lytic viruses during release of their progeny Consequence of differences in metabolic needs between the virus and the host cell

Syncytia
Multinucleated gaint cells formed from the fusion of host cells Unwieldy (difficult to carry or manage because of size, shape, weight, or complexity) and face premature death infected cells have virus adsorption proteins on their surface help in binding with uninfected cells in forming syncytia (HIV) Inclusion bodies - Intracellular granules developed in the infected host cells often useful for virus identification purposes

Cell mediated immunity

Virus infected host cells are recognized by the immune system and destroyed an important mechanism for cytopathic effects Virus infected cells are distinguished from uninfected cells through recognition of presence of viral proteins and destruction

Mechanisms of Viral Pathology

Antibody dependent cellular cytotoxicity (ADCC)
Antibodies (produced in response to the viral proteins present on the host cell membrane) bind to the surface infected cells Natural killer cells recognize presence of antibody bound infected host cells and destroy them

Cyto-toxic T-cell mediated immunity

Infected cells do not display the viral proteins on their surface Partially broken down intracellular viral proteins are brought in contact with Major Histocompatibility Complex (MHC) proteins and are together displayed on the surface of cells Cytotoxic T lymphocytes (CTLs), a type of white blood cells, capable of reversibly interacting with MHC proteins, strongly bind to altered MHC proteins and induced host cell destruction

Latent infection
Cell mediated immunity often forces the infection to become latent only to re-emerge upon immuno-depression Development of latent infection development on bodys response to viral infection and the type of viral infection

Viruses and Cancer

Cancer
Uncontrolled growth eventually forms a single cell into a clone of tumour cells these cells can in turn disseminate and spread to other parts of the body A healthy cell to become cancer cell a series of changes (including genetic changes) must occur These changes slowly release the cell from the multiple checks and balances that control normal growth of the cell Cancer takes many years to develop after exposure to a risk factor hence cancer is a disease of middle and older age

Viruses associated with cancer

Viruses are associated with 20% of the cancers the viruses associated with cancer in humans include
Human T-lymphotropic virus 1 Human papillomavirus Hepatitis B and Hepatitis C Kapasis sarcoma associated herpes virus Epstein-Barr virus

Both DNA viruses and retroviruses can cause cancer

These are capable of persisting in the host cell after the initial infection (virus evades the hosts immune response)

Viruses and Cancer

How viruses can cause cancer?
Virus infection alone is not enough to cause cancer a series of other essential events are needed Can remove/incorporate genes/genetic material into host cells Can cause cancer by two mechanisms
Directly cause cancer: Products of the viral genome enhance growth potential and/or survival of the host cell Indirectly cause cancer: Virus acts as a cofactor for tumour (severe immunosuppression by HIV allows other viruses to cause uncontrolled cell growth)

Probable ways of casuing cancer are

Animal cells have proto-oncogenes insertion of DNA of the virus into host chromosome mutates proto-oncogene into oncogene and this causes cancer Insertion of viral DNA near a gene that regulates cell growth and division can increase the latters transcription and cause cancer Viruses may produce proteins that bind to the tumor suppressors and transform cells into tumor cells

Control of Viral Diseases

Antibiotics are useless viruses do not have their own chemistry or metabolism to interfere with Certain drugs can interfere with replication of viruses within host cells
Acyclovir interferes with replication of herpes virus in skin cells Azidothymidine (AZT) interferes with HIV replication in lymphocytes Amantadine interferes with influenza virus

Interferon protein produced by infected host cells and released to adjacent host cells result in antiviral factors production and interfere with infection drug for future antiviral therapy Stimulation of immune system Viral infection stimulates host cells to produce antibodies Antibodies neutralize the attachment sites and interfere with viral attachment Vaccines - through stimulating the immune system these make host cells to produce antibodies before they are infected by virus

Control of Viral Diseases (contd..)

