Introduction to Virology

3000BC

History Smallpox was endemic in China by 1000BC. In response, the practice of variolation was developed. Recognizing that survivors of smallpox outbreaks were protected from subsequent infection, variolation involved inhalation of the dried crusts from smallpox lesions like snuff, or in later modifications, inoculation of the pus from a lesion into a scratch on the forearm of a child.

The concept of virus Edward Jenner (1798), introduced the term virus in microbiology. Virus in Greek means poison. Edward Jenner noticed that milk maids who infected with cowpox develop immunity against smallpox. He inoculated a boy with the vesicle fluid taken from the hand of infected maid. The boy developed sustained immunity against smallpox.

The concept of virus. Edward Jenner assumed that the vesicle fluid that has been taken from the hand of the milk maid contained a poison ( virus ), that was responsible for immunity.

9.1 General Properties of Viruses Virus: Viruses are the obligate intracellular element that cannot replicate independently of a living (host) cell Virology: the study of viruses Virus particle (virion): extracellular form of a virus –Exists outside host and facilitates transmission from one host cell to another –Contains nucleic acid genome surrounded by a protein coat and, in some cases, other layers of material © 2012 Pearson Education, Inc.

General characteristics of viruses Viruses are smaller than bacteria, they range in size between nanometer ( nm ). Viruses contain only one type of nucleic acid, either DNA or RNA, but never both. Viruses consist of nucleic acid surrounded by a protein coat. Some viruses have additional lipoprotein envelope. Viruses lack cellular organelles, such as mitochondria and ribosomes.

General characteristics of viruses Viruses are obligate cellular parasites. They replicate only inside living cells. Viruses replicate through replication of their nucleic acid and synthesis of the viral protein. Viruses do not multiply in chemically defined media. Viruses do not undergo binary fission. Virus particles can only be observed by an electron microscope

Challenges the way we define lifedefine life viruses do not respire, nor do they display irritability 应急性 ; they do not move they do not grow they do most certainly reproduce, and may adapt to new hosts.

Virus structure, classification and replication

Viruses defined Obligate intracellular parasites

Virion capsomeres Nucleocapsid (a nucleocapsid without a genome is a capsid) enveloped virus envelope A virion nucleocapsid

13 VIRAL STRUCTURE – SOME TERMINOLOGY virus particle = virion protein which coats the genome = capsid capsid + genome = nucleocapsid may have an envelope

Terminology Virion: The complete virus particle. Capsid: The protein coat that surrounds nucleic acid. Nucleocapsid: The nucleic acid plus the capsid. Capsomeres: The structural protein units that made up the capsid. Defective virus: the virus cannot replicate by its own, it requires helper virus. Nanometer : milli-micron.

Genome The genome of a virus can be either DNA or RNA DNA-double stranded (ds): linear or circular Single stranded (ss) : linear or circular RNA- ss:segmented or non-segmented ss:polarity+(sense) or polarity – (non-sense) ds: linear (only reovirus family)

Basic virus structure

Nature of Viruses Viral genome is packaged in protein coat

Virion Capsid Viral core envelope

Viral core The viral nucleic acid genome, In the center of the virion, : Control the viral heredity and variation, responsible for the infectivity.

Viral Capsid The protein shell, or coat, that encloses the nucleic acid genome. Functions: a. Protect the viral nucleic acid. b. Participate in the viral infection. c. Share the antigenicity

9.2 Nature of the Virion Viral Structure –Capsid: the protein shell that surrounds the genome of a virus particle (Figure 9.2) Composed of a number of protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid –Capsomere: subunit of the capsid Smallest morphological unit visible with an electron microscope © 2012 Pearson Education, Inc.

Figure 9.3 Nucleocapsid Nucleic acid Capsid (composed of capsomeres) Envelope Capsid Nucleic acid Naked virus Enveloped virus © 2012 Pearson Education, Inc.