Vaccines
Consist of viruses altered in a way not to replicate in the host cells but stimulate the immune system First vaccine was used by Jenner (1798) against smallpox - contained live vaccinia (cowpox) virus.

Three types Live attenuated vaccines: Mutant viral strains produce an asymptomatic infection in host.

Examples: Polio (oral, Sabin vaccine), measles, yellow fever, mumps, rubella, and chickenpox. Advantages: Better immune response Disadvantages: May cause disease due to contamination, genetic instability, or residual virulence

Killed or inactivated vaccines: Virus is typically grown in eggs or cell culture and inactivated with formalin.
Examples: Polio (Salk vaccine), rabies, influenza A & B. Advantages: Immunization with little or no risk of infection. Disadvantages: less effective, inactivation may alter viral antigens.

Recombinant vaccines: Viral subunits are produced by genetically engineered cells - Example: Hepatitis B
Advantages: Little or no risk of infection. Disadvantages: Less effective immune response.

Important human viruses

Infectious diseases causing most deaths worldwide in 1998 and contribution by viruses
Disease
Acute Respiratory* Diarrheal diseases

Cause
Bacterial or viral Bacterial or viral

Deaths/year
4,400,000 3,200,000

Tuberculosis
Malaria Hepatitis B Measles AIDS Neonatal Tetanus

Bacterial
Protozoan Viral Viral Viral Bacterial

3,100,000
3,100,000 2,000,000 1,500,000 1,000,000 600,000

*: Pneumonia, bronchitis, influenza, etc.

HIV and AIDS

HIV (Human Immunodeficiency Virus)
Discovered by Luc Montagneir of the Pasteur Institute in 1984 An enveloped retrovirus with dsRNA

Replication
Has receptor sites on CD4 cells Penetrates CD4 cell through fusion of envelop with host cell membrane Genome gets integrated into the host genome as proviral DNA and can remain latent for a median period of 10 years Turning on the viral genome can occur from other infections, stress or shock, drug abuse, alcohol abuse, nutrition, lack or too much of exercise, sun burn, etc. Turning on of the HIV genome results in death usually within 2 years

Transmission
by exposure to infected body fluids, like, blood, semen, vaginal secretions and breast milk (sex, needle, blood to blood contact and mother to child are main routes)

HIV life cycle

HIV and AIDS

AIDS (Acquired Immune Deficiency Syndrome) caused by HIV results in failue of immune system and death usually results from opportunistic infections
Immune system can be cellular (cells phagocytize) or humoral (destruction or inactivation by antibodies)

Characteristics and symptoms

Acute infection lasts for 2 weeks characterized by viremia (fever, headache, weakness and muscle and joint aches) CD4 cell count is normal (1200/mm3) Asymptomatic disease virus is latent in CD4 cells CD4 cell count is <1000/mm3 HIV positive antibodies can be detected in blood but no symptoms of illness Symptomatic disease CD4 cell count is<600/mm3 HIV genome is turned on and symptoms of illness begin to appear symptoms include chronic fatigue, night sweats, diarrhea and weight loss body becomes susceptible to infections Advanced disease CD4 cell count is <200/mm3 characterized by severe opportunistic infections

HIV and AIDS

Testing for HIV
ELISA (Enzyme Linked Immunosorbant Assay) test (a blood test)
If positive the same sample should be tested again if positive again then should go for Western Blot Test

Western Blot Test (a test for the HIV viral antigens)

Treatment
No cure AZT (Azidothymidine) which can inhibit reverse transcription can be used As combination therapy AZT is used along with 3TC and protease inhibitor Vaccine for HIV not feasible HIV mutates very rapidly during reverse transcription

Influenza Virus
Enveloped ssRNA (negative) virus of helical shape Genome is divided into 8 segments Nucleo-capsid has transcriptase enzyme

Infection/replication cycle Has two antigens on the spikes of the envelope (neuraminidase and hemagglutin) Breakdown of these antigens is needed for penetration
Enzymes needed for the breakdown are found in the respiratory tract of mammals and digestive tract of birds