Nucleocapsid The core of a virus particle consisting of the genome plus a complex of proteins. complex of proteins = Structural proteins +Non- Structural proteins (Enzymes &Nucleic acid binding proteins)

Symmetry of Nucleocapsid Helical Cubic /Icosahedral Complex

Helical symmetry

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28 Adenovirus

SHAPES MAY DIFFER BUT… T4 Bacteriophage Tobacco Mosaic Virus Influenza Virus Head Tail sheath DNA Tail fiber RNA Capsid Surface proteins Membrane envelope RNA Capsid proteins All viruses have 1. Chromosome-like part that carries hereditary information – The Core 2. Protein coat: Protects hereditary information and provides the shape! The Capsid

Size and Shape Methods Size of Viruses Shapes of Viruses

Introduction to Virology Recognizing the shape, size, and structure of different viruses is critical to the study of disease Viruses have an inner core of nucleic acid surrounded by protein coat known as an envelope Most viruses range in sizes from 20 – 250 nanometers

Shape of Viruses Spherical Rod-shaped Brick-shaped Tadpole-shaped Bullet-shaped Filament

Shapes of Viruses :Spherical

Shapes of Viruses :Rod-shaped

Shapes of Viruses :Brick-shaped.

Tadpole-shaped

Shapes of Viruses :Bullet-shaped

Shapes of Viruses :Filament

39 White, DO and Fenner, FJ. Medical Virology, 4 th Ed Virus particle = virion

T4 Bacteriophage

Structure of viruses A – naked, not containing an envelope aroud capsid B – enveloped, containing an envelope around the capsid

Properties of enveloped viruses Envelope is sensitive to – Drying – Heat – Detergents – Acid Consequences – Must stay wet during transmission – Transmission in large droplets and secretions – Cannot survive in the gastrointestinal tract – Do not need to kill cells in order to spread Adapted from Murray, P.R. Rosenthal K.S., Pfaller, M.A. (2005) Medical Microbiology, 5th edition, Elsevier Mosby, Philadelphia, PA Box 6-5

Genome The classification of viruses is based on the type of nucleic acid contained within RNA viruses---also known as a retrovirus DNA viruses

Classification of viruses Viruses are divided into two large groups: RNA containing viruses.RNA containing viruses. DNA containing viruses.DNA containing viruses.

Viral Genomes Nucleic Acid DNA RNA Double Stranded Positive Negative RNADNA Single Stranded Double Stranded Single Stranded

Virus Genomes

DNA viruses adenovirus Papillomavirus Herpesvirus Parvo virus Hepatitis B virus Molluscum contagiosum (Pox virus)

RNA viruses Influenza viruses Rotavirus Enterovirus Paramyxovirus Rift valley fever

Replication Viruses replicate within a host cell while utilizing the host cell’s nucleic acids.

52 BASIC STEPS IN VIRAL LIFE CYCLE ADSORPTION PENETRATION UNCOATING AND ECLIPSE SYNTHESIS OF VIRAL NUCLEIC ACID AND PROTEIN ASSEMBLY (maturation) RELEASE

Steps in virus replication 1-Adsorption (attachment ). Viruses must recognize and bind to specific cellular receptors on the surface of the infected cell via particular glycoproteins.

Steps in virus replication 2--Penetration. A- Enveloped viruses that has the ability to form syncytia ( multi-nucleated giant cell ) enter the cell through fusion of the viral envelope with cell plasma membrane( eg. Paramyo and herpes viruses ). 2- The remaining enveloped viruses enter the cell through endocytosis.

Entry of enveloped viruses, fusion of the viral envelope.

Steps in virus replication B- Unenveloped viruses enter the cell either by endocytosis ( endosome lyses as with adenoviruses) or by forming a pore in the membrane of the cell. The viral RNA is then released inside the cell (picornaviruses).

Endocytosis Endocytosis involves invagination of the cell membrane to form vesicles in the cell cytoplasm. Infected viruses are then engulfed inside these vesicles. Each vesicle fuses with a lysosome to form lysosomal vesicle. The viral envelope fuses with lysosomal membrane and the viral nucleocapsid is expelled into the cytoplasm.

Endocytosis.

Steps in virus replication 3- Uncoating. Release of the viral genome from its protective capsid to enable the viral nucleic acid to replicate. 4- Transcription. Synthesis of m-RNA. 5-Translation. The viral genome is translated using cell ribosomes into structural and non-structural proteins.

Steps in viral replication 6- Replication of the viral nucleic acid. 7-Assembly. New virus genomes and proteins are assembled to form new virus particles. 8-Release. Enveloped viruses are released by budding from the infected cells. Unenveloped viruses are released by rupture of the infected cells.

Release of enveloped viruses by budding

62 PENETRATION - ENVELOPED VIRUSES from Schaechter et al, Mechanisms of Microbial Disease, 3rd ed, 1998

63 smallpox virus cytoplasmic assembly and maturation F. A. Murphy, School of Veterinary Medicine, University of California, Davis.

64 HIV budding and maturation Hsiung, GD et al., Diagnostic Virology 1994 p204 (D. Medina)

65 HIV – mature form Briggs JA et al. Structure. (2006) 14:15-20

Why Study Viruses

(From Medical Microbiology, 4 th ed., Murray, Rosenthal, Kobayashi & Pfaller, Mosby Inc., 2002, Fig ) Under attack!

Why Study Viruses Viruses are capable of infecting all forms of life – Vertebrates, prokaryotes, fungi, algae Most abundant form of life – Bacteriophages are extremely abundant – Estimated tailed bacteriophages Excellent molecular biology tools

Viruses& Human Health ‏ Human Health ‏ June 23, SBI3C

Some examples of generalised viral infections:

Measles

Viral haemorrhagic fever zoonosis

Rabies Motor neurone

Source of infection : Shedding virussusceptible Man > 99% animals zoonosis

Routes of entry: sexual Inhalation inoculation Blood organ t/plant ingestion Congenital / vertical

“vertical transmission” Some viruses can cross the placenta Infection during pregnancy can damage the foetus e.g. Rubella, Cytomegalovirus

September 19, 2015SBI3C80 Viral diseases are difficult to treat because: 1.No drug is available to kill viruses in the body 2. Some viruses are lysogenic  can remain dormant for years (hide inside cells) ex. a) Herpes Simplex Virus I (HSV I) (cold sores ) b) HIV 3.some viruses are cause cells to become cancerous 80 (AIDS) ex. Human Papiloma Virus (HPV) (genital warts) (cervical cancer)

September 19, 2015SBI3C81SBI3C81 vaccines: only true protection against viral diseases people are given a dead or weakened form of the virus builds up an army of WBC’s & antibodies to kill the living virus immediately before it can reproduce ex. polio vaccine, hepatitis B vaccine Protection Against Viral Diseases

Viral Diseases-Examples Influenza Rabies HIV Hepatitis

Poliovirus

Poliovirus Enterovirus. Possesses a RNA genome. Transmitted by the faecal oral route. Cause of gastrointestinal illness and poliomyelitis. Properties of the virus

Poliovirus Infection Gut Virus Infection Virus excretion in the faeces Viraemia Non-neuronal tissues Neuronal tissues Paralysis

Incidence of Poliomyelitis Number of cases (in thousands) A B Poliovirus vaccines A: Salk – killed inactivated vaccine. B: Sabin – live attenuated vaccine

Influenza A virus Myxovirus Enveloped virus with a segmented RNA genome Infects a wide range of animals other than humans Undergoes extensive antigenic variation Major cause of respiratory infections Properties of the virus

Influenza A virus Infection Spread by respiratory route Virus infects cells of the respiratory tract Destruction of respiratory epithelium Secondary bacterial infections Altered cytokine expression leading to fever e.g interleukin-1 and interferon

Spread of influenza virus

Respiratory Tract

SBI3C91 Structure of HIV

September 19, 2015SBI3C92SBI3C92 AIDS HIV (Human Immunodeficiency Virus) virus that causes AIDS RNA core (retrovirus) can only infect helper T cells (type of white blood cell) cannot survive outside the body because glycoprotein membrane around its capsid dries out can only be transmitted from 1 bodily fluid to another ex. 1. blood to blood: needles, transfusions, toothbrushes 2. semen & vaginal secretions 3.breast milk