Virus enters host cells by endocytosis Disintegration of envelope and capsid releases the genome and RNA dependent RNA transcriptase into cell
RNA replicates in the host cell nucleus

Influenza Virus
Replication/infection cycle (contd..)
Prior to release by budding hemagglutinin and neuraminidase molecules are inserted onto membrane After release of influenza virus the host cell dies

Have no RNA proof reading enzymes

RNA transcriptase makes nucleotide insertion errors (1 in 10,000) Every new manufactured influenza virus is thus a mutant

Commonly infects birds and mammals and known as flu

Water fowl are reservoirs of influenza viruses Bird flu, human flu, Dog flu, Swine flu and Horse flu

Three types
Influenza-A: responsible for the pandemics infects humans, pigs, chicken, horses and birds (also seals and whales) Influenza-B: infects only humans Influenza-C: not important human pathogen

Influenza Virus
Sub-types of influenza-A
H1N1 causative of Spanish flu H2N2 causative of Asian flu H3N2 causative of Hong Kong flu H5N1 a current pandemic threat (currently it is mostly bird flu) H1N2 (endemic in humans and pigs), H7N2, H7N3, H7N7 (has unusual zoonotic potential), H9N2, H10N7
Hear H and N are antigens present on the spikes of the envelope

Transmission
Highly contagious - can make many people ill in a short period of time - transmits through contact with droplets from the nose and throat of infected person who is coughing and sneezing Disease infects the nose, throat or lungs Often breaks out as an epidemic and spreads from town to town and country to country - an area can have epidemic conditions for four to six weeks

Influenza Virus
Symptoms

Onset of symptoms range from 18 to 72 hours

First indication is chills and chilly sensation; Fever with temperature 102 to 103F during first few days; Many develop aches and pains throughout the body (more pronounced in the back and legs) Other symptoms include fatigue, irritated watering of eyes, loss of smell, nasal congestion, nausea and vomiting, reddened eyes, skin, mouth and throat, running nose, pharyngitis (sore throat), and sneezing Many of the symptoms are caused by the huge production of interferon from influenza infected cells Common cold like symptoms! - more severe than the common cold and can even lead to death

Influenza Virus
Effects of infection
Recovery takes about 1 to 2 weeks, but can be deadly for the weak, old or chronically ill people Some develop life-threatening complications like pneumonia, bronchitis, sinus and ear infections Peak prevalence in winter (appears year round in tropics) Spreads rapidly around the world in seasonal epidemics (WHO estimates 250000 to 500000 deaths) Kills millions in pandemic years (usually occur following major genetic changes in the virus)

Prevention
Vaccination - highly variable effectiveness (due to high mutability) - confers protection only for a few years Infection by unexpected strains possible even in the same season of vaccination Vaccination takes a few days for becoming effective may provide only partial coverage for the unexpected strains Vaccination can lead to appearance of general infection symptoms which are usually not severe and long lasting Vaccine (killed or inactivated viruses) can be allergic Personal health and hygiene is important for avoiding or minimizing influenza

Influenza Virus
Treatment
Plenty of rest drinking of lot of liquids avoiding alcohol and tobacco Use of acetaminophen to relieve fever and muscle aches associated with flu Avoid Asprin can lead to Reye syndrome (potentially fatal disease of liver)

H5N1 sub-type of influenza-A

Has high lethality and virulence and is a current pandemic threat Currently it is mostly a bird flu (avian influenza) and endemic in many bird populations of south-east Asia No evidence suggesting its human to human transmission or air borne transmission Has potential to mutate into a strain that is capable of efficient human-to-human transmission

Hepatitis B virus
Causes liver disease It is cause for the current epidemics in parts of Asia and Africa 3-6% of the world population is currently infected
10% is infected in Southeast Asia and Africa, and only 1% in North America and Europe

An icosahedral enveloped virus with partially double stranded DNA genome

a long and a short strand of DNA overlap each other and form a closed circle

Size is 40-48 nm

Hepatitis B Virus
Replication cycle
DNA genome upon entry through endocytosis relocates itself into host cell nucleus and transcribe mRNA This mRNA is translated into viral polymerase and core proteins In the cytoplasm DNA genome transcribes pre-genome RNA Viral polymerase and the pre-genome RNA along with the core proteins are used in the assembly of core particles Within the core particles reverse transcription of the pregenome RNA occurs and nucleocapsid results! The particle obtains envelope through entering the endoplasmic reticulum The virus particle comes out of the ER as a transport vesicle and enters the galgi apparatus From galgi it comes out as a vesicle and gets released from the cells through vesicle merger with the cell membrane

Hepatitis B Virus
Transmission of the disease
By exposure to body fluids containing the virus (saliva, blood and semen) - mechanisms of transmission include Unprotected sex and direct contact with infected individuals blood and blood products transfusions reuse of contaminated needles and syringes vertical transmission from mother to child during birth

Disease development
Response of the hosts immune system results in both hepatocellular damage and viral clearance Infected cells are killed, antiviral cytokines capable of purging out virus from viable cells are produced and virus elimination also by lymphocytes Antigen non-specific inflammatory cells and platelets facilitate accumulation of lymphocytes into the liver Bodys ability to clear infection depends on persons age
Only 5% of the infected newborns can clear infection 70% of infected children of 1 to 6 years age can clear infection 95% of infected adults or older children can clear infection If infection not cleared then infected becomes chronic carrier

Hepatitis B Virus
Symptoms
Infection is acute/chronic & incubation period is 2-6 mon. Acute infection
It begins with general ill health, loss of appetite, nausea, vomiting, body aches and mild fever The illness progresses into jaundice (acute viral hepatitis) and lasts for a few weeks and then gradually improves A few patients develop more severe liver disease known as fulminant hepatic failure and even death

Chronic infection
Poor immune response is responsible Patient experiences fatigue Associated with chronic inflammation of liver can leads to liver cirrosis over several years time Dramatically increases the incidence of liver cancer (2nd most important cause after smoking for liver cancer)

In some the infection can be entirely asymptomatic Hepatitis D requires concomitant infection with hepatitis B
Coinfection increases the risk of cirrosis and liver cancer

Hepatitis B Virus (HBV)

Diagnosis
Serum or blood tests are used and infection is detected by detecting presence of viral antigens or antibodies by host Screening for Hepatitis B surface Antigen (HBsAg)
Can be detected only during a small window period may not be present during early infection and may not be detectable at later stage of infection

Screening for HBeAg (Hepatitis B e antigen)

Appears shortly after the appearance of HBsAg Presence indicates much higher rate of viral replication Some variants of HBV do not produce this antigen During natural course of infection this antigen is cleared

Anti-HBs antibodies for HBsAg Clearing of infection also clears the HBsAg and also anti-HBs Antibodies of the HB core antigen (anti HBc-IGM) Anti-HBe (antibodies to the e antigen)
Appearance is associated with decline in viral replication

PCR tests can also be used for detecting and measuring the amount of viral nucleic acid in the clinical specimen

Hepatitis B Virus (HBV)

Treatment
For chronic cases following treatment is recommended
Antivirals such as lamivudine and adefovir USFDA (food and drug administration) approved Entecavir, and EU commission approved PEGASYS Immune system modulators such as interferon alpha Combination therapy does not offer any advantages Chronic carriers should avoid alcohol consumption

Treatment with antibodies is suggested for Infants born to HBV positive mothers and for individuals exposed to HBV Therapy generally works through reducing viral load and helping hosts immune system in clearing infection

Prevention
Vaccination is highly effective
Vaccines based on the viral proteins are used vaccination of newborns is recommended Boosters not needed (but recommended for health workers - 10 yr.)