SBI3C93 Transmission of AIDS (Worldwide) ‏ HIV in Body Fluids Semen 11,000 Vaginal Fluid 7,000 Blood 18,000 Amniotic Fluid 4,000 Saliva 1 Average number of HIV particles in 1 mL of these body fluids

September 19, SBI3C94

SBI3C95 Source: UNAIDS, 2006 Report on the Global AIDS Epidemic, 2006 HIV Prevalence Worldwide Adults Ages with HIV 15.01% % 5.01% % 1.01% - 5.0% 0.51% - 1.0% 0.0% - 0.5% Not available

Transmission of Viruses Respiratory transmission Influenza A virus Faecal-oral transmission Enterovirus Blood-borne transmission Hepatitis B virus Sexual Transmission HIV Animal or insect vectors Rabies virus

Treatment and Prevention of Virus Infections Antivirals Vaccines and immunisation

Antiviral Targets Attachment/Entry Nucleic acid replication Virus protein processing Virus maturation

Viruses and Human Tumours Epstein Barr Virus Burkitt’s Lymphoma Human papillomavirus Benign warts Cervical Carcinoma Human T-cell Leukaemia Virus (HTLV-1) Leukaemia Hepatitis C virus Liver carcinoma

Virus-induced tumours Virus Infection Uninfected Cell ? [] Uncontrolled cell growth and tumour formation

Virus-induced transformation Normal cellsTransformed cells

Virus-Induced Tumours Virus infects cell. Virus nucleic acid, as DNA, integrates into cellular genome. Virus causes changes in cellular gene expression. Uncontrolled cell multiplication and tumour formation.

The cultivation of viruses is complex and includes three common methods Chicken egg culture Cell culture Animal inoculation

Cultivation of Viruses A. Chick Embryos: Virus growth in an embryonated chick egg may result in the death of the embryo (eg, encephalitis virus), the production of pocks or plaques on the chorioallantoic membrane (eg, herpes, smallpox, vaccinia), the development of hemagglutinins in the embryonic fluids or tissues (eg, influenza), or the development of infective virus (eg, polio virus type 2).

Cultivation of Viruses B. Tissue Cultures: Primary cultures are made by dispersing cells (usually with trypsin) from host tissues. In general, they are unable to grow for more than a few passages in culture, as secondary cultures. - Diploid cell strains are secondary cultures which have undergone a change that allows their limited culture (up to 50 passages) but which retain their normal chromosome pattern. - Continuous cell lines are cultures capable of more prolonged (perhaps indefinite) culture which have been derived from cell strains or from malignant tissues They invariably have altered and irregular numbers of chromosomes.

HeLA, Hep-2, Detroit-6, KB, Vero, Fibroblasts of human embryou, Kidney of rhesus monkey, WI-38, RD, Primary cultures of chiken fibroblasts Cell Cultures

107 CYTOPATHIC EFFECT ANY DETECTABLE CHANGES IN THE HOST CELL –MORPHOLOGICAL CHANGES

108 Hockley et al. J Gen Virol 69: uninfectedHIV infected (at higher magnifcation)

109 CYTOPATHIC EFFECT ANY DETECTABLE CHANGES IN THE HOST CELL –MORPHOLOGICAL CHANGES –DEATH –APOPTOSIS –INDEFINITE GROWTH

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113 tissue culture cells epithelialepithelioidfibroblastic slides from CDC

114 epithelial cells - adenovirus uninfected early infectionlate infection slides from CDC

115 epithelial cells - respiratory syncytial virus uninfectedrespiratory syncytial virus slides from CDC

116 fibroblastic cells - herpes simplex virus uninfected early infection late infection slides from CDC

117 fibroblastic cells - poliovirus uninfected early infectionlate infection slides from CDC

Cytopathic Effect (cpe) AdenovirusHerpes virus