HIV positive patients apparently have inferior antibody response to HB vaccination

Poliovirus
General information
Causative agent for polio (a disease causing damage to the nervous system and paralysis) Most common in infants and young children (often called as infantile paralysis) Greatest risk areas include primarily Indian subcontinent and to a lesser extent West and Central Africa Number of cases reported around the world are just around one thousand
50,000 cases were recorded in 1975 Only 1115 cases have been recorded in 2006 uptill 29th August all from four countries (Nigeria, India, Pakistan and Afganistan) Nigeria accounted for 2/3rd of the cases

Polio virus
Non-segmented, linear ssRNA+ virus Non-enveloped virus

Poliovirus
Life cycle of Polio Virus
Only one, of about 200 viruses encountering, enters a host cell Binds to the receptor site conformational changes occur in the capsid (is it preparation for uncoating?) Models of entry of virus into the host cell
Injection of just genome into host cell cytoplasm Receptor protein mediated endocytosis

Viral ssRNA acts as mRNA and translates into a single long polyprotein, which in turn cleaves to form the proteins involved in the replication and packaging and the viral copier proteins RNA replication is carried out by RNA polymerase first nonsense strand is formed and from it RNA genome is produced Host cells own protein synthesis is stopped Viral ssRNA enters the immature capsid formed from the selfassembly of capsid proteins and mature capsid is formed Assembled viral particles wait for cell lysis for their release and infection of neighboring cells

Life cycle of Poliovirus

Poliovirus
Infection and disease development
Poliovirus can infect anterior horn cells of spinal cord, dorsal root ganglia, motor neurons, skeletal muscles and lymphoid cells Enters the host body orally and infects intestinal wall (lymphoid tissue underlying the mucosa) Multiplies in number and enters blood (viremia) From blood the virus infects other tissues
Has special affinity to the cell bodies of motor neurons (which carry commands to muscles) Invasion of nerve cells can cause paralysis of muscles Which muscles are affected depends which nerve cells are infected

Damage is caused mainly by cytopathic effects of the virus In rare cases oral polio vaccine can revert to virulent form and cause vaccine derived polio

Poliovirus
90% of the infections are almost asymptomatic or their disease is indistinguishable from influenza 9% of the infections develop into non-paralytic polio Only 1% of the infections, that too if not immunized, develop into paralytic polio
Of these 10% of the cases result in death, 40% of the cases in partial recovery with permanent paralysis, and full recovery in 50% of the cases 79% of the paralytic polio cases are spinal (19% of these may be with bulbar symptoms) 2% of all the paralytic polio cases are bulbar polio

Symptoms
Incubation period is 3 to 35 days and symptoms of infection start appearing after 7 to 14 days of infection Early symptoms of infection include fatigue, fever, vomiting, headache and pain in the neck and back and muscle pain Symptoms of non-paralytic polio include fever, vomiting, abdominal pain, lethargy and irritability, and some muscles becoming tender Post polio syndrome: additional symptoms in people survived polio after decades (muscle weakness, extreme fatigue, etc.)

Poliovirus
Diagnosis
By blood test to detect antipolio antibodies By virus isolation and culturing

Transmission
Called as the disease of civilization The infected excrete virus in the feces Through fecal contaminated water and food Hands contaminated with stool of the infected is major source The infected is the most contagious source from a few days before to a few days after the start of symptoms In rare cases oral vaccine can cause polio in immuno-compromised individuals, attenuated virus, even without reversion, can cause severe disease

Treatment
There is no treatment

Poliovirus
Prevention
Preventable by immunization and by better sanitation Two types of polio vaccines
Inactivated Polio Vaccine (IPV):
It is (formalene) inactivated polio virus developed by Jonas Salk of University of Pittsburgh and given as injection less effective in preventing spread among non-vaccinated persons, but causes no polio disease

Oral Polio Vaccine (OPV):

Live attenuated (weakened virus) vaccine (by Albert Sabin) produced by passing the virus through non-human cells at subphysiological temperature Indirectly protects other susceptible persons through this virus spread, but In rare cases cause vaccine derived polio

Recommended schedule for vaccination

2 doses of IPV (at 2 and 4 months age), and 2 doses OPV (at 12-18 months and 4-6 years age) 4 doses of only IPV (at 2, 4, 12-18 months and 4-6 years age) 4 doses of only OPV (at 2, 4, 6-18 months and 4-6 years age) Booster dose for people traveling to areas of polio prevelance

Dengue Virus
Dengue virus and dengue fever
Three levels of pathogenicity
Typical Dengue Fever, Dengue Hemorrhagic Fever (DHF), and Dengue Shock Syndrome (DSS)

Caused by four serotypes of the virus

Flavivirus serotypes DEN-1, DEN-2, DEN-3 and DEN-4 First infection leads to the development of long-lasting, nonoverlapping immunity (a serotype can infect only once!) Second infection by some other serotype increases risk of severe dengue manifestation resulting in DHF and DSS

Found in tropics, mostly during and shortly after the raining season, and has geographical spread similar to that of malaria
If mosquitoes develop resistance to cooler climates the disease can spread even to temperate climates

A major international public health concern

Prevalent in 100 countries, 2.5 billion people exposed and annually 100 million people infected, 0.25 million get DHF/DSS & 25,000 die Epidemics of more severity occur every 5 or 6 years once and currently many regions are experiencing increase in dengue cases

Dengue Virus
Dengue virus
Enveloped virus with ssRNA+ genome Has single open reading frame encoding a polyprotein

Replication
Virus particle binds to host cell via interactions between its surface glycoproteins and poorly defined host cell receptors Receptor mediated endocytosis internalizes the virion After uncoating the viral RNA is translated at the rER
Uncoated genome translates into polyprotein Poly-protein is co and post-translationally processed into both structural and non-structural proteins RNA replication occurs in close association with cell membrane

Virus particles are thought to be assembled by budding into the endoplasmic reticulum Assembled virus particles are transported through host secretary pathway In the mosquito the virus multiplies in its salivary glands

Dengue Virus
Transmission
Transmitted by mosquitoes Aedes aegypte and Aedes albopictus
Mosquitoes become infected when they bite infected humans Once infected remains able to transmit dengue for its entire life

Not contagious from person to person but can be transmitted through transfusion of blood or blood products while they are still febrile

Disease development
Infected body releases cytokines that cause the endothelial tissue to become permeable and this results in hemorrhagic fever and fluid loss from blood vessels Antibody dependent enhancement secondary infections by other serotypes Internal bleeding is represented by dark color stools and other bleeding at surfaces by red rashes

Dengue Virus
Symptoms
Incubation period is 4 days and symptoms appear within 5 to 6 days after infection Symptoms of typical dengue
High fever (105F) Severe headache and retroorbital pain (pain behind the eye) Nausea and vomiting Rashes appear after 3-4 days of infection second rash may also develop later in the disease Some of the infected may go through several weeks to months of feeling of tired and/or depressed

Symptoms of Dengue Hemorrhagic Fever (DHF)

All those symptoms of typical dengue Marked damage to blood and lymph vessels Bleeding from nose, gums or under the skin causing purplish bruishes Can cause death (about 5% mortality rate)

Dengue Virus
Symptoms
Symptoms of Dengue Shock Syndrome (DSS)
Include all the symptoms of typical dengue fever and of DHF Fluids leaking outside the blood vessels Massive bleeding Shock (very low BP) Can cause death (about 40% mortality rate)

Clinically platelet count drops (Thrombocytopenia)

Normal platelet count is 1,50,000 to 4,50,000/mm3 Droping below 75,000 in hemorrhagic cases and below 50,000 in case of hemorrhagic cases is considered serious

Hemoconcentration Hemorrhagic phenomena (bleeding)

Diagnosis
By doing two blood tests in 2 to 3 weeks apart for detecting antibodies of the virus

Dengue Virus
Treatment
No specific treatment and mainstay of treatment is supportive therapy, primarily based on fluid replacement
Keeping up oral intake of fluids to prevent dehydration and significant hemoconcentration
if unable to maintain this supplementing with intravenous fluids

Platelet transfusion recommended when their count falls below 50,000 for non-hemorrhage cases and below 75,000 for hemorrhage/ Getting plenty of body rest and taking medicines to reduce fever to help in recovery
Classic dengue fever lasts for 6 to 7 days and one recovers completely from the fever within 2 weeks Use of acetaminophen and other pain reducing medicines (Asprin should be avoided) Use of drugs like corticosteroids or carbazochrome sodium sulfonate to stabilize capillary permeability and avoid plasma leakage

With proper treatment mortality rate for dengue can be brought down to less than 1 in 1000

Dengue Virus
Prevention
Through mosquito control
Public spraying Application of larvicide to standing water Eradicating pools of standing water Rendering mosquitoes sterile

Special precautions to avoid contact with mosquitoes

Usually bite during day time (early morning before day break and late afternoon before dark) Use of mosquito nets and repellants, and covering exposed skin, use of DEET, meta-N,N-diehtyltoluamide (an insect ripellant chemical) impregnated bednets Avoiding endemic areas

Vaccination
May take few more years for commercial availability of dengue vaccines Vaccine development is associated with a problem of achieving rapid and robust protection of host against all the four serotypes of dengue virus at the same time

Chikungunya virus
Name from Swahili for that which bends up (position victim takes to relieve joint pain) Also known as Buggy creek virus Causative of chikungunya fever First described by Marion Robinson and WHR Lumsden (1955) Major epidemics appearing after 7-8 years and sometimes after as much as 20 years India is experiencing after 20 years
As on 10-10-2006, 151 districts from 8 states/provinces (AP, Andaman & Nicobar, Tamil Nadu, Karnataka, Maharashtra, Gujrat, MP, Kerala and Delhi) are affected 1.25 million cases reported In some areas the attack reached 45% - though not life threatening caused deaths (125 in Kerala)

The virus and the fever

ssRNA+ genome Enveloped virus

Chikungunya virus
Transmission
Highly infective and disabling, but not transmittable between people Spreads by Aedes aegypti mosquito
Virus reportedly suffered mutation and can now be transmitted also by Aedes albopictus (tiger mosquito)

Most likely also dispensed as an aerosol decontamination by common disinfectants , moist heat and drying is possible

Symptoms and Diagnosis

Incubation period is 3-12 days Sudden severe headache, chills, fever, joint and muscle pain (joints of extermities become swollen and painful to be touched), nausea and vomiting, sometimes rash may appear Most recover within 3-5 days some may suffer joint pain for months It is rarely life threatening Detection of antigen or antibody in the blood sample

Chikungunya virus
Treatment
No specific therapy is available Supportive care through treating the symptoms (mitigating pain and fever using anti-inflammatory drugs) Chloroquine may be effective in treating Rest, and movement and mild exercise tend to improve stiffness and morning arthralgia

Prevention
Vaccine is not available Vector control

Plant Viruses
Plant virus is the first virus to be discovered (Tobacco Mosoic Virus) still relatively less understood than other viruses Most are ssRNA viruses, without envelope and with rod shaped capsids having protein units arranged in a spiral Host specificity is relatively less but generally more stable and remain infectious in environment for a longer time No attachment mechanism is known
have no specific mechanism for entering the host cell (cell wall and cuticle are obstacles) entry depends on injuries (damage by weather) or on transmission via invertabrates (insects and nematodes) animal transmitter sometimes acts as an intermediate host (plant virus or animal virus?)

Mechanisms of spread include

Horizontal transmission plant is infected by virus from external source Vertical transmission virus is inherited from parent through both asexual and sexual reproduction

Vascular system is often used for spreading the virus in the plant Viral diseases in plants are relatively less frequent monocultures may favour spread of viral diseases in plants

Plant Viruses
Plants have defense against the viral infection (only a few can infect and an infected virus can be inherited only a few successive plant generations) Hyper sensitivity (cells in the immediate surroundings of the primary site of infection die off) is used as a means of effective protection against the virus Symptoms Primary symptoms (at the primary site of infection) and secondary symptoms (spreading throughout the plant) Mosaic leaf patterns of light and dark green areas Deformed or involuted leaves (occur if infected during during leaf developmental stage) Chlorosis (lightened leaf areas due to breakdown of chlorophyll around the primary site of infection) Necroses (withered areas) Yellowish look from loss of chlorophyll but carotenoids retention Infections can be latent (asymptomatic viral multiplication) Finding cure for plant viruses is difficult hence focus is on reducing occurrence and transmission of viruses

Viroids
Tiny strands of RNA interfering mostly with plants metabolism and cause disease Considered as escaped introns and also as sub-viral particles Consists of a short stretch of highly complementary, circular, single stranded RNA without the protein coat Genome has some double stranded regions (extensive intramolecular base pairing is responsible) Potato spindle tuber viroid, Cadang-cadang disease in palms, rice yellow mottle sobemovirus (RYMV), citrus exocortis, etc. Only human disease known as caused by viroid is Hepatitis D Multiplication Presumably multiplied with the aid of RNA polymerase-II and the RNA synthesis follows rolling circle mechanism Do not encode proteins themselves Pathogenicity Occur mainly in warm climates (and transmitted by seed/pollen!) Apparently prevent correct cutting out of the introns Infected plants show distorted growth

Prions
Subviral proteinaceous infectious particles Name prion is coined by Stanley B. Prusiner of Univ. of Calif. Prions are found in mammals - prion like proteins are also found in some fungi and other non-mammalian animals Found in plasma membrane highest concentration in the cells of central nervous system PrP (prion related protein) The protein by which the prion is made of Found throughout the body (even in healthy people and animals) in the membranes of cells - organisms have genes (PRNP gene) coding for the prions 2 different conformational types (secondary structure differs)
Normal form of PrP (PrPc) - c refers to cellular Functions are not yet known Infectious form of PrP (PrPSc) - Sc refers to scapie - aberrant prion Resistant to denaturation by protease, heat, radiation (including UV radiation which breaks down nucleic acid) and formalin treatments (potency or infectivity however is reduced) Responds to the agents that disrupt proteins

Prions represent a special case wherein mere change of shape or conformation biological properties of a protein can altered

Prions
Aberrant prion can act as a template for refolding a normal prion into an aberrant prion Protein-X is believed to mediate this refolding protein-X is a type of choperone that binds to a newly synthesized protein and ensures proper folding that provides secondary or tertiary structure to it Prion diseases can be inherited (a mutated PRNP gene coding for aberrant prion is responsible) PRNP gene can be mutated and some of the mutations make PrPc more likely to spontaneously change into PrPSc Believed to infect and propagate through refolding of a normal prion into an aberrant prion

Prions
Diseases caused by prions Transmissible spongiform encephalopathies (TSEs) was the first identified prion Scrapie and screutzfeldt jacob disease are examples for prion caused diseases All diseases are fatal and untreatable (vaccine is however under development) Prions affect structure of the brain or other neural tissue Apparently influence the course of the disease by altering ionic homeostatis in the brain However, lack of normal prions or presence of aberrant prions, which causes the disease is not clear Transmission of prion disease from one species to another (aberrant prions from one species serving as a template fore refolding normal prions of another species) is a rare event Bovine Spongiform Encephalopathy (BSE, Mad cow disease) was due to the crossing of the species barrier (sheep to cow) Can the bovine prions be passed to humans?